Reviewers, Volume 20* (2006) - Genes & Developmentgenesdev.cshlp.org/content/20/24/local/back-matter.pdf · Reviewers, Volume 20* (2006) The editors would like to thank the Editorial

Reviewers, Volume 20* (2006)The editors would like tothank the Editorial Boardand the following scientistswho were kind enough toreview papers and provideadvice during 2006.

*From October 20, 2005 toOctober 18, 2006

Abate-Shen, CoryAbraham, RobertAbrams, JohnAccili, DomenicoAdams, RalfAffolter, MarkusAgami, ReuvenAhmad, KamiAhringer, JulieAkashi, KoichiAkhtar, AsifaAlitalo, KariAlt, FrederickAltman, SidneyAltmann, MichaelAmasino, RichardAmbros, VictorAnderson, KathrynAnderson, PaulAndino, RaulAndrophy, ElliotAparicio, OscarArber, SilviaArcher, CharlesArcher, TrevorArnheiter, HeinzArnosti, DavidAroian, RaffiArpin, MoniqueArtandi, StevenAshe, MarkAshrafi, KavehAshworth, AlanAster, JonAttardi, LauraAugenlicht, LeonardAusio, JuanAutexier, ChantalAuwerx, JohanAvner, PhilipBaldwin, AlbertBalmain, AllanBarbacid, MarianoBardeesy, NabeelBarlow, DeniseBaron, RolandBartek, JiriBartel, BonnieBartolomei, MarisaBasler, KonradBass, BrendaBaulcombe, DavidBaylin, StephenBeachy, Philip

Becker, PeterBelmonte, Juan CarlosBender, TimothyBenfey, PhilipBenjamin, LauraBentley, DavidBerger, JamesBernards, RenéBertolotto, CorineBesharse, JosephBestor, TimothyBetsholtz, ChristerBianco, PieroBickmore, WendyBielinsky, AnjaBier, EthanBirchler, James A.Bishop, DouglasBisseling, TonBissell, MinaBlackwell, T. KeithBlasco, MariaBlenis, JohnBlobel, GerdBoeke, JefBohmann, DirkBohr, VilhelmBoone, CharlesBotchan, MichaelBourrat, FranckBoyce, BrendanBrandt, UlrichBrindle, PaulBriscoe, JamesBrisken, CathrinBrockdorff, NeilBrodsky, FrancesBronner-Fraser, MarianneBrown, Nicholas H.Brown, MylesBrugge, JoanBrunet, AnneBrunner, MichaelBuck, MartinBudd, RalphBuratowski, StephenBurge, ChristopherBurgess, SeanBusslinger, MeinradCaceres, JavierCalame, KathrynCallis, JudyCamper, SallyCantor, AlanCantor, SharonCapel, BlancheCarlson, MarianCarmichael, GordonCarpousis, AgamemnonCarr, AntonyCarrington, JamesCasadevall, ArturoCashel, MichaelCavalli, Giacomo

Cedar, HowardChalker, DouglasChang, SandyChartrand, PascalChen, JunjieChen, TaipingChen, XiaojiangChen, XinbinCheresh, DavidChien, KennethChory, JoanneChuong, Cheng-MingCimprich, KarleneClarke, DuncanClevers, HansClurman, BruceCoffin, JohnCohen-Fix, OrnaCole, CharlesCollins, KathleenColot, VincentConstam, DanielCook, SimonCooney, AustinCooper, JonathanCorces, VictorCortez, DavidCosta, RobertCostantino, PaoloCostanzo, VincenzoCôté, JacquesCoulombe, PierreCoupland, GeorgeCourey, Albert J.Cowburn, DavidCox, MichaelCrabtree, GeraldCrews, StephenCrooke, ElliottCumano, AnaCyert, MarthaD’Andrea, Alan DavidDang, ChiDangl, JeffDarlington, GretchenDarnell, RobertDarst, Sethde Crombrugghe, Benoitde Lange, TitiaDe Robertis, EdwardDean, CarolineDedhar, ShoukatDent, SharonDePamphilis, MelvinDePinho, RonaldDerynck, RikDesplan, ClaudeDillin, AndrewDix, DavidDixit, VishvaDlugosz, AndrzejDoherty, AidanDonehower, LawrenceDotto, G. Paolo

3488 GENES & DEVELOPMENT

Downs, JessicaDownward, JulianD’Souza-Schorey, CrislynDubcovsky, JorgeDubiel, WolfgangDuBois, RaymondDuboule, DenisDunlap, JayDunphy, WilliamDunwoodie, SallyDurocher, DanielDurston, A. J.Dutta, AnindyaDyer, MichaelDynlacht, BrianDyson, NicholasEcker, JosephEdgar, BruceEggenschwiler, JonathanEilers, MartinEmerman, MichaelEmerson, CharlesEngel, James DouglasEspinosa, JoaquinFaessler, ReinhardFankhauser, ChristianFarnham, PeggyFeil, RobertFeldheim, DavidFelsenfeld, GaryFelsher, Dean WaltonFerguson, StuartFerguson-Smith, AnneFerrari, SimoneFerraro, MarinaFessler, JohnFields, StanFilipowicz, WitoldFischer, UtzFischle, WolfgangFisher, AmandaFitzgerald, GarretFlavell, RichardFodde, RiccardoFoiani, MarcoFornace, AlbertFox, CatherineFreeman, MatthewFreiman, RichardFriedman, ScottFunabiki, HironoriGage, FredGall, JosephGallie, BrendaGarabedian, MichaelGarcia, JosephGartenberg, MarcGasser, SusanGatti, MaurizioGautier, JeanGeballe, AdamGebelein, BrianGeiduschek, E. PeterGeijsen, NielsGermino, GregoryGerondakis, Steve

Geyer, PamelaGhosh, SankarGiaccia, AmatoGiancotti, FilippoGiegé, RichardGiguere, VincentGill, GraceGilmartin, GregoryGilmour, DavidGilson, EricGiovannini, MarcoGlass, ChristopherGoldsmith, BetsyGoodell, MargaretGoodrich, JustinGoridis, ChristoGorospe, MyriamGossler, AchimGottesman, MichaelGourse, RichardGrabowski, PaulaGraf, ThomasGrapin-Botton, AnneGraveley, BrentonGraves, BarbaraGray, WilliamGreen, MichaelGreen, PamelaGreene, WarnerGreenstein, DavidGreenwald, IvaGremigni, VittorioGrewal, ShivGridley, ThomasGroden, JoannaGross, CarolGrosveld, FrankGrove, ElizabethGrummt, IngridGrunstein, MichaelGuan, Kun-LiangGuidos, CynthiaGuillemot, FrançoisGurdon, JohnGuthrie, ChristineGutkind, J. SilvioGyurkovics, HenrikHahn, StevenHajnal, AlexHalazonetis, ThanosHall, MichaelHandel, Mary AnnHardin, PaulHardtke, ChristianHardwick, KevinHarfe, BrianHarper, J. WadeHarris, PeterHartmann, ChristineHarvey, RichardHauschka, StephenHay, NissimHe, XiHeard, EdithHebrok, MatthiasHeisenberg, Carl-Philipp

Heitman, JosephHekimi, SiegfriedHelin, KristianHellen, ChristopherHelliwell, ChrisHemann, MichaelHengartner, MichaelHengge, RegineHengst, LudgerHenikoff, SteveHennig, LarsHennighausen, LotharHerlyn, MeenhardHernandez, NouriaHerrera, PedroHerrmann, BernhardHickson, IanHiggs, DouglasHinton, BarryHiom, KevinHoang, TrangHochstrasser, MarkHockenbery, DavidHolland, EricHolley, ScottHollingsworth, NancyHopper, AnitaHorsthemke, BernhardHoury, WalidHuang, DavidHuang, YingqunHuang, Z. JoshHuberman, JoelHughes, StephenHunter, TonyHurlin, PeterHuttner, WielandIbba, MichaelImlay, JamesImler, Jean-LucIngham, PhilipInzé, DirkIp, TonyIsh-Horowicz, DavidIsrael, AlainIto, KoreakiIzaurralde, ElisaJackson, DaveJackson, IanJames, DavidJasin, MariaJiang, JinJohnson, CarlJohnson, GaryJohnson, PeterJohnson, RandallJohnson, ReidJohnstone, RoseJones, JonathanJones, StephenJonkers, JosJoshua-Tor, LeemorJoyce, JohannaKadesch, TomKaelin, WilliamKaestner, Klaus

GENES & DEVELOPMENT 3489

Kageyama, RyoichiroKalcheim, ChayaKalderon, DanielKalluri, RaghuKamakaka, RohintonKanaar, RolandKaplan, Daniel LeeKarch, FrancoisKarin, MichaelKarlseder, JanKarpen, GaryKarsenty, GerardKastan, MichaelKaufman, PaulKaufman, RandalKay, SteveKeeney, ScottKelly, DanielKemler, RolfKepinski, StefanKhorasanizadeh, SepidehKiebler, MichaelKim, StuartKim, V. NarryKimble, JudithKimelman, DavidKimmel, AlanKingston, RobertKitajewski, JanKleckner, NancyKleene, KennethKlein, HannahKnippschild, UweKnowles, BarbaraKo, LanKobayashi, TakehikoKoff, AndrewKooter, JanKoromilas, AntonisKoshland, DouglasKoumenis, ConstantinosKowalczykowski, StephenKraus, William LeeKrek, WilhelmKroll, KristenKroos, LeeKushner, PeterKuwabara, PatriciaLa Thangue, NicholasLabib, KarimLadurner, PeterLambert, PaulLamond, Angus IainLandau, NathanielLang, RichardLasko, PaulLassar, AndrewLaub, MichaelLavoie, BrigitteLaybourn, PaulLeach, StevenLee, IlhaLee, JeannieLees-Miller, SusanLehmann, AlanLehmann, Ruth

Lehner, ChristianLemischka, IhorLemke, GregLeonhardt, HeinrichLeptin, MariaLeutz, AchimLeyser, OttolineLichten, MichaelLin, ChentaoLingner, JoachimLiu, HaopingLiu, QinghauLiu, YiLloyd, AlisonLloyd, RichardLloyd, RobertLohmann, JanLondono Vallejo, José-ArturoLongo, ValterLorsch, JonLosada, AnaLowe, ScottLowndes, NoelLozano, GuillerminaLu, XinLukas, JiriLuo, LiqunLykke-Andersen, JensLyko, FrankMa, HongMa, QiufuMacKeigan, JeffMaina, FlavioMajumder, SadhanMak, TakMalter, JamesMandl, ChristianManfredi, JamesMangelsdorf, DavidManiatis, TomMaquat, LynneMarino, SilviaMarmorstein, RonenMarston, AdeleMartin, CathieMarzluff, WilliamMason, PhilipMassagué, JoanMassé, EricMasson, PatrickMatsuoka, MakotoMatusik, RobertMatzke, MarjoriMaurizi, MichaelMazin, AlexanderMcConnell, SusanMcInerny, ChristopherMcInnes, RoderickMcKay, RonMcKeon, FrankMcMahon, MartinMcStay, BrianMeans, AnthonyMeier, ThomasMelchior, FraukeMerlino, Glen

Merrill, BradleyMerrow, MarthaMeyuhas, OdedMichael, MatthewMichalides, RobMichalik, LilianeMigliaccio, Anna RitaMikkola, MarjaMillar, SarahMills, AleaMinna, JohnMitchell, AaronMoazed, DaneshMoll, UteMontminy, MarcMoore, ClaireMorimoto, RichardMorrison, DeborahMorrison, SeanMostov, KeithMueller, JuergMueller, UlrichMullins, MaryMundy, JohnMurphy, Coleen, TMurphy, KennethMurre, CornelisMuthuswamy, SenthilNakatani, YoshihiroNakayama, KeiichiNarita, MasashiNeufeld, ThomasNevins, JosephNewton, KimNey, PaulNickoloff, JacNiehrs, ChristofNilsen, TimothyNilsson, OveNishiwaki, KiyojiNiwa, HitoshiNomura, MasayasuNorio, PaoloNovitch, BennettNusse, RoelNussenzweig, AndreNussenzweig, MichelO’Farrell, PatrickOhno, ShigeoOlson, EricOlsson, LennartOlwin, BradleyO’Malley, BertOren, MosheOro, AnthonyOrr-Weaver, TerryOsborne, TimothyOsley, Mary AnnOursler, Merry JoOwen-Hughes, TomPagano, MichelePandolfi, Pier PaoloPanning, BarbaraParada, LuisPardue, Mary-LouParker, Malcolm


Parker, RoyParo, RenatoParsons, RamonPasero, PhilippePasquinelli, AmyPatel, KetanPaterson, BrucePawson, TonyPear, WarrenPeifer, MarkPellegrini, LucaPelletier, JerryPellman, DavidPerkins, NeilPerlmann, ThomasPerrimon, NorbertPeter, MarcusPeterlin, B. MatijaPeters, AntoinePeters, GordonPeters, Jan MichaelPeterson, CraigPetrini, JohnPfanner, NikolausPines, JonathonPirrotta, VincenzoPlasterk, RonaldPogliano, KitPogliano, JoePosas, FrancescPourquié, OlivierPouyssegur, JacquesPrice, CarolynPrice, DavidPrivalsky, MartinProudfoot, NicholasPryciak, PeterPrywes, RonRabbitts, TerryRadtke, FreddyRaff, JordanRao, AnjanaReed, RobinReed, StevenReich, NancyReik, WolfRenkawitz, RainerReppert, StevenRice, PhoebeRichard, StéphaneRichards, EricRigby, PeterRine, JasperRoberts, JamesRobertson, ElizabethRobine, SylvieRoeder, RobertRoenneberg, TillRomeo, TonyRon, DavidRoop, DennisRosbash, MichaelRosenfeld, Michael G.Rosenthal, NadiaRoth, DavidRoth, Frederick

Rothenberg, EllenRougvie, AnnRoussel, MartineRudnicki, MichaelRushlow, ChristineRustgi, AnilRyan, KevinSabatini, DavidSaint, RobertSanes, JoshuaSatoh, NoriSauvageau, GuyScadden, DavidSchaefer, EberhardSchatz, DavidSchedl, PaulSchedl, TimothyScheiffele, PeterScheres, BenSchier, AlexanderSchleif, RobertSchlissel, MarkSchmid, RolandSchmitt, ClemensSchneider, DavidScholer, HansSchübeler, DirkSchulz, CordulaSchupbach, TrudiSchuurmans, CarolSchwabe, JohnSchwartz, MartinSchweisguth, FrançoisSchweitzer, RonenSchwob, EtienneScrable, HeidiSelker, EricSen, GanesSengupta, PialiSeydoux, GeraldineSharpless, NormanShen, Che-Kun J.Shen, KangShen, MichaelSherr, CharlesSherratt, DavidShi, YangShiekhattar, RaminShilatifard, AliShore, DavidShyu, Ann-BinSibley, David L.Sicinski, PiotrSilhavy, ThomasSimanis, ViestursSimon, M. CelesteSinger, RobertSingh, HarinderSiomi, HaruhikoSiomi, MikikoSjogren, CamillaSkapek, StephenSlater, ClarkeSlauch, JamesSlingerland, JoyceSliwkowski, Mark

Smith, JeffreySmith, LaurieSmith, SusanSokol, SergeiSolnica-Krezel, LiliannaSolomon, MarkSommer, LukasSonenberg, NahumSontheimer, EricSpector, DavidSpiegelman, BruceSpradling, AllanSprague, GeorgeSrivastava, DeepakSt. Johnston, DanielStallcup, MichaelStamenkovic, IvanStanek, DavidStaskawicz, BrianStemple, DerekStenlund, ArneStern, ClaudioStern, DavidStewart, Colin L.Storey, KateStrasser, AndreasStrober, WarrenStruhl, KevinStrunnikov, AlexanderStucki, ManuelSullivan, WilliamSun, Tai-PingSurani, AzimSvejstrup, JesperSymington, LorraineTabin, CliffTajbakhsh, ShahragimTakabe, TeruhiroTam, PatrickTanaka, EllyTapscott, StephenTatar, MarcTaub, RebeccaTaylor, Stephente Riele, HeinTheurkauf, WilliamThiele, DennisThomas, GeorgeThorner, JeremyThummel, CarlTimmers, MarcTissenbaum, HeidiTlsty, TheaToczyski, DavidToda, TakashiTomlinson, AndrewTomoda, ToshiTontonoz, PeterTora, LaszloTownes, TimTrainor, PaulTreisman, RichardTremethick, DavidTrumpp, AndreasTsai, Li HueiTsukiyama, Toshio


Tyers, MichaelTyler, JessicaUhlmann, FrankUitterlinden, AndréValcárcel, Juanvan Aalten, DaanVan Aelst, Lindavan Heyningen, Veronicavan Lohuizen, MaartenVance, VickiVasioukhin, ValeriVaux, DavidVenkitaraman, AshokVerrijzer, C. PeterVirshup, DavidVisconti, PabloVisvader, JaneVoinnet, OlivierVousden, KarenWagner, ErwinWahl, GeoffreyWahli, WalterWainwright, BrandonWalker, JohnWallace, ValerieWalter, JohannesWandersman, CécileWang, Xiao-FanWarburton, DavidWarner, JonathanWassarman, KarenWasserman, StevenWatanabe, YoshinoriWechsler-Reya, RobertWeinert, TedWeinzierl, RobertWeiss, MitchellWellinger, RaymundWerb, ZenaWest, AdamWhitby, MatthewWhite, EileenWhite, MichaelWhitman, MalcolmWickner, SueWillard, HuntingtonWillis, AnneWingler, AstridWinston, FredWittenberg, CurtWodarz, AndreasWolberger, CynthiaWorkman, JerryWotton, DavidWright, ChristopherWright, AndrewWu, LiziWynshaw-Boris, AnthonyXavier-Neto, JoséXie, TingXiong, YueXu, H. EricXu, Rui-MingXu, YangYamamoto, MasayukiYamasaki, Lili

Yaniv, MosheYoule, Richard J.Yuan, JunyingZakian, VirginiaZambetti, GerardZaret, KennethZarkower, DavidZeller, RolfZetter, BruceZhang, PuminZhou, Ming MingZhou, PengboZhu, Jian-KangZoghbi, Huda YahyaZou, Lee


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Author Index, Volume 20 (2006)Aakre, M.E., 3147Abate-Shen, C., 784Abaza, I., 368, 380Adams, D.J., 1880Adams, R.H., 1829Admire, A., 159Afelik, S., 1441Agathocleous, M., 3036Ahlgren, U., 2208Aiba, H., 3487Aikawa, Y., 1321Ait-Si-Ali, S., 3324Akashi, K., 3010Åkerfelt, M., 836Akhtar, A., 871Akira, S., 1435Aldridge, C., 2315Aldridge, P.D., 2315Alekseyenko, A.A., 848Alisch, R.S., 210Alitalo, K., 1829Allen, E., 2673Allende, J., 1800Allis, C.D., 2580Alt, F.W., 1256Alvarez, D.E., 2238Álvarez-Barrientos, A., 307,

747Amasino, R.A., 898Amasino, R.M., 3244Amato, M.A., 3036Amon, A., 2887Amsterdam, A., 3117Andersen, P., 1331Andersen, R.O., 3464Anderson, K., 2018Andino, R., 2985Andréasson, C., 1563Andrés, V., 307, 747Andrews, C.A., 1162Antoch, M.P., 1868Antonchuk, J., 2018Antoniewski, C., 2985Antonini, D., 1028Arcangeli, M.L., 2096Arinobu, Y., 3010Arsham, A.M., 557Asayesh, A., 2208Aster, J.C., 2096Avner, Pl, 2787Aylon, Y., 2687Azvolinsky, A., 3104Babiarz, J.E., 700Babitzke, P., 2605Baer, R., 1721Baetz, K., 660Bagley, S., 2421Bailey, J., 1829Bajard, L., 2450Baldwin, A.S., 225Balla, J., 2902Bangs, F.K., 1365Bantignies, F., 501Bardeesy, N., 1218, 3130

Barlow, D.P., 1203Baroux, C., 1081Bart, R., 1215Bartel, D.P., 3407Bashirullah, A., 3453, 3464Bassler, B.L., 2754Batista, D., 2871Baugh, L.R., 3342Baus, D., 473Baylin, S.B., 3215Beard, P., 2024Beaudet, A.L., 2859Becker, P.B., 858Beckmann, K., 368Bedogni, B., 3366Beh, J., 2728Behm-Ansmant, I., 391, 1885Behringer, R.R., 2937Ben-Asouli, Y., 1621Bender, M.A., 1447Bendig, G., 2361Benková, E., 2902Bennetzen, J.L., 1250Bentley, D.L., 954Berenger, H., 101Berger, J.H., 3130Berger, S.L., 966, 2580Bergink, S., 1343Bergsland, M., 3475Berlanga, J.J., 87Berleth, T., 1015Bernards, A., 3311Berns, A., 1975Berry, B., 2985Berthelet, F., 2871Berthelet, S., 660Bertone, P., 435Bessler, J.B., 3104Besson, A., 47, 1511Beuter, C., 2421Beyret, E., 1709Bi, C., 1470Bialek, P., 2937Bilodeau, S., 2871Birchall, C., 2315Birchmeier, C., 2465Bishop, D.K., 1685, 2593Bjerke, G., 601Blacklow, S.C., 2096Blagoev, B., 113Blankschien, M., 1776Blanpain, C., 3022Blencowe, B.J., 153Bogan, E., 2279Bohmann, D., 101Boiko, A.D., 236Boldyreff, B., 1800Boller, T., 537Bor, Y.-C., 1597Borghi, L., 1667Bork, P., 1885Borneman, A.R., 435Bornstein, S., 1331Boualem, A., 3084

Bougdour, A., 884Bouveret, R., 1667Boyer, D.F., 253Bracken, A.P., 1123Bradley, A., 1880Brakebusch, C., 571Brandina, I., 1609Breeden, L.L., 2266Breitbart, H., 411Brenman, J.E., 2773Brennecke, J., 2769Brenner, H.R., 1800Bresnick, E.H., 2739Brill, S., 3311Briscoe, J., 1365Brito, I.L., 2887Brockman, J.M., 2713Brodigan, T.M., 3395Brodnicki, T., 1175Brodu, V., 1817Bromleigh, C., 185Bronson, R., 675Broome Powell, M., 3366Brown, M., 2513Brown-Swigart, L., 2527Brue, T., 2871Brunner, M., 297, 1061Buchanan, F.G., 77Buchou, T., 1800Buckingham, M.E., 2450Buckman, C., 2135Bultman, S.J., 1744Buratowski, S., 660Burkart, A., 2193Burke, B., 307, 747Burt, D.W., 1365Buszczak, M., 977Buxton, P., 1365Buza-Vidas, N., 2018Bylebyl, G.R., 966Byron, R., 1447Cabernard, C., 3464Caldwell, S.D., 174Calléja, C., 1525Camacho, M.M., 784Cantor, S.B., 34Cao, Y., 675Carey, M.F., 3049Carles, C., 2030Carotta, S., 933Carpenter, L.R., 660Carrasco, L., 87Carreira, S., 3426Carroll, C.W., 449Carroll, J.S., 2513Casanova, J., 1817Cavalli, G., 501Celli, G., 2648Cha, J., 2552Cha, Y.I., 77Chagraoui, J., 2110Chambon, P., 1525, 2024Chang, Y., 836Chapellier, B., 1525

Chappell, T.G., 2279Chaumeil, J., 2223Chédin, S., 2030Chen, B., 1485Chen, D.Y., 2397Chen, H., 927, 1150Chen, H.B., 648Chen, H.-J., 1933Chen, J., 1721Chen, M-.L., 1569Chen, W.S., 1569Chen, X., 47, 2580, 2961,

3372Chen, X.S., 2373Chen, Y., 1441Chen, Y.-T., 2937Chen, Z., 2629Cheng, C., 1715Cheng, C.-H., 2067Cheng, E.H.-Y., 2397Cheng, H.-L., 1256Cheng, K.H., 3130Cheng, Y., 1790Cheung, W.L., 2580Cheusova, T., 1800Chevallierr, O., 1429Chia, W., 3453Chiang C.-M., 2383Chin, H.G., 3049Chin, L., 2149Chinchilla, D., 537Chiorino, G., 1028Choi, K., 1651Chow, B., 1998Christiaen, L., 2728Christianson, J., 2193Chrostek, A., 571Chu, G.C., 3130Chu, Z., 1250Chua, N.-H., 3255Chytil, A., 3147Citterio, E., 1343Clark, B.S., 1470Clarke, D.J., 1162Cleary, M.D., 429Cogswell, P., 225Cohen, S.M., 417, 913, 2769Cohen, S.N., 2082Colaiácovo, M.P., 1986Coleman, N., 1880Coletti, D., 3440Coll, O., 380Collins, K., 28, 531, 2848Colomb, S., 501Combier, J.-P., 3084Cooper, M.P., 2996Corcoran, L.M., 933, 1175Corless, C.L., 1331Corvera, S., 2193Coulombe, P., 2110Coulombe, P.A., 1353Coupland, G., 898Coutu, P., 2355Covello, K.L., 557


Cowley, G.S., 3311Craven, R.A., 2421Creemers, E.E., 1545Crespi, M., 3084Crevillen, P., 3079Crews, S.T., 2773Culi, J., 1636Curry, J.D., 1539Czuchra, A., 571Dahme, T., 2361Dai, X., 1790Dailey, G.M., 1899Danielian, P.S., 3117Dantuma, N.P., 1343Danzl, N., 159Darnell Jr., J.E., 3372Das, R., 1100Dasgupta, S., 2121Daubas, P., 2450Dauwalder, B., 723Davenport, M., 990Davey, M.G., 1365Davidson, B., 2728Davis, R.J., 2701Dean, C., 3079de Billy, F., 3084De Carlo, S., 1485de Carvalho, C.E., 1986de Crombrugghe, B., 2492Dedhar, S., 2355Déjardin, J., 501de Laat, W., 2349de Lange, T., 2648, 3238del Bianco, C., 2096Denat, L., 3426DePinho, R.A., 1218, 3130Devgan, V., 1028de Waard, H., 1343de Wit, E., 858Díaz-Martínez, L.A., 1162Di Cristofano, A., 1569Diernfellner, A., 297Dietrich, N., 1123Dimitrov, S., 3324Dimitrova, N., 3238Disteche, C.M., 1848di Vignano, A.T., 1028Dixon, M.P., 1175Dlugosz, A.A., 3161Doe, C.Q., 429, 2618, 3464Doerks, T., 1885Dokmanovic, M., 966Donaldson, A.D., 1874Dorsey, J., 2580Dorsey, J.A., 966Dotto, G.P., 1028Doukoumetzidis, K., 2279Douziech, M., 807Dreyfuss, G., 355Drouin, J., 2871Du, L.-L., 1583Dubey, C., 2024Dubois, N., 2024DuBois, R.N., 77Dubova, I., 3232Dufu, K., 1100

Dunaway, S., 3104Duncan, K., 368Dunphy, W.G., 772Earley, K., 1283Economides, K.D., 784Eeckhoute, J., 2513Eferl, R., 2306Eisenman, R.N., 16Elenko, M., 1100El Fatimy, R., 836Eliseenkova, A.V., 185Elledge, S.J., 334Ellermeier, C.D., 1911El-Yahyaoui, F., 3084Emerson, B.M., 601Enari, M., 1087Encinas, M., 321Enciso, A.J., 1283Endo, Y., 1525Engel, J.D., 1379Entelis, N., 1609Eppig, J.J., 2713Erdjument-Bromage, H., 2383,

2996Erickson, S.L., 1162Ermilov, A., 3161Eskin, J.A., 3249Espinosa, J.M., 601Essers, M.A.G., 2024Estay, I.S., 276Esteban, M., 87Estève, P.-O., 3049Evan, G.I., 2527Evans, A.M., 486Evans, R.M., 1308Evsikov, A.V., 2713Fagan, B.M., 1187Fan, P.-D., 1496Fardeau, V., 836Favry, E., 2030Feehery, G.R., 3049Feldt, M., 1100Felsher, D., 2096Feng, J., 1470Feng, Z., 267Ferris, J., 3161Fields, S., 174Figarella-Branger, D., 2871Filomatori, C.V., 2238Fink, G.R., 1150Fischle, W., 1110Fisher, D.E., 2149Fisher, J.K., 2397Fishman, M.C., 2361Fleig, U., 2421Fleischer, T.C., 1294Fodor, B.D., 1557Fogel, M.A., 3269Foo, C., 2985Ford, E., 1075Fornara, F., 898Fraser, P., 1379Frey, B.J., 153Friml, J., 1015, 2902Fritsch, C., 1110Frock, R.L., 486

Frugier, F., 3084Fu, B., 1250Fu, D., 531Fu, S., 1721Fuchs, E., 3022Fujitani, S., 253, 3147Fujitani, Y., 253, 1435, 3147Fukushige, T., 3395Fuller, M.T., 2580Furuta, Y., 147Gage, F.H., 210, 1308Gagliardini, V., 1081Galjart, N., 2349Gamarnik, A.V., 2238Gamas, P., 3084Gangisetty, O., 3049Gannon, M., 253Gao, F.-B., 2793Gao, P., 675Garcia, B.A., 2566Garcia-Perez, J.L., 210Garraway, L.A., 2149Garrenton, L.S., 1946Garry, D.J., 1692Gatta, G.D., 1028Gaurente, L., 1075Gauthier, Y., 2871Gavin, A.-C., 1800Gaye, N., 1429Ge, X., 1250Geballe, A.P., 915Gebauer, F., 368, 380Gebuhr, T.C., 1744Geistlinger, T.R., 2513Georgiev, P., 345Gerdes, K., 113Gerstein, M., 435Ghyselinck, N.B., 1525Giaccia, A.J., 3366Giancotti, F.G., 1057Gierl, M.S., 2465Gilfillan, G.D., 858Giménez-Abián, J.F., 1162Girard, S., 2110Gitton, Y., 836Glasheen, B.M., 1899Glass, C.K., 1405Gocheva, V., 543Goding, C.R., 3426Goldin, R., 1262Gomes, N.P., 601Gonzalez, F.J., 2293González, J.M., 307, 747Gonzalez, M.A., 1880Goodall, J., 3426Gorbacheva, V.Y., 1868Gordan, J.D., 557Gore, S.L., 282Gorska, A.E., 3147Gottesman, S., 884, 2338Govek, E.-E., 2639Govin, J., 2580Graba, Y., 101Graber, J.H., 2713Gradin, K., 3366Grallert, A., 2421

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Sheridan, S., 1685Sherratt, D.J., 1727Shi, W., 2728Shi, X., 1692Shi, Y.-F., 2355Shia, W.-J., 2507Shigematsu, H., 3010Shilatifard, A., 643, 2487Shindo, C., 3079Shiojima, I., 3347Shiota, M., 253Shiraiwa, T., 1435Shmueli, A., 2687Shu, L., 2961Siddiqui, Y., 1331Sierra, J., 586Silva, M., 1283Silver, P.A., 3249Simon, M.C., 557Sims III, R.J., 2779Sinclair, D.A., 3249Singh, P., 2713Singh, R.R., 2943Sinha-Hikim, A.P., 147Siomi, H., 2214Siomi, M.C., 2214Sistonen, L., 836Skarnes, W.C., 22Skovgaard, O., 2121Slee, E., 1262Smale, S.T., 282Smallwood, A., 3049Smith, C.S., 1651Smith, T.G., 1365Snyder, M., 435Sobhian, B., 34Solecki, D.J., 2639Solnica-Krezel, L., 77Solter, D., 2713Somers, G.W., 3453Sonobe, S., 1004Soyano, T., 1004Spector, D.L., 784Spiegelman, B.M., 2996Splinter, E., 2349Spradling, A.C., 977Sprague Jr., G.F., 1045Sridharan, R., 282Srivastava, D., 2327Sroga, G.E., 1899St. Arnaud, R., 2355Stamataki, D., 1365Stanger, B.Z., 1218Stark, A., 1885, 2769Stauber, R.H., 473Steele, S.J.S., 1268Stein, R.W., 253Stein, S., 473Steitz, J.A., 138Stepniak, E., 2306Sterner, D.E., 966Sternglanz, R., 1256Stevens, S.L., 2673Stevens, W., 159Sticht, H., 1800Storz, G., 2338


Stratakis, C., 2871Straub, T., 858Strehle, M., 2465Strein, C., 368Su, J., 1262Sugiyama, D., 654, 1974Sumara, G., 2306Sumara, I., 2306Summers, M.K., 2410Sun, F.-L., 1959Sung, S., 3244Surzenko, N., 1187Sutton, A., 1256Suzuki, K., 2605Suzuki, Y., 423Svoboda, P., 1744Swartz, J., 1597Swiss, V.A., 784Symington, L.S., 2479Szeto, D.P., 1923Szostek, S.A., 601Tachibana, K.-e.K., 1880Takahashi, Y., 1004Takaki, S., 2018Takatsu, K., 3010Takeda, A., 1732Takeda, K., 1435Takeda, S., 2397Talianidis, I., 2293Talukder, A.H., 2943Tanaka, K., 1429Tanaka, M., 1365Tang, C.-F., 1331Tanizawa, Y., 3296Taranova, O.V., 1187Tarassov, I., 1609Tardif, J.-C., 2355Tardiff, D.F., 2055Taubert, S., 1137Taya, Y., 1087Tchoudakova, A.V., 3311Teboul, L., 1511Teleman, A.A., 417, 913Telling, A., 1447Tempst, P., 2383, 2996Tenen, D.G., 3010Testori, A., 3426Therrien, M., 807Thomas, D.Y., 734Thomas, T., 1175Thompson, C.B., 1Thompson, D., 2315Thomson, J.M., 2202Thorner, J., 1946Thornton, B.R., 449, 3069Ti, S.-C., 2067Tickle, C., 1365Tilghman, S.M., 1268Ting, A.H., 3215Tjian, R., 1458Tobias, J., 2096Toczyski, D.P., 449, 3069Tollkuhn, J., 2739Tomioka, M., 2955Tomoda, T., 2639Tong, X., 1353

Torres, J.Z., 3104Torres-Arzayus, M.I., 2513Tran, K.D., 3464Trano, N., 2361Treisman, J.E., 795Trejo, J., 3407Tronche, F., 2293Trotta, C.R., 939Trouillet, D., 836Trumpp, A., 2024Truong, A.B., 3185Tsai, C.-C., 525Tsai, J.-W., 1384Tsai, T.-F., 2859Tsubouchi, H., 1766Tsukiyama, T., 1732Tsumura, A., 3382Turck, F., 898Tuschl, T., 3255Ueda, S., 1321Urban, S., 3054Valcárcel, J., 1679Valencia-Sanchez, M.A., 515Vallee, R.B., 1384Vallette-Kasic, S., 2871van Amerongen, R., 1975VanderWaal, K.E., 1162van der Weyden, L., 1880Van Gilst, M.R., 1137van Rij, R.P., 2985Vanselow, J.T., 2660Vanselow, K., 2660van Steensel, B., 858Vaquero, A., 1256Varmus, H.E., 1496Vas, A.C., 1162Vasudevan, S., 138Vaucheret, H., 759, 3407Ventoso, I., 87Vermeulen, W., 1343Vernié, T., 3084Vidal, M., 2279Vidalain, P.-O., 2279Viegas, W., 1283Villén. J., 2887Vincent, C., 898Vives, V., 1262Voit, R., 1075Voss, A.K., 1175Vykhovanets, O.V., 1868Wachi, M., 113Wagner, E.F., 2306Wai, C., 2096Waldor, M.K., 3269Walker, J.A., 3311Walsh, D., 461Walsh, K., 3347Wang, D., 1331Wang, F., 2793Wang, H., 3453Wang, J., 1028Wang, J.-C., 689Wang, L., 525Wang, M., 159Wang, S., 1250Wang, T.-F., 2067

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Subject Index, Volume 20 (2006)3D nuclear organization

Xist RNA role in (Chaumeil et al.),2223–2237

3�-end processingrole of Rat1 in coupling to transcrip-

tion termination (Luo et al.),954–965

3� UTReffect on upstream open reading

frames (Sachs and Geballe),915–921 Perspective

post-transcriptional control of Her-2mRNA (Mehta et al.), 939–953

5� UTRpost-transcriptional control of Her-2

mRNA (Mehta et al.), 939–9539p21 locus

in pancreatic ductal adenocarcinoma(Hezel et al.), 1218–1249 Re-view

A

AAA+ ATPase assemblyregulated assembly and function of the

transcriptional activator NtrC(De Carlo, et al.), 1485–1495

Acetylationas a dynamic signal for transcriptional

response (Rosenfeld et al.),1405–1428 Review

H2A.Z acetylation and heterochroma-tin boundaries (Babiarz et al.),700–710

of H2AZ Lys 14 is associated with ge-nome-wide gene activity inyeast (Millar et al.), 711–722

Htzl acetylation by NuA4 (Keogh etal.), 660–665

of Stat1 (Krämer et al.), 473–485Acetylcholine receptor (AChR)

regulation of aggregation at neuromus-cular junction (Cheusova et al.),1800–1816

Acinar-to-ductal transitioninduced by PDX-1 through Stat3 acti-

vation (Miyatsuka et al.), 1435–1440

ACS (ARS consensus sequence)identification in yeast by comparative

genomics (Nieduszynski et al.),1874–1879

ActinDia1 effect on polymerization (Car-

reira et al.), 3426–3439localization in tracheal invagination

(Brodu and Casanova), 1817–1828

MreB–RNAP interaction and chromo-some segregation (Kruse et al.),113–124

Adaptationnatural variation in FLC silencing

(Shindo et al.), 3079–3083

Adaptive immunityleukemia and lymphoma as cost of

(Schlissel et al.), 1539–1544 Per-spective

Adhesionmatrix metalloproteinase liberation of

ninjurin A ectodomain to signalloss of cell adhesion (Zhang etal.), 1899–1910

AdipogenesisKeystone meeting summary (Corvera

et al.), 2193–2201 Meeting Re-view

Adrenal tumorsdeletion of akt1 and inhibition of tu-

morigenesis in Pten+/− mice(Chen et al.), 1569–1574

AFM (atomic force microscopy)dengue viral RNA synthases (Filoma-

tori et al.), 2238–2249Aging

early aging caused by BMAL1 defi-ciency (Kondratov et al.), 1868–1873

life span increase in TOR mutants(Powers et al.), 174–184

p53 role in (Mendrysa et al.), 16–21role of mammalian sirtuins in (Haigis

and Guarente), 2913–2921 Re-view

AGL19repression by Polycomb-group pro-

teins (Schönrock et al.),1667–1678

Ago. See ArgonauteAhr (aryl hydrocarbon (dioxin) receptor)

(Kim et al.), 2806–2819AKAP–HDAC3–Aurora B–HP1 pathway

(Li et al.), 2566–2579Akt

deletion of suppression of tumor de-velopment in Pten+/− mice(Chen et al.), 1569–1574

p53–IGF-1–AKT–TOR pathway inter-actions (Levine et al.), 267–275Review

PI3 kinase–AKT pathway, in mela-noma (Chin et al.), 2149–2182Review

regulation of cardiac growth and coro-nary angiogenesis (Shiojima andWalsh), 3347–3365 Review

Sin1 role in Akt phosphorylation andsignaling (Yang et al.), 2820–2832

Allelic seriesSOX2 mutations and (Taranova et al.),

1187–1202Alphaviruses, eIF2-independent transla-

tion in (Ventoso et al.), 87–100

Alternative splicingCD44 coupled with Ras activation

(Cheng et al.), 1715–1720

global analysis of (Pan et al.), 153–158as means to expand hth (homothorax)

functional diversity (Noro etal.), 1636–1650

modulation of organizer activity ofFGF8 in the brain (Olsen et al.),185–198

Anagenkeratins roles during hair follicle cy-

cling (Tong and Coulombe),1353–1364

Anaphase-promoting complex (APC)architectural map of (Thornton et al.),

449–460Emil inhibition of (Miller et al.), 2410–

2420inhibition of �-catenin inside the

nucleus (Xiong and Kotake),637–642 Perspective

role in regulation of cell cycle progres-sion (Thornton and Toczyski),3069–3078 Review

role in Wnt signaling (Willert andJones), 1294–1404 Review

as target of casein kinase I in Wnt sig-naling (Price), 399–410 Review

Angelman syndrome (AS)Rbbp1/Arid4b and Rbbp1l1/Arid4b

regulation of imprinting (Wu etal.), 2859–2870

AngiogenesisIL-1� mediation of Myc angiogenic

switch (Shchors et al.), 2527–2538

regulation of coronary by Akt/PKB sig-naling pathway (Shiojima andWalsh), 3347–3365 Review

taxane resistance by Txr1 and TSP-1(Lih et al.), 2082–2095

Animal behaviorRho activation of neurotransmitter re-

lease, effect of (McMullan etal.), 65–76

AnopthalmiaSOX2 mutations and (Taranova et al.),

1187–1202Anti-adaptor protein

IraP as (Bougdour et al.), 884–897Antimicrobial peptides

resistance by regulated intramem-brane proteolysis in Bacillussubtilis (Ellermeier and Losick),1911–1922

Anti-repressioncontrol of flagellar motility by (Shen et

al.), 3283–3295Antisense RNA

oocyte expression (Evsikov et al.),2713–2727

Antisense transcriptionKcnq1ot1 transcript mediation of CpG

island imprinting at KvDMR(Mancini-DiNardo et al.), 1268–1282


Xist promoter regulation by Tsix (Na-varro et al.), 2787–2792

AntisilencingSAS-mediated acetylation of histone

H4 Lys16 (Shia et al.), 2507–2512

Antiviral defense/responseeIF2� phosphorylation (Ventoso et al.),

87–100role of Argonaute 2 in (van Rij et al.),

2985–2995AP-1

AP-1-dependent HPV chromatin tran-scription (Wu et al.), 2383–2396

suppression through interaction of c-Fos with lamin A/C (Ivorra etal.), 307–320

APCarchitectural map of (Thornton et al.),

449–460Emil inhibition of (Miller et al.), 2410–

2420inhibition of �-catenin inside the

nucleus (Xiong and Kotake),637–642 Perspective

role in regulation of cell cycle progres-sion (Thornton and Toczyski),3069–3078 Review

role in Wnt signaling (Willert andJones), 1294–1404 Review


APC tumor suppressoreffect on �-catenin activation and

H3K4 methylation at Wnt tar-get genes (Sierra et al.), 586–600

Apical ectodermal cap (Kawakami et al.),3232–3237

ApoptosisASPP2 stimulation of p53 family

(Vives et al.), 1262–1267epigenetic modulation of JNK signal-

ing (Miotto et al.), 101–112GLA-3 from C. elegans, role of (Kriti-

kou et al.), 2279–2292inhibition of p53-induced by Bcl-3 ex-

pression (Kashatus et al.), 225–235

keratins roles during hair follicle cy-cling (Tong and Coulombe),1353–1364

p21, role of (Gomes et al.), 601–612programmed cell necrosis (Zong and

Thompson), 1–15 Reviewrole for TSP1 in (van Amerongen and

Berns), 1975–1981 Perspectiverole of p53 in tumor suppression and

aging (Mendrysa et al.), 16–21role of SIRT7 in (Ford et al.),

1075–1080roles of clathrin in p53 regulation

(Enari et al.), 1087–1099specificity of E2F1 (Hallstrom and

Nevins), 613–623Arabidopsis

auxin synthesis and plant develop-

ment (Cheng et al.), 1790–1799

CMV 2b inhibition of AGO1-mediatedcleavage (Zhang et al.), 3255–3268

diversity of miRNAs and siRNAs in(Rajagopalan et al.), 3407–3425

flagellin-induced endocytosis of FLS2(Robatzek et al.), 537–542

hormone perception (Chow and Mc-Court), 1998–2008 Review

MEDEA autoregulation and genomicimprinting (Baroux et al.), 1081–1086

natural variation in FLC silencing(Shindo et al.), 3079–3083

Polycomb-group (PcG) proteins andvernalization response (Schön-rock et al.), 1667–1678

rRNA gene silencing requirement forHDA6 (Earley et al.), 1283–1293

spatial control of flowering (Searle etal.), 898–912

VIL1 role in photoperiod and vernal-ization (Sung et al.), 3244–3248

ARE (AU-rich element)endotoxic shock in AUF/knockout

mice (Lu et al.), 3174–3184ARF

ARF–MDM2–P53 pathway, in mela-noma (Chin et al.), 2149–2182Review

in pancreatic ductal adenocarcinomaReview (Hezel et al.), 1218–1249

Arginine methylationrole in silent chromatin formation (Yu

et al.), 3249–3254Argonaute

antiviral function of (van Rij et al.),2985–2995

GW182 interaction with (Behm-Ans-mant), 1885–1898

piwi-interacting RNAs in mammaliantestes (Kim), 1993–1997 Review

Argonaute1 (AGO1)Cucumber mosaic virus-encoded 2b

suppressor (Zhang et al.), 3255–3268

Arid4bregulation of imprinting by (Wu et al.),

2859–2870Aromatic alcohols

autostimulation of morphogenesis infungi (Chen and Fink),1150–1161

ARS (autonomously replication se-quences)

identification in yeast by comparativegenomics (Nieduszynski et al.),1874–1879

ARS consensus sequence (ACS)identification in yeast by comparative


Aryl hydrocarbon (dioxin) receptor (Ahr)(Kim et al.), 2806–2819

Arylpyrazole compoundseffect on glucocorticoid receptor activ-

ity (Wang et al.), 689–699AS (Angelman syndrome)

Rbbp1/Arid4b and Rbbp1l1/Arid4bregulation of imprinting (Wu etal.), 2859–2870

ASPP2as tumor suppressor gene (Vives et al.),

1262–1267Association studies, in bone diseases

(Ralston and de Crombrugghe),2492–2506 Review

Asymmetric divisionof Drosophila larval neuroblasts (Lee

et al.), 3464–3474; (Wang et al.),3453–3463

AtAGO1 (Zhang et al.), 3255–3268ATM, MDC1 effect on (Dimitrova and

de Lange), 3238–3243Atomic force microscopy (AFM)

dengue viral RNA synthases (Filoma-tori et al.), 2238–2249

AtPIN genesrole in leaf vascular patterning (Scar-

pella et al.), 1015–1027ATR

Claspin effect on phosphorylation ofChk1 (Yoo, et al.), 772–783

UV-induced ubiquitylation of histoneH2A (Bergink et al.), 1343–1352

Atrophinas nuclear receptor corepressors (Wang

et al.), 525–530TLX interaction with (Zhang et al.),

1308–1320Atypical protein kinase C (aPKC)/Numb

cortical polarity (Lee et al.),3464–3474

AUF/knockout miceendotoxic shock in (Lu et al.), 3174–

3184AUG

3� UTR effects on uORFs (Sachs andGeballe), 915–921 Perspective

AU-rich element (ARE)endotoxic shock in AUF/knockout

mice (Lu et al.), 3174–3184Aurora-A

regulation of a PKC/Numb cortical po-larity and spindle orientation(Lee et al.), 3464–3474

as tumor suppressor (Wang et al.),3453–3463

Aurora-Bhistone deacetylase pathway modula-

tion of (Li et al.), 2566–2579Autoinducer discrimination in Vibrio

harveyi (Zhu et al.), 2754–2767Autonomously replication sequences

(ARS)identification in yeast by comparative



Aux/IAA–ARF (indole-3-acetic acid-auxin response factor) signalingpathway (Sauer et al.), 2902–2911

AuxinArabidopsis leaf vein patterning con-

trol by polar auxin transport(Scarpella et al.), 1015–1027

biosynthesis and control plant devel-opment (Cheng et al.), 1790–1799

transport (Sauer et al.), 2902–2911transport and venation patterning

(Scheres and Xu), 922–926 Per-spective

Axinas scaffold for casein kinase I phos-

phorylation in Wnt signaling(Price), 399–410 Review

Axin translocationrole of MACF1 in (Chen et al.), 1933–

1945Axon outgrowth, neuronal polarity and

(Solecki et al.), 2639–2647 Re-view

B

�1 integringenetic test of integrin activation (Py-

layeva and Giancotti), 1057–1060 Perspective

�-cateninAPC counteraction of (Sierra et al.),

586–600APC inhibition of inside the nucleus

(Xiong and Kotake), 637–642Perspective

Cdc42 control of turnover in skin (Wuet al.), 571–585

effect on TGF-� activity in humanmesenchymal stem cells (Jian etal.), 666–674

mechanism of Wnt/�-catenin signal-ing (Willert and Jones), 1394–1404 Review

regulation of vertebrate limb regenera-tion (Kawakami et al.), 3232–3237


�-globin locusCTCF-mediated effects (Splinter et

al.), 2349–2354role in erythroid differentiation

(Ragoczy et al.), 1447–1457�-paravin (Affixin) (Bendig et al.), 2361–

2372�TrCP

association with APC (Sierra et al.),586–600

role in Gli protein destruction (Hunt-zicker et al.), 276–281

BACH-1BRCA1/BARD1 activation by DNA

damage (Greenberg et al.), 34–46

Bacillus subtilisprotease governing regulated intra-

membrane proteolysis and re-sistance to antimicrobial pep-tides in (Ellermeier and Losick),1911–1922

Bacterial blightrice Xa13 gene and disease resistance

(Chu et al.), 1250–1255Bapx1(Nkx3.2), effect on splenopancre-

atic interrelationship (Asayeshet al.), 2208–2213

BARD1activation by DNA damage (Greenberg

et al.), 34–46Basal cell carinoma

induction by Gli protein accumulation(Huntzicker et al.), 276–281

Basement membraneMT-MMP-dependent remodeling (Ho-

tary et al.), 2673–2686Basic helix-loop-helix (bHLH) transcrip-

tion factorsHes1 (Zhu et al.), 2739–2753role in neurogenesis (Bergsland et al.),

3475–3486B-cell commitment

repression of Flt3 by Pax5 (Holmes etal.), 933–938

Bcl-3suppression of p53 activation (Kasha-

tus et al.), 225–235Binding network

as master regulator of development inyeast (Borneman), 435–448

Biofilm formation (Suzuki et al.), 2605–2617

BMAL1 deficiencyearly aging caused by (Kondratov et

al.), 1868–1873BMI1

E4F1 mediation of function in hema-topoietic cells (Chagraoui et al.),2110–2120

BMP signalingmesodermal progenitor cell specifica-

tion (Szeto and Kimelman),1923–1932

Bone massgenetic regulation of (Ralston and de

Crombrugghe), 2492–2506 Re-view

Bone morphogenic protein (BMP)dephosphorylation of BMP-activated

Smad (Chen et al.), 648–653;(Ralston and de Crombrugghe),2492–2506 Review

BRAF mutations, in melanoma (Chin etal.), 2149–2182 Review

BrainAurora-A as tumor suppressor in fly

(Wang et al.), 3453–3463role of LIS1 in development (Vallee

and Tsai), 1384–1393 Perspec-tive

BRCA1

activation by DNA damage (Greenberget al.), 34–46

effect of Chk1 phosphorylation (Yoo,et al.), 772–783

ubiquitination of CtIP (Cheng et al.),1721–1726

BRCA2in pancreatic ductal adenocarcinoma

(Hezel et al.), 1218–1249 Re-view

BRCT domainCtIP-binding partner (Cheng et al.),

1721–1726Brd4

E2-Brd4 transcriptional silencer (Wu etal.), 2383–2396

Breast cancerCCND1 regulation by estrogen (Eeck-

houte et al.), 2513–2526Brg1

glucocorticoid receptor feedback andresistance (Bilodeau et al.),2871–2886

regulation of zygotic genome activa-tion in the mouse (Bultman etal.), 1744–1754

BTG2mediation of anti-Ras function of p53

(Boiko et al.), 236–252

C

Cadherinsrole in tissue morphogenesis (Halbleib

and Nelson), 3199–3214 ReviewCaenorhabditis elegans

genetic redundancy for PTEN func-tions (Suzuki and Han), 423–428

GLA-3 control of MAPK signaling(Kritikou et al.), 2279–2292

inositol monophosphatase (Tanizawaet al.), 3296–3310

insulin-like signaling for integrativebehavior (Kodama et al.), 2955–2960

MDT-15 integration of fatty acid me-tabolism regulation (Taubert etal.), 1137–1149

muscle specification (Baugh andHunter), 3342–3346 Perspective

neuronal polarity (Solecki et al.),2639–2647 Review

Rho activation of neurotransmitter re-lease (McMullan et al.), 65–76

transcriptional regulation of body wallmuscle (Fukushige et al.), 3395–3406

Cajal bodySm protein association (Fu and Col-

lins), 531–536Calcium

programmed cell necrosis, role in(Zong and Thompson), 1–15 Re-view

sensor and transcription regulation


(Rosenfeld et al.), 1405–1428Review

Calorie restrictionrole of mammalian sirtuins in (Haigis

and Guarente), 2913–2921 Re-view

Calpainsin programmed cell necrosis (Zong and

Thompson), 1–15 ReviewCancer

ASPP2 as tumor suppressor gene(Vives et al.), 1262–1267

Bcl-3 suppression of p53 activation(Kashatus et al.), 225–235

cachexia (Schwarzkopf et al.), 3440–3452

components of cofactor complexes assensors for inflammatory sig-nals in (Rosenfeld et al.), 1405–1428 Review

derepression of the her-2 uORF (Mehtaet al.), 939–953

EGFR-dependent lung cancer in mice(Politi et al.), 1496–1510

epigenetics (Ting et al.), 3215–3231Review

genetic analysis of cysteine cathepsinin (Gocheva et al.), 543–556

genome-wide mapping of Polycombtarget genes (Bracken et al.),1123–1136

IL-1� mediation of Myc angiogenicswitch (Shchors et al.), 2527–2538

leukemia and lymphoma as cost ofadaptive immunity (Schlissel etal.), 1539–1544 Perspective

loss of transforming growth factor-�type II receptor promotes meta-static head-and-neck squamoscell carcinoma (Lu et al.), 1331–1342

matrix metalloproteinase-dependentbasement membrane remodel-ing (Hotary et al.), 2673–2686

melanoma proliferation and invasive-ness, control of (Carreira et al.),3426–3439

pancreatic ductal adenocarcinoma(Hezel et al.), 1218–1249 Re-view

PDX-1 induction of acinoductal meta-plasia in the pancreas (Miyat-suka et al.), 1435–1440

PGE2 regulation of cell motility (Chaet al.), 77–86

regulation of microRNA processing(Thomson et al.), 2202–2207

regulation of Oct-4 by HIF-2� (Covelloet al.), 557–570

role of Smad4 in pancreatic (Bardeesyet al.), 3130–3146

Taspase1 overexpression (Takeda etal.), 2397–2409

Cancer therapydeletion of akt1 and inhibition of tu-


role of p53 in tumor suppression andaging (Mendrysa et al.), 16–21

Capacitationtranslation during sperm capaciation

(Gur and Breitbart), 411–416Cardiac contractility, integrin-linked ki-

nase and (Srivastava and Yu),2327–2331 Perspective

Cardiac stretch sensor (Bendig et al.),2361–2372

Cardiomyopathy, from targeted ablationof ILK (White et al.), 2355–2360

Casein kinaserole in regulation of Neurospora circa-

dian clock (He et al.), 2552–2565

serine phosphorylation of MuSK andregulation of acetylcholine re-ceptor aggregation (Cheusova etal.), 1800–1816

in Wnt and Hh signaling (Price), 399–410 Review

Caspasesin programmed cell necrosis (Zong and

Thompson), 1–15 ReviewCastor

regulation of neuroblast competence(Cleary and Doe), 429–434

specification of motor neuron identity(Grosskortenhaus et al.), 2618–2627

Catagenkeratins roles during hair follicle cy-


Catalytic ribonucleoproteinrole for RNase P in Pol III transcription

(Reiner et al.), 1621–1635Catenation

topoisomerase II checkpoint and (An-drews et al.), 1162–1174

Cathespinscathepsin K, osteoporosis and (Ralston

and de Crombrugghe),2492–2506 Review

in programmed cell necrosis (Zong andThompson), 1–15 Review

CBFA1 gene, osteoporosis and (Ralstonand de Crombrugghe), 2492–2506 Review

CCAAT enhancer-binding protein � (C/EBP�) (Iwasaki et al.), 3010–3021

CCND1, regulation by estrogen (Eeck-houte et al.), 2513–2526

CCR4:NOT complex, recruitment byGW182 (Behm-Ansmant), 1885–1898

CD44, coupled with Ras signaling(Cheng et al.), 1715–1720

CD47 receptor, taxane cytotoxicity and(Lih et al.), 2082–2095

Cdc20anaphase-promoting complex (APC)

architecture (Thornton et al.),449–460

APC role in cell cycle progression(Thornton and Toczyski), 3069–3078 Review

Cdc42control differentiation and �-catenin

turnover in skin (Wu et al.),571–585

Cdh1anaphase-promoting complex (APC)


CDK. See Cyclin-dependent kinaseCDKN2A locus, in melanoma (Chin et

al.), 2149–2182 ReviewCds1

autophosphorylation (Xu et al.), 990–1003

dimerization (Xu et al.), 990–1003two-stage mechanism for activation in

fission yeast (Xu et al.),990–1003

CDT1 (Sansam et al.), 3117–3129CDT2 (Sansam et al.), 3117–3129Cdx2

geminin interaction with (Gonzalez etal.), 1880–1884

Ceh-18interaction with daf-18 (Suzuki and

Han), 423–428Cell cycle

CD44 coupled with Ras activation(Cheng et al.), 1715–1720

control of ribonucleotide reductase lo-calization (Lee and Elledge),334–344

estrogen regulation of progression inbreast cancer (Eeckhoute et al.),2513–2526

Hcm1 regulation of S-phase-specifictranscription (Pramila et al.),2266–2278

Hedgehog and (Locker et al.), 3036–3048

histone modification-dependent and-independent pathways for re-cruitment of checkpoint proteinCrb2 to double-strand breaks(Du et al.), 1583–1596

Ino80 and checkpoint adaptation (Pa-pamichos-Chronakis et al.),2437–2449

regulation of condensin-dependentlinkages (Lam et al.), 2973–2984

regulation of CycA by PcG proteins inDrosophila (Martinez et al.),501–513

RNPC1 regulation of (Shu et al.),2961–2972

Taspase1 coordinated cell prolifera-tion (Takeda et al.), 2397–2409

Cell deathnecrotic (Zong and Thompson), 1–15

ReviewCell differentiation. See Differentiation


Cell growth controlcrystal structure of SV40 large T-anti-

gen bound to p53 (Lilyestrom etal.), 2373–2382

Cell migrationp27kip1 promotion of neuronal

(Nguyen et al.), 1511–1524Cell motility

promotion by PGE2 signaling (Cha etal.), 77–86

Cell proliferationrole of SIRT7 in (Ford et al.), 1075–

1080Cell signaling

rhomboid proteins and (Urban), 3054–3068 Review

Cell sortingrole of cadherins in (Halbleib and Nel-

son), 3199–3214 ReviewCell transformation

crystal structure of SV40 large T-anti-gen bound to p53 (Lilyestrom etal.), 2373–2382

Central nervous system developmentneuronal polarity (Solecki et al.),

2639–2647 Reviewc-Fos

AP-1 suppression through interactionwith lamin A/C (Ivorra et al.),307–320

Chameau HATantagonism of JNK/AP-1 dependent

transcription (Miotto et al.),101–112

ChaperoneeIF4F assembly by a viral chaperone

(Walsh and Mohr), 461–472�28-dependent FlgM secretion (Al-

dridge et al.), 2315–2326Checkpoint

adaptation, regulation by Ino80 andSwr1 (Papamichos-Chronakis etal.), 2437–2449

control and structure-specific regula-tion of Claspin (Yoo, et al.),772–783

control of ribonucleotide reductase lo-calization (Lee and Elledge),334–344

DTL/CDT2 role in G2/M checkpoint(Sansam et al.), 3117–3129


increase in cycles of chromosome in-stability by defects in (Admireet al.), 159–173

topoisomerase II in budding yeast (An-drews et al.), 1162–1174

two-stage activation of Cds1 (Xu etal.), 990–1003

Checkpoint kinasesBRCA1/BARD1 DNA damage-response

functions (Greenberg et al.), 35–46

Chickentalpid3 gene and Hedgehog signaling

(Davey et al.), 1365–1377ChIP. See Chromatin immunoprecipita-

tion (ChIP)Chk1

role of Claspin in ATF-dependentphosphorylation (Yoo, et al.),772–783

Chk2damage-inducible, BRCA1 super-com-

plex formation (Greenberg etal.), 35–46

Chondrocyte maturation, inhibition byRunx2 (Hinoi et al.), 2937–2942

Chordate heart, development and evolu-tion (Satou and Satoh), 2634–2638 Perspective

ChromatinAPC inhibition of �-catenin on (Xiong

and Kotake), 637–642 Perspec-tive

compaction, role of H4 Ser1 phos-phorylation in (Wendt and Shi-latifard), 2487–2491 Perspective

DNMT1 and G9a coordination ofmethylation (Estève et al.),3089–3103

estrogen regulation of cyclin D1 ex-pression (Eeckhoute et al.),2513–2526



Jmjd2b antagonism of pericentricH2K9me3 (Fodor et al.), 1557–1562

link to ribosomal proteins (Ni et al.),1959–1973

looping, CTCF mediation of (Splinteret al.), 2349–2354

modifications as signals for dynamictranscriptional modulation(Rosenfeld et al.), 1405–1428Review

NER-dependent histone ubiquityla-tion (Bergink et al.), 1343–1352

quantitative chromatin immunopre-cipitation (Papp and Müller),2041–2054

regulation by PcG proteins in Dro-sophila (Martinez et al.), 501–513

regulation of inflammatory response(Ramirez-Carrozzi et al.), 282–296

role of P68 RNA helicase in transcrip-tional deactivation by promot-ing RNA release (Buszczak andSpradling), 977–989

Rrm3p DNA helicase, global replica-

tion effects of (Azvolinsky etal.), 3104–3116


silent, sister chromatid cohesion in(Huang and Moazed), 132–137Perspective

SirT2 deacetylation of histone H4 dur-ing mitosis (Vaquero et al.),1256–1261

Tid1 and Rad54 control of distributionof Dmc1 (Holzen et al.), 2593–2604

X-chromosome-wide profiling ofMSL-1 distribution and dosagecompensation in Drosophila(Legube et al.), 871–883

Chromatin immunoprecipitation (ChIP)arylpyrazole regulation of glucocorti-

coid receptor (Wang et al.), 689–699

checkpoint adaptation (Papamichos-Chronakis et al.), 2437–2449

cotranscriptional splicing in yeast(Lacadie et al.), 2055–2066

genomic reprogramming (Zanton andPugh), 2250–2265

hypaxial myogenesis (Bajard et al.),2450–2464

MSL complex targeting of active geneson X (Alekseyenko et al.), 848–857

Neurospora circadian clock regulationexperiments (He et al.), 2552–2565

profiling of MSL-1 distribution anddosage compensation (Legube etal.), 871–883

target hub proteins as master regula-tors (Borneman), 435–448

Taspase1 coordination of cell prolif-eration (Takeda et al.), 2397–2409

Tid1-mediated dissociation of Dmc1(Holzen et al.), 2593–2604

Chromatin modificationin cancer epigenetics (Ting et al.),

3215–3231 ReviewMSL complex targeting of active genes

on X (Alekseyenko et al.), 848–857


Chromatin remodelingenzymes (Papamichos-Chronakis et

al.), 2437–2449gene-specific binding of Drosophila

DCC (Gilfillan et al.), 858–870Chromatin transcription

silencing by E2-Brd4 (Wu et al.), 2383–2396

Chromosomal translocationleukemia and lymphoma as cost for

adaptive immunity (Schlissel etal.), 1539–1544 Perspective

Chromosome instability


cycles associated with fragile sites andincreased by defects in DNAreplication and checkpoint con-trols (Admire et al.), 159–173

Chromosome organizationEscherichia coli (Wang et al.), 1727–

1731Chromosome replication

RIDA (regulatory inactivation ofDnaA) in Escherichia coli (Riberet al.), 2121–2134

Chromosome segregationEscherichia coli chromosome arm

(Wang et al.), 1727–1731Htzl acetylation by NuA4 (Keogh et

al.), 660–665mitotic-like mechanism in Vibrio

cholerae (Fogel and Waldor),3269–3282

MreB and RNA polymerase interac-tion in E. coli (Kruse et al.), 113–124

role of condensin in (Lam et al.), 2973–2984

Cias target of casein kinase I in Hedge-

hog signaling (Price), 399–410Review

Ciona intestinalisFGF signaling and heart development

in (Davidson et al.), 2728–2738Circadian clock/rhythm


PER-dependent rhythms in CLK phos-phrylation and E-box binding(Yu et al.), 723–733

PER phosphorylation (Vanselow et al.),2660–2672

phoscillators in (Merrow et al.), 2629–2633 Perspective

phosphorylation-dependent FRQmaturation in Neurospora(Shafmeier et al.), 297–306

regulation in Neurospora (He et al.),2552–2565

transcriptional and post-transcrip-tional regulation of the circa-dian clock of cyanobacteria andNeurospora (Brunner andSchafmeier), 1061–1074 Review

cis-elementPdx1 in foregut organ differentiation

and pancreas function (Fujitaniet al.), 253–266

c-Junliver regeneration, control of (Stepniak

et al.), 2306–2314CK2

serine phosphorylation of MuSK andregulation of acetylcholine re-ceptor aggregation (Cheusova etal.), 1800–1816

CLASP (Grallert et al.), 2421–2436Claspin, structure-specific regulation of

(Yoo, et al.), 772–783Class-switch recombination (CSR)

leukemia and lymphoma as cost foradaptive immunity (Schlissel etal.), 1539–1544 Perspective

Clathrinrole in p53-mediated transcription

(Enari et al.), 1087–1099CLCN7 gene, osteoporosis and (Ralston

and de Crombrugghe), 2492–2506 Review

CleavageCMV 2b inhibition of AGO1-mediated

(Zhang et al.), 3255–3268CLF

AGL19 repression in vernalizationpathway (Schönrock et al.),1667–1678

CLIP170, 2421–2436CLOCK (CLK)

PER-dependent rhythms in phos-phorylation (Yu et al.), 723–733

c-Mycrepression of p21Cip1 during papillo-

magenesis (Oskarsson et al.),2024–2029

as target of Notch1 in T-cell acutelymphoblastic leukemia/lym-phoma (Weng et al.), 2096–2109

Cnk (connector enhancer of Ksr)Aveugle interaction with (Roignant et

al.), 795–806KSR/CNK/HYP role in RAS-depen-

dent RAF activation (Douziechet al.), 807–819

Coactivatorcross-talk and transcriptional output

(Marr et al.), 1458–1469myocardin family of transcriptional

coactivators (Pipes et al.), 1545–1556 Review

Cockayne syndromeCSA-dependent degradation of CSB

(Groisman et al.), 1429–1434Cohesion

chromosome arm (Lam et al.), 2973–2984

inhibition of homologous recombina-tion by a cohesin-associatedclamp complex (Huang et al.),2887–2901

Cold-shock domain, in UNR (upstreamof N-ras) protein (Duncan et al.),368–379

Collagencollagen type I�1 (COLIA1), osteopo-

rosis and (Ralston and de Crom-brugghe), 2492–2506 Review


Comparative genomicsidentifying origins by phylogenetics

(Nieduszynski et al.), 1874–1879

Competence

regulation of neuroblast (Cleary andDoe), 429–434

Condensinchromosome arm cohesion during mi-

tosis and (Lam et al.), 2973–2984

Conditional knock-intyrosine regulation of integrin func-

tion (Chen et al.), 927–932Conditional somatic mutagenesis

nuclear receptors and epidermis differ-entiation (Calléja et al.), 1525–1538

Congenital anomalies of kidneys and thelower urinary tract (CAKUT)

RET signaling in kidney development(Jain et al.), 321–333

Connector enhancer of Ksr (Cnk)Aveugle interaction with (Roignant et

al.), 795–806KSR/CNK/HYP role in RAS-depen-

dent RAF activation (Douziechet al.), 807–819

Constitutive transport element (CTE)Wilms’ tumor 1 gene (+KTS) isoform

functions with (Bor et al.),1597–1608

Coregulatorsa coactivator/corepressor/epigenetic code

for integrating signal-dependentprograms of transcriptional re-sponse (Rosenfeld et al.), 1405–1428 Review

Coronary angiogenesisAkt signaling and (Shiojima and

Walsh), 3347–3365 ReviewCoronary vascular development

fibroblast growth factor regulation ofHedgehog activation essentialfor (Noro et al.), 1657–1666

Corticogenesisrole of HSF2 in radial cortical migra-

tion (Chang et al.), 836–847Cotranscription

phosphoCTD of RNA polymerase II(Phatnani and Greenleaf), 2922–2936 Review

Cotranscriptional RNA processesinfluence on genome stability (Li and

Manley), 1838–1847 ReviewCounterdefense, of Cucumber mosaic

virus-encoded 2b suppressor(Zhang et al.), 3255–3268

Coupling transcription to splicing (Daset al.), 1100–1109

CPEB. See Cytoplasmic polyadenylationelement-binding protein (CPEB)

CpG-island methylation by Dmnt3a andDnmt3b (Oda et al.), 3382–3394

Crb2pathways of recruitment to double-

strand breaks (Du et al.), 1583–1596

Cricket Paralysis virus (CrPV) (van Rij etal.), 2985–2995

Crossing over


reduction when Rad51 is the only re-combinase (Tsubouchi andRoeder), 1766–1775

Cross-linking factor 1 (Chen et al.),1933–1945

Crossveinless-c gene, effect on trachealinvagination in Drosophila(Brodu and Casanova), 1817–1828

CSArole in degradation of CSB by ubiquit-

in–proteasome pathway (Grois-man et al.), 1429–1434

CSBCSA-dependent degradation of (Grois-

man et al.), 1429–1434Csm1, suppression of rDNA recombina-

tion (Huang et al.), 2887–2901CsrA (carbon store regulator A) (Suzuki

et al.), 2605–2617CTCF

boundary, of Xist promoter (Navarro etal.), 2787–2792

mediation of chromatin looping(Splinter et al.), 2349–2354

CTEWilms‘ tumor 1 gene (+KTS) isoform

functions with (Bor et al.),1597–1608

C-terminal-binding protein (CtBP)association with APC (Sierra et al.),

586–600mechanism of Wnt/�-catenin signal-

ing (Willert and Jones),1394–1404 Review

C-terminal repeat domain (CTD)of RNA polymerase II (RNAPII) (Phat-

nani and Greenleaf), 2922–2936Review

CtIPBRCA1/BARD1 activation by DNA

damage (Greenberg et al.), 34–46ubiquitination by BRCA1 (Cheng et

al.), 1721–1726Cucumber mosaic virus-encoded 2b pro-

tein (Zhang et al.), 3255–3268CUL4 (He et al.), 2949–2954; (Sansam et

al.), 3117–3129Cullin

anaphase-promoting complex (APC)architecture (Thornton et al.),449–460

E3 ligases (He et al.), 2949–2954Cushing disease

misexpression of Brg1 and HDAC2 in(Bilodeau et al.), 2871–2886

Cut5histone modification-independent re-

cruitment of Crb2 to DSBs (Duet al.), 1583–1596

Cyanobacteriacircadian clock regulation in (Brunner

and Schafmeier), 1061–1074 Re-view

Cyclic transcriptionmechanism of Wnt/�-catenin signal-

ing (Willert and Jones), 1394–1404 Review

CyclinCyclin A, regulation by PcG proteins

in Drosophila (Martinez et al.),501–513

cyclin D1 (CCND1) oncogene, regula-tion by estrogen (Eeckhoute etal.), 2513–2526

Hedgehog signaling in retinal stemcells (Locker et al.), 3036–3048

p27 turnover (Besson et al.), 47–64Cyclin-dependent kinase (CDK)

cyclin-dependent kinase 5 (Cdk5), ef-fect of heat-shock factor 2 on ac-tivity of (Chang et al.), 836–847

p27 turnover (Besson et al.), 47–64Cyclooxygenase

PGE2 signaling and cell motility dur-ing gastrulation (Cha et al.), 77–86

Cysteine cathepsinrole in multistage tumorigenesis (Go-

cheva et al.), 543–556Cyst formation, splenopancreatic inter-

relationship and (Asayesh etal.), 2208–2213

CytokinesLNK inhibition of thrombopoietin-

mediated hematopoietic stemcell expansion (Buza-Vidas etal.), 2018–2023

regulation of inflammatory responseby chromatin (Ramirez-Car-rozzi et al.), 282–296

role in endotoxic shock (Lu et al.),3174–3184

Cytokinesisregulation by MAPK via NtMAP65-1

(Sasabe et al.), 1004–1014Cytoplasmic polyadenylation element-

binding protein (CPEB)Pumilio-2 control of (Padmanabhan

and Richter), 199–209senescence control by (Groisman et

al.), 2701–2712Cytoskeletal signaling

role of myocardin family of transcrip-tional coactivators (Pipes et al.),1545–1556 Review

D

daf-16daf-18 interaction (Suzuki and Han),

423–428daf-18

genetic redundancy for functions of(Suzuki and Han), 423–428

DAG kinaseRho interaction with (McMullan et

al.), 65–76DBT (DOUBLE-TIME) kinase

destabilization of PER and CLK by (Yuet al.), 723–733

DCAKs (Sansam et al.), 3117–3129DCP1:DCP2 decapping complexes

GW182 interaction with (Behm-Ans-mant), 1885–1898

DDB1 (He et al.), 2949–2954Deadenylation

role of GW182 (Behm-Ansmant),1885–1898

Decapentaplegicdephosphorylation by pyruvate dehy-

drogenase phosphatase (Chen etal.), 648–653

Decappingrole of GW182 (Behm-Ansmant),

1885–1898Degradation, role in regulation of the

Neurospora clock (He et al.),2552–2565

Degradosome (Suzuki et al.), 2605–2617DegU (Shen et al.), 3283–3295Demethylation


Dendritesspineless regulation of diversity (Kim

et al.), 2806–2819transcriptional regulation of develop-

ment in (Parrish et al.), 820–835Dendritic morphogenesis, spineless role

in (Crews and Brenman), 2773–2778 Perspective

Dengue virus, mechanism of viral RNAsynthesis (Filomatori et al.),2238–2249

Dentatorubral-pallidoluysian atrophy(DRPLA) (Riley and Orr), 2183–2192 Review

Dephosphorylationof phosphotyrosine on STAT1 dimers

(Mertens et al.), 3372–3381Desmin

effect of lamin A/C deficiency on(Frock et al.), 486–500

Development�1 integrin activation, requirement for

(Pylayeva and Giancotti), 1057–1060 Perspective

FGF in Ciona heart development (Dav-idson et al.), 2728–2738

FGF regulation of Hedgehog activationand coronary development(Noro et al.), 1651–1666

GLA-3 from C. elegans, role of (Kriti-kou et al.), 2279–2292

hepatocyte regulatory networks (Kyr-mizi et al.), 2293–2305


Insm1 in endocrine development (Gi-erl et al.), 2465–2478

melanoma and (Chin et al.), 2149–2182 Review

muscle stem cells (Shi and Garry),1692–1708 Review

Pdm and Cas specify late-born neuro-


nal identity (Grosskortenhauset al.), 2618–2627

PGE2 signaling in early development(Cha et al.), 77–86

requirement of Aveugle for EGFR sig-naling (Roignant et al.), 795–806

role of LIS1 in brain development(Vallee and Tsai), 1384–1393Perspective

role of monocytic leukemia zinc fingerprotein (Thomas et al.), 1175–1186

role of XA13 in pollen development(Bart et al.), 1215–1217 Perspec-tive; (Chu et al.), 1250–1255

splenopancreatic interrelationship(Asayesh et al.), 2208–2213

TLX coordination of retinal develop-ment (Zhang et al.), 1308–1320

transcriptional regulation of dendritedevelopment (Parrish et al.),820–835

translation regulatory cascades (Va-sudevan et al.), 138–146 Per-spective

DFIin quorom sensing (Zhu et al.), 2754–

2767Dia1

regulation by Mitf (Carreira et al.),3426–3439

Diabetes mellitusKeystone meeting summary (Corvera


Dicerinhibition by Drosophila C virus

dsRNA-binding domain protein(van Rij et al.), 2985–2995

Tetrahymena homologues (Lee andCollins), 28–33

Differentiationof GATA-1-null cells (Kitajima et al.),

654–659genome-wide mapping of Polycomb

target genes (Bracken et al.),1123–1136

monocytic leukemia zinc-finger pro-tein (MOZ) role in hematopoi-esis (Katsumoto et al.), 1321–1330

Notch–p63 cross-talk in keratinocytes(Nguyen et al.), 1028–1042

Notch regulation of diversification ofprecurors (Zhu et al.), 2739–2753

Notch signaling in epidermal (Blan-pain et al.), 3022–3035


p27kip1 promotion of neuronal(Nguyen et al.), 1511–1524

p53 and PW1 regulation of muscle ho-meostasis (Schwarzkopf et al.),3440–3452

p63 regulation of epidermal (Truong etal.), 3185–3197


regulation of cardiomyocyte differen-tiation and embryonic heartgrowth by Akt signaling (Shio-jima and Walsh), 3347–3365 Re-view

role of Aveugle during photoreceptor(Roignant et al.), 795–806

role of PIAS1 and Msx1 in myoblasts(Lee et al.), 784–794



Dioxin receptor (Ahr) (Kim et al.), 2806–2819

Disease resistancerole of xa13 gene in plants (Bart et al.),

1215–1217 Perspective; (Chu etal.), 1250–1255

Dishevelled (DVI)as casein kinase I target in Wnt signal-

ing (Price), 399–410 ReviewDLX-2

Evf-2 noncoding RNA as transcrip-tional coactivator of Dlx-2 (Fenget al.), 1470–1484

DMBA/TPA-induced tumorigenesis (Os-karsson et al.), 2024–2029

Dmc1Hed1 attenuation of Rad51 in yeast

(Tsubouchi and Roeder), 1766–1775

recombinase Rad51 interaction with(Sheridan and Bishop), 1685–1691 Perspective

Tid1/Rdh54 promoter of dissociation(Holzen et al.), 2593–2604

Dmnt3a/Dnmt3b (Oda et al.), 3382–3394DnaA gene expression, Hda protein ef-

fect on (Riber et al.), 2121–2134DNA binding


role in regulation of the Neurosporaclock (He et al.), 2552–2565

specificity of Msx1 homeoprotein (Leeet al.), 784–794

DNA-binding proteinsPhoRC (Pho-repressive complex) (Kly-

menko et al.), 1110–1122DNA damage

Bcl-3 inhibition of p53 response to(Kashatus et al.), 225–235

DTL/CDT2 role in G2/M checkpoint(Sansam et al.), 3117–3129

liver function without telomeres(Lazzerini Denchi et al.), 2648–2653

MDC1 acceleration of nonhomolo-gous end-joining of dysfunc-

tional telomeres (Dimitrova andde Lange), 3238–3243

nucleotide excision repair-dependentmonoubiquitylation of histoneH2A (Bergink et al.), 1343–1352

response by BRCA1/BARD1-contain-ing complexes (Greenberg etal.), 34–46

ribonucleotide reductase localization,effect on (Lee and Elledge), 334–344

ubiquitinated CtIP and (Cheng et al.),1721–1726

DNA methylationin cancer epigenetics (Ting et al.),

3215–3231 Reviewof CpG island KvDMR of mouse chro-

mosome 7 and effect on im-printing (Mancini-DiNardo etal.), 1268–1282

regulation of long-range gene silencingof an X-linked homeobox genecluster (Oda et al.), 3382–3394

DNA repairchromatin remodeling enzyme regula-

tion of cell cycle checkpoint ad-aptation (Papamichos-Chro-nakis et al.), 2437–2449


Rep and PriA limitation of RecA activ-ity during replication fork repair(Mahdi et al.), 2135–2147

SIRT6 regulation of (Haigis andGuarente), 2913–2921 Review

V(D)J recombination and transposition(Reddy et al.), 1575–1582

DNA replication. See ReplicationDNMT1, coordination of chromatin

methylation (Estève et al.),3089–3103

Dosage compensationchromosome-wide gene-specific tar-

geting of the Drosophila dosagecompensation complex (Gilfil-lan et al.), 858–870

male-specific lethality (MSL) distribu-tion on X chromosome (Schü-beler), 749–753 Perspective

MSL complex targeting of active geneson X (Alekseyenko et al.), 848–857; (Heard and Disteche),1848–1867 Review

UNR and SXL corepression of MSL-2translation (Duncan et al.), 368–379

UNR repression of msl-2 mRNAtranslation (Abaza et al.), 380–389

X-chromosome-wide profiling (Legubeet al.), 871–883

Dosage regulationSOX2 as regulator of retinal neural

progenitor competence (Taranovaet al.), 1187–1202

Double-strand break repair


V(D)J recombination and transposition(Reddy et al.), 1575–1582

Double-strand breaksparallel pathways recruiting Crb2 to

DSBs (Du et al.), 1583–1596DOUBLE-TIME (DBT) kinase

destabilization of PER and CLK by (Yuet al.), 723–733

DPC4in pancreatic ductal adenocarcinoma


Drosharegulation of microRNA processing

(Thomson et al.), 2202–2207Drosophila

antiviral function of Ago2 (van Rij etal.), 2985–2995

Aurora-A regulation of neuroblast self-renewal (Lee et al.), 3464–3474;(Wang et al.), 3453–3463

cell shape remodeling in tracheal in-vagination (Brodu and Casa-nova), 1817–1828

coactivator cross-talk (Marr et al.),1458–1469

developmental roles of hth HDlessvariants (Noro et al.),1636–1650

EGF receptor signaling pathway, re-quirement for Raf activation byAveugle in (Roignant et al.),795–806

epigenetic modulation of JNK signal-ing (Miotto et al.), 101–112

gene-specific binding of dosage com-pensation complex (Gilfillan etal.), 858–870

histone H4 Ser1 phosphorylation dur-ing gametogenesis(Krishnamoorthy et al.),2580–2592

HOX gene control by histone methyl-transferases (Papp and Müller),2041–2054

KSR/CNK/HYP role in RAS-depen-dent RAF activation (Douziechet al.), 807–819

matrix metalloproteinase liberation ofninjurin A ectodomain to signalloss of cell adhesion (Zhang etal.), 1899–1910

microRNA denoising of feedbackloops (Cohen et al.), 2769–2772Perspective

microRNA in neuronal precursorspecification (Li et al.),2793–2805

miR-278 regulation of energy metabo-lism (Teleman and Cohen),417–422

neurofibromatosis 1 mutants (Walkeret al.), 3311–3323

neuronal polarity (Solecki et al.),2639–2647 Review

P68 RNA helicase regulation of tran-

scriptional deactivation (Buszc-zak and Spradling), 977–989

vPdm and Cas specify late-born neuronalidentity (Grosskortenhaus etal.), 2618–2627

Piwi association with rasiRNA in flies(Saito et al.), 2214–2222

regulation of CycA by PcG proteins in(Martinez et al.), 501–513

regulation of dendrite development(Crews and Brenman),2773–2778 Perspective


rhomboid proteins in (Urban),3054–3068 Review

ribosomal protein L22 (Ni et al.),1959–1973

RNAi control of telomere length(Savitsky et al.), 345–354

role of GW182 in mRNA decay (Behm-Ansmant), 1885–1898

spineless regulation of dendritic diver-sity (Kim et al.), 2806–2819

SRF-myocardin partnership in (Pipeset al.), 1545–1556 Review


UNR and SXL corepress MSL-2 trans-lation (Duncan et al.), 368–379


Drosophila C virus (DCV) (van Rij et al.),2985–2995

DRpd3 HDACantagonism of JNK/AP-1 dependent


DSfmbt proteinHOX gene silencing and (Klymenko et

al.), 1110–1122DsRNA-binding protein

RNAi suppressor of Drosophila C vi-rus (van Rij et al.), 2985–2995

DTL (Sansam et al.), 3117–3129DVI (Dishevelled)

as casein kinase I target in Wnt signal-ing (Price), 399–410 Review

DyneinSchizosaccharomyces pombe CLASP

and (Grallert et al.), 2421–2436Dyskeratosis congenita, telomere main-

tenance in (Wong et al.), 2848–2858

Dyskerin (Wong et al.), 2848–2858

E


E2FJab1 as specificity factor for E2F1-in-

duced apoptosis (Hallstrom andNevins), 613–623

Taspase1 and (Takeda et al.),2397–2409

E4F1BMI1 function in hematopoietic cells,

mediation of (Chagraoui et al.),2110–2120

EB1, antagonism by Peg1 (Grallert et al.),2421–2436

ECF � factoractivation in Bacillus subtilis by regu-

lated intramembrane proteoly-sis (Ellermeier and Losick),1911–1922

EGFR. See Epidermal growth factor re-ceptor (EGFR)

EIF2�

recognition of initiation codon context(Pisarev et al.), 624–636

resistance of late alphavirus mRNA toeIF2� phosphorylation (Ventosoet al.), 87–100

EIF4Ein fully grown oocytes (Evsikov et al.),

2713–2727EIF4F

assembly by a viral chaperone (Walshand Mohr), 461–472

phosphorylation, herpes simplex vi-rus-1 and (Walsh and Mohr),461–472

EJC (exon junction complex)SMG-1 phosphorylation of Upf1 on

(Kashima et al.), 355–367Electroporation

p27kip1 functions in neurogenesis(Nguyen et al.), 1511–1524

ELM2 domainof Atrophin proteins (Wang et al.),

525–530Embryogenesis, role of cadherins in (Hal-

bleib and Nelson), 3199–3214Review

Embryonic lethalityin MACF1−/− mice(Chen et al.), 1933–

1945Embryonic stem cells. See Stem cellsEmerin

role in skeletal muscle satellite celldifferentiation (Frock et al.),486–500

Emery-Dreifuss muscular dystrophyrole of lamin A/C and emerin defi-

ciency in (Frock et al.), 486–500Emil

as pseudosubstrate inhibitor of APC/C(Miller et al.), 2410–2420

Endocrine developmentInsm1 in (Gierl et al.), 2465–2478

Endocytosisof the pattern recognition receptor

FLS2 in Arabidopsis (Robatzeket al.), 537–542

EndodermPdx1 and p48 conversion of endoderm

to pancreas (Afelik et al.), 1441–1446


Endometrial carcinomadeletion of akt1 and inhibition of tu-


Endoplasmic reticulum (ER) stressinflammation and (Corvera et al.),

2193–2201 Meeting ReviewEndoreduplication

genetic ablation of geminin in themouse (Gonzalez et al.), 1880–1884

hepatocytes with telomere deprotec-tion and fusion (Lazzerini Den-chi et al.), 2648–2653

Endotoxic shock, in AUF/knockoutmice (Lu et al.), 3174–3184

Enhancerestrogen regulation of cyclin D1 ex-

pression (Eeckhoute et al.),2513–2526

targeted deletion of the Pdx1 enhancer(Fujitani et al.), 253–266

Enhancer-binding proteinregulated assembly and function of the


Enolaseas cofactor of tRNA targeting toward

mitochondria (Entelis et al.),1609–1620

Environmental sensingregulation of transcription factor by re-

ceptor-activated proteolysis re-sponse to membrane sensor(Andréasson et al.), 1563–1568

Epidermal growth factorin pancreatic ductal adenocarcinoma


Epidermal growth factor receptor (EGFR)Aveugle role in Raf activation in EGF

receptor signaling pathway(Roignant et al.), 795–806

cell shape remodeling in Drosophilatracheal invagination (Broduand Casanova), 1817–1828

lung cancer induction by mutant(Politi et al.), 1496–1510

Epidermal tumorigenesisc-Myc repression of p21Cip1 during

papillomagenesis (Oskarsson etal.), 2024–2029

Epidermisdifferentiation, nuclear receptors and

(Calléja et al.), 1525–1538Notch signaling in epidermal differen-

tiation (Blanpain et al.), 3022–3035

p63 in epidermal proliferation and dif-ferentiation (Truong et al.),3185–3197

Epigenetic regulationXist promoter regulation by Tsix (Na-

varro et al.), 2787–2792Epigenetics

cancer (Ting et al.), 3215–3231 Review

a coactivator/corepressor/epigeneticcode for integrating signal-de-pendent programs of transcrip-tional response (Rosenfeld etal.), 1405–1428 Review



JNK signaling (Miotto et al.), 101–112natural variation in FLC silencing

(Shindo et al.), 3079–3083rRNA gene silencing requirement for

HDA6 (Earley et al.), 1283–1293two types of imprinted cis-acting si-

lencers (Pauler and Barlow),1203–1206 Perspective

VIL1 role in photoperiod and vernal-ization (Sung et al.), 3244–3248

X inactivation and dosage compensa-tion (Heard and Disteche),1848–1867 Review

Epithelial-to-mesenchymal transitionmouse models (Bardeesy et al.),3130–3146

ERFin SURF (SMG-1–Upf1–eRF1–eRF3)

complex (Kashima et al.), 355–367

ER (endoplasmic reticulum) stressinflammation and (Corvera et al.),

2193–2201 Meeting ReviewErythroid cell

differentiation, �-globin locus positionand activity during (Ragoczy etal.), 1447–1457

differentiation of GATA-1-null cells(Kitajima et al.), 654–659

Escherichia colichromosome organization (Wang et

al.), 1727–1731chromosome segregation in (Kruse et

al.), 113–124regulation of �s stability by IraP (Boug-

dour et al.), 884–897RIDA and chromosome replication

(Riber et al.), 2121–2134�32-mediated heat-shock response

(Nonaka et al.), 1776–1789Estrogen

CCND1 regulation by (Eeckhoute etal.), 2513–2526

Estrogen receptor �

osteoporosis and (Ralston and deCrombrugghe), 2492–2506 Re-view

transcriptional network (Eeckhoute etal.), 2513–2526

Etsin Ciona heart development (Davidson

et al.), 2728–2738Eukaryotic initiation factor

in fully grown oocytes (Evsikov et al.),2713–2727


Evf-2 noncoding RNAtranscription from Dlx-5/6 ultracon-

served region and cuntion asDlx-2 transcriptional coactiva-tor (Feng et al.), 1470–1484

Evolutionchordate heart (Satou and Satoh),

2634–2638 Perspectiveconservation of replication origin se-

quences (Nieduszynski et al.),1874–1879


of pre-mRNA splicing (Izquierdo andValcárcel), 1679–1684 Perspec-tive

X inactivation and dosage compensa-tion (Heard and Disteche),1848–1867 Review

Exon junction complex (EJC)SMG-1 phosphorylation of Upf1 on

(Kashima et al.), 355–367Export. See RNA exportEye development

Hedgehog-regulated localization ofVax2 (Kim and Lemke), 2833–2847

requirement of Aveugle for EGFR sig-naling (Roignant et al.), 795–806

F

Familial advanced sleep phase syndrome(FASPS) (Vanselow et al.), 2660–2672

Fatty acid metabolismregulation by MDT-15 in C. elegans

(Taubert et al.), 1137–1149Feedback control/regulation

denoising by miRNAs (Cohen et al.),2769–2772 Perspective

of morphogenesis in fungi by aromaticalcohols (Chen and Fink), 1150–1161



Female cell lineUNR protein functional role in (Dun-

can et al.), 368–379Fertility

role of xa13 gene in plants (Bart et al.),1215–1217 Perspective

Fertilizationeffect of inhibition of protein transla-

tion (Gur and Breitbart), 411–416

FGF8 subfamily


regulation of the organizing activityof, 185–198

FGF18Runx2 enhanced expression of (Hinoi

et al.), 2937–2942FGF receptors

structure of complex with FGF8 sub-family (Olsen et al.), 185–198

Fibroblast growth factor (FGF)in pancreatic ductal adenocarcinoma


regulation of Hedgehog activation andcoronary vascular development(Noro et al.), 1651–1666

Fibroblastsgenome-wide mapping of Polycomb

target genes (Bracken et al.),1123–1136

FIS genesvregulatory interactions in Arabidopsis

(Baroux et al.), 1081–1086Flagella

motility, in Listeria monocytogenes(Shen et al.), 3283–3295

�28-dependent FlgM secretion (Al-dridge et al.), 2315–2326

Flavin monooxygenaseauxin biosynthesis by YUC flavin mo-

nooxygenases (Cheng et al.),1790–1799

Flavivirusmechanism of dengue virus RNA syn-

thesis (Filomatori et al.), 2238–2249

FLC. See FLOWERING LOCUS CFlo8

role in regulation of development inyeast (Borneman), 435–448

Flower developmentauxin biosynthesis by YUC flavin mo-


Floweringspatial control of flowering in Arabi-

dopsis (Searle et al.), 898–912VIL1 role in photoperiod and vernal-

ization (Sung et al.), 3244–3248FLOWERING LOCUS C (FLC)

FLC-independent vernalization path-way, Polycomb-group proteinrepression of AGL19 in (Schön-rock et al.), 1667–1678

FLC silencing, natural variation in(Shindo et al.), 3079–3083

spatial control of flowering in Arabi-dopsis (Searle et al.), 898–912

VIL1 regeneration of exprression (Sunget al.), 3244–3248

FLOWERING LOCUS M (FLM)VIL1 regeneration of expression (Sung

et al.), 3244–3248FLS2, flagellin-induced endocytosis (Ro-

batzek et al.), 537–542Flt3

regulation by Pax5 (Holmes et al.),

933–938Fluorescence in situ hybridization (FISH)

studyglobin locus position (Ragoczy et al.),

1447–1457Forebrain development


Foregut differentiationPdx1 role in (Fujitani et al.), 253–266

ForkheadHcm1 regulation of S-phase-specific

transcription (Pramila et al.),2266–2278

Foseffects of Chameau and DRpd3 on

(Miotto et al.), 101–112FoxA1 (Eeckhoute et al.), 2513–2526FOXO

cardiac growth and Akt signaling(Shiojima and Walsh), 3347–3365 Review

Fragile sitescycles of chromosome instability (Ad-

mire et al.), 159–173FREQUENCY (FRQ) protein

phosphorylation-dependent matura-tion (Shafmeier et al.), 297–306

phosphorylation of WHITE COLLARcomplex (He et al.), 2552–2565

Fungi. See also Yeast; specific speciesfeeback control of morphogenesis by

aromatic alcohols (Chen andFink), 1150–1161

G

G9a, coordination of chromatin methyl-ation (Estève et al.), 3089–3103

Gametogenesishistone H4 Ser1 phosphorylation dur-

ing (Krishnamoorthy et al.),2580–2592

GAP (GTPase-Activating Protein) (Walkeret al.), 3311–3323

GastrulationPGE2 signaling in zebrafish (Cha et

al.), 77–86GATA-1-null cells, differentiation of

(Kitajima et al.), 654–659GATA-2 (Iwasaki et al.), 3010–3021GDNF

mediation of RET signaling in kidneydevelopment (Jain et al.), 321–333

Geminingenetic ablation in mouse (Gonzalez et

al.), 1880–1884Gene activation

corepressor/coactivator exchange and(Rosenfeld et al.), 1405–1428Review

Gene expressiongene-specific binding of Drosophila

DCC (Gilfillan et al.), 858–870


polyglutamine disease and transcrip-tion regulation (Riley and Orr),2183–2192 Review

profiling, in fully grown oocytes (Evsi-kov et al.), 2713–2727

Gene insulation, CTCF effects on (Splin-ter et al.), 2349–2354

General transcription factors (GTFs),preinitiation complex and (Zan-ton and Pugh), 2250–2265

Gene regulationmyocardin family of transcriptional

coactivators (Pipes et al.), 1545–1556 Review

regulated assembly and function of thetranscriptional activator NtrC(De Carlo, et al.), 1485–1495

regulatory networks for developmentand evolution of the chordateheart (Satou and Satoh), 2634–2638 Perspective

�28-dependent FlgM secretion (Al-dridge et al.), 2315–2326

Gene silencingE2-Brd4 transcriptional silencer (Wu et

al.), 2383–2396HDA6 requirement for rRNA gene si-

lencing (Earley et al.), 1283–1293

Kcnq1ot1 transcript mediation of CpGisland imprinting at KvDMR(Mancini-DiNardo et al.), 1268–1282

long-range of the Rhox gene cluster byDnmt3a/Dnmt3b (Oda et al.),3382–3394

nucleolar dominance (McStay), 1207–1214 Perspective

two types of imprinted cis-acting si-lencers (Pauler and Barlow),1203–1206 Perspective

Genetic redundancyfor PTEN functions (Suzuki and Han),

423–428Genetics

malignant melanoma (Chin et al.),2149–2182 Review


Genome compactionhistone H4 Ser1 phosphorylation and

(Krishnamoorthy et al.), 2580–2592

Genome rearrangementTetrahymena thermophila small

RNAs, role of (Lee and Collins),28–33

Genome stabilityHcm1 regulation of S-phase-specific

transcription (Pramila et al.),2266–2278

histone modification-dependent and


-independent pathways for re-cruitment of checkpoint proteinCrb2 to double-strand breaks(Du et al.), 1583–1596

influence of cotranscriptional pro-cesses on (Li and Manley),1838–1847 Review

Genomic imprintingArid4b and Arid4b, regulation of (Wu

et al.), 2859–2870Kcnq1ot1 transcript mediation of CpG

island imprinting at KvDMR(Mancini-DiNardo et al.), 1268–1282

MEDEA autoregulation in Arabidop-sis (Baroux et al.), 1081–1086

two types of imprinted cis-acting si-lencers (Pauler and Barlow),1203–1206 Perspective

Genomic instabilitydue to V(D)J recombination-associated

transposition (Reddy et al.),1575–1582

leukemia and lymphoma as cost ofadaptive immunity (Schlissel etal.), 1539–1544 Perspective

Genomic reprogramming (Zanton andPugh), 2250–2265

Genomicsmalignant melanoma (Chin et al.),

2149–2182 Reviewtarget hub proteins as master regula-

tors (Borneman), 435–448Genomic stem cell


Germ celldevelopment, H4 Ser1 phosphoryla-

tion and (Wendt and Shilati-fard), 2487–2491 Perspective

role of WT1 in germ cell developmentand survival (Rao et al.), 147–152

Germlinedevelopment, role of GLA-3 from C.

elegans in (Kritikou et al.),2279–2292

RNAi control of telomere length inDrosophila (Savitsky et al.),345–354

Germline small RNAs (gsRNAs)in mouse spermatogenic cells (Grivna

et al.), 1709–1714from mouse testes (Watanabe et al.),

1732–1743GGDEF-EAL (Suzuki et al.), 2605–2617GLA-3, control of MAPK signaling (Kri-

tikou et al.), 2279–2292Gli

degradation signals (Huntzicker et al.),276–281

requirement for talpid3 gene in Hedge-hog pathway (Davey et al.),1365–1377

Glucocorticoid receptor

effect of arylpyrazole compounds on(Wang et al.), 689–699

Glucocorticoid receptor ligandarylpyrazole compounds as (Wang et

al.), 689–699Glucose homeostasis, SIRT1 regulation

of (Haigis and Guarente), 2913–2921 Review

Glutamate dehydrogenase, SIRT4 inhibi-tion of (Haigis and Guarente),2913–2921 Review

Glycolysisenolase as cofactor of tRNA targeting

toward mitochondria (Entelis etal.), 1609–1620

GmaR (Shen et al.), 3283–3295Granulocyte/monocyte progenitors

(GMPs), order of transcriptionfactor expression (Iwasaki etal.), 3010–3021

GSK-3cardiac growth and Akt signaling

(Shiojima and Walsh), 3347–3365 Review

gsRNAs. See Germline small RNAs(gsRNAs)

GTPase-Activating Protein (GAP) (Walkeret al.), 3311–3323

GW182linkage of miRNA pathway to mRNA

decay (Behm-Ansmant), 1885–1898

H

H2Anucleotide excision repair-dependent

monoubiquitylation of (Berginket al.), 1343–1352

H2A.Zacetylation and heterochromatin

boundares (Babiarz et al.), 700–710

acetylation by NuA4 (Keogh et al.),660–665

Htzl-K14 acetylation and genome-wide gene activity (Millar et al.),711–722

incorporation at subtelomeric regionsin Saccharomyces cerevisiae(Shia et al.), 2507–2512

nucleosomes (Zanton and Pugh),2250–2265

H3K4 methylationAPC counteraction of (Sierra et al.),

586–600H3K9me3

Jmjd2b antagonism at pericentric het-erochromatin (Fodor et al.),1557–1562

H4SAS-mediated acetylation of Lys16

(Shia et al.), 2507–2512Ser1 phosphorylation (Wendt and Shi-

latifard), 2487–2491 PerspectiveSer1 phosphorylation during gameto-

genesis (Krishnamoorthy et al.),2580–2592

Hair folliclecycling, role of keratins during (Tong

and Coulombe), 1353–1364tumorigenesis and Gli protein accu-

mulation (Huntzicker et al.),276–281

Hammerhead ribozymecotranscriptional splicing, effect on

(Lacadie et al.), 2055–2066HAND

role in body wall myogenesis (Fuku-shige et al.), 3395–3406

HAP2 (Combier et al.), 3084–3088Hcm1

regulation of S-phase-specific tran-scription (Pramila et al.), 2266–2278

HDA6effect on rRNA gene silencing (Earley

et al.), 1283–1293HDAC. See Histone deacetylase (HDAC)Hda protein

DnaA protein inactivation by (Riber etal.), 2121–2134

Hdm2increase with Bcl-3 expression (Kasha-

tus et al.), 225–235Head-and-neck squamos cell carcinoma

(HNSCC)promotion by loss of TGF� type II re-

ceptor (Lu et al.), 1331–1342Heart

development and evolution of chor-date (Satou and Satoh), 2634–2638 Perspective

development, FGF regulation ofHedgehog activation and (Noroet al.), 1651–1666


regulation of cardiac growth and coro-nary angiogenesis by Akt signal-ing (Shiojima and Walsh), 3347–3365 Review

Heat shockeffect on histone variant mH2A1.1

(Ouararhni et al.), 3324–3336full and partial genome-wide assembly

and disassembly of the yeasttranscription machinery in re-sponse to (Zanton and Pugh),2250–2265

�32-mediated response (Nonaka et al.),1776–1789

Heat-shock factor 2, role of (Chang etal.), 836–847

Hed1Red-Hed regulation (Sheridan and

Bishop), 1685–1691 PerspectiveHedgehog. See also Sonic hedgehog (Shh)

casein kinase I in Hedgehog signaling(Price), 399–410 Review

Gli protein mediation of effects (Hunt-zicker et al.), 276–281


in pancreatic cancer (Pasca de Magli-ano et al.), 3161–3173


Patched, functional domains of (Lu etal.), 2539–2551

in retinal stem cells (Locker et al.),3036–3048

role of fibroblast growth factor in coro-nary development (Noro et al.),1651–1666

talpid3 gene and (Davey et al.), 1365–1377

tectonic modulation of Hedgehog sig-naling (Reiter and Skarnes), 22–27

Vax2 localization in the developingeye (Kim and Lemke), 2833–2847

HelicaseP68 RNA helicase (Buszczak and Spra-

dling), 977–989PriA helicase, limitation on RecA ac-

tivity during replication by(Mahdi et al.), 2135–2147

Rrm3p DNA helicase, global replica-tion effects of (Azvolinsky etal.), 3104–3116

Sgs1/BLM helicases, dissociation of D-loops by (Symington andHeyer), 2479–2486 Perspective

HematopoiesisE4F1 mediation of BMI1 function in

hematopoietic cells (Chagraouiet al.), 2110–2120

essential roles of MOZ in (Katsumotoet al.), 1321–1330

LNK inhibition of thrombopoietin-mediated hematopoietic stemcell expansion (Buza-Vidas etal.), 2018–2023

order of transcription factor expression(Iwasaki et al.), 3010–3021


Hepatocyte growth factor (HGF)in pancreatic ductal adenocarcinoma


Hepatocytesendoreduplication (Lazzerini Denchi

et al.), 2648–2653regulatory networks in (Kyrmizi et al.),

2293–2305Her-2

post-transcriptional control of Her-2mRNA (Mehta et al.), 939–953

Herpes simplex virus-1 (HSV-1)translation initiation factor complex

assembly by viral chaperone(Walsh and Mohr), 461–472

Hes1 (Blanpain et al.), 3022–3035HES/HERP family members

role of Notch–p63 cross-talk in kera-

tinocytes (Nguyen et al.), 1028–1042

HeT-ARNAi control of telomere length in

Drosophila (Savitsky et al.),345–354

Heterochromatinarginine methylation and (Yu et al.),

3249–3254Jmjd2b antagonism of pericentric

H2K9me3 (Fodor et al.), 1557–1562


Heterochromatin boundariesNuA4-dependent acetylation of

H2A.Z (Babiarz et al.), 700–710Hfq

antisense RNA and (Suzuki et al.),2605–2617

sRNA modulation of outer membraneproteins (Guillier et al.), 2338–2348 Review

HIF1�. See Hypoxia-inducible factor 1�

Higher-order chromatin structure (Splin-ter et al.), 2349–2354

High-osmolarity glycerol (HOG) path-way

Ste50p link to Ste11p MEKK (Wu etal.), 734–746

High-throughput sequencingmiRNAs and siRNAs in Arabidopsis

(Rajagopalan et al.), 3407–3425Histone

H1 link to ribosomal protein L22 (Niet al.), 1959–1973

H3 Lys4 methylation (Sims and Rein-berg), 2779–2786 Perspective

H4 Lys16 aectylation (Shia et al.),2507–2512

H4 Ser1 phosphorylation during game-togenesis (Krishnamoorthy etal.), 2580–2592

H4 Ser1 phosphorylation in chromatincompaction and germ cell de-velopment (Wendt and Shilati-fard), 2487–2491 Perspective


nucleosome displacement in tran-scription (Workman), 2009–2017 Review

variant mH2A down-regulation ofPARP-1 activity (Ouararhni etal.), 3324–3336

Histone acetylationeffects of Chameau and DRpd3 on

(Miotto et al.), 101–112Htzl-K14 acetylation and genome-

wide gene activity (Millar et al.),711–722

Histone acetyltransferaseantagonism of JNK/AP-1 dependent


Htzl acetylation by NuA4 (Keogh et

al.), 660–665monocytic leukemia zinc finger pro-

tein (Thomas et al.), 1175–1186monocytic leukemia zinc-finger pro-

tein (MOZ) role in hematopoi-esis (Katsumoto et al.), 1321–1330

Histone codeCrb2 recruitment to double-strand

breaks (Du et al.), 1583–1596H2A.Z acetylation and heterochroma-

tin boundaries (Babiarz et al.),700–710

modulation of histone deacetylasepathway (Li et al.), 2566–2579

Histone deacetylase (HDAC)acetylation of Stat1 (Krämer et al.),

473–485Atrophin proteins as nuclear receptor

corepressors (Wang et al.), 525–530

DRpd3 and antagonism of JNK/AP-1dependent transcription (Miottoet al.), 101–112

HDAC2, glucocorticoid receptor feed-back and resistance (Bilodeau etal.), 2871–2886

regulation of mitosis (Li et al.), 2566–2579


Histone deacetylase (HDAC) inhibitorinductor of Stat1 acetylation by

(Krämer et al.), 473–485Histone deacetylation

SirT2 deacetylation of histone H4 dur-ing mitosis (Vaquero et al.),1256–1261

Histone demethylationof H3K9me3 by Jmjd2b (Fodor et al.),

1557–1562Histone lysine methyltransferase

Crb2 recruitment to double-strandbreaks (Du et al.), 1583–1596

Histone methylationAPC effect on (Willert and Jones),

1394–1404 ReviewCrb2 recruitment to double-strand

breaks (Du et al.), 1583–1596H3 Lys4 (Sims and Reinberg),

2779–2786 PerspectiveHOX genes, control of (Papp and

Müller), 2041–2054PhoRC binding to methylated his-

tones (Klymenko et al.), 1110–1122

prevention of AGL19 locus by vernal-ization (Schönrock et al.), 1667–1678

Histone methyltransferase (HMTase)HOX gene control by (Papp and

Müller), 2041–2054Histone modification

in cancer epigenetics (Ting et al.),3215–3231 Review


gene-specific binding of DrosophilaDCC (Gilfillan et al.), 858–870



in vernalization (Sung et al.), 3244–3248


Histone post-transcriptional modifica-tions

sumoylation as negative regulator inyeast (Nathan et al.), 966–976

HLH-1role in body wall myogenesis (Fuku-

shige et al.), 3395–3406Hmt1 (Yu et al.), 3249–3254HMTase (histone methyltransferase)

HOX gene control by (Papp andMüller), 2041–2054

HND-1role in body wall myogenesis (Fuku-

shige et al.), 3395–3406HNF-4� (Kyrmizi et al.), 2293–2305HOG (high-osmolarity glycerol) pathway

Ste50p link to Ste11p MEKK (Wu etal.), 734–746

Holliday junctionRep and PriA limitation of RecA activ-

ity during replication fork repair(Mahdi et al.), 2135–2147

Homeobox genesDNA-binding specificity of Msx1 ho-

meoprotein (Lee et al.), 784–794Homeodomain

functions of homeodomain-containingand homeodomain-less iso-forms encoded by homothorax(Noro et al.), 1636–1650

Homeodomain transcription factorsEvf-2 function as Dlx-3 transcriptional

coactivator (Feng et al.), 1470–1484

Homologous recombinationdynamics of (Symington and Heyer),

2479–2486 PerspectiveHomothorax

developmental roles of hth HDlessvariants (Noro et al.), 1636–1650

Hormonesplant hormone receptors (Chow and

McCourt), 1998–2008 ReviewHOX

functions of homeodomain-containingand homeodomain-less iso-forms encoded by homothorax(Noro et al.), 1636–1650

PcG/trxG control of (Papp and Müller),2041–2054

Pho-repressive complex (PhoRC) inter-action with (Klymenko et al.),1110–1122

HPV (human papillomavirus)


H-rasoverexpression and promotion of head-

and-neck squamos cell carci-noma (Lu et al.), 1331–1342

Hsp70, as a mH2A1.1 target gene(Ouararhni et al.), 3324–3336

Hst2deacetylation of histone H4 during mi-

tosis (Vaquero et al.), 1256–1261HSV-1 (herpes simplex virus-1)

translation initiation factor complexassembly by viral chaperone(Walsh and Mohr), 461–472

Htz1acetylation and heterochromatin

boundares (Babiarz et al.), 700–710

checkpoint adaptation (Papamichos-Chronakis et al.), 2437–2449


Human mesenchymal stem cells�-catenin mediation of TGF-� activity

(Jian et al.), 666–674Hunchback


Huntington diseasepolyglutamine disease and transcrip-

tion regulation (Riley and Orr),2183–2192 Review

Hypaxial myogenesis (Bajard et al.),2450–2464

Hypertrophycardiac myocytes (Shiojima and

Walsh), 3347–3365 ReviewHyphen (HYP)


Hypomorphic mutants, Sox2 (Okubo etal.), 2654–2659

Hypoxiaeffects on stem cell function, embry-

onic development, and tumorgrowth (Covello et al.), 557–570

premature senescence from (Welfordet al.), 3366–3371

Hypoxia-inducible factor 1� (HIF1�)MIF activation and delay of senes-

cence (Welford et al.), 3366–3371

senescence delay (Maity and Kou-menis), 3337–3341 Perpective

Hypoxia-inducible factor 2� (HIF-2�),regulation of Oct-4 (Covello etal.), 557–570

I

Ichthyosisnuclear receptors and epidermis differ-

entiation (Calléja et al.), 1525–1538

ICP6as chaperone for eIF4F assembly

(Walsh and Mohr), 461–472IGF. See Insulin-like growth factor (IGF)ILK. See Integrin-linked kinase (ILK)Imprinting. See also Genomic imprint-

ingArid4b and Arid4b, regulation of (Wu

et al.), 2859–2870X inactivation and dosage compensa-

tion (Heard and Disteche),1848–1867 Review

InflammationKeystone meeting summary (Corvera


selective and atagonistic functions ofSWI/SNF and Mi-2� nucleo-some remodeling complexesduring (Ramirez-Carrozzi et al.),282–296

Initiationrecognition of initiation codon context

(Pisarev et al.), 624–636INK4A

INK4A–CDK4/6–RB pathway, inmelanoma (Chin et al.), 2149–2182 Review


Innate immunityflagellin-induced endocytosis of FLS2

(Robatzek et al.), 537–542Ino80 (Papamichos-Chronakis et al.),

2437–2449Inositol monophosphatase, regulation of

synapses and behavior by (Tani-zawa et al.), 3296–3310

Inside-out signalingtyrosine regulation of integrin func-

tion (Chen et al.), 927–932Insm1 (insulinoma-associated 1, IA-1)

gene (Gierl et al.), 2465–2478Insulin


insulin-like signaling for integrativebehavior (Kodama et al.), 2955–2960

SIRT1 regulation of (Haigis andGuarente), 2913–2921 Review

Insulin-like growth factor (IGF)cardiac growth and Akt signaling




Integrative behaviorinsulin-like signaling for (Kodama et

al.), 2955–2960


Integringenetic test of integrin activation (Py-

layeva and Giancotti), 1057–1060 Perspective

tyrosine regulation of function (Chenet al.), 927–932

Integrin-linked kinase (ILK)cardiac contractility and (Srivastava

and Yu), 2327–2331 Perspectivetargeted ablation of (White et al.),

2355–2360zebrafish heart contractility, control of

(Bendig et al.), 2361–2372Interactions


Interferon �

inductor of Stat1 acetylation by(Krämer et al.), 473–485

Interferon-responsive genesNotch–p63 cross-talk in keratinocytes

(Nguyen et al.), 1028–1042Interleukin1� (IL-1�)

mediation of Myc angiogenic switch(Shchors et al.), 2527–2538


Intermediate filamentkeratins roles during hair follicle cy-


Intestinal polypsdeletion of akt1 and inhibition of tu-


IntestineInsm1 in endocrine development (Gi-

erl et al.), 2465–2478Intramembrane proteolysis (Urban),

3054–3068 ReviewInvasion


IraP, regulation of RssB activity by(Bougdour et al.), 884–897

J

Jab1as specificity factor for E2F1-induced

apoptosis (Hallstrom and Nev-ins), 613–623

Jmjd2b hydroxylaseantagonism of H3Kp trimethylation at

pericentric heterochromatin(Fodor et al.), 1557–1562

JNK signalingepigenetic modulation of (Miotto et

al.), 101–112

K

Kcnq1ot1transcript elongation and genomic im-

printing of neighboring genes(Mancini-DiNardo et al.), 1268–1282

KeratinocytesCdc42 function in (Wu et al.), 571–585evidence that a retinoic acid cannot be

the RXR-activating ligand inmouse epidermis keratinocytes(Calléja et al.), 1525–1538

keratin 17 modulation of hair folliclecycling (Tong and Coulombe),1353–1364

Notch–p63 cross-talk in (Nguyen etal.), 1028–1042

Keratin, role during hair rollicle cycling(Tong and Coulombe), 1353–1364

Keystone meeting: obesity and diabetes(Corvera et al.), 2193–2201Meeting Review

Kidney development, RET signaling in(Jain et al.), 321–333

Kinase. See also specific kinasesSps1 (Krishnamoorthy et al.), 2580–

2592Knock-in mutant

Neurospora ck-1a (He et al.), 2552–2565

Knockout mice, studies withASPP2 as tumor suppressor gene

(Vives et al.), 1262–1267loss of transforming growth factor-�

type II receptor promotes meta-static head-and-neck squamoscell carcinoma (Lu et al.), 1331–1342

KrasHedgehog/Ras in pancreatic cancer

(Pasca de Magliano et al.), 3161–3173

molecular pathogenesis of pancreaticcancer (Rustgi), 3049–3053 Per-pective

overexpression and promotion of head-and-neck squamous cell carci-noma (Lu et al.), 1331–1342


Smad4 in pancreas development andcancer (Bardeesy et al.), 3130–3146

TGF-� signaling, blockade of (Ijichi etal.), 3147–3160

Krüppelregulation of neuroblast competence

(Cleary and Doe), 429–434KSR (kinase suppressor of RAS)

RAF activation (Douziech et al.), 807–819

L

L22 ribosomal protein (Ni et al.), 1959–1973

LactationMTA3 repression of Wnt4 pathway in

(Zhang et al.), 2943–2948Lamin A/C

AP-1 suppression through interactionwith c-Fos (Ivorra et al.), 307–320

role in skeletal muscle satellite celldifferentiation (Frock et al.),486–500

Lats2-p53 feedback loop (Aylon et al.),2687–2700

LBK1/STK11 tumor suppressorin pancreatic ductal adenocarcinoma


Leaf developmentcontrol of vascular patterning by polar

auxin transport (Scarpella et al.),1015–1027

Learning and memoryinsulin-like signaling for integrative

behavior (Kodama et al.), 2955–2960

LEFas target of casein kinase I in Wnt sig-

naling (Price), 399–410 ReviewLeigh syndrome French Canadian vari-

ant (LSFC) (Cooper et al.), 2996–3009

Let-7regulation of microRNA processing

(Thomson et al.), 2202–2207Leucine-rich repeat (LRR)-based hor-

mone receptors (Chow and Mc-Court), 1998–2008 Review

Leucine zipperc-Fos–lamin A/C interaction (Ivorra et

al.), 307–320Leukemia


Notch1 induction of c-Myc in (Wenget al.), 2096–2109

Life spanextension in yeast by decreasing TOR

pathway signaling (Powers etal.), 174–184

Limbhypaxial myogenesis (Bajard et al.),

2450–2464regeneration regulation by Wnt/�-

catenin signaling (Kawakami etal.), 3232–3237

Linkage studies, in bone diseases (Rals-ton and de Crombrugghe),2492–2506 Review

LipidmiR-278 effect on (Teleman and Co-

hen), 417–422Lipoprotein receptor-related protein 5

(LRP5), osteoporosis and (Rals-ton and de Crombrugghe),2492–2506 Review


LIS1 (Vallee and Tsai), 1384–1393 Per-spective

Lissencephaly (Vallee and Tsai), 1384–1393 Perspective

Listeria monocytogenes, flagellar motil-ity in (Shen et al.), 3283–3295

Lithium, sensitivity of inositol mono-phosphatase (Tanizawa et al.),3296–3310

Liverc-Jun/p53/p21/p38 in liver regenera-

tion (Stepniak et al.), 2306–2314regulatory networks in hepatocytes

(Kyrmizi et al.), 2293–2305LNK

inhibition of thrombopoietin-medi-ated hematopoietic stem cellexpansion (Buza-Vidas et al.),2018–2023

Localizationcontrol of ribonucleotide reductase lo-

calization through an anchoringmechanism involving Wtm1(Lee and Elledge), 334–344

Locus control regionassociation of the murine �-globin lo-

cus with engaged transcriptionfactories during erythroid matu-ration (Ragoczy et al.), 1447–1457

Long Interspersed Element-1 (LINE-1)retrotransposons

translation of (Alisch et al.), 210–224Looping, chromatin (Splinter et al.),

2349–2354LPRPRC (Cooper et al.), 2996–3009LRP6

MACF1 interaction with (Chen et al.),1933–1945


LRP130regulation of energetics in Leigh syn-

drome (Cooper et al.), 2996–3009

Lrs4, supression of rDNA recombination(Huang et al.), 2887–2901

Lung cancerEGFR induced (Politi et al.), 1496–

1510Ras-dependent, role of p27 in (Besson

et al.), 47–64LuxO/LuxR (Zhu et al.), 2754–2767Lysosomes


M

MACF1 (microtubule actin cross-linkingfactor 1) (Chen et al.), 1933–1945

MACF1-knockout mice (Chen et al.),1933–1945

Macrophage

regulation of inflammatory responseby chromatin (Ramirez-Car-rozzi et al.), 282–296

MAD (Mother against Decapentaplegic)dephosphorylation by pyruvate dehy-


Mad2topoisomerase II checkpoint and (An-

drews et al.), 1162–1174Malaria, rhomboid proteins and (Urban),

3054–3068 ReviewMale-specific lethal 1 (MSL1)

binding study using chromatin immu-noprecipitation and microarrays(Gilfillan et al.), 858–870

Male-specific lethal 2 (MSL-2)translation repression by UNR (Abaza

et al.), 380–389UNR and sex-lethal (SXL) corepression

of 368-379 (Duncan et al.), 368–379

Male-specific lethal (MSL) complexdistribution on X chromosome (Schü-

beler), 749–753 Perspectivetargeting of active genes on X chromo-

some (Alekseyenko et al.), 848–857

X-chromosome-wide profiling of dis-tribution (Legube et al.),871–883

Malignant melanomagenetics and therapeutics in the geno-

mic era (Chin et al.), 2149–2182Review

MAML1function in myogenesis (Shen et al.),

675–688Mammary gland

MTA3 repression of Wnt4 pathway in(Zhang et al.), 2943–2948

MAP65/PRC1effect of phosphorylation by MAP ki-

nase (Sasabe et al.), 1004–1014MAPK. See Mitogen-activated protein

kinase (MAPK)Mass spectrometry

use in proteomic screens of translationcomplexes (Fleischer et al.),1294–1307

Master regulatorstarget hub proteins as (Borneman),

435–448Maternal effect gene, in fully grown oo-

cytes (Evsikov et al.), 2713–2727Maternal-effect mutation

BRG1 regulation of zygotic genome ac-tivation (Bultman et al.), 1744–1754

Math3 (Zhu et al.), 2739–2753Matrix metalloproteinases (MMPs)

basement membrane remodeling (Ho-tary et al.), 2673–2686

liberation of ninjurin A ectodomain tosignal loss of cell adhesion(Zhang et al.), 1899–1910

Maturation-promoting factor (Miller etal.), 2410–2420

MBT repeatin dSfmbt protein (Klymenko et al.),

1110–11222MDC1 (mediator of DNA damage check-

point 1), acceleration of nonho-mologous end-joining of dys-functional telomeres (Dimi-trova and de Lange), 3238–3243

Mdm2. See Murine double-minute gene2 (Mdm2)

MEDEAautoregulation and imprinted gene ex-

pression in Arabidopsis (Barouxet al.), 1081–1086

Mediatorinteraction with TFIID (Marr et al.),

1458–1469role in integration of regulation of

fatty acid and metabolism in C.elegans (Taubert et al.),1137–1149

Medicago truncatula, control of nodula-tion in (Combier et al.), 3084–3088

MEF2C (myocyte enhancer factor 2C)MAML1 interaction with (Shen et al.),

675–688Meiosis

Hed1 attenuation of Rad51 in yeast(Tsubouchi and Roeder), 1766–1775

Red-Hed regulation (Sheridan andBishop), 1685–1691 Perspective

roles of SUMOylation in yeast (Chenget al.), 2067–2081

SUMO regulation of meiotic synap-tonemal complex formation (deCarvalho and Colaiácovo),1986–1992 Perspective


MEKK (mitogen extracellular signal-regulated kinase kinase)

role of Ste50p in regulation (Wu et al.),734–746

Melanomacontrol of proliferation and invasive-

ness by Mitf regulation of Dia1(Carreira et al.), 3426–3439

genetics and therapeutics of (Chin etal.), 2149–2182 Review

Membrane proteases (Urban), 3054–3068Review

Mesenchymal stem cells (MSCs)�-catenin mediation of TGF-� activity

(Jian et al.), 666–674Mesoderm

role of MACF1 in Wnt signaling (Chenet al.), 1933–1945

Mesodermal progenitor cellsspecification in zebrafish (Szeto and

Kimelman), 1923–1932Mesp (Davidson et al.), 2728–2738Metaplasia




Metastasisloss of transforming growth factor-�

type II receptor promotes meta-static head-and-neck squamoscell carcinoma (Lu et al.), 1331–1342

Metastatic tumor antigen 3 (MTA3)(Zhang et al.), 2943–2948

Methylation. See also DNA methyl-ation; Histone methylation

control of HOX genes (Papp andMüller), 2041–2054

DNMT1 and G9a coordination ofchromatin (Estève et al.), 3089–3103

Mga1as master regulator of development in

yeast (Borneman), 435–448MH2A1.1, PARP-1 down-regulation by

(Ouararhni et al.), 3324–3336Mi-2�

anti-inflammatory function of(Ramirez-Carrozzi et al.), 282–296

Mice. See MouseMicF, OmpF modulation by (Guillier et

al.), 2338–2348 ReviewMicroapthalmia

SOX2 mutations and (Taranova et al.),1187–1202

Microarray analysisof alternative splicing and nonsense-

mediated mRNA decay controlof gene expression (Pan et al.),153–158





�32-mediated heat-shock response(Nonaka et al.), 1776–1789taxane resistance by Txr1 andTSP-1 (Lih et al.), 2082–2095

Microphthalmia-associated transcrip-tion factor (Mitf) (Carreira etal.), 3426–3439

microRNA (miRNA)CMV 2b interference with pathways

in Arabidopsis (Zhang et al.),3255–3268

control of nodule development (Com-bier et al.), 3084–3088

control of translation and mRNA deg-radation (Valencia-Sanchez etal.), 515–524 Review

denoising feedback loops (Cohen etal.), 2769–2772 Perspective

diversity in Arabidopsis thaliana (Ra-jagopalan et al.), 3407–3425

GW182 linking of the miRNA path-way to mRNA decay (Behm-Ansmant), 1885–1898


in neuronal precursor specification (Liet al.), 2793–2805

pathways in plants (Vaucheret), 759–771 Review


regulation of microRNA processingand cancer implications (Thom-son et al.), 2202–2207

small RNAs from mouse germline(Watanabe et al.), 1732–1743

tissue-specific RNAi compared (Rao etal.), 147–152

Microtubulecytokinesis regulation by MAP kinase

via NtMAP65-1 (Sasabe et al.),1004–1014

Microtubule-associated proteinsNtMAP65-1 regulation of cytokinesis

(Sasabe et al.), 1004–1014Mid-hindbrain organizer

regulation of the organizing activityof, 185–198

Migration inhibitory factor (MIF)activation by HIF1� (Welford et al.),

3366–3371senescence delay (Maity and Kou-

menis), 3337–3341 PerpectiveMigration, neuronal polarity and


miRNA. See MicroRNA (miRNA)Mitf

oncogene, in melanoma (Chin et al.),2149–2182 Review

regulation of p27 via Dia1 (Carreira etal.), 3426–3439

Mitochondriaenolase as cofactor of tRNA targeting

toward mitochondria (Entelis etal.), 1609–1620

PPAR� coactivator-1� (PGC-1�) (Cor-vera et al.), 2193–2201 MeetingReview


sirtuins (Haigis and Guarente), 2913–2921 Review

Mitochondrial-type ribosomestranslation in mammalian sperm (Gur

and Breitbart), 411–416Mitogen-activated protein kinase

(MAPK)KSR/CNK/HYP role in RAS-depen-

dent RAF activation (Douziech

et al.), 807–819in pancreatic ductal adenocarcinoma


phosphorylation, Aveugle role in (Roi-gnant et al.), 795–806

regulation of cytokinesis via Nt-MAP65-1 (Sasabe et al.), 1004–1014

repression by c-Jun/AP-1 (Stepniak etal.), 2306–2314

Mitogen-activated protein kinase(MAPK) scaffold protein

membrane targeting of Ste5 (Garren-ton et al.), 1946–1958

Mitogen-activated protein kinase(MAPK) signaling

C. elegans GLA-3 control of (Kritikouet al.), 2279–2292


in melanoma (Chin et al.), 2149–2182Review

Mitogen extracellular signal-regulatedkinase kinase (MEKK)

role of Ste50p in regulation (Wu et al.),734–746

MitosisAKAP–HDAC3–Aurora B–HP1 path-

way (Li et al.), 2566–2579condensin complex in chromosome

arm cohesion (Lam et al.), 2973–2984

Emil as pseudosubstrate inhibitor ofAPC/C (Miller et al.), 2410–2420

SirT2 deacetylation of histone H4 dur-ing (Vaquero et al.), 1256–1261

Mitotic checkpointtopoisomerase II in budding yeast (An-

drews et al.), 1162–1174MIWI

in mouse spermatogenic cells (Grivnaet al.), 1709–1714

Mixed-lineage leukemia (MLL) proteinsMLL1/MLL2/SET1, �-catenin asso-

ciation with (Sierra et al.), 586–600

proteolysis of (Takeda et al.),2397–2409

MMPs. See Matrix metalloproteinases(MMPs)

MODYPdx1 enhancers ad targets for (Fujitani

et al.), 253–266MogR (Shen et al.), 3283–3295Molecular genetics

of osteoporosis (Ralston and de Crom-brugghe), 2492–2506 Review

Pax3 activation of Myf5 (Bajard et al.),2450–2464

Molecular sensora coactivator/corepressor/epigenetic code

for integrating signal-dependentprograms of transcriptional re-


sponse (Rosenfeld et al.), 1405–1428 Review

Monoallelic regulationX inactivation and dosage compensa-

tion (Heard and Disteche),1848–1867 Review

Monocytic leukemia zinc-finger protein(MOZ)

in hematoprotein development(Thomas et al.), 1175–1186

role in maintenance of hematopoieticstem cells (Katsumoto et al.),1321–1330

Morphogenesiscell shape remodeling in tracheal in-

vagination (Brodu and Casa-nova), 1817–1828

feeback control by aromatic alcoholsin fungi (Chen and Fink), 1150–1161

Mother against Decapentaplegic (MAD)dephosphorylation by pyruvate dehy-


MouseASPP2 as tumor suppressor gene

(Vives et al.), 1262–1267�-globin locus position and activity

(Ragoczy et al.), 1447–1457BRG1 regulation of zygotic genome ac-

tivation (Bultman et al.), 1744–1754

Cdc42 control of cell differentiationand �-catenin turnover in skin(Wu et al.), 571–585

deletion of akt1 and inhibition of tu-morigenesis in Pten+/− mice(Chen et al.), 1569–1574

development and tectonic modulationof Hedgehog signaling (Reiterand Skarnes), 22–27


EGFR-dependent lung cancer (Politi etal.), 1496–1510

evidence that a retinoic acid cannot bethe RXR-activating ligand inmouse epidermis keratinocytes(Calléja et al.), 1525–1538


fully grown oocyte transcriptome(Evsikov et al.), 2713–2727

genetic ablation of geminin in (Gonza-lez et al.), 1880–1884

histone H4 Ser1 phosphorylation dur-ing gametogenesis (Krishnamoor-thy et al.), 2580–2592

Insm1 in endocrine development (Gi-erl et al.), 2465–2478


keratins roles during hair follicle cy-


liver function without telomeres(Lazzerini Denchi et al.), 2648–2653

loss of transforming growth factor-�type II receptor promotes meta-static head-and-neck squamoscell carcinoma (Lu et al.), 1331–1342

monocytic leukemia zinc finger pro-tein (Thomas et al.), 1175–1186

monocytic leukemia zinc-finger pro-tein (MOZ) role in hematopoi-esis (Katsumoto et al.),1321–1330

p27 stability and tumor suppression(Besson et al.), 47–64


regulating Mdm2 and p53 in (Poy-urovsky and Prives), 125–131Perspective

role of MACF1 in Wnt signaling (Chenet al.), 1933–1945

role of p53 in tumor suppression andaging (Mendrysa et al.), 16–21


small RNAs in the mouse testis(Grivna et al.), 1709–1714




Mouse embryonic fibroblasts (MEFs),Taspase1 deficiency (Takeda etal.), 2397–2409

Mouse modelHedgehog/Ras in pancreatic cancer

(Pasca de Magliano et al.), 3161–3173


of pancreatic islet cell carcinogenesis(Gocheva et al.), 543–556

Mrc1p (Azvolinsky et al.), 3104–3116Mrcl TQ repeats

Cds1 activation (Xu et al.), 990–1003Mre11/Rad50/NBS1 (M/R/N)

BRCA1/BARD1, DNA damage-spe-cific interactions with (Green-berg et al.), 34–46

MreBinteraction with RNA polyerase in

chromosome segregation (Kruseet al.), 113–124

MRFs. See Myogenic regulatory factors(MRFs)

mRNA decay/degradationcontrol by miRNAs and siRNAs (Va-

lencia-Sanchez et al.), 515–524Review

of cytokine mRNAs (Lu et al.), 3174–3184

role of GW182 (Behm-Ansmant),1885–1898

mRNA quality controlassembly pathway of surveillance

complex (Behm-Ansmant andIzaurralde), 391–398 Perspective

mRNA stability, in fully grown oocytes(Evsikov et al.), 2713–2727

mRNPUNR and SXL corepression of MSL-2

translation (Duncan et al.), 368–379

MRTF (myocardin-related transcriptionfactor)

interaction with SRF (serum responsefactor) (Pipes et al.), 1545–1556Review

MSCs (mesenchymal stem cells)�-catenin mediation of TGF-� activity

(Jian et al.), 666–674MSH signaling


MSI1AGL19 repression in vernalization

pathway (Schönrock et al.),1667–1678

MSL. See Male-specific lethal (MSL)complex

MSL1. See Male-specific lethal 1 (MSL1)MSL-2. See Male-specific lethal 2 (MSL-

2)Msn2

effect of decreased TOR activity on(Powers et al.), 174–184

Msx1DNA-binding specificity, role of

PIAS1 in conferring (Lee et al.),784–794

MTA3 (metastatic tumor antigen 3)(Zhang et al.), 2943–2948

MTF-1interaction with TFIID and Mediator

(Marr et al.), 1458–1469MtHAP2-1 (Combier et al.), 3084–3088MT-MMP-dependent basement mem-

brane remodeling (Hotary et al.),2673–2686

mTORAkt signaling and (Shiojima and

Walsh), 3347–3365 ReviewSin1 as component of (Yang et al.),

2820–2832Mud2

cotranscriptional splicing, effect on(Lacadie et al.), 2055–2066

Multigene familyin mouse fully grown oocyte transcrip-

tome (Evsikov et al.), 2713–2727Munc13

Rho effects on (McMullan et al.), 65–76


Murine double-minute gene 2 (Mdm2)Lats2–p53 feedback loop (Aylon et al.),

2687–2700regulating in mice (Poyurovsky and

Prives), 125–131 Perspectiverole in tumor suppression and aging

(Mendrysa et al.), 16–21Muscle cachexia

regulation by a p53–PW1/Peg3-depen-dent pathway (Schwarzkopf etal.), 3440–3452

Muscle development (Shi and Garry),1692–1708 Review

Muscle differentiationp53 and PW1 regulation of muscle ho-

meostasis (Schwarzkopf et al.),3440–3452

Muscle regeneration (Shi and Garry),1692–1708 Review

Muscle stem cells (Shi and Garry), 1692–1708 Review

Muscular dystrophyrole of MAML1 in (Shen et al.), 675–

688MuSK

casein kinase 2-dependent serine phos-phorylation of (Cheusova et al.),1800–1816

Myc. See also c-MycCPEB inhibition of myc RNA transla-

tion (Groisman et al.), 2701–2712

IL-1� mediation of Myc angiogenicswitch (Shchors et al.), 2527–2538

Myoblastsdifferentiation, PIAS1–Msx1 interac-

tion (Lee et al.), 784–794role of lamin A/C and emerin inn dif-

ferentiation (Frock et al.), 486–500

Myocardin family of transcriptional co-activators (Pipes et al.), 1545–1556 Review

MyoDconservation of regulators and redun-

dancy in C. elegans (Baugh andHunter), 3342–3346 Perspective

effect of lamin A/C deficiency on(Frock et al.), 486–500

transcriptional regulation of body wallmuscle in C. elegans (Fukushigeet al.), 3395–3406

Myogenesisconservation of regulators and redun-


MAML1 function in (Shen et al.), 675–688

myocardin family of transcriptionalcoactivators (Pipes et al.), 1545–1556 Review

Pax3 activation of Myf5 (Bajard et al.),2450–2464

role of lamin A/C and emerin in (Frocket al.), 486–500

transcriptional regulation of body wallmuscle in C. elegans (Fukushigeet al.), 3395–3406

Myogenic regulatory factors (MRFs)conservation of regulators and redun-


early body wall muscle developmentin C. elegans (Fukushige et al.),3395–3406

myo-inositol monophosphatase, regula-tion of synapses and behavior by(Tanizawa et al.), 3296–3310

Myopathy (Shi and Garry), 1692–1708Review

Myosin, localization in tracheal invagi-nation (Brodu and Casanova),1817–1828

MZoepmesodermal progenitor cell specifica-


N

Nat-siRNA (natural cis-antisense tran-scripts)

regulation of gene expression in plants(Vaucheret), 759–711 Review

Natural variation in Arabidopsis vernal-ization response (Shindo et al.),3079–3083

ncRNA. See Noncoding RNA (ncRNA)Necrosis

programmed cell (Zong and Thomp-son), 1–15 Review

NEDD9 gene, in melanoma (Chin et al.),2149–2182 Review

NER (nucleotide excision repair)monoubiquitylation of histone H2A

(Bergink et al.), 1343–1352Neural circuit

for integrative behavior in C. elegans(Kodama et al.), 2955–2960

Neural patterningtectonic modulation of Hedgehog sig-

naling (Reiter and Skarnes), 22–27

NeuroblastAurora-A regulation of self-renewal

(Lee et al.), 3464–3474; (Wang etal.), 3453–3463

competence, regulation of (Cleary andDoe), 429–434

Pdm and Cas specify late-born neuro-nal identity (Grosskortenhauset al.), 2618–2627

Neurodegenerationprevention of retinal dystrophy by

nuclear receptor TLX (Zhang etal.), 1308–1320

Neurodegenerative diseasepolyglutamine disease and transcrip-

tion regulation (Riley and Orr),2183–2192 Review

Neurofibromatosis type 1 (NF1) (Walker

et al.), 3311–3323Neurogenesis

microRNA in neuronal precursorspecification (Li et al.),2793–2805

multiple functions of p27 in (Nguyenet al.), 1511–1524

polarity proteins in (Solecki et al.),2639–2647 Review

Neurogeninstabilization by p27kip1 (Nguyen et al.),

1511–1524Neuromuscular junction

casein kinase 2-dependent serine phos-phorylation of MuSK regulationof acetylcholine receptor aggre-gation at (Cheusova et al.),1800–1816

Neuronneurofibromatosis/expression in larval

(Walker et al.), 3311–3323spineless regulation of dendritic diver-

sity (Kim et al.), 2806–2819transcriptional regulation of dendrite

development (Parrish et al.),820–835

Neuronal polarity, in CNS development(Solecki et al.), 2639–2647 Re-view

Neuronal properties, Sox4/Sox11 estab-lishment of (Bergsland et al.),3475–3486

Neuron function, SIRT1 role in (Haigisand Guarente), 2913–2921 Re-view

Neurosporacircadian clock regulation (Brunner

and Schafmeier), 1061–1074 Re-view; (He et al.), 2552–2565

maturation of circadian clock protein(Shafmeier et al.), 297–306

Neurotransmitter releaseRho activation of (McMullan et al.),

65–76NFIC, 2513–2526NF�B. See Nuclear factor �BNHES

MDC1 acceleration of nonhomolo-gous end-joining of dysfunc-tional telomeres (Dimitrova andde Lange), 3238–3243

Ninjurin Aliberation by matrix metalloproteinase

to signal loss of cell adhesion(Zhang et al.), 1899–1910

Nitrogen-regulatory protein C (NtrC)structural studies of (De Carlo, et al.),

1485–1495Nodal

mesodermal progenitor cell specifica-tion (Szeto and Kimelman),1923–1932

Nodulation, microRNA control of (Com-bier et al.), 3084–3088

Non-cell autonomy (Walker et al.),3311–3323


Noncoding RNA (ncRNA)as cis-acting domain silencers (Pauler

and Barlow), 1203–1206 Per-spective

Evf-2 function as Dlx-3 transcriptionalcoactivator (Feng et al.), 1470–1484


miRNAs and siRNAs in Arabidopsis(Rajagopalan et al.), 3407–3425


Nonsense-mediated mRNA decay(NMD)

assembly pathway of surveillancecomplex (Behm-Ansmant andIzaurralde), 391–398 Perspective

microarray of alternative splicing (Panet al.), 153–158

trigger by SMG-1 phosphorylation ofUpf1 on exon junction complex(Kashima et al.), 355–367

NotchAurora-A (Wang et al.), 3453–3463cross-regulation with p63 in keratino-

cytes (Nguyen et al.), 1028–1042in epidermal differentiation (Blanpain

et al.), 3022–3035induction of c-Myc in T-cell leuke-

mia/lymphoma (Weng et al.),2096–2109

MAML1 function in myogenesis (Shenet al.), 675–688


regulation of precursor diversification(Zhu et al.), 2739–2753

NtrCstructural studies of (De Carlo, et al.),

1485–1495NuA4

acetylation by Htzl (Keogh et al.), 660–665

acetylation of H2A.Z and heterochro-matin boundaries (Babiarz etal.), 700–710

Nuclear evelopec-Fos–lamin A/C interaction at (Ivorra

et al.), 307–320Nuclear factor �B (NF�B)

acetylation of Stat1, effect of (Krämeret al.), 473–485

Bcl-3 effect on (Kashatus et al.), 225–235


Nuclear Hormone Receptor NHR-49regulation of fatty acid metabolism C.

elegans (Taubert et al.),1137–1149

Nuclear organization

�-globin locus position and activity(Ragoczy et al.), 1447–1457

phosphoCTD of RNA polymerase II(Phatnani and Greenleaf), 2922–2936 Review

Xist RNA and (Chaumeil et al.), 2223–2237

Nuclear periphery�-globin locus position and activity

(Ragoczy et al.), 1447–1457Nuclear receptor

Atrophin proteins as corepressors of(Wang et al.), 525–530

Brg1 and HDAC2 in glucocorticoid re-ceptor (Bilodeau et al.),2871–2886


Nuclear translocation, of Vax2 (Kim andLemke), 2833–2847

Nucleolar dominanceerasure of histone acetylation by Ara-

bidopsis HDA6 mediates large-scale gene silencing in (Earley etal.), 1283–1293

as a model for rRNA gene silencing(McStay), 1207–1214 Perspec-tive

Nucleosomedisplacement in transcription (Work-

man), 2009–2017 ReviewmH2A1.1-associated (Ouararhni et

al.), 3324–3336remodeling regulation of inflamma-

tory response by chromatin(Ramirez-Carrozzi et al.), 282–296

Nucleotide contextrecognition of initiation codon context

(Pisarev et al.), 624–636Nucleotide excision repair (NER)

monoubiquitylation of histone H2A(Bergink et al.), 1343–1352

Numbcortical polarity and spindle orienta-

tion (Lee et al.), 3464–3474as target of Aurora-A (Wang et al.),

3453–3463NuRD

Mi-2�/NuRD complexes during in-flammatory response (Ramirez-Carrozzi et al.), 282–296

NutrientsTOR pathway signaling and effect on

life span (Powers et al.), 174–184

O

ObesityKeystone meeting summary (Corvera


Oct4geminin interaction with (Gonzalez et

al.), 1880–1884

HIF-2� regulation by (Covello et al.),557–570

O-linked GlcNAc transferase (Shen etal.), 3283–3295

OmpA/OmpC/OmpF, regulating withsRNAs (Guillier et al.), 2338–2348 Review

Oncogenic RasBTG2 mediation of anti-Ras function

of p53 (Boiko et al.), 236–252Oocyte maturation

translation regulatory cascades (Va-sudevan et al.), 138–146 Per-spective

Oocyte-to-embryo transition (OET)(Evsikov et al.), 2713–2727

Open braintectonic effect on neural patterning

(Reiter and Skarnes), 22–27ORC (origin recognition complex)

identification in yeast by comparativegenomics (Nieduszynski et al.),1874–1879

Organismal growth control, non-cell au-tonomy (Walker et al.), 3311–3323

OrganogenesisNotch regulation of diversification of

precurors (Zhu et al.), 2739–2753

Pdx1 in foregut organ differentiationand pancreas function (Fujitaniet al.), 253–266


oriCMreB–RNAP interaction and chromo-

some segregation (Kruse et al.),113–124

Osteoporosis, genetics of (Ralston and deCrombrugghe), 2492–2506 Re-view

Outer membrane proteins, sRNA modu-lation of (Guillier et al.), 2338–2348 Review

Outside-in signalingtyrosine regulation of integrin func-

tion (Chen et al.), 927–932Oxidative stress premature senescence

from (Welford et al.), 3366–3371

P

p16Taspase1 and (Takeda et al.), 2397–

2409p21

mRNA stability regulation by RNPC1(Shu et al.), 2961–2972


role in p53 pathway (Gomes et al.),601–612

transcription of (Wood and Shilati-fard), 643–647 Perspective


p21Cip1

repression by c-Myc (Oskarsson et al.),2024–2029

p27regulation by Mitf (Carreira et al.),

3426–3439p27Kip1

function in neurogenesis (Nguyen etal.), 1511–1524

stability, subcellular localization, andtumor suppression (Besson etal.), 47–64

p35heat-shock factor 2 role in regulation

of (Chang et al.), 836–847p38


p48ectopic expression with Pdx1 and con-

version of endoderm to pancreas(Afelik et al.), 1441–1446

p53ASPP2 cooperation in tumor suppres-

sion (Vives et al.), 1262–1267BTG2 mediation of anti-Ras function

of (Boiko et al.), 236–252crystal structure of SV40 large T-anti-


IGF-1–AKT–TOR pathway interac-tions (Levine et al.), 267–275Review

Lats2–p53 feedback loop (Aylon et al.),2687–2700

p21 induction by (Shu et al.),2961–2972



P-TEFb function in the p53 pathway(Gomes et al.), 601–612

regulating in mice (Poyurovsky andPrives), 125–131 Perspective

regulation of muscle cachexia(Schwarzkopf et al.), 3440–3452


RNPC1 as direct target of (Shu et al.),2961–2972

role (Mendrysa et al.), 16–21role of clathrin in regulation (Enari et

al.), 1087–1099suppression by expression of Bcl-3

proto-oncogene (Kashatus etal.), 225–235

transcription of p21 (Wood and Shilati-fard), 643–647 Perspective

p53AIP1 promoterclathrin heavy chain binding to (Enari

et al.), 1087–1099p63

epidermal proliferation and differen-

tiation (Truong et al.),3185–3197


vertebrate limb regeneration and(Kawakami et al.), 3232–3237

p68 RNA helicaseregulation of transcriptional deactiva-

tion by promotion of RNA re-lease from chromatin (Buszczakand Spradling), 977–989

p300clathrin stabilization of p53–p300 in-

teraction (Enari et al.), 1087–1099

Paf1cotranscriptional splicing, effect on

(Lacadie et al.), 2055–2066PAMP (pathogen-associated molecular

pattern)regulation of PRR activities by subcel-

lular compartmentalization(Robatzek et al.), 537–542

PancreasInsm1 in endocrine development (Gi-

erl et al.), 2465–2478splenopancreatic interrelationship

(Asayesh et al.), 2208–2213Pancreas development

Pdx1 and p48 conversion of endodermto pancreas (Afelik et al.), 1441–1446

PDX-1 induction of acinoductal meta-plasia (Miyatsuka et al.), 1435–1440

Pdx1 role in (Fujitani et al.), 253–266Pancreas-specific knockout (Ijichi et al.),

3147–3160Pancreatic and duodenal homeobox fac-

tor 1 (PDX-1)acinar-to-ductal metaplasia induced

through Stat3 activation (Miya-tsuka et al.), 1435–1440

ectopic expression with Ptf1a/p48and conversion of endoderm topancreas (Afelik et al.), 1441–1446

Pancreatic cancergenetics and biology of (Hezel et al.),

1218–1249 ReviewHedgehog/Ras in (Pasca de Magliano

et al.), 3161–3173molecular pathogenesis (Rustgi),

3049–3053 Perpectiverole for cysteine cathepsin genes in

(Gocheva et al.), 543–556role of Smad4 in (Bardeesy et al.),

3130–3146Papillomagenesis

c-Myc represses p21Cip1 during (Os-karsson et al.), 2024–2029

ParA/ParB proteins, of Vibrio cholerae(Fogel and Waldor), 3269–3282

PARP-1, histone in mH2A1.1 down-regulation of (Ouararhni et al.),3324–3336

Patched, functional domains in (Lu etal.), 2539–2551

Pathogen-associated molecular pattern(PAMP)

regulation of PRR activities by sub-cellular compartmentalization(Robatzek et al.), 537–542

Pathwayassembly pathway of surveillance

complex (Behm-Ansmant andIzaurralde), 391–398 Perspective

Aveugle role in Raf activation in EGFreceptor signaling pathway(Roignant et al.), 795–806


Pattern-recognition receptors (PRRs)flagellin receptor FLS2 in Arabidopsis

(Robatzek et al.), 537–542Pax3

activation of Myf5 during myogenesis(Bajard et al.), 2450–2464

Pax5regulation of Flt3 by (Holmes et al.),

933–938Pax6 gene

Vax2 repression of (Kim and Lemke),2833–2847

Pax7regulation of muscle cachexia

(Schwarzkopf et al.), 3440–3452P-bodies


Pcf11role in recruitment of Rat1 to elonga-

tion complex (Luo et al.), 954–965

PcG. See Polycomb group (PcG)PDK1


Pdmregulation of neuroblast competence

(Cleary and Doe), 429–434specification of motor neuron identity

(Grosskortenhaus et al.), 2618–2627

PDP (pyruvate dehydrogenase phospha-tase)

Smad dephosphorylation by (Chen etal.), 648–653

Pds1topoisomerase II checkpoint and (An-

drews et al.), 1162–1174Pdx1

acinar-to-ductal metaplasia inducedthrough Stat3 activation (Miya-tsuka et al.), 1435–1440

ectopic expression with Ptf1a/p48 andconversion of endoderm to pan-creas (Afelik et al.), 1441–1446


Pdx1 enhancertargeted deletion of (Fujitani et al.),

253–266Peg1 (Grallert et al.), 2421–2436Peg3

regulation of muscle cachexia (Schwarz-kopf et al.), 3440–3452

PERcircadian rhythms in CLK phosphory-

lation and E-box binding (Yu etal.), 723–733

PER2 phosphorylation, differential ef-fects of (Vanselow et al.), 2660–2672

PerichondriumRunx2 expression in (Hinoi et al.),

2937–2942Peripheral nervous system (PNS)

microRNA in neuronal precursorspecification (Li et al.), 2793–2805

PESTFRQ phosphorylation (Shafmeier et

al.), 297–306PGC-1�

regulation of energetics in Leigh syn-drome (Cooper et al.), 2996–3009

Phd1as master regulator of development in

yeast (Borneman), 435–448Pheromone response, role of Ste5 (Gar-

renton et al.), 1946–1958Pho-repressive complex (PhoRC)

binding to DNA and methylated his-tones (Klymenko et al.), 1110–1122

Phoscillator (Merrow et al.), 2629–2633Perspective

Phosphoinositide 3-kinase (PI3K)antagonism by PTEN (Suzuki and

Han), 423–428cardiac growth and Akt signaling



PI3 kinase–AKT pathway, in mela-noma (Chin et al.), 2149–2182Review

Phosphorylationcasein kinase 2-dependent serine phos-

phorylation of MuSK (Cheusovaet al.), 1800–1816

Claspin regulation (Yoo, et al.), 772–783

CtIP binding of BRCA1 BRCT domain(Cheng et al.), 1721–1726

differential effects of PER2 (Vanselowet al.), 2660–2672

regulation of daily timing by (Merrowet al.), 2629–2633 Perspective

RNA polymerase II C-terminal repeatdomain (Phatnani and Green-leaf), 2922–2936 Review

of RS domain (Shen and Green), 1755–1765


of Upf1 by SMG-1 (Kashima et al.),355–367

Phosphotyrosine-binding (PTB) domainbinding of � integrin (Chen et al.), 927–

932Photoperiod

PHD finger protein VIL1 involvementin (Sung et al.), 3244–3248


Photoreceptordifferentiation, requirement of

Aveugle for (Roignant et al.),795–806

Phragmoplastregulation by MAPK via NtMAP65-1

(Sasabe et al.), 1004–1014Phyllotaxis (Sauer et al.), 2902–2911Phylogenetics

identifying origins by (Nieduszynskiet al.), 1874–1879

PI3K. See Phosphoinositide 3-kinase(PI3K)

PI3-kinase-like kinase (PIKK)damage-inducible, BRCA1 super-com-

plex formation (Greenberg etal.), 35–46

PIAS proteinsDNA-binding specificity on the Msx1

homeoprotein (Lee et al.), 784–794

role in transcriptional regulation(Sharrocks), 754–758 Perspec-tive

PIN (prostate intraepithelial neoplasia)deletion of akt1 and inhibition of tu-


PIN polarity (Sauer et al.), 2902–2911piRNAs. See Piwi-interacting RNAsPit1 (Zhu et al.), 2739–2753Pituitary

Notch regulation of diversification ofprecurors (Zhu et al.), 2739–2753

Pituitary tumorBrg1 and HDAC2 in glucocorticoid re-

ceptor (Bilodeau et al.), 2871–2886

Piwiassociation with rasiRNA in flies

(Saito et al.), 2214–2222interaction of GW182 with AGO1

PIWI domain (Behm-Ansmant),1885–1898


Piwi-interacting RNAs (piRNAs)in mouse spermatogenic cells (Grivna

et al.), 1709–1714piwi-interacting RNAs in mammalian

testes (Kim), 1993–1997 ReviewPKB signaling pathway

regulation of cardiac growth and coro-nary angiogenesis (Shiojima andWalsh), 3347–3365 Review

PKRresistance of late alphavirus mRNA to

eIF2� phosphorylation (Ventosoet al.), 87–100

Plant homeodomain (PHD) finger-con-taining protein VIN3-LIKE 1(VIL1), role in photoperiod andvernalization (Sung et al.),3244–3248

Plants. See also ArabidopsisArabidopsis leaf vein patterning con-

trol by polar auxin transport(Scarpella et al.), 1015–1027

auxin in biosynthesis effect on devel-opment (Cheng et al.), 1790–1799


polar auxin transport and venationpatterning (Scheres and Xu),922–926 Perspective

post-transcriptional small RNA path-ways (Vaucheret), 759–771 Re-view

Plasma membranemembrane targeting of Ste5 (Garren-

ton et al.), 1946–1958Plasmodium

rhomboid proteins in (Urban), 3054–3068 Review

Pleckstrin-homology (PH) domain, ofSte5 (Garrenton et al.), 1946–1958

Pluripotencygenetic ablation of geminin in the

mouse (Gonzalez et al.), 1880–1884

Polar auxin transportcontrol of leaf vein patterning (Scar-

pella et al.), 1015–1027control of leaf vein patterning (Scheres

and Xu), 922–926 PerspectivePolarity

atypical protein kinase C (aPKC)/Numb cortical polarity (Lee etal.), 3464–3474

auxin flow and (Sauer et al.), 2902–2911

neuronal (Solecki et al.), 2639–2647Review

PIN polarity (Sauer et al.), 2902–2911Pollen development

role of XA13 in (Bart et al.), 1215–1217Perspective; (Chu et al.), 1250–1255

Polo-like kinases (Miller et al.), 2410–2420

Polyadenylation


Pumilio-2 effect on (Padmanabhan andRichter), 199–209

Polycomb group (PcG)as antagonistic regulators of HOX

genes (Papp and Müller), 2041–2054

dependent Cyclin A repression in Dro-sophila (Martinez et al.),501–513

E4F1 mediation of BMI1 function inhematopoietic cells (Chagraouiet al.), 2110–2120

genome-wide mapping of target genes(Bracken et al.), 1123–1136

MEDEA autoregulation and imprintedgene expression in Arabidopsis(Baroux et al.), 1081–1086

protein complex with sequence-spe-cific DNA-binding and selectivemethyl-lysine-binding activi-ties (Klymenko et al.),1110–1122

repression of the floral activatorAGL19 in the FLC-independentvernalization pathway (Schön-rock et al.), 1667–1678

Polycomb response elements (PREs)HOX genes, control of (Papp and

Müller), 2041–2054Pho-repressive complex (PhoRC) bind-

ing to (Klymenko et al.), 1110–1122

Polyglutamine disease and transcriptionregulation (Riley and Orr),2183–2192 Review

Polynucleotide phosphorylase (Suzuki etal.), 2605–2617

POMC (proopiomelanocortin) generepression, Brg1 and HDAC2 role in

(Bilodeau et al.), 2871–2886Positive feedback loop


Post-transcriptional gene silencing(PTGS)

small RNA pathways in plants(Vaucheret), 759–771 Review

Post-transcriptional regulationof circadian clock of cyanobacteria and

Neurospora (Brunner andSchafmeier), 1061–1074 Review

of microRNAs and its implications forcancer (Thomson et al.), 2202–2207

WT1(+KTS) enhancement of transla-tion (Bor et al.), 1597–1608

Post-translationalFRQ functions (Shafmeier et al.), 296–

306PPAR� (�)

role in epidermis keratinocytes (Cal-léja et al.), 1525–1538

Prader-Willi syndrome (PWS)Rbbp1/Arid4b and Rbbp1l1/Arid4b

regulation of imprinting (Wu etal.), 2859–2870

PRBeffect of lamin A/C deficiency on

(Frock et al.), 486–500Precursor cells, Notch regulation of di-

versification (Zhu et al.), 2739–2753

Preinitiation complex (Zanton andPugh), 2250–2265

Premature termination codonmicroarray analysis of alternative

splicing and nonsense-mediatedmRNA decay to control geneexpression (Pan et al.), 153–158

Pre-mRNA splicingcoupling transcription to splicing (Das

et al.), 1100–1109evolution (Izquierdo and Valcárcel),

1679–1684 PerspectivePREs. See Polycomb response elements

(PREs)Presenilin (Urban), 3054–3068 ReviewPriA helicase, limitation on RecA activ-

ity during replication by (Mahdiet al.), 2135–2147

Primitive streakin MACF1−/− mice(Chen et al.), 1933–

1945Pro-B cells

Pax5 repression of Flt3 (Holmes et al.),933–938

Procambiumcontrol of vascular patterning by polar

auxin transport (Scarpella et al.),1015–1027

Progenitor cellsCdc42 control of differentiation (Wu et

al.), 571–585differentiation of GATA-1-null cells

(Kitajima et al.), 654–659hypoxia effects on (Covello et al.),

557–570multiple temporal identity factors and

neuroblast competence (Clearyand Doe), 429–434

Pax5 repression of Flt3 in pro-B cells(Holmes et al.), 933–938

regulation of mesodermal specifica-tion in zebrafish (Szeto andKimelman), 1923–1932

role of LIS1 in brain development(Vallee and Tsai), 1384–1393Perspective

SOX2 as regulator of retinal neural pro-genitor competence (Taranovaet al.), 1187–1202


Programmed cell necrosis (Zong andThompson), 1–15 Review

Proliferation, p63 regulation of epider-mal (Truong et al.), 3185–3197

Promoterhistone variant mH2A1.1 effect on

(Ouararhni et al.), 3324–3336quorom sensing-controlled (Zhu et

al.), 2754–2767

�32-mediated heat-shock response(Nonaka et al.), 1776–1789

Proopiomelanocortin (POMC) generepression, Brg1 and HDAC2 role in

(Bilodeau et al.), 2871–2886Prop1 (Zhu et al.), 2739–2753Prostaglandin


Proteasesgenetic analysis of cysteine cathepsin

in cancer (Gocheva et al.), 543–556


ProteasomeGli protein destruction by (Huntzicker

et al.), 276–281Protein kinase. See also specific kinases

resistance of late alphavirus mRNA toeIF2� phosphorylation (Ventosoet al.), 87–100

Protein localization, by inositol mono-phosphatase (Tanizawa et al.),3296–3310

Protein multimerizationPatched (Ptc) membrane protein (Lu et

al.), 2539–2551Protein phosphorylation. See also Phos-

phorylationPER-dependent rhythms in CLK phos-

phrylation and E-box binding(Yu et al.), 723–733

Protein–protein interactionPIAS1 and Msx1 homeoprotein (Lee et

al.), 784–794Protein stability

destabilization of CLK and PER byDOUBLE-TIME (DBT) kinase(Yu et al.), 723–733

Protein translation. See TranslationProtein turnover

Patched (Ptc) membrane protein (Lu etal.), 2539–2551

Proteolysisregulated intramembrane in Bacillus

subtilis (Ellermeier and Losick),1911–1922

regulation of transcription factor la-tency by receptor-activated pro-teolysis (Andréasson et al.),1563–1568

Proteomicsscreens of translation complexes

(Fleischer et al.), 1294–1307Protocadherins (Halbleib and Nelson),

3199–3214 ReviewProto-oncogene

Bcl-3 suppression p53 activation (Kas-hatus et al.), 225–235

PRRs (pattern-recognition receptors)flagellin receptor FLS2 in Arabidopsis

(Robatzek et al.), 537–542PrsW protease, from Bacillus subtilis

(Ellermeier and Losick), 1911–1922


Pseudouridineribosomal RNA modification in dys-

keratosis congenita (Wong etal.), 2848–2858

PTB (phosphotyrosine-binding) domainbinding of � integrin (Chen et al.), 927–

932P-TEFb

function in the p53 pathway (Gomeset al.), 601–612

PTENcardiac growth and Akt signaling



genetic redundancy for functions of(Suzuki and Han), 423–428


regulation of expression by nuclear re-ceptor TLX (Zhang et al.), 1308–1320

Ptf1aectopic expression with Pdx1 and

conversion of endoderm topancreas (Afelik et al.), 1441–1446

pancreatic ductal adenocarcinoma (Iji-chi et al.), 3147–3160

PTGS (post-transcriptional gene silenc-ing)

small RNA pathways in plants(Vaucheret), 759–771 Review

PU.1MOZ (monocytic leukemia zinc-

finger protein) interaction with(Katsumoto et al.), 1321–1330

PUFA (polyunsaturated fatty acid)regulation og metabolism in C. el-

egans (Taubert et al.), 1137–1149

Pumilio-2regulation of translation (Padmanab-

han and Richter), 199–209PW1

regulation of muscle cachexia (Schwarz-kopf et al.), 3440–3452

Pyruvate dehydrogenase phosphatase(PDP)

Smad dephosphorylation by (Chen etal.), 648–653

Q

Quorom sensingfeeback control of morphogenesis by

aromatic alcohols (Chen andFink), 1150–1161

in Vibrio harveyi (Zhu et al.), 2754–2767

by yeast (Sprague and Winans), 1045–1049 Perspective

R

Race-specific resistancerice Xa13 gene and disease resistance

(Chu et al.), 1250–1255Rad51

Dmc1 interaction (Sheridan andBishop), 1685–1691 Perspective

Hed1 attenuation of (Tsubouchi andRoeder), 1766–1775

Rad54dissociation of (Symington and Heyer),

2479–2486 PerspectiveTid1 and (Holzen et al.), 2593–2604

Radial cortical migration, role of HSF2 in(Chang et al.), 836–847

Radial migrationp27kip1 promotion of neuronal

(Nguyen et al.), 1511–1524Radiation response, senescence and (Ma-

ity and Koumenis), 3337–3341Perpective

Rafactivation by KSR (Douziech et al.),

807–819Aveugle role in activation in EGF re-

ceptor signaling pathway (Roi-gnant et al.), 795–806


RAR�

role in epidermis keratinocytes (Cal-léja et al.), 1525–1538

RasBTG2 mediation of anti-Ras function

of p53 (Boiko et al.), 236–252family of proto-oncogenes, in mela-

noma (Chin et al.), 2149–2182Review

Hedgehog/Ras in pancreatic cancer(Pasca de Magliano et al.), 3161–3173

KSR activation of RAF (Douziech etal.), 807–819

lung tumorigenesis and p27 (Besson etal.), 47–64

overexpression and promotion of head-and-neck squamos cell carci-noma (Lu et al.), 1331–1342


Ras association (RA)-like domainrole in Ste50p function (Wu et al.),

734–746rasiRNAs, Piwi association with (Saito

et al.), 2214–2222Ras signaling



in non-cell-autonomous growth con-trol (Walker et al.), 3311–3323

Rat1role in RNA pol II termination (Luo et

al.), 954–965Rb

BTG2 effect on (Boiko et al.), 236–252Rbbp1/Arid4b and Rbbp1l1/Arid4b,

regulation of imprinting by (Wuet al.), 2859–2870

RBP-JNotch signaling in epidermal differen-

tiation (Blanpain et al.),3022–3035

Rdh54/Tid1dissociation of Dmc1–dsDNA fila-

ments (Symington and Heyer),2479–2486 Perspective

rDNA. See Ribosomal DNAReactive oxygen species


RecARep and PriA limitation of RecA activ-

ity during replication fork repair(Mahdi et al.), 2135–2147

RecA homologsHed1 attenuation of Rad51 in yeast


RecBCD, replication fork repair and(Mahdi et al.), 2135–2147

Receptor-activated proteolysisregulation of transcription factor la-

tency by (Andréasson et al.),1563–1568

Receptor-like kinaseFLS2 in Arabidopsis (Robatzek et al.),

537–542Receptor tyrosine kinase

activation, in melanoma (Chin et al.),2149–2182 Review

Aveugle role in Raf activation in EGFreceptor signaling pathway(Roignant et al.), 795–806


Recessive generice Xa13 gene and disease resistance

(Chu et al.), 1250–1255RecFOR, replication fork repair and

(Mahdi et al.), 2135–2147Recombinase Rad51

Dmc1 interaction (Sheridan andBishop), 1685–1691 Perspective

RecombinationHed1 attenuation of Rad51 in yeast


Red-Hed regulation of (Sheridan andBishop), 1685–1691 Perspective


Red-Hed regulation of recombination(Sheridan and Bishop), 1685–1691 Perspective

Regeneration, regulation of vertebrate


limb (Kawakami et al.),3232–3237

Regulated intramembrane proteolysis(Urban), 3054–3068 Review

Regulated localizationcontrol of ribonucleotide reductase lo-

calization through an anchoringmechanism involving Wtm1(Lee and Elledge), 334–344

Regulated proteolysisregulation of �s stability by IraP (Boug-

dour et al.), 884–897regulation of transcription factor la-

tency by receptor-activated pro-teolysis (Andréasson et al.),1563–1568

Regulation3� UTR effects on upstream ORFs (Sa-

chs and Geballe), 915–921 Per-spective

histone sumoylation as negative regu-lator (Nathan et al.), 966–976

MEDEA autoregulation and imprintedgene expression in Arabidopsis(Baroux et al.), 1081–1086

Red-Hed regulation of recombination(Sheridan and Bishop), 1685–1691 Perspective

roles of clathrin in p53 regulation(Enari et al.), 1087–1099

SOX2 as regulator of retinal neural pro-genitor competence (Taranovaet al.), 1187–1202


tyrosine regulation of integrin func-tion (Chen et al.), 927–932

Regulatory cascades, translation (Va-sudevan et al.), 138–146 Per-spective

Regulatory networks, in hepatocytes(Kyrmizi et al.), 2293–2305

RENT (regulator of nucleolar silencingand telophase exit) (Huang etal.), 2887–2901

ReorientationSTAT1 dephosphorylation domain

shifts (Mertens et al.), 3372–3381

Repeat-associated small interferingRNAs (rasiRNAs), Piwi associa-tion with (Saito et al.), 2214–2222

Rep helicase, limitation on RecA activ-ity during replication by (Mahdiet al.), 2135–2147

Replicationcheckpoint, two-stage activation of

Cds1 (Xu et al.), 990–1003chromosome instability increased by

defects in (Admire et al.), 159–173

DTL/CDT2 role in G2/M checkpoint

(Sansam et al.), 3117–3129Rrm3p DNA helicase, global replica-

tion effects of (Azvolinsky etal.), 3104–3116

Replichores, Escherichia coli (Wang etal.), 1727–1731

Repressionanti-repression, control of flagellar

motility by (Shen et al.), 3283–3295

trans-repression of POMC gene (Bilo-deau et al.), 2871–2886

trans-repression sensors and signals(Rosenfeld et al.), 1405–1428Review

Reproductive isolation (Evsikov et al.),2713–2727

Response elementarylpyrazole compound effect on glu-

cocorticoid (Wang et al.), 689–699

REST/NRSF (Bergsland et al.), 3475–3486

RETsignaling in kidney development (Jain

et al.), 321–333Retina

retinal dystrophy prevention bynuclear receptor TLX (Zhang etal.), 1308–1320


Retinal progenitor identitySOX2 as regulator of retinal neural pro-

genitor competence (Taranovaet al.), 1187–1202

Retinal stem cellsHedgehog signaling in (Locker et al.),

3036–3048Retroelements, in fully grown oocytes

(Evsikov et al.), 2713–2727Retrotransposons

derived siRNAs in oocytes and germ-line small RNAs in testes (Wa-tanabe et al.), 1732–1743


RNAi control of telomere length inDrosophila (Savitsky et al.),345–354

translation of mammalian LINE-1(Alisch et al.), 210–224

RhabdomyosarcomaASPP2 as tumor suppressor gene

(Vives et al.), 1262–1267RhoA

p27kip1 promotion of neuronal mi-gration by blocking signal-ing (Nguyen et al.), 1511–1524

presynaptic activation of neurotrans-mitter release in C. elegans(McMullan et al.), 65–76

RhoGAPeffect on tracheal invagination in Dro-

sophila (Brodu and Casanova),1817–1828

Rho GTPasesCdc42 control of cell differentiation

and �-catenin turnover in skin(Wu et al.), 571–585

Rhomboid proteins (Urban), 3054–3068Review

Rho signalingrole of myocardin family of transcrip-

tional coactivators (Pipes et al.),1545–1556 Review

Rhox cluster silencing by Dnmt3a/Dnmt3b (Oda et al.), 3382–3394

Ribonucleotide reductase (RNR)Wtm1 nuclear anchor for (Lee and

Elledge), 334–344Ribosomal DNA (rDNA)

recombination, cohesion clamp and(Huang et al.), 2887–2901

silencing, Tof2 (Huang et al.), 2887–2901

Ribosomal RNA (rRNA)gene silencing and nucleolar domi-

nance (McStay), 1207–1214 Per-spective

gene silencing requirement for HDA6(Earley et al.), 1283–1293

pseudouridine modification in dys-keratosis congenita (Wong etal.), 2848–2858

SIRT7 association with active rRNAgenes (Ford et al.), 1075–1080

Ribosomeproteomic screens of translation com-

plexes (Fleischer et al.), 1294–1307


Ribosome biogenesiscontrol by RNA polymerase I activity

(Laferté et al.), 2030–2040coordination of RNA Pol I, II, and III

activities (Michels and Hernan-dez), 1982–1985 Perspective

Ribozymecotranscriptional splicing, effect on

(Lacadie et al.), 2055–2066Rice

roled xa13 gene in fertility and diseaseresistance (Bart et al.), 1215–1217 Perspective

xa13 gene functions (Chu et al.), 1250–1255

Rictor, as component of mTOR (Yang etal.), 2820–2832

RIDA (regulatory inactivation of DnaA),in Escherichia coli (Riber et al.),2121–2134

RINGO/Spy mRNA translationPumilio-2 control of (Padmanabhan

and Richter), 199–209RISC

antiviral function of Ago2 (van Rij etal.), 2985–2995


regulation of microRNA processing(Thomson et al.), 2202–2207

R-loopinfluence on genome stability (Li and

Manley), 1838–1847 ReviewRNA cyclization, dengue virus genome

(Filomatori et al.), 2238–2249RNA decay. See also mRNA decay/deg-

radationspecificity factor for CsrB (Suzuki et

al.), 2605–2617RNA-dependent silencing


RNA exportrole of P68 helicase in (Buszczak and

Spradling), 977–989Wilms’ tumor 1 (WT1) gene (+KTS iso-

form) function with a CTE toenhance translation from an un-spliced RNA with a retained in-tron (Bor et al.), 1597–1608

RNA helicaseP68 regulation of transcriptional deac-

tivation (Buszczak and Spra-dling), 977–989

RNA interference (RNAi)as antiviral immune defense mecha-

nism in Drosophila (van Rij etal.), 2985–2995

control of telomere length (Savitsky etal.), 345–354

endogenous small RNAs in Tetrahy-mena (Lee and Collins), 28–33


study of TFIID and Mediator interac-tion (Marr et al.), 1458–1469


RNAi suppressor, of Drosophila C virus(van Rij et al.), 2985–2995

RNA polymerasecoordination of RNA Pol I, II, and III

activities (Michels and Hernan-dez), 1982–1985 Perspective

interaction with MreB polyerase inchromosome segregation (Kruseet al.), 113–124

RNA-dependent RNA polymerasemechanism of dengue virusRNA synthesis (Filomatori etal.), 2238–2249

RNA polymerase I (pol I)control of ribosome biogenesis (Laferté

et al.), 2030–2040SIRT7 activation of (Ford et al.), 1075–

1080RNA polymerase II (pol II)

distribution during erythroid matura-tion (Ragoczy et al.), 1447–1457

functional coupling to spliceosome as-

sembly (Das et al.), 1100–1109p21, role of (Gomes et al.), 601–612phosphorylation of C-terminal repeat

domain (Phatnani and Green-leaf), 2922–2936 Review

role of Tar1 in transcription termina-tion (Luo et al.), 954–965

RNA polymerase III (polIII)role for RNase P in Pol III transcription

(Reiner et al.), 1621–1635RNase P

role in RNA polymerase III transcrip-tion (Reiner et al.), 1621–1635

RNA silencingcucumber mosaic virus 2b suppressor

inhibition of AGO1-mediatedcleavage (Zhang et al.), 3255–3268


RNA synthesismechanism of dengue virus (Filoma-

tori et al.), 2238–2249RNPC1

p21 mRNA stability regulation by(Shu et al.), 2961–2972

Rnr2, Wtm1 is nuclear anchor for (Leeand Elledge), 334–344

ROCK-dependent invasiveness, Mitfdepletion effect on (Carreira etal.), 3426–3439

Root development, lateral (Sauer et al.),2902–2911

RpoSstability regulation by IraP (Bougdour

et al.), 884–897Rrm3p DNA helicase, global replication

effects of (Azvolinsky et al.),3104–3116

rRNA. See Ribosomal RNA (rRNA)RS domain

mechanism of function (Shen andGreen), 1755–1765

RssBIraP interaction with activity of (Boug-

dour et al.), 884–897RSS fragment transposition

detection and quantification of (Schlis-sel et al.), 1539–1544 Perspec-tive

RTK. See Receptor tyrosine kinaseRunx2 (Hinoi et al.), 2937–2942RuvABC, replication fork repair and

(Mahdi et al.), 2135–2147

S

�32

heat-shock response (Nonaka et al.),1776–1789

�E-regulated sRNAs (Guillier et al.),2338–2348 Review

�s

stability regulation by IraP (Bougdouret al.), 884–897

�w

activation in Bacillus subtilis by regu-lated intramembrane proteoly-sis (Ellermeier and Losick),1911–1922

S6Kcardiac growth and Akt signaling


Saccharomycesidentifying origins by phylogenetics

(Nieduszynski et al.), 1874–1879

Saccharomyces cerevisiaeanaphase-promoting complex (APC)


chromosome arm cohesion during mi-tosis (Lam et al.), 2973–2984

cotranscriptional splicing (Lacadie etal.), 2055–2066

enolase as cofactor of tRNA targetingtoward mitochondria (Entelis etal.), 1609–1620

feeback control of morphogenesis byaromatic alcohols (Chen andFink), 1150–1161


histone H4 Ser1 phosphorylation and(Krishnamoorthy et al.), 2580–2592






proteomic screens of translation com-plexes (Fleischer et al.), 1294–1307


role of protein arginine methylation inthe formation of silent chroma-tin (Yu et al.), 3249–3254

roles of SUMOylation in yeast meiosis(Cheng et al.), 2067–2081

Rrm3p DNA helicase (Azvolinsky etal.), 3104–3116

SAS-mediated acetylation of histoneH4 Lys16 (Shia et al.), 2507–2512




SAGAH2A.Z acetylation (Babiarz et al.),

700–710SAM domain. See Sterile � motif (SAM)

domainSANT domain

of Atrophin proteins (Wang et al.),525–530

SAS (Something About Silencing)aectylation of histone H4 Lys16 (Shia

et al.), 2507–2512Satellite cells

muscle stem cells (Shi and Garry),1692–1708 Review

Scaffold proteinKSR in Drosophila (Douziech et al.),

807–819mitogen-activated protein kinase

(MAPK) (Garrenton et al.),1946–1958

Schizosaccharomyces pombeCLIP170-associated protein (CLASP)

(Grallert et al.), 2421–2436parallel pathways recruiting Crb2 to

DSBs (Du et al.), 1583–1596two-stage activation of Cds1 (Xu et

al.), 990–1003Sclerostin (SOST) gene, osteoporosis and

(Ralston and de Crombrugghe),2492–2506 Review

Seed developmentMEDEA autoregulation and imprinted

gene expression in Arabidopsis(Baroux et al.), 1081–1086

Segregation. See Chromosome segrega-tion

Selector genefunctions of homeodomain-containing

and homeodomain-less iso-forms encoded by homothorax(Noro et al.), 1636–1650

Self-renewalAurora-A regulation of (Lee et al.),

3464–3474; (Wang et al.), 3453–3463



SenescenceCPEB control of (Groisman et al.),

2701–2712delayed (Maity and Koumenis), 3337–

3341 PerpectiveE4F1 mediation of BMI1 function in

hematopoietic cells (Chagraouiet al.), 2110–2120

HIF1� delay of premature (Welford etal.), 3366–3371

Senseless (sens), inhibition of expressionby miRNA (Li et al.), 2793–2805

Sensora coactivator/corepressor/epigenetic

code for integrating signal-de-pendent programs of transcrip-tional response (Rosenfeld etal.), 1405–1428 Review


Sensory organ precursors (SOPs), mi-croRNA specification of (Li etal.), 2793–2805

Serine–arginine (SR) proteinsmechanism of RS domain function

(Shen and Green), 1755–1765Sertoli cell


Serum response factor (SRF)myocardin family of transcriptional

coactivators association with(Pipes et al.), 1545–1556 Review

Sex-lethal (SXL) proteincorepression of msl-2 translation with

UNR (Duncan et al.), 368–379UNR interaction with (Abaza et al.),

380–389Sex-specific function

UNR and SXL corepression of msl-2translation (Duncan et al.), 368–379

Sexual developmentrole of XA13 in pollen development

(Chu et al.), 1250–1255Sgs1/BLM helicases

dissociation of D-loops by (Symingtonand Heyer), 2479–2486 Perspec-tive

Shh. See Sonic hedgehog (Shh)Short hairpin RNA (shRNA) library

search for mediators of tumor suppres-sion (Boiko et al.), 236–252

Short interfering RNAs. See siRNAsSignaling. See also Akt; Hedgehog; Wnt

signalingAveugle role in Raf activation in EGF

receptor signaling pathway(Roignant et al.), 795–806



mechanism of Wnt/�-catenin signal-ing (Willert and Jones),1394–1404 Review



talpid3 gene and Hedgehog signaling(Davey et al.), 1365–1377

tyrosine regulation of integrin func-tion (Chen et al.), 927–932

Signal transduction


integral membrane protein anchor forSte50p/Ste11p in HOG pathway(Wu et al.), 734–746

regulated intramembrane proteolysis(Ellermeier and Losick), 1911–1922



Silencing. See also Gene silencing; RNAsilencing

effect of H2A.Z acetylation (Babiarz etal.), 700–710



Silent chromatinrole of arginine methylation in (Yu et

al.), 3249–3254sister chromatid cohesion in (Huang

and Moazed), 132–137 Perspec-tive

Silent-Information Regulator (SIR) pro-teins

effect of H2A.Z acetylation (Babiarz etal.), 700–710

Sin1, identification as TORC2 compo-nent (Yang et al.), 2820–2832

Sir2mammalian homologs (Haigis and

Guarente), 2913–2921 ReviewrDNA silencing (Huang et al.), 2887–

2901role of protein arginine methylation in

the formation of silent chroma-tin (Yu et al.), 3249–3254

siRNAscontrol of translation and mRNA deg-

radation (Valencia-Sanchez etal.), 515–524 Review

diversity in Arabidopsis thaliana (Ra-jagopalan et al.), 3407–3425

from mouse oocytes (Watanabe et al.),1732–1743

pathways in plants (Vaucheret), 759–771 Review


SIRT1-7roles in physiology, aging and calorie

restriction (Haigis and Guarente),2913–2921 Review

SirT2deacetylation of histone H4 during mi-

tosis (Vaquero et al.), 1256–1261

SirtuinSIRT7 activation of RNA Pol I tran-


scription by (Ford et al.), 1075–1080

Sister chromatid cohesionrequirement for the condensin com-

plex in (Lam et al.), 2973–2984in silent chromatin (Huang and

Moazed), 132–137 PerspectiveSite-1 cleavage, of RsiW in Bacillus sub-

tilis (Ellermeier and Losick),1911–1922

Skeletal musclecasein kinase 2-dependent serine phos-

phorylation of MuSK (Cheusovaet al.), 1800–1816

regulation of cachexia (Schwarzkopf etal.), 3440–3452

SkinCdc42 control of cell differentiation

and �-catenin turnover in skin(Wu et al.), 571–585



Slicer (Saito et al.), 2214–2222Smad

dephosphorylation by pyruvate dehy-drogenase phosphatase (Chen etal.), 648–653

SMAD4in pancreatic ductal adenocarcinoma


role in pancreatic development andcancer (Bardeesy et al.), 3130–3146

Small interfering RNAs. See siRNAsSmall, noncoding RNA gene

role of RNase P in RNA polymerase IIItranscription of (Reiner et al.),1621–1635

Small RNAsendogenous small RNAs in Tetrahy-

mena (Lee and Collins), 28–33from mouse germline (Watanabe et

al.), 1732–1743in mouse spermatogenic cells (Grivna

et al.), 1709–1714pathways in plants (Vaucheret), 759–

771 Reviewpiwi-interacting RNAs in mammalian

testes (Kim), 1993–1997 ReviewSMG-1

phosphorylation of Upf1 on exon junc-tion complex (Kashima et al.),355–367

SMG-1–Upf1–eRF1–eRF3 complex (SURF)binding to exon junction complex, ef-

fect of (Kashima et al.), 355–367Smith autoantigen

telomerase and Cajal body associationwith (Fu and Collins), 531–536

Smoas target of casein kinase I in Hedge-

hog signaling (Price), 399–410Review

Smooth musclerole of myocardin family of transcrip-

tional coactivators in (Pipes etal.), 1545–1556 Review

Sm proteinstelomerase and Cajal body association

with (Fu and Collins), 531–536SOC1

AGL19 and (Schönrock et al.), 1667–1678

Sok2role in regulation of development in

yeast (Borneman), 435–448Somatic hypermutation (SHM)

leukemia and lymphoma as cost foradaptive immunity (Schlissel etal.), 1539–1544 Perspective

Something About Silencing (SAS)aectylation of histone H4 Lys16 (Shia

et al.), 2507–2512Somite

mesodermal progenitor cell specifica-tion (Szeto and Kimelman),1923–1932

Sonic hedgehog (Shh). See also Hedgehogcoexpression of Dlx-2,5, and 6 and

Evf-2 transcripts in the brain(Feng et al.), 1470–1484

Gli protein mediation of effects (Hunt-zicker et al.), 276–281



SOPs (sensory organ precursors), mi-croRNA specification of (Li etal.), 2793–2805

SOST (sclerostin) gene, osteoporosis and(Ralston and de Crombrugghe),2492–2506 Review

Sox2as dose-dependent regulator of retinal

neural progenitor competence(Taranova et al.), 1187–1202

in taste bud development (Okubo etal.), 2654–2659

Sox4/Sox11, control of neurogenesis(Bergsland et al.), 3475–3486

Specification of trunk and tail somites inthe zebrafish blastula (Holley),1831–1837 Perspective

Spermsmall RNAs in mouse spermatid

(Grivna et al.), 1709–1714translation in (Gur and Breitbart), 411–

416Spermatogenesis

histone H4 Ser1 phosphorylation dur-ing (Krishnamoorthy et al.),2580–2592

small RNAs and (Grivna et al.), 1709–1714

WT1 role in (Rao et al.), 147–152Spinal bulbar muscular atrophy (SBMA)

(Riley and Orr), 2183–2192 Re-view

Spindle orientationAurora-A regulation of (Lee et al.),

3464–3474Spineless

dendrite morphogenesis and (Crewsand Brenman), 2773–2778 Per-spective

regulation of dendritic diversity (Kimet al.), 2806–2819

regulation of diversity (Kim et al.),2806–2819

Spinocerebellar ataxia (SCA) (Riley andOrr), 2183–2192 Review

Splenopancreatic interrelationship (Asayeshet al.), 2208–2213

Spliceosome assemblyfunctional coupling of RNAP II tran-

scription to (Das et al.), 1100–1109

mechanism of RS domain function(Shen and Green), 1755–1765

Splicing. See also Alternative splicingcotranscriptional splicing in yeast

(Lacadie et al.), 2055–2066evolution of pre-mRNA (Izquierdo and

Valcárcel), 1679–1684 Perspec-tive

global analysis of alternative splicing(Pan et al.), 153–158

mechanism of RS domain function(Shen and Green), 1755–1765

Sporulationhistone H4 Ser1 phosphorylation and

(Krishnamoorthy et al.), 2580–2592

Sps1 (Krishnamoorthy et al.), 2580–2592

SPS (Ssy1-Ptr3-Ssy5)-sensorregulation of transcription factor Stp1

(Andréasson et al.), 1563–1568SRF

role in body wall myogenesis (Fuku-shige et al.), 3395–3406

SRNAsmodulating the outer membrane with

(Guillier et al.), 2338–2348 Re-view

in quorom sensing (Zhu et al.), 2754–2767

Srs2/UvtDdissociation of Rad51/RecA-ssDNA

filaments (Symington andHeyer), 2479–2486 Perspective

Starvationregulation of �s stability by IraP (Boug-

dour et al.), 884–897Stat1

acetylation of (Krämer et al.), 473–485dephosphorylation domain shifts

(Mertens et al.), 3372–3381Stat3

PDX-1 induction of acinoductal meta-


plasia (Miyatsuka et al.), 1435–1440

Ste5membrane targeting of (Garrenton et

al.), 1946–1958Ste12

role in regulation of development inyeast (Borneman), 435–448

Ste20Ste5 interaction with (Garrenton et

al.), 1946–1958Ste50p

role in MEKK regulation (Wu et al.),734–746

Stem cellsAurora-A regulation of neuroblast self-

renewal (Lee et al.), 3464–3474;(Wang et al.), 3453–3463

�-catenin mediation of TGF-� activityin human mesenchymal (Jian etal.), 666–674

cancer epigenetics (Ting et al.), 3215–3231 Review

Cdc42 control of cell differentiationand �-catenin turnover in skin(Wu et al.), 571–585



Hedgehog signaling and the retina(Locker et al.), 3036–3048

hypoxia effects on (Covello et al.),557–570


melanoma (Chin et al.), 2149–2182 Re-view


muscle (Shi and Garry), 1692–1708 Re-view


Notch signaling in epidermal differen-tiation (Blanpain et al.), 3022–3035


regulation of DNA methylation in theRhox cluster in (Oda et al.),3382–3394


Sterile � motif (SAM) domainAveugle protein (Roignant et al.), 795–

806HYP protein (Douziech et al.), 807–819

in Ste50p and Ste11p (Wu et al.), 734–746

Stp1regulation by receptor-activated prote-

olysis (Andréasson et al.), 1563–1568

SUMO (small ubiquitin-related modi-fier)

regulation of synaptonemal complexformation during meiosis (deCarvalho and Colaiácovo),1986–1992 Perspective

role of SUMOylationin yeast meiosis(Cheng et al.), 2067–2081

Sumoylationof histones as negative regulator in

yeast (Nathan et al.), 966–976Msx1 (Lee et al.), 784–794

Surface plasmon resonance (SPR)receptor-binding specificity of FGF8

subfamily (Olsen et al.), 185–198

Surveillance complexassembly pathway (Behm-Ansmant

and Izaurralde), 391–398 Per-spective

SUV39H1 (Estève et al.), 3089–3103SV40 large T-antigen


Swi/SnfBRG1 regulation of zygotic genome ac-


function during inflammatory re-sponse (Ramirez-Carrozzi etal.), 282–296

glucocorticoid receptor trans-repres-sion (Bilodeau et al.), 2871–2886

Tid1/Rdh54 (Holzen et al.), 2593–2604

Swr1 (Papamichos-Chronakis et al.),2437–2449

SWR1-Comrole in H2A.Z acetylation (Babiarz et

al.), 700–710SXL. See Sex-lethal (SXL) proteinSymbiosis, in Medicago nodulation

(Combier et al.), 3084–3088Synapse

casein kinase 2-dependent serine phos-phorylation of MuSK regulationof acetylcholine receptor aggre-gation at (Cheusova et al.),1800–1816

inositol monophosphatase effect on(Tanizawa et al.), 3296–3310

Synaptic vesicle releaseRho activation in C. elegans (McMul-

lan et al.), 65–76Synaptogenesis, neuronal polarity and


Synaptonemal complexformation, SUMO-mediated regula-

tion of (de Carvalho and Colaiá-covo), 1986–1992 Perspective


Synthetic screengenetic redundancy for PTEN func-

tions (Suzuki and Han), 423–428

T

TaillessAtrophin interaction with (Wang et

al.), 525–530talpid3 gene

Hedgehog signaling and (Davey et al.),1365–1377

Target hub proteinsas master regulators of development in

yeast (Borneman), 435–448Targeting


TARTRNAi control of telomere length in

Drosophila (Savitsky et al.),345–354

Ta-siRNAs (trans-acting siRNAs)pathways in plants (Vaucheret), 759–

771 ReviewTAS4 gene (Rajagopalan et al.), 3407–

3425Taspase1 (Takeda et al.), 2397–2409Taste bud development, Sox2 in (Okubo

et al.), 2654–2659Taxane resistance

mechanism of (van Amerongen andBerns), 1975–1981 Perspective

by Txr1 and TSP-1 (Lih et al.), 2082–2095

T-box genesmesodermal progenitor cell specifica-


T-cell lymphoblastic leukemias andlymphomas

Notch1 induction of c-Myc in (Wenget al.), 2096–2109

TCFas target of casein kinase I in Wnt sig-

naling (Price), 399–410 ReviewTCIRG1 gene, osteoporosis and (Ralston

and de Crombrugghe), 2492–2506 Review

Tec1, role in regulation of developmentin yeast (Borneman), 435–448

Tectonic, Hedgehog modulation by (Re-iter and Skarnes), 22–27

Telomerase reverse transcriptase (TERT)in dyskeratosis congenita (Wong et

al.), 2848–2858Telomerase ribonucleoprotein

Sm protein association (Fu and Col-lins), 531–536

Telomerase RNA, telomere length limi-


tation by (Wong et al.), 2848–2858

Telomerelength control by RNAi (Savitsky et

al.), 345–354length in dyskeratosis congenita

(Wong et al.), 2848–2858liver function without (Lazzerini Den-

chi et al.), 2648–2653MDC1 acceleration of nonhomolo-

gous end-joining of dysfunc-tional telomeres (Dimitrova andde Lange), 3238–3243

NuA4-dependent acetylation ofH2A.Z (Babiarz et al.), 700–710

shortening and dysfunction in pancre-atic ductal adenocarcinoma(Hezel et al.), 1218–1249 Re-view

Telomeric silencinghistone sumoylation as negative regu-

lator (Nathan et al.), 966–976Temperature-dependent regulation, of

flagellar motility (Shen et al.),3283–3295

Temporal patterningPdm and Cas specify late-born neuro-

nal identity (Grosskortenhauset al.), 2618–2627

terCMreB–RNAP interaction and chromo-

some segregation (Kruse et al.),113–124

Testispiwi-interacting RNAs in mammalian

testes (Kim), 1993–1997 ReviewTetrahymena thermophila

endogenous small RNAs in (Lee andCollins), 28–33

Tetraploidy checkpoint (Aylon et al.),2687–2700

TFIIDinteraction with Mediator (Marr et al.),

1458–1469TFIIS

cotranscriptional splicing, effect on(Lacadie et al.), 2055–2066

TGF-�, HIF-2� effects on (Covello et al.),557–570

TGF-�. See Transforming growth fac-tor-�

Therapeuticsmalignant melanoma (Chin et al.),

2149–2182 ReviewThermotaxis

in Caenorhabditis elegans (Kodama etal.), 2955–2960; (Tanizawa etal.), 3296–3310

Thresholdingdenoising feedback loops by (Cohen et

al.), 2769–2772 PerspectiveThrombopoietin


Thrombospondin-1taxane resistance by (Lih et al.), 2082–

2095Thyroid tumors


Tid1/Rdh54 Dmc1 dissociation and(Holzen et al.), 2593–2604

Timing, of neuroblast gene expression(Grosskortenhaus et al.), 2618–2627

Tissue differentiationrole of cadherins in (Halbleib and Nel-

son), 3199–3214 ReviewTissue growth


TLXcoordination of retinal development

by (Zhang et al.), 1308–1320TNF�. See Tumor necrosis factor-�Tof2 (Huang et al.), 2887–2901Tongue, Sox2 in taste bud development

(Okubo et al.), 2654–2659TopBP1

BRCA1/BARD1, DNA damage-spe-cific interactions with (Green-berg et al.), 34–46

Topoisomerase II (Topo II)checkpoint in budding yeast (Andrews

et al.), 1162–1174TOR

decreased pathway signaling and lifespan extension (Powers et al.),174–184


TORC2, Sin1 as component of (Yang etal.), 2820–2832

Toxoplasma, rhomboid proteins in (Ur-ban), 3054–3068 Review

TPRanaphase-promoting complex (APC)


Tracheal developmentmatrix metalloproteinase liberation of

ninjurin A ectodomain to signalloss of cell adhesion (Zhang etal.), 1899–1910

Trachealess patterning gene (Brodu andCasanova), 1817–1828

Tracheal invaginationcell shape remodeling in Drosophila

(Brodu and Casanova), 1817–1828

Trans-acting siRNA. See ta-siRNAsTranscription

active occupation of transcriptionalspace (Fraser and Engel), 1379–1383 Perspective

chromosome-wide gene-specific tar-geting of the Drosophila dosage

compensation complex (Gilfil-lan et al.), 858–870

a coactivator/corepressor/epigenetic codefor integrating signal-dependentprograms of transcriptional re-sponse (Rosenfeld et al.), 1405–1428 Review

coactivator cross-talk (Marr et al.),1458–1469

cotranscriptional splicing in yeast(Lacadie et al.), 2055–2066

CTCF effects (Splinter et al.), 2349–2354


epigenetic modulation of JNK signal-ing (Miotto et al.), 101–112

estrogen regulation of cyclin D1 ex-pression (Eeckhoute et al.),2513–2526

functional coupling of RNAP II tran-scription to spliceosome assem-bly (Das et al.), 1100–1109


nucleosome displacement (Workman),2009–2017 Review

P68 RNA helicase regulation of tran-scriptional deactivation (Buszc-zak and Spradling), 977–989


requirement of clathrin heavy chainfor p53-mediated (Enari et al.),1087–1099

ribosome biogenesis, control of (La-ferté et al.), 2030–2040

role for RNase P in Pol III transcription(Reiner et al.), 1621–1635

role of histone H1 and ribosomal pro-tein L22 (Ni et al.), 1959–1973

�32-mediated heat-shock response(Nonaka et al.), 1776–1789

SIRT7 activation of RNA polymerase I(Ford et al.), 1075–1080

X-chromosome-wide profiling of MSL-1distribution and dosage com-pensation in Drosophila (Le-gube et al.), 871–883

Transcriptional activationregulated assembly and function of the


Transcriptional coactivatorsMAML1 and MEF2C interaction (Shen

et al.), 675–688MDT-15 regulation of fatty acid me-

tabolism in C. elegans (Taubertet al.), 1137–1149

monocytic leukemia zinc finger pro-tein (Thomas et al.), 1175–1186

MOZ as coactivator for AML1 (Katsu-moto et al.), 1321–1330


myocardin family of (Pipes et al.),1545–1556 Review

Transcriptional regulationBRG1 regulation of zygotic genome ac-


c-Fos-lamin A/C interaction (Ivorra etal.), 307–320

of circadian clock of cyanobacteria andNeurospora (Brunner andSchafmeier), 1061–1074 Review

of dendrite development (Parrish etal.), 820–835



of p21 by p53 family (Shu et al.), 2961–2972


role of histone H1 and ribosomal pro-tein L22 (Ni et al.), 1959–1973

role of PIAS proteins (Sharrocks), 754–758 Perspective

Transcriptional repressionof Flt3 by Pax5 (Holmes et al.), 933–

938by histone variant mH2A1.1 (Ouararhni

et al.), 3324–3336Transcriptional silencing


Transcriptional subordinationof RXR to RAR partner in epidermis

keratinocytes (Calléja et al.),1525–1538

Transcription-coupled repair (TCR)pathway

role of CSA and CSB in (Groisman etal.), 1429–1434

Transcription elongationmutants, effect on cotranscriptional

splicing (Lacadie et al.), 2055–2066

nucleosome displacement (Workman),2009–2017 Review

p21, role of (Gomes et al.), 601–612Transcription factors

GATA-1 and erythroid differentiation(Kitajima et al.), 654–659


hepatocyte (Kyrmizi et al.), 2293–2305order of expression (Iwasaki et al.),

3010–3021Ptf1a (Ijichi et al.), 3147–3160�28-dependent FlgM secretion (Al-

dridge et al.), 2315–2326symbiotic nodule development in

Medicago (Combier et al.),3084–3088

Transcription initiationnucleosome displacement (Workman),

2009–2017 ReviewTranscription termination

models (Rosonina et al.), 1050–1056Perspective

role of Rat1 in coupling mRNA 3�-endprocessing to (Luo et al.), 954–965

Transcriptomemouse fully grown oocyte (Evsikov et

al.), 2713–2727Transfer RNA (tRNA)


processing, role for RNase P in Pol IIItranscription (Reiner et al.),1621–1635

TransformationNotch1 induction of c-Myc in T-cell

leukemia lymphoma (Weng etal.), 2096–2109

Transforming growth factor-� (TGF-�)HIF-2� effects on (Covello et al.), 557–

570Transforming growth factor-� (TGF-�)

�-catenin mediation of activity in hu-man mesenchymal stem cells(Jian et al.), 666–674

pancreas-specific blockade of signaling(Ijichi et al.), 3147–3160


Smad4 effect on (Bardeesy et al.),3130–3146

type II receptor (Ijichi et al.),3147–3160

Transforming growth factor-� (TGF-�1)effect on head-and-neck squamos cell

carcinoma (Lu et al.), 1331–1342

osteoporosis and (Ralston and deCrombrugghe), 2492–2506 Re-view

Transforming growth factor-� type II re-ceptor

promotion of head-and-neck squamoscell carcinoma from loss of (Luet al.), 1331–1342

TransgenicSox2 expression (Okubo et al.), 2654–

2659Translation

control by miRNAsand siRNAs (Va-lencia-Sanchez et al.), 515–524Review

mammalian LINE-1 (Alisch et al.),210–223

in mammalian sperm (Gur and Breit-bart), 411–416


Pumilio-2-regulated (Padmanabhan

and Richter), 199–209recognition of initiation codon context

(Pisarev et al.), 624–636regulatory cascades (Vasudevan et al.),

138–146 Perspectiveresistance of late alphavirus mRNA to

eIF2� phosphorylation (Ventosoet al.), 87–100

Translational control/regulationCPEB and senescence, 2701–2712eIF4F assembly by a viral chaperone

(Walsh and Mohr), 461–472by miRNAsand siRNAs (Valen-

cia-Sanchez et al.), 515–524 Re-view

UNR and sex-lethal (SXL) corepressionof msl-2 translation (Duncan etal.), 368–379


WT1(+KTS) enhancement of transla-tion (Bor et al.), 1597–1608

Transpositionleukemia and lymphoma as cost for


V(D)J recombination and (Reddy et al.),1575–1582

Trans-repressionsensors and signals (Rosenfeld et al.),

1405–1428 ReviewTrans-specification

Pdx1 and p48 conversion of endodermto pancreas (Afelik et al.), 1441–1446

TRF2deletion in hepatocytes, effect of

(Lazzerini Denchi et al.), 2648–2653

inhibition, effect of (Dimitrova and deLange), 3238–3243

TrimerPatched (Ptc) membrane protein (Lu et

al.), 2539–2551Trinucleotide repeats


Trithorax group (trxG) proteinsas antagonistic regualtors of HOX

genes (Papp and Müller), 2041–2054

regulation of CycA (Martinez et al.),501–513

tRNA. See Transfer RNA (tRNA)Trophoblast

genetic ablation of geminin in themouse (Gonzalez et al.), 1880–1884

TrxG. See Trithorax group (trxG) pro-teins

TSC (Yang et al.), 2820–2832Tsix, Xist promoter regulation (Navarro

et al.), 2787–2792TTX-7 (Tanizawa et al.), 3296–3310


Tumorgrowth, hypoxia effects on (Covello et

al.), 557–570IL-1� mediation of Myc angiogenic

switch (Shchors et al.), 2527–2538

Tumorigenesisc-Myc represses p21Cip1 during papil-

lomagenesis (Oskarsson et al.),2024–2029

control of Gli protein accumulation(Huntzicker et al.), 276–281

p27, role of (Besson et al.), 47–64role for cysteine cathepsin genes in

(Gocheva et al.), 543–556Tumor microenvironment

role for cysteine cathepsin genes in(Gocheva et al.), 543–556

Tumor necrosis factor-� (TNF�)cachexia, association with (Schwarz-

kopf et al.), 3440–3452keratin 17 modulation of hair follicle

cycling (Tong and Coulombe),1353–1364


Tumor suppressionp53 role in (Mendrysa et al.), 16–21

Tumor suppressorASPP2 (Vives et al.), 1262–1267Aurora-A (Wang et al.), 3453–3463BTG2 mediation of anti-Ras func-

tion of p53 (Boiko et al.), 236–252


p27 stability and (Besson et al.), 47–64viral oncoprotein and (Liu and Mar-

morstein), 2332–2337 Perspec-tive

Twist-1 (Hinoi et al.), 2937–2942Two-cell embryo, arrest by maternal

BRG1 depletion (Bultman etal.), 1744–1754

Two-component signal transductionregulated assembly and function of

the transcriptional activatorNtrC (De Carlo, et al.), 1485–1495

Txr1taxane resistance by (Lih et al.), 2082–

2095Txr1-mediated thrombospondin re-

pression (van Amerongen andBerns), 1975–1981 Perspective

Type III secretion�28-dependent FlgM secretion (Al-

dridge et al.), 2315–2326Tyrosine kinase inhibitor

response of EGFR-dependent lung can-cer in mice (Politi et al.), 1496–1510

Tyrosine phosphorylationregulation of � integrin function (Chen

et al.), 927–932

U

UbiquitinAPC role in cell cycle progression

(Thornton and Toczyski), 3069–3078 Review

cullin E3 ligases (He et al.), 2949–2954Ubiquitination

of CtIP (Cheng et al.), 1721–1726nucleotide excision repair-dependent

monoubiquitylation of histoneH2A (Bergink et al.), 1343–1352

as a signal for transcriptional dynamic(Rosenfeld et al.), 1405–1428Review

ubiquitination-based hormone recep-tors (Chow and McCourt),1998–2008 Review

Ubiquitin–proteasome systemCSA-dependent degradation of CSB

(Groisman et al.), 1429–1434nucleotide excision repair-dependent

monoubiquitylation of histoneH2A (Bergink et al.), 1343–1352

Ubiquitin-protein ligases (Miller et al.),2410–2420

Ulp2 degradation (Cheng et al.), 2067–2081

Ultraconserved regionEvf-2 transcription from Dlx-5/6 (Feng

et al.), 1470–1484UNC-13

Rho effects on (McMullan et al.), 65–76

UNC-120role in body wall myogenesis (Fuku-

shige et al.), 3395–3406UNR (upstream of N-ras) protein

corepression of msl-2 translation withsex-lethal (SXL) (Duncan et al.),368–379

repression of msl-2 mRNA translation(Abaza et al.), 380–389

Upf1phosphorylation by SMG-1 (Kashima

et al.), 355–367Upstream open reading frames (uORFs)

3� UTR effects on (Sachs and Geballe),915–921 Perspective

derepression of Her-2 uORD by post-transcriptional control (Mehtaet al.), 939–953

V

Vascular developmentauxin biosynthesis by YUC flavin mo-


auxin flow and polarity (Sauer et al.),2902–2911

Vascular patterningcontrol by polar auxin transport (Scar-

pella et al.), 1015–1027Vax2 localization in the developing eye

(Kim and Lemke), 2833–2847

VEGFHIF-2� effects on (Covello et al.), 557–

570in pancreatic ductal adenocarcinoma


Vein patterningcontrol by polar auxin transport (Scar-

pella et al.), 1015–1027; (Scheresand Xu), 922–926 Perspective

Vernalizationnatural variation in FLC silencing

(Shindo et al.), 3079–3083PHD finger protein VIL1 involvement

in (Sung et al.), 3244–3248Polycomb-group protein repression of

AGL19 in FLC-independentpathway (Schönrock et al.),1667–1678


VERNALIZATION INSENSITIVE 3(VIN3) (Sung et al.), 3244–3248

Vibrio harveyi, autoinducer discrimina-tion in (Zhu et al.), 2754–2767

VIN3-LIKE 1 (VIL1) (Sung et al.), 3244–3248

Viral oncoproteincrystal structure of SV40 large T-anti-


tumor suppressor and (Liu and Mar-morstein), 2332–2337 Perspec-tive

Viral siRNAseffect in plants (Vaucheret), 759–771

ReviewViral suppressor

Cucumber mosaic virus-encoded 2b(Zhang et al.), 3255–3268

ViruseIF2-independent translation in alpha-

viruses (Ventoso et al.), 87–100mechanism of dengue virus RNA syn-

thesis (Filomatori et al.), 2238–2249

Vitamin D receptor (VDR), osteoporosisand (Ralston and de Crombrug-ghe), 2492–2506 Review

V(D)J recombinationgenomic instability due to (Reddy et

al.), 1575–1582leukemia and lymphoma as cost for


W

WD (He et al.), 2949–2954WD40 (He et al.), 2949–2954WHITE COLLAR (WC) complex (He et

al.), 2552–2565White Collar Complex (WCC), FRQ in-

teraction with (Shafmeier et al.),297–306


Wilm’s tumor 1 transcription factorrole (Rao et al.), 147–152WT1(+KTS) enhancement of transla-

tion (Bor et al.), 1597–1608Wnt4 signaling

MTA3 repression of (Zhang et al.),2943–2948

Wnt signalingAPC counteraction of �-catenin acti-

vation and H3K4 methylation(Sierra et al.), 586–600

APC inhibition of �-catenin on chro-matin (Xiong and Kotake), 637–642 Perspective

casein kinase I in (Price), 399–410 Re-view

mechanism of Wnt/�-catenin signal-ing (Willert and Jones),1394–1404 Review


regulation of vertebrate limb regenera-tion (Kawakami et al.), 3232–3237

role of MACF1 in (Chen et al.), 1933–1945

Sox2 and taste bud development(Okubo et al.), 2654–2659

Wt1. See Wilm’s tumor 1 transcriptionfactor

Wtm1, as nuclear anchor for Rnr2 (Leeand Elledge), 334–344

X

Xa13 generole in fertility and disease (Bart et al.),

1215–1217 PerspectiveX chromosome


MSL complex targets active genes on(Alekseyenko et al.), 848–857


XenopusPdx1 and p48 conversion of endoderm

to pancreas (Afelik et al.), 1441–1446

Pumilio-2-regulated translation, 199–209

retinogenesis (Locker et al.), 3036–3048

structure-specific regulation of Claspin(Yoo, et al.), 772–783

X inactivationdosage compensation and (Heard and

Disteche), 1848–1867 ReviewXist promoter regulation by Tsix (Na-

varro et al.), 2787–2792

Xist RNA and nuclear organization(Chaumeil et al.), 2223–2237


Xist RNA and nuclear organization(Chaumeil et al.), 2223–2237

XlHbox8ectopic expression with Ptf1a/p48 and

conversion of endoderm to pan-creas (Afelik et al.), 1441–1446

Y

YaiBregulation of RssB activity by IraP

(Bougdour et al.), 884–897Yeast

anaphase-promoting complex (APC)architecture (Thornton et al.),449–460

APC role in cell cycle progression(Thornton and Toczyski), 3069–3078 Review

chromosome arm cohesion during mi-tosis (Lam et al.), 2973–2984

chromosome instability and fragilesites in (Admire et al.), 159–173

cotranscriptional splicing (Lacadie etal.), 2055–2066




Hed1 attenuation of Rad51 in meiosis(Tsubouchi and Roeder), 1766–1775




identifying origins by phylogenetics(Nieduszynski et al.), 1874–1879



parallel pathways recruiting Crb2 toDSBs (Du et al.), 1583–1596


quorom sensing by (Sprague andWinans), 1045–1049 Perspective

Red-Hed regulation (Sheridan andBishop), 1685–1691 Perspective


ribosome biogenesis, control of (La-ferté et al.), 2030–2040

role of protein arginine methylation inthe formation of silent chroma-tin (Yu et al.), 3249–3254


Rrm3p DNA helicase (Azvolinsky etal.), 3104–3116

SAS-mediated acetylation of histoneH4 Lys16 (Shia et al.), 2507–2512

Schizosaccharomyces pombe CLASPand (Grallert et al.), 2421–2436

sporulation, histone H4 Ser1 phos-phorylation and (Krishnamoor-thy et al.), 2580–2592



topoisomerase II checkpoint (Andrewset al.), 1162–1174

two-stage activation of Cds1 (Xu etal.), 990–1003

YUC flavin monooxygenases, auxin bio-synthesis by (Cheng et al.),1790–1799

Z

ZebrafishILK control of heart contractility (Ben-

dig et al.), 2361–2372mesodermal progenitor cell specifica-



retinogenesis (Locker et al.), 3036–3048

specification of trunk and tail somites(Holley), 1831–1837 Perspective

Zinc-finger factor Insm1 (Gierl et al.),2465–2478

Zip1, binding of SUMO-conjugated pro-teins (Cheng et al.), 2067–2081

Zip3, as SUMO E3 ligase (Cheng et al.),2067–2081

Zygotic genome activation (ZGA)regulation by maternal BRG1 (Bult-

man et al.), 1744–1754


Documents

Reviewers, Volume 20* (2006) - Genes & Developmentgenesdev.cshlp.org/content/20/24/local/back-matter.pdf · Reviewers, Volume 20* (2006) The editors would like to thank the Editorial