Epigenetic Mechanisms of Gene Regulation Monograph 32

Edited by Vincenzo E.A. Russo, Max-Planck- Institut fiir Molekulare Genetik; Robert A. Martienssen, Cold Spring Harbor Laboratory; Arthur D. Riggs, Beckman Research Institute of the City of Hope

Many inheritable changes in gene function are not explained by changes in the DNA sequence. Such epigenetic mechanisms are known to influe- nce gene function in most complex organisms and include effects such as transposon function, chromosome imprinting, yeast mating type switching and telomeric silencing. In recent years, epigenetic effects have become a major focus of research activity. This monograph, edited by three well-known biologists from different specialties, is the first to review and synthesise what is known about these effects across all species, particularly from a molecular perspective, and will be of inter- est to everyone in the fields of molecular biology and genetics.

CONTENTS Introduction (A.D. Riggs et al.) Historical Overview of Epigenetic Mechanisms DNA Methylation in Eukaryotes: 20 Years On (R. Holliday); Overview of Epigenetic Mechanisms (A.D. Riggs, T.N. Porter) DNA Methylation Gene Silencing in Mammalian Cells (R. Holliday et al.); DNA Methyltransferases in Mammalian Development and Genome Defense (T.H. Bestor); The Mutational Burden of 5- Methylcytosine (A.S. Yang et al.); Plant Methyltransferases and Their Targets in the Plant Genome (R.L.P. Adams et al.); Mechanism of DNA Demethylation in Vertebrates and Its Biological Significance (J.-P. Jost); The Role of DNA Methylation in Plant Development (E.J. Finnegan); Methy- lation-related Epigenetic Signals in Bacterial DNA (J. Casadesfis, J. Torreblanca); DNA Modification and Restric- tion: Selfish Behavior of an Epigenetic System (I. Kobay- ashi)

Paramutation, Imprinting and X-Inactivation Organization and Control of Imprinted Genes: The Common Features (J.F.-X. Ainscough, M.A. Surani); Genomic Im- printing and Modifier Genes in the Mouse (J. Walter et al.); Establishment of Imprinted Methylation Patterns during De- velopment (R. Shemer, A. Razin); X-Chromosome Inactiva- tion and Epigenetic Mechanisms (A.D. Riggs, T.N. Porter);

X-Chromosome Inactivation: XCE and the Candidate Region for the X-Inactivation Center (P. Avner); Epigenetic Silenc- ing and Activation of a Maize r Gene (J.L. Kermicle); b and pl Paramutation in Maize: Heritable Transcription States Pro- grammed during Development (V.L. Chandler et al.); DNA Methylation of Flower Color Transgenes in Petunia hybrida (P. Meyer) Repeated Genes and Gene Silencing Position-effect Variegation in Drosophila: Recent Progress (S. Henikoff); Control and Function of DNA Methylation in Neurospora crassa (A.T. Hagemann, E.U. Selker); Silencing of the Gene hph in Neurospora crassa (V.E.A. Russo et al.); Prokaryotic Model of Epigenetic Inactivation: Chromosomal Silencing in Bacillus subtilis Fusion Products (V. Grandjean et al.); Stable Epigenetic States in Differentiated Plant Cells: Implications for Somaclonal Variation and Gene Silencing in Transgenic Plants (M.A. Matzke, A.JM. Matzke); Sense Co- suppression of Flower Color Genes: Metastable Morphology- based Phenotypes and the Prepattem-threshold Hypothesis (R.A. Jorgensen et al.); Analysis of a Tobacco Transgene Locus That Triggers Both Transcriptional and Posttranscrip- tional Silencing (H. Vaucheret et al.); Epigenetic Modifica- tions and Gene Silencing in Plants (F. Meins, Jr.) Nuclear Organization and Chromatin Structure Transcriptional Silencing in the Fission Yeast: A Manifesta- tion of Higher Order Chromosome Structure and Functions (R.C. Allshire); Transcriptional Silencing of the Yeast Mating-type Genes (S.G. Holmes et al.); Stable Chromatin States Regulating Homeotic Genes in Drosophila (V. Pir- rotta); The Role of Polycomb Group and Trithorax Group Chromatin Complexes in the Maintenance of Determined Cell States (R. Paro, P.J. Harte); Histones, Histone Modifica- tions, and the Inheritance of Chromatin Structure (S.U. Kass, A.P. Wolffe) Transposable Elements and Viruses The Silencing of Human Immunodeficiency Virus (D.P. Bed- narik); CpG Suppression in HIV-1 Versus HIV-2: Correla- tion with Pathogenicity and Possible Implications for the De- sign of Antiretroviral Vaccines (J.W. Nyce); Epigenetic Regulation of the Maize Spm Transposable Element (N. Fedoroff); Epigenetic Silencing of Mu Transposable Ele- ments in Maize (R.A. Martienssen) Appendices Essentials of Plant Development (R.A. Martienssen); Essen- tials of Mouse Development (A.D. Riggs) Reprints Paramutation: Directed Genetic Change (R.A. Brink et al); DNA Modification Mechanisms and Gene Activity during Development (R. Holliday, J.E. Pugh); X Inactivation, Dif- ferentiation, and DNA Methylation (A.D. Riggs)

1997, 692 pp., illus., color plates, glossary, index Cloth $125 ISBN 0-87969-490-4

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6 e n e S Development

VOLUME 11 NUMBER 11 PAGES 1357-1492 June 1, 1997

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J. Adams (Melbourne, Australia) J. Beckwith (Boston, USA) A. Berns (Amsterdam, The Netherlands) E. Blackburn (San Francisco, USA) D. Bohmann (Heidelberg, Germany) J. Brugge (Cambridge, USA) T. Cech (Boulder, USA) P. Chambon (Strasbourg, France) N.-H. Chua (New York, USA} S. Courtneidge (Redwood City, CA USA) S. Elledge (Houston, USA) R. Evans (La Jolla, USA) G. Fink (Cambridge, USA) P. Goodfellow (Harlow, UK) S. Gottesman (Bethesda, USA) C. Gross (San Francisco, USA) R. Grosschedl (San Francisco, USA) M. Groudine (Seattle, USA) L. Guarente (Cambridge, USA) E. Hafen (Zurich, Switzerland) S. Hake (Albany, CA USA) A. Hall (London, UK) R. Harland (Berkeley, USA) E. Harlow (Charlestown, USA) W. Herr (Cold Spring Harbor, USA) J. Hodgkin (Cambridge, UK) J.H.J. Hoeijmakers (Rotterdam, The

Netherlands) R. Horvitz (Cambridge, USA) P. Ingham (Sheffield, UK)

Y.-N. Jan {San Francisco, USA) T. Jessell (New York, USA} N. Jones (London, UK} J. Kadonaga {La Jolla, USA) R. Lehmann {New York, USA) M. Levine (Berkeley, USAI D. Livingston (Boston, USA) J. Manley (New York, USA) R. Martienssen (Cold Spring Harbor, USA) M. Mathews (Newark, NJ USA} W. McGinnis (La Jolla, USA} R. McKay (Bethesda, USA) S. McKnight {Dallas, USA) A. McMahon ICambridge, USA} L. Parada (Dallas, USAI C. Prives (New York, USA} U. Schibler (Geneva, Switzerland} J. Schlessinger (New York, USA) P. Sharp (Cambridge, USA} C. SheEr (Memphis, USA} D. Solter (Freiburg, FRG} P. Soriano (Seattle, USA} J. Steitz (New Haven, USA) P. Stragier (Paris, Francel M. Takeichi {Kyoto, Japan} T. Taniguchi (Tokyo, Japanl S. Ti lghman {Princeton, USA) R. Tjian {Berkeley, USA} M. Wiglet (Cold Spring Harbor, USA)

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Contents GENES & DEVELOPMENT June 1, 1997

Research papers

Homeodomain factor Nkx2-5 controls left/right asymmetric expression of bHLH gene eHand during murine heart development Christine Biben and Richard P. Harvey

1357

A family of LIM domain-associated cofactors confer transcriptional synergism between LIM and Otx homeodomain proteins Ingolf Bach, Catherine Carri~re, Heather P. Ostendorff, Bogi Andersen, and Michael G. Rosenfeld

1370

Human TAFn135 potentiates transcriptional activation by the AF-2s of the retinoic acid, vitamin D3, and thyroid hormone receptors in mammalian cells Gabrielle Mengus, Michael May, Lucie CarrG Pierre Chambon, and Irwin Davidson

1381

Klumpfuss, a putative Drosophila zinc finger transcription factor, acts to differentiate between the identities of two secondary precursor cells within one neuroblast lineage Xiaohang Yang, Sami Bahri, Thomas Klein, and William Chia

1396

The role of cyclin-dependent kinase 5 and a novel regulatory subunit in regulating muscle differentiation and patterning Anna Philpott, Elena B. Porto, Marc W. Kirschner, and Li-Huei Tsai

1409

The anl l locus controlling flower pigmentation in petunia encodes a novel WD-repeat protein conserved in yeast, plants, and animals Nick de Vetten, Francesca Quattrocchio, Joseph Mol, and Ronald Koes

1422

Mitogenic stimulation of resting T cells causes rapid phosphorylation of the transcription factor LSF and increased DNA-binding activity Janet L. Volker, Lucia E. Rameh, Quan Zhu, James DeCaprio, and Ulla Hansen

1435

pRB and p107/p130 are required for the regulated expression of different sets of E2F responsive genes Robert K. Hurford, Jr., David Cobrinik, Myung-Ho Lee, and Nicholas Dyson

1447

(continued)

Cyclin E-CDK2 is a regulator of p27 Kipl Robert J. Sheaff, M a r k Groudine , M a t t h e w Gordon, James M. Roberts , and Bruce E. C l u r m a n

1464

Cyclin E-induced S phase without activation of the pRb/E2F pathway Jiri Lukas, T h o m a s Herzinger , Klaus Hansen , Mar ia Cr i s t i na Moroni , Dal ia Resn i t zky , Kris t ian Hel in , S teven I. Reed, and Jiri Bar tek

1479

Cover Homeobox and bHLH genes in mouse heart development. Shown is a transverse section of an LS-II stage embryo showing eHand expression in the heart tube, with distinct caudal expression domains and enhanced expressions on the left side of the heart in the caudal domain. (For details, see Biben and Harvey, p. 1357.1