7/27/2019 EPI EXAM

http://slidepdf.com/reader/full/epi-exam 1/12

Review

Epigenomics of cancer e emerging new concepts

Melanie R. Hassler a , b, Gerda Egger a , *

a Clinical Institute of Pathology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austriab Department of Internal Medicine I, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria

a r t i c l e i n f o

Article history:Received 6 March 2012Accepted 9 May 2012Available online 17 May 2012

Keywords:Cancer epigeneticsChromatinNuclear architectureDNA methylationHistone modi cationlncRNA

a b s t r a c t

The complexity of the mammalian genome is regulated by heritable epigenetic mechanisms, which

provide the basis for differentiation, development and cellular homeostasis. These mechanisms act onthe level of chromatin, by modifying DNA, histone proteins and nucleosome density/composition. Duringthe last decade it became clear that cancer is de ned by a variety of epigenetic changes, which occur inearly stages of disease and parallel genetic mutations. With the advent of new technologies we are juststarting to unravel the cancer epigenome and latest mechanistic ndings provide the rst clue as to howaltered epigenetic patterns might occur in different cancers. Here we review latest ndings on chromatinrelated mechanisms and hypothesize how their impairment might contribute to the altered epigenomeof cancer cells.

Ó 2012 Elsevier Masson SAS. All rights reserved.

1. Epigenetic mechanisms and their basal functions

In order to gain access to the fundamental information of theDNA sequence to produce cell type speci c gene expressionsignatures, a highly regulated organization of DNA into chromatinis essential. Long-range silencing of repetitive sequences andformation of silent heterochromatin but also DNA access for tran-scription in euchromatin or DNA replication are dependent onepigenetic mechanisms including DNA methylation, histonemodi cation and remodeling, and non-coding RNA. These mecha-nisms are interrelated and need to be stably maintained during celldivisions to conserve cellular identity but also react to cell intrinsicsignals during development or to external factors to adopt toaltered environmental cues.

1.1. DNA methylation

The modi cation of the C5 position of the cytosine base(5 mC) isfound in approximately 70 e 80% of CpG dinucleotides in somaticmammalian cells and to some extend in non-CpG sequences inembryonic stem cells (ESC) [1,2] . DNA methylation is the basis fordifferent epigeneticphenomena such as imprinting,X chromosomeinactivation or the formationof heterochromatin [3] . Generally, DNAmethylation of promoter regions inversely correlates with gene

expression ( Fig. 1). Exceptions are CpG islands, which are found inabout 60% of promoters [4] . They have a high CpG density and areusually kept free of methylation independent of their activity state[5,6] . However, in cancercellspromoter CpG islands tend to becomehypermethylated, which then causes silencing of the underlyinggene [7] . Intragenic methylation is found at repetitive sequencessuchas satelliterepeatsand remnantsof retroviral insertionssuch asLINEs and SINEs in human DNA [1,8] . Gene body methylation ispresent in highly expressed genes and it has been speculated thatthis may repress transcriptional noise from alternative start sites,inhibit antisense transcription or direct RNA splicing and relates toreplication timing [9e 12] . A direct role for alternative splicing hasrecently been attested to methylation-sensitive CTCF binding andpolymerase II pausing at CTCF bound exon boundaries [13] .Comparison of the methylome of different hematopoietic lineageshas identi ed a large number of hypomethylated regions (HMRs),which can be constitutive or lineage-speci c and colocalize withtranscription factor binding sites [14] . Furthermore, complexpatterns of methylation were detected in progenitor cells in HMRs,which resolved in a lineage-speci c fashion to methylated ordemethylatedregions, reminiscent of a bivalenthistonemethylationstate found in progenitor cells [14] . Similarly, the deciphering of themouse methylome revealed regions of low methylation at distalregulatory elements, which was linked to binding of tissue speci ctranscriptionfactors [15] (Fig.1). Thus,recentreportshave identi edgenomic regions, which are associated with distinct DNA methyla-tion patterns regulating gene expression pro les and chromatincompartmentalization.

* Corresponding author. Tel.: þ 43 1 40400 6389; fax: þ 43 1 40400 5179.E-mail address: gerda.egger@meduniwien.ac.at (G. Egger).

Contents lists available at SciVerse ScienceDirect

Biochimie

j o u rn a l h o mep ag e : www.e l sev i e r. co m/ l o ca t e / b i o ch i

0300-9084/$ e see front matter Ó 2012 Elsevier Masson SAS. All rights reserved.

doi: 10.1016/j.biochi.2012.05.007

Biochimie 94 (2012) 2219 e 2230

7/27/2019 EPI EXAM

http://slidepdf.com/reader/full/epi-exam 2/12

Although DNA methylation is a very stable epigenetic mark,

which is passed on to subsequent cell generations, reprogramming

of DNA methylation occurs during gametogenesis and after fertil-

ization or after arti

cial reprogramming of somatic cells into

Fig.1. Complex epigenetic patterns demarcate distinct genomic regions. Genome-wide approaches have provided information on the different epigenetic characteristics of de nedgenomic loci. (Top) DNA methylation levels and chromatin states are indicated for an intragenic region, subdivided in expressed and silent status (red color indicates expressed, bluecolor silent genes). DNA methylation within promoter regions of genes negatively correlates with expression levels of the gene except in CpG islands, which are usually kept free of methylation (CpG island, CGI within green rectangle; red line, methylation level of expressed gene; blue line, methylation level of repressed gene; TSS, transcription start site). Innon-CGI promoters (crossed out green rectangle) transcriptional activity inversely correlates with DNA methylation of the promoter. Upstream enhancers (DRE, distant regulatoryelement) are demethylated in active genes, whereas they are methylated in repressed genes. Gene body methylation is elevated in expressed genes and shows characteristic spikesat exon-intron boundaries (indicated by black dashed lines). Furthermore, expressed and silent genes are marked by characteristic chromatin marks, nucleosome density andhistone variants, which together re ect the on/off state of a gene (see middle panel of gure). Note that only selected histone modi cation marks are listed. NDR indicatesnucleosome depleted regions in enhancers, promoters and 3 0 regions of active genes. BLOCs and LOCKs designate large silent gene-rich regions marked by repressive histone marksH3K27me3 and H3K9me2, respectively. (Bottom) DNA methylation levels and chromatin composition including histone modi cations, grade of compaction and histone variants areindicated for intergenic regions and heterochromatin. Inverted arrows on top indicate inverted repeats. These regions show generally high levels of DNA methylation and areassociated with repressive histone marks.

M.R. Hassler, G. Egger / Biochimie 94 (2012) 2219 e 22302220

7/27/2019 EPI EXAM

http://slidepdf.com/reader/full/epi-exam 3/12

induced pluripotent stem cells (iPSC) [16] . Furthermore, differen-tiation speci c demethylation was observed in hematopoieticprogenitors [17] and in murine erythroid progenitors, whichwas associated with high DNA replication rates, arguing fora mechanism of passive demethylation [18] . Modi cation of 5 mCvia oxidation by the TET family of proteins to 5-hydroxymethyl-cytosine (5hmC) or via deamination to thymine by AID/APOBEC1followed by base excision repair (BER) was proposed as a possiblemechanism for DNA demethylation [17] . High levels of 5hmC havebeen detected in brain tissue and ESCs, which might be a prereq-uisite for active demethylation by the action of DNA glycosylases orpassive demethylation during replication [19] .

1.2. Histone modi cation and remodeling

The coiling of DNA around nucleosome particles is the basis forthe organization of eukaryotic genomes. A multitude of differentposttranslational modi cations of the core histone proteins (H2A,H2B, H3 and H4) allows for demarcation of speci c chromatinregions and states, as illustrated by recent genome-wide chromatinmodi cation mapping studies (reviewed in [20] ) (Fig. 1). Histonemodi cations can be dynamically added or removed and associatewith both active and repressed regions of chromatin. To date morethan a dozen different histone modi cations have been detected,which can modify more than 150 conserved residues withinhistone proteins [21] . This number of different modi cations hasa high combinatorial potential, which would yield a hugelycomplex histone code [22] and it is under debate, whether sucha code exists or whether histone modi cations are a consequenceand mere re ection of dynamic processes altering DNA accessibilitysuch as transcription factor or RNA polymerase II (RNAPII) bindingor chromatin remodeling [23] . Generally, certain histone modi -cations such as acetylation or phosphorylation are thought tochange chromatin structure by altering the net positive charge of the histone proteins, thereby rendering the underlying DNAsequence information more accessible [24] . Alternatively, histone

modi cations can be recognized by speci c protein domains (e.g.bromodomains, Tudor domains, chromodomains), which in turnmight enforce or stabilize the chromatin signature and providea platform for the recruitment of additional factors [25,26] .Intriguingly, chromatin regulators encompassing histone modi ersand histone modi cation binding proteins are present in a combi-natorial fashion at distinct genomic loci and frequently bringtogether regulators associated with opposing activities [27] . Thismight occur counterintuitive, but could provide a dynamic systemfor ne-tuning gene e xpression programs or rapid response toaltered signals and highlights the importance of a balanced level of chromatin regulators for normal cell function.

Distinct histone modi cations correlate with distinct genomicregions ( Fig. 1); for example H3K4 trimethylation (H3K4me3) with

promoters; H3K4 monomethylation (H3K3me1) with enhancers;H3K9 acetylation and H3K27 acetylation (H3K9ac, H3K27ac) withactiveregulatory regions; H3K36trimethylation (H3K36me3),H3K79dimethylation (H3K79me2) and H4K20 monomethylation(H4K20me1) with transcribed regions and intron/exon usage;H3K27trimethylation (H3K27me3) with Polycomb repressed regions; orH3K9 trimethylation H3K9me3 with pericentromeric heterochro-matin [20,28] . In Drosophila developmental enhancers are markedbyheterogeneous histone modi cations including H3K4me1, H3K27ac,H3K79me3 and H3K27me3 and the co-occurrence of H3K27ac,H3K79me3 and RNAPII was correlated with the spatio e temporaltiming of enhancer activity [29] . The H3K4me1 appeared to repre-sent a general mark presenton enhancers irrespectiveof their activitystate and cell type speci city, which was in contrast to earlier reports

[30,31] , but is in line with a recent report demonstrating that

Polycomb repressed genes tend to keep permissive enhancers indifferentiated cells, which are marked by the histone variant H2AZand H3K4me1 [32] . Presumably, developmental plasticity is estab-lished through so-called bivalent histone modi cations, whichcombine the active H3K4me3 with the inactive H3K27me3 mark inESC on silent developmental and differentiation speci c genes.Duringdifferentiation,these regions canbe resolved into eitheractiveH3K4me3 orinactiveH3K27me3marksandenablerapidactivationorsilencing of the underlying genes [33,34] .

Aside from gene regulatory functions, which occur in a relativelylocal and con ned chromatin region, histone modi cations can alsospan large regions, as exempli ed by X chromosome inactivation infemale mammals [35] . Large chromatin blocks of H3K27me3associated with gene silencing have been identi ed on mammalianautosomes [36] , and H3K9me2 modi ed regions in the megabasesize have been found in differentiated mammalian cells correlatingwith silenced genes [37] (Fig. 1).

Further, exchange of canonical histones by variants is connectedto transcriptional activity as well as chromatin structure. Examplesinclude macroH2A on the inactive X chromosome [38] , CENP-A atcentromeres [39] or g H2AX at DNA double strand breaks [40] . Thehistone variants H2AZ and H3.3 are enriched at active promotersand enhancers [41,42] (Fig. 1). Additionally, H3.3 can be incorpo-rated into telomeres and pericentromeric chromatin [43 e 45] .Deposition of histone variants can be replication coupled or inde-pendent and an interesting function has been attested to H3.3recently. H3.3 deposition via the chaperone HIRA was linked locallyto RNAPII occupancy at sites of active transcription and a moreglobal gap- lling mechanism to protect genome integrity duringtranscription or replication was proposed [46] .

DNAaccessibilitycanbe affectedby the structure of nucleosomesand their interaction with DNA by exchanging canonical histoneswith histone variants or by histone modi cations, respectively.Additionally, the position and the density of nucleosomes on theDNAstringcan determinethe levelof accessibility.Activegeneshavecharacteristic nucleosome depleted regions (NDRs) anked by

positioned nucleosomes upstream of their transcription start sites,which contain binding sequences for transcription factors [47] .Repressed genes usually lack a NDR, but DNA sequence, binding of transcription factors and the action of chromatin remodelingcomplexes has been suggested to act in a multistep process todetermine local nucleosome composition and density [48] (Fig. 2).

1.3. Non-coding RNA

In recent years, it has become increasingly clear that non-codingRNAs are important modulators of chromatin regulation and geneexpression. Whole genome and transcriptome sequencingdemonstrated that at least 90% of the genome is actively tran-scribed, although less than 2% represent protein-coding genes.

Thus, the non-coding part of the transcriptome became a new focusin gene expression and regulation [49 e 52] .Currently, two major groups of non-coding RNA players can be

distinguished: small ncRNAs and long ncRNAs (lncRNAs) [52,53] .SmallncRNAsare processed fromlongerprecursorsand comprise,inaddition to transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), thewell-studied microRNAs (miRNAs), piwi interacting RNAs (piRNAs),small nuclear RNAs (snoRNAs) and other less well-characterizedRNAs (for a detailed review on these types of ncRNA and theirfunction see [54,55] ). Long ncRNAs (lncRNAs), on theother hand,area heterogenous class of mRNA-like transcripts from 200 nt upto 100 kb which do not code for proteins [53] . They can be tran-scribed from sense or antisensestrand,in a bidirectional wayso thata coding transcript of the opposite strand is initiated in close prox-

imity, fromintronic sequences processed froma transcript and from

M.R. Hassler, G. Egger / Biochimie 94 (2012) 2219 e 2230 2221

7/27/2019 EPI EXAM

http://slidepdf.com/reader/full/epi-exam 4/12

intergenic regions between two genes [56] . Recent studies suggestthat they make up the bulk of the human transcriptome, excludingribosomal and mitochondrial RNA [57,58] . Functional lncRNAsful ll important regulatory roles in gene expression and regulationby assembling protein complexes and localizing them to theirgenomic target DNA sequence [59] . Long intergenic non-codingRNAs (lincRNAs) have been identi ed at intergenic sites outside

protein-coding genes containing H3K4me3 and H3K36me3domains [60] . Many of these biological active lincRNAs can phys-ically associate with chromatin remodeling complexes such asPCR2 [61] and are needed for pluripotency and differentiation [62](Table 1 ).

Another class of non-coding RNAs constitute the recentlydiscovered transcribed ultraconserved regions (T-UCRs) [63,64] ,which are transcribed from evolutionary ultraconserved regionsfound in the human, rat and mouse genome [65] . They showaberrant expression in several cancers, including adult chroniclymphocytic leukemia, colorectal and hepatocellular carcinomasand neuroblastomas [64 e 66] . Although distinct T-UCR expressionsignatures are associated with speci c cancer types and their highsequence conservation across species argues for functional prop-erties, their precise mode of action in the cell is still unknown [64] .

Noteworthy, a recently introduced method called ChIRP (Chro-matin Isolation by RNA Puri cation) has the potency to shed lighton the complexity of RNA-chromatin or RNA-DNA-protein inter-actions on a genome-wide scale. This technology was used to mapgenome-wide interaction sites of three different lncRNAs includingHOTAIR, and has revealed focal, sequence-speci c binding atnumerous sites in the genome [67] .

1.4. Interrelations of different epigenetic mechanisms and targeting of epigenetic modi cations

The different epigenetic layers described above are interrelatedand can both reinforce each other and inhibitopposing functions. Inorder to establish a repressive chromatin environment DNA meth-ylation and repressive histone modi cations are combined withinthe same chromatin regions. Methylation of H3K9 is found inregions of DNA methylation, whereas H3K4me3 and DNA methyl-ation occur mutually exclusive. Different HMTs including G9a,SUV39H1, EZH2 can direct DNA methylation via direct or indirectrecruitment of DNMTs [68 e 70] , which might bea mechanism for denovo methylation of DNA in ESC but appears to be nonessential formaintenance of methylation in differentiated cells [71] .

The ubiquitin multi-motif protein UHRF1 is a central player intargeting repressive chromatin marks. It contains a SRA domain,which binds to hemimethylated DNA, a Tudor domain binding tomethylated H3 (H3K9me3) and a PHD nger interacting with anunmodi ed arginine residue within H3 (H3R2) [72 e 74] . Further-more, UHRF1 interacts with DNMTs, G9a and HDAC1 and therebyunit es various enzymes that can provide a repressive chromatinenvironment [75 e 77] . Interestingly, UHRF1 also recruits the H2AK5actetyltransferase TiP60 thus integrating a multitude of differentepigenetic signals [78] . A further example for the link betweenDNA methylation and histone modi cations represent methyl Cbinding proteins such as MeCP2, which interact with co-repressorcomplexes including HDACs and HMTs [79,80] . Interestingly,a recent report shows that components of the piRNA pathway are

required to target de novo DNA methylation to an imprinted region

Setting epigenetic marks

secondary(sequence independent)

readers of PTM/ DNA methylation

CM CM

noncoding RNA

CM

primary(sequence specific)

intrinsic DNA sequence

sequence specific transcription factors

CM

TF

noncoding RNA

CM

M B P

HMBP

A/T

Fig. 2. Setting the epigenetic marks. Establishment of a speci c chromatin environ-ment can be dependent or independent on DNA sequence. The intrinsic DNA sequenceshows different af nities for nucleosomes. A/T sequences are generally repellingnucleosomes, whereas G/C sequences are more favorable for nucleosome incorpora-tion in vitro (left, top). Regular phasing of A/T dinucleotides might help bend the DNAand facilitate positioning of nucleosomes (left, top). Additionally, sequence-speci ctranscription factors are involved in establishing a de ned chromatin state byrecruiting chromatin remodelers (CM) and in uence nucleosome positioning/deple-tion and histone modi cations of adjacent nucleosomes (left, middle). Alternatively,non-coding RNA can serve as a scaffold to recruit chromatin remodelers in a sequencedependent fashion (left, bottom). As a second route, trans acting factors can bind tomethylated DNA or speci c chromatin modi cations and recruit chromatin modifyingcomplexes, which is essential for maintenance or spreading of epigenetic information(right, top). Also, non-coding RNA can span large regions of chromatin (e.g. XIST on theinactive X chromosome) in a sequence independent fashion and enforce a speci c

chromatin environment (right, bottom). Gray cylinders, nucleosomes; black lines,DNA; red line, speci c DNA motif; TF, transcription factor; CM, chromatin modi cation/remodeling complex; black circles, methylated DNA; pink line, non-coding RNA; MBP,methyl DNA binding protein; HMBP, histone modi cation binding protein; smallcolored circles and hexagons indicate different histone modi cations as indicated inFig. 1.

Table 1Selected lncRNAs and interaction partners.

lncRNA Interaction/Target Function References

Polycomb repressive complexes (PCR)XIST PCR2 Silencing of X chromosome [84]HOTAIR PCR2 Targets PCR2 complex to HOXD

locus[118]

ANRIL PCR2 and PCR1 Targets PCR complexes to

INK4b-ARF-INKa locus

[119 e 121]

Histone methyltransferases (HMTs)AIR HMT G9a Si lencing of maternally expressed

Igf2r/Slc22a2/Slc22a3[87]

Kcnq1ot1 PCR2 and HMT G9a Lineage-speci c silencing of theKcnq1 locus

[88]

HOTTIP WDR5/MLL Activation of the HOXA cluster [170]Histone demethylasesHOTAIR LSD1/CoREST/REST HOXD locus regulation, silencing

of neuronal speci c genes[171]

Transcription factors/mRNA processing lincRNA-

p21Repressive hnRNP-Kcomplex

Targets hnRNP-K to repress p53target genes

[90]

NRON NFAT Affects transcription factor acitvi ty [172]PANDA NF-YA Del imits apoptosis by inhibit ing

NF-YA[91]

miRNAsPTENP1 miR-17, miR-19 Decoy for miRNAs targeting tumor

suppressor PTEN[124]

HULC miR-372 Upregulated in liver cancer [125]l inc MD1 miR-133 Regulat ion of muscle

differentiation[173]

M.R. Hassler, G. Egger / Biochimie 94 (2012) 2219 e 22302222

7/27/2019 EPI EXAM

http://slidepdf.com/reader/full/epi-exam 5/12

of the mouse genome implicating that selective methylation of imprinted regions can be regulated by non-coding piRNAs [81] .

Although we can dissect different functional genomic areas bytheir chromatin modi cation pattern, we still don ’ t understand themechanism underlying this patterning and whether epigeneticmarks such as posttranslational histone modi cations are cause orconsequence of chromatin states [23] (Fig. 2). Evidence is accu-mulating, that the DNA sequence per se is at least in part able todirect chromatin structure and modi cation. This involves posi-tioning of nucleosomes in a sequence dependent manner [82] .Additional binding of transcription factors and recruitment of chromatin remodeling complexes are essential to demarcate activeregions and to adjust nucleosome composition, occupancy andpositioning [48] . Interestingly, de novo methylation of DNA is alsomediated by genetic elements, which are found in promoters andcontain binding motifs for transcription factors [83] .

Another targeting mechanism of epigenetic modi cations relieson lncRNAs, which function as “ adaptor platforms ” for interactionsbetween chromatin and chromatin remodeling complexes and areableto recruitand directchromatinremodelingcomplexes tospeci cloci in thegenome [59] (Fig.2 ). The longest-known examples for thisare lncRNAs involvedin epigenetic silencing and imprinting, such asthe X-inactivation promoting lncRNA XIST, which recruits the Poly-comb repressive complex (PRC) to silence the X chromosome fromwhich it is transcribed [84] and TSIX, which is transcribed from theopposite strand and regulates XIST levels during X-inactivation [85] .Other lncRNAs involved in imprinting processes are the paternallyexpressed lncRNA AIR, which is required for silencing the maternallyexpressed protein-coding genes Igf2r/Slc22a2/Slc22a3 [86] andinhibits expression by targeting the H3K9histone methyltransferaseG9a to the Slc22a3 promoter [87] , and paternally expressed lncRNAKcnq1ot1, which mediates lineage-speci c silencing of the Kcnq1locus byinteractionwith thePRC2 complex andG9a HMTin placenta,but not in fetal liver [88] .

Furthermore, loss of function studies and analyses of custom-designed microarrays demonstrate involvement of functional

lncRNAs in development and differentiation [62,89] . Speci c sets of lncRNAs are needed to keep embryonic stem cells in a pluripotentstate and promote differentiation by association with not onlychromatin modi ers but also speci c transcription factors such asSOX2 and REST [89] .

lncRNAs can also contribute to modulation of cell cycle networksin the cell, such as the recently discovered lincRNA-p21, which isinduced by p53and mediates gene repression of p53target genes byassociating with repressor complex heterogeneous nuclear ribo-nucleoprotein K (hnRNP-K) and targeting the complex to previouslyactive genes [90] . Other examples for lncRNAs in the p53 networkare the p53-induced lncRNA PANDA and the maternally expressedgene 3 (MEG3). PANDA is transcribed from the CDKN1A locus anddelimitsapoptosisafterDNAdamage [91] byspeci callybinding and

inhibiting NF-YA, a nuclear transcription factor that is responsiblefor activating genes related to apoptosis. MEG3 can activate bothp53-dependent and p53-independent pathways and has tumorsuppressive functions [92] . Interestingly, it was shown that partialreplacement of MEG3 RNA with unrelated sequences did not alterp53 activation, indicating that lncRNA function largely depends onsecondary structures and that lack of sequence conservation, whichis observed for many lncRNAs, does not affect functionality.

2. Alterations in cancer

2.1. Altered epigenetic patterns

The epigenome of cancer cells displays numerous alterations in

comparison to the epigenome of their normal counterpart. Changes

in DNA methylation include a genome-wide loss and a regional gainof DNA methylation. This causes on one hand genomic instabilityand deregulation of tissue speci c and imprinted genes and on theother hand silencing of tumor suppressor genes e controlling cellcycle, apoptosis or DNA repair e by hypermethylation of theirpromoter CpG islands [3,7] . Interestingly, no global hypo-methylation but rather a directed hypomethylation at satelliterepeats could be detected in malignant peripheral nerve sheathtumors using a genome-wide approach [93] .

Unusually high frequency of DNA methylation at CpG rich siteswas termed CIMP (for CpG island methylator phenotype) and was rst identi ed in colorectal cancer [94] . CIMP is associated withdiverse clinicopathological characteristics such as patient age,gender, tumor location, microsatellite instability and geneticmutationin the BRAF gene [95] . Interestingly, CIMPcan alsobe foundin other tumor entities such as glioma or breast cancer, where it alsoallows for a sub-classi cation of tumors and determines metastaticpotential, respectively [96,97] . In analogy to genetic mutation,tumorsseemto accumulate higher levels of DNAmethylationduringtumor progression and genome-wide pro ling of DNA methylationhas proven useful for tumor classi cation of different tumor types[98 e 100] . These de ned alterations arecurrentlyevaluated for theiruse as biomarkers for diagnosis,prognosis and prediction of therapyresponse for different cancers [101] .

Another target of aberrant DNA methylation in cancer are CpGisland shores, de ned as approximately 2 kb regions surroundingCpG islands. These regions were initially identi ed hyper-methylated in colorectal cancer and represent regions of tissuespeci c methylation in normal tissues [102] . Methylation of shoreregions is related to gene expression and has also been detected indifferent tumor cell lines and nerve sheath tumors [93,103] . Incontrast, no differential methylation of shore regions was detectedin different lineages of the murine immune system [104] .

Tumor heterogeneity presents an obstacle for therapeuticintervention and cure. Stochastic methylation variability wasdetected in cancer speci c differentially methylated regions

(cDMRs), which might contribute to tumor heterogeneity [105] .Further, large hypervariable blocks covering half the genome showdifferences in gene expression patterns, involving genes thatregulate tumor-associated processes such as cell division andmatrix remodeling [105] . This heterogeneity of methylationpatterns might be the foundation for the selective advantage of tumor cells and provide a cellular mechanism of evolution [106] .

Additional insight into the cancer methylome has been gainedfrom a recent study in primary colon cancer [107] . Single CpGresolution genome-wide bisul te sequencing enabled the identi- cation of large hypomethylated regions, covering more than half of the genome. These regions coincided with late replication fociand nuclear lamina associated domains. This study thus proposesthe 3D chromatin architecture to be involved in epigenetic

reprogramming in cancer cells. Another link between chromatinarchitecture and DNA hypermethylation of tumor suppressor genesstems from the nding that loss of CTCF binding in multiple tumorcell lines coincides with silencing of p16 INK4a and the loss of anupstream chromatin boundary [108] .

Numerous changes in modi cation patterns have also beenobserved at the level of posttranslational histone modi cations[109] . The loss of repressive heterochromatin is re ected bya depletion of repressive histone marks such as H4K20me3 andH4K16ac in these regions [110] . Further, H3K27me3 seems to occurmutually exclusive to DNA methylation and promote de novosilencing of genes in different cancers [6,111] . Many developmentalgenes that are silenced by H3K27me3 in embryonic stem cells aresilenced by DNA methylation in cancer cells, establishing an

epigenetic switch from a dynamic to a more stable silencing system

M.R. Hassler, G. Egger / Biochimie 94 (2012) 2219 e 2230 2223

7/27/2019 EPI EXAM

http://slidepdf.com/reader/full/epi-exam 6/12

that promotes a stem cell-like signature of cancer cells [112 e 114] .Generally, changes in histone modi cation patterns were reportedin a variety of tumors and correlated to tumor stage and prognosis,however with contradicting results [109] . Since histone modi ca-tion patterns are very dynamic and can be easily erased byopposing enzymes, it seems that a regulated balance of thesemodi ers needs to be present within a cell. Shifting the balance toeither side might therefore result in different outcomes and eitherpromote or restrict tumor proliferation. This is highlighted by therecent nding that the histone deacetylase HDAC1, which waspreviously associated with cell cycle arrest, can induce tumorproliferation in a teratoma mouse model [115,116] .

Altered epigenetic patterns in cancer cells are also associatedwith the deregulation of lncRNAs and subsequent re-positioning of chromatin modifying complexes. For example, increased expres-sion of the lincRNA HOTAIR was found in primary and metastaticbreast tumors [117] . Overexpression of HOTAIR, which is normallyexpressed antisense to the HOXC locus during development andtargets the PCR2 complex to the HOXD locus [118] , leads to differentPCR2 occupancy at chromatin sites, altered H3K27 methylationpatterns resembling those of embryonic broblasts and increasedcancer invasiveness in breast cancer cells [117] . Another lncRNAinvolved in targeting of PCR complexes to tumor suppressor genesis antisense non-coding RNA in the INK4 locus (ANRIL) [119,120] .ANRIL is transcribed from the antisense strand at the INK4b-ARF-INK4a locus, which is an important regulator of cell cycleprogression, apoptosis and cellular senescence [121,122] . Byrecruiting PCR1 and PCR2 complexes to form heterochromatinsurrounding the INK4b-ARF-INK4a locus, ANRIL mediates silencingof these tumor suppressor genes.

According to an interesting new hypothesis non-coding RNAscan, besides assembling chromatin complexes and modulating cellcycle networks, act as decoys for miRNAs when they containspeci c microRNA binding sites. This in turn has implications onthe expression of other mRNAs and regulatory networks normallytargeted by the respective miRNA [123] . An example for this

competing endogenous RNA (ceRNA) is the transcribed PTENP1pseudogene, which contains many microRNA response elements(MREs) also present in the tumor suppressor PTEN. PTENP1 hasbeen shown to be able to regulate cellular levels of PTEN bydetracting miRNAs from PTEN mRNA and is selectively lost incancer, indicating a tumor suppressor function [124] . Anotherexample for an oncogenic “ endogenous sponge ” is the highlyupregulated in liver cancer (HULC) lncRNA, which sequesters miR-372 and in turn induces its own transcriptional up-regulation inliver cancer [125] .

2.2. Mutations in epigenetic enzymes

Chromatin modifying enzymes such as HMTs, histone acetyl-

transferases (HATs) and HDACs have been implicated in thepathology of leukemia, either as direct or indirect partners of oncofusion proteins [126] . The HATs MOF, MOZ or p300/CBP andthe HMT MLL are frequently found in translocations in acutemyeloid leukemia (AML) [127] , whereas indirect recruitment of co-repressor complexes including HDACs has been found in PML/RARalpha and PLZF/RARalpha fusions in acute promyelocyticleukemia (APL) [128,129] .

Advances in next generation sequencing technologies haveresu lted in the discovery of novel somatic mutations drivingdifferent cancers [130] . Intriguingly, numerous chromatin relatedenzymes and proteins were among the newly identi ed genes[109,131] . For example, the HMT EZH 2, which has previously beenattested oncogenic potential in different solid cancers such as

prostate or breast cancer, is frequently mutated in hematological

malignancies together with other members of the PRC2 such as EEDand SUZ12 [132] . Interestingly, inactivating mutations were iden-ti ed in myeloid disorders [133,134] and in T-ALL (acute lympho-blastic leukemia) [135] , whereas activating mutations leading tohyper-trimethylation of H3K27me3 were associated with twomutations (Y641, A6779) in follicular lymphoma and other B-celllymphomas [136 e 138] .

Mutations associated with DNA methylation have also beendescribed in hematological disorders. The de novo methyltransfer-ase DNMT3a was found mutated in acute myeloid leukemia (AML)and myelodysplastic syndrome [139 e 141] . The family of TETproteins has been implicated in DNA demethylation in ES cells andis frequently found mutated in myeloid disorders [142] . This isrelated to lower levels of 5-hydroxymethyl-Cytosine (5hmC) butsurprisingly also to DNA hypomethylation in affected patients[143] . TET function can also be affected by mutations in IDH 1 andIDH 2 genes, which cause accumulation of 2-hydroxyglutarateinhibiting TET2 [144] . Somatic mutations of IDH 1 have been asso-ciated with a CIMP phenotype in glioma [96] . An oncogenic coop-eration was suggested recently for DNMT3a and TET 2 in T-celllymphoma indicated by a frequent co-occurrence of mutations inboth genes, where 73% of patients with DNMT3a mutations alsoharbored TET 2 mutations [145] .

Two recent publications independently demonstrated thatmutations at two critical sites of posttranslational modi cations inthe histone H3 variant H3.3 are frequently detected in differentforms of brain tumors [146,147] . Schwatzentruber et al. furtherfound somatic mutations in the H3.3-ATRX-DAXX chromatinremodeling pathway, which is needed for the incorporation of histone H3.3 into pericentromeric heterochromatin, in 44% of pediatric glioblastoma multiforme (GBM). This was accompaniedby alternative telomere lengthening highlighting the importantrole of H3.3 for genome integrity and chromatin architecture [46] .

An unexpected role in chromatin regulation was recentlyascribed to the tumor suppressor BRCA1 [148] . Using nestin-Crespeci c deletion of Brca1 in murine neural stem cells, Zhu et al.

discovered an impaired heterochromatin structure in knockoutcells, which was associated with increased transcription of satellite,repeats. This was due to the loss of histone H2A ubiquitylationat pericentromeric heterochromatin, which was dependent on theubiquitin ligase function of BRCA1. Increased transcription of satel-lite repeats was associated with DNA damage and genomic insta-bility and was also detected in BRCA1 de cient murine and humanbreast cancers. Thus, the authors propose that the tumor suppres-sive function of BRCA1 might be largely dependent on its regulationof pericentromeric heterochromatin, which allows for controlledcell division and genomeintegrity [148] . Overexpression of satelliterepeats wasalso identi ed in pancreaticand other epithelial cancerslately, indicating that disruption of heterochromatin may result ingenomic instability in a variety of human cancers [149] .

2.3. Possible causes of aberrant epigenetic patterns

In order to recognize the source of aberrant epigenetic patterns,we need to understand how epigenetic pathways work in theirnormal environment. Recent literature has provided us severaloptions ( Fig. 3). First, alterations of epigenetic patterns such asaberrant DNA methylation could arise stochastically due to loss of delity or mutation of epigenetic enzymes [109] . This is supportedby the nding that aging results in a loss of the global DNA meth-ylation content [150] and by a large heterogeneity in genome-widemethylation patterns of different cancers [105] .

The nucleus has to accommodate DNA in an ordered fashion,to allow for regulated gene expression. Using Hi-C to resolve

the 3-dimensional genome architecture, Liebermane

Aiden et al.

M.R. Hassler, G. Egger / Biochimie 94 (2012) 2219 e 22302224

7/27/2019 EPI EXAM

http://slidepdf.com/reader/full/epi-exam 7/12

constructed spatial proximity maps identifying regions of segre-gated open and closed chromatin states [151] . This suggestsa territorial arrangement of nuclear architecture, which is sup-ported by the nding that heterochromatic regions and repressedgenes tend to be associated with the nuclear lamina,whereas activechromatin is moved away from the lamina [152,153] . Clustering of Polycomb regulated HOX genes and the organization of repressivechromatin into Polycomb bodies lends further support to these

ndings [154] . Actively transcribed regions of the genome havebeen thought to cluster in so-called “ transcription factories ” [155] .Recent data substantiate this model, which suggests that genesregulated by speci c transcription factors are clustered and loopedaround factories of concentrated RNAPII [156] . The rst 3D inter-action map of RNAPII occupied sites was recently established usingchromatin interaction analysis by paired-end-tag sequencing(ChIA-PET) [157] . RNAPII dependent interaction sites consist of extensive promoter e promoter interactions between proximal anddistant genes yielding multi-gene complexes that cooperativelyregulate their activity and are enriched for active chromatin marks.One might envision a model, in which speci c transcription factorsassemble genes via promoter/enhancer binding assisted byproteins involved in chromatin looping and organization such as

CTCF, cohesin or chromatin remodelers [156e

160] . Nuclear struc-ture including chromatin texture is altered in tumor cells and usedby pathologists for diagnosis of malignancy. Molecularly this wouldhold a considerable potential for large-scale rearrangements of genomic organization causing deregulated gene expressionpatterns and aberrant chromatin structure, which is in line withrecent ndings related to aberrant DNA methylation in cancer cellsand provides a second route to altered epigenetic patterning incancer [37,105,107,161] .

Finally, alterations in the cancer epigenome might result frommistargeting or altered composition of epigenetic complexes. Byinducing cellular oxidative stress O ’ Hagan et al. showed, thata complex consisting of DNMTsand HDACs is formedand recruitedtothe sites of damaged DNA. Components of the complex are recruitedfromnon-GC-rich toGC-rich areas. Theauthors detect similarchanges

in an in vivo in ammatory model and suggest, that delocalization of key epigenetic enzymes upon cellular stress might be the cause of global and local epigenetic alterations of cancer cells [162] .

2.4. Signaling to the cancer epigenome

Epigenetic patterns are initially established as a consequence of developmental cues and are maintained even after the initiating

signal is removed. For example, early differentiation programs areturned on in response to speci c transcription factors and areupheld in the determined lineage. Nonetheless the epigenomeretains some level of plasticity and can be shaped by environmentalfactors. Polycomb group (PcG) proteins are essential to maintainthe cellular memory by acting in these aforementioned ways of both stabilizing cell fate decisions but also regulating geneexpression patterns in response to extrinsic signals [163] . This hasbeen exempli ed by the induction of transdetermination inDrosophila via suppression of PcG proteins by JNK kinase signaling[164] , which links upstream kinase signaling with chromatinmodi cations. A further connection between kinase signaling inresponse to external factors and PcG proteins has been made bythe nding that the PRC2 component EZH2 can be directly

phosphorylated at different sites by a number of cell cycle depen-dent and stress induced kinases [165] . Although the effects of sitespeci c phosphorylation of EZH2 are somewhat controversial, itcan be anticipated that they regulate EZH2 interaction with otherPRC members, enzymatic activity or targeting to chromatin sites.Aside from modi cation of chromatin related proteins, stressinduced kinases can directly modify histone tail residues asrecently demonstrated for JNK during stem cell differentiation intoneurons [166] . Recent work has identi ed numerous upstreamkinases that directly act on chromatin in response to cytokines,growth factors or ultraviolet light and are involved in transcrip-tional regulation, chromatin condensation, apoptosis and DNAdamage repair [167] . Combinatorial histone modi cation patternshave been observed among the many possible modi cations of

histone tails. Related to histone phosphorylation, a crosstalk

Fig. 3. Altered nuclear and epigenomic structure of cancer cells. In normal cells, the nucleus is subdivided into active (yellow) and inactive (gray) territories. Inactive territories arelocated close tothe nuclear lamina (blue circle) and contain inactive, hypermethylated regions (black circles) that are tightly packed into nucleosomes with repressive histone marks(red cylinders). Active regions are found in the nuclear center, and contain “ transcription factories ” (green shapes), which are composed of speci c transcription factors, RNAPII,chromatin remodelers and CTCF/cohesin proteins for looping chromatin into these areas. Promoters of active genes (red lines) are unmethylated (white circles) and marked by

positive histone marks (green cylinders). Permanent stress (such as chronic in ammation (CI), UV exposure, reactive oxygen species (ROS)) might induce a stable epigenetic switchvia mutation in epigenetic enzymes (I), mistargeting or altered composition of epigenetic complexes (II) or altered nuclear architecture linked to stress speci c gene expressionpatterns (III). The altered nuclear morphology of cancer cells is associated with re-arranged active and inactive territories and chromatin, global DNA demethylation (white circles)and local DNA hypermethylation at CpG islands, which results in silencing of underlying genes (indicated by blue lines, black circles within blue lines indicate methylated promoterCpG islands). Transcription factories contain a tumor cell speci c set of proteins (red shapes) such as transcription factors and maintain a tumor cell speci c gene expression pro le.

M.R. Hassler, G. Egger / Biochimie 94 (2012) 2219 e 2230 2225

7/27/2019 EPI EXAM

http://slidepdf.com/reader/full/epi-exam 8/12

between phosphorylation and acetylation of neighboring residueshas been detected. For example, H3S10 phosphorylation is facili-tating the acetylation of the nearby H3K9/K14 marks and has animportant function for the induction of different genes in responseto stress (for details see also review by Sawicka and Seiser thisissue). Additionally, phosphorylation of the H3 tail can alleviate therepressive function of histone methylation on H3K9 and H3K27 byreleasing HP1 or PRC2 from chromatin, respectively [167] . Thus,kinase signaling targets transcription factors, chromatin modi ersand chromatin itself to robustly induce transcriptional responses toexternal stimuli and if deregulated might lead to local and globalchanges in chromatin structure and gene expression patterns asobserved in various cancers.

3. Conclusions

Research of the last decade has highlighted the essential role of epigenetic alterations in cancer development and progression[168] . Latest technologies have allowed for the analysis of thecancer epigenome and have resulted in important discoveries,which provide the basis for new concepts of how epigeneticalterations might emerge. We are now able to look at the cancerepigenome from a bird ’ s eyes view and we are just beginning tounderstand how alterations in nuclear architecture and globalchromatin, as observed by pathologists since more than 150 years,are related to epigenetic mechanisms [169] . Based on latest litera-ture we can envision different pathways that might cause epige-netic alterations in cancer cells as observed by genome-wideepigenomic pro ling ( Fig. 3). (I) Mutations in chromatin relatedenzymes such as DNMTs, histone modi ers or chromatin remod-elers might induce stochastic changes in the epigenome causingglobal changes in chromatin. (II) Faulty targeting (e.g. by lncRNAs ortranscription factors) or altered composition of epigeneticcomplexes can lead to global and gene speci c changes in theepigenetic signature. (III) Changes in the spatio e temporal organi-

zation of nuclear architecture or loss of boundaries might causealtered nuclear territories, disrupt ordered epigenetic patterns andinduce altered gene expression programs. All three pathways couldresult from altered external signaling due to permanent stress andact in concert to lock in the cancer epigenome.

Acknowledgments

This work was supported by funds from the Austrian ScienceFund FWF (V102-B12), the Oesterreichische Nationalbank (Anni-versary Fund, project number 13061) and the EU-FP7 (Marie CurieInternational Reintegration grant 230984). We are thankful toFernando Reyes for assistance in gure design.

References

[1] Y. Li, J. Zhu, G. Tian, N. Li, Q. Li, M. Ye, H. Zheng, J. Yu, H. Wu, J. Sun, H. Zhang,Q. Chen, R. Luo, M. Chen, Y. He, X. Jin, Q. Zhang, C. Yu, G. Zhou, Y. Huang,H. Cao, X. Zhou, S. Guo, X. Hu, X. Li, K. Kristiansen, L. Bolund, J. Xu, W. Wang,H. Yang, J. Wang, R. Li, S. Beck, X. Zhang, The DNA methylome of humanperipheral blood mononuclear cells, PLoS Biol. 8 (2010) e1000533.

[2] R. Lister, M. Pelizzola, R.H. Dowen, R.D. Hawkins, G. Hon, J. Tonti-Filippini, J.R. Nery, L. Lee, Z. Ye, Q.M. Ngo, L. Edsall, J. Antosiewicz-Bourget, R. Stewart,V. Ruotti, A.H. Millar, J.A. Thomson, B. Ren, J.R. Ecker, Human DNA methyl-omes at base resolution show widespread epigenomic differences, Nature462 (2009) 315 e 322.

[3] M. Berdasco, M. Esteller, Aberrant epigenetic landscape in cancer: howcellular identity goes awry, Dev. Cell 19 (2010) 698 e 711.

[4] S. Sharma, T.K. Kelly, P.A. Jones, Epigenetics in cancer, Carcinogenesis 31(2010) 27 e 36.

[5] D. Takai, P.A. Jones, Comprehensive analysis of CpG islands in human chro-

mosomes 21 and 22, Proc. Natl. Acad. Sci. USA 99 (2002) 3740e

3745.

[6] E.N. Gal-Yam, G. Egger, L. Iniguez, H. Holster, S. Einarsson, X. Zhang, J.C. Lin,G. Liang, P.A. Jones, A. Tanay, Frequent switching of Polycomb repressivemarks and DNA hypermethylation in the PC3 prostate cancer cell line, Proc.Natl. Acad. Sci. USA 105 (2008) 12979 e 12984.

[7] G. Egger, G. Liang, A. Aparicio, P.A. Jones, Epigenetics in human disease andprospects for epigenetic therapy, Nature 429 (2004) 457 e 463.

[8] J.A. Yoder, C.P. Walsh, T.H. Bestor, Cytosine methylation and the ecology of intragenomic parasites, Trends Genet. 13 (1997) 335 e 340.

[9] M.P. Ball, J.B. Li, Y. Gao, J.H. Lee, E.M. LeProust, I.H. Park, B. Xie, G.Q. Daley,G.M. Church, Targeted and genome-scale strategies reveal gene-body

methylation signatures in human cells, Nat. Biotechnol. 27 (2009)361 e 368.

[10] A.K. Maunakea, R.P. Nagarajan, M. Bilenky, T.J. Ballinger, C. D ’ Souza,S.D. Fouse, B.E. Johnson, C. Hong, C. Nielsen, Y. Zhao, G. Turecki, A. Delaney,R. Varhol, N. Thiessen, K. Shchors, V.M. Heine, D.H. Rowitch, X. Xing, C. Fiore,M. Schillebeeckx, S.J. Jones, D. Haussler, M.A. Marra, M. Hirst, T. Wang, J.F. Costello, Conserved role of intragenic DNA methylation in regulatingalternative promoters, Nature 466 (2010) 253 e 257.

[11] N. Shenker, J.M. Flanagan, Intragenic DNA methylation: implications of thisepigenetic mechanism for cancer research, Br. J. Cancer 106 (2012) 248 e 253.

[12] D. Aran, G. Toperoff, M. Rosenberg, A. Hellman, Replication timing-relatedand gene body-speci c methylation of active human genes, Hum. Mol.Genet. 20 (2010) 670 e 680.

[13] S. Shukla, E. Kavak, M. Gregory, M. Imashimizu, B. Shutinoski, M. Kashlev,P. Oberdoerffer, R. Sandberg, S. Oberdoerffer, CTCF-promoted RNA poly-merase II pausing links DNA methylation to splicing, Nature 479 (2011)74 e 79.

[14] E. Hodges, A. Molaro, C.O. Dos Santos, P. Thekkat, Q. Song, P.J. Uren, J. Park, J. Butler, S. Ra i, W.R. McCombie, A.D. Smith, G.J. Hannon, Directional DNAmethylation changes and complex intermediate states accompany lineagespeci city in the adult hematopoietic compartment, Mol. Cell 44 (2011)17 e 28.

[15] M.B. Stadler, R. Murr, L. Burger, R. Ivanek, F. Lienert, A. Scholer, C. Wirbelauer,E.J. Oakeley, D. Gaidatzis, V.K. Tiwari, D. Schubeler, DNA-binding factorsshape the mouse methylome at distal regulatory regions, Nature 480 (2011)490 e 495.

[16] D.D. De Carvalho, J.S. You, P.A. Jones, DNA methylation and cellular reprog-ramming, Trends Cell Biol. 20 (2010) 609 e 617.

[17] H. Ji, L.I. Ehrlich, J. Seita, P. Murakami, A. Doi, P. Lindau, H. Lee, M.J. Aryee,R.A. Irizarry, K. Kim, D.J. Rossi, M.A. Inlay, T. Serwold, H. Karsunky, L. Ho,G.Q. Daley, I.L. Weissman, A.P. Feinberg, Comprehensive methylome map of lineage commitment from haematopoietic progenitors, Nature 467 (2010)338 e 342.

[18] J.R. Shearstone, R. Pop, C. Bock, P. Boyle, A. Meissner, M. Socolovsky, GlobalDNA demethylation during mouse erythropoiesis in vivo, Science 334 (2011)799 e 802.

[19] K. Williams, J. Christensen, M.T. Pedersen, J.V. Johansen, P.A. Cloos,

J. Rappsilber, K. Helin, TET1 and hydroxymethylcytosine in transcription andDNA methylation delity, Nature 473 (2012) 343 e 348.[20] V.W. Zhou, A. Goren, B.E. Bernstein, Charting histone modi cations and the

functional organization of mammalian genomes, Nat. Rev. Genet. 12 (2011)7e 18.

[21] M. Tan, H. Luo, S. Lee, F. Jin, J.S. Yang, E. Montellier, T. Buchou, Z. Cheng,S. Rousseaux, N. Rajagopal, Z. Lu, Z. Ye, Q. Zhu, J. Wysocka, Y. Ye, S. Khochbin,B. Ren, Y. Zhao, Identi cation of 67 histone marks and histone lysine cro-tonylation as a new type of histone modi cation, Cell 146 (2011)1016 e 1028.

[22] T. Jenuwein, C.D. Allis, Translating the histone code, Science 293 (2001)1074 e 1080.

[23] S. Henikoff, A. Shilatifard, Histone modi cation: cause or cog? Trends Genet.27 (2011) 389 e 396.

[24] A.P. Wolffe, J.J. Hayes, Chromatin disruption and modi cation, Nucleic AcidsRes. 27 (1999) 711 e 720.

[25] S.D. Taverna, H. Li, A.J. Ruthenburg, C.D. Allis, D.J. Patel, How chromatin-binding modules interpret histone modi cations: lessons from professionalpocket pickers, Nat. Struct. Mol. Biol. 14 (2007) 1025 e 1040.

[26] K.E. Gardner, C.D. Allis, B.D. Strahl, Operating on chromatin, a colorfullanguage where context matters, J. Mol. Biol. 409 (2011) 36 e 46.

[27] O. Ram, A. Goren, I. Amit, N. Shoresh, N. Yosef, J. Ernst, M. Kellis, M. Gymrek,R. Issner, M. Coyne, T. Durham, X. Zhang, J. Donaghey, C.B. Epstein, A. Regev,B.E. Bernstein, Combinatorial patterning of chromatin regulators uncoveredby genome-wide location analysis in human cells, Cell 147 (2011)1628 e 1639.

[28] J. Ernst, P. Kheradpour, T.S. Mikkelsen, N. Shoresh, L.D. Ward, C.B. Epstein,X. Zhang, L. Wang, R. Issner, M. Coyne, M. Ku, T. Durham, M. Kellis,B.E. Bernstein, Mapping and analysis of chromatin state dynamics in ninehuman cell types, Nature 473 (2011) 43 e 49.

[29] S. Bonn, R.P. Zinzen, C. Girardot, E.H. Gustafson, A. Perez-Gonzalez,N. Delhomme, Y. Ghavi-Helm, B. Wilczynski, A. Riddell, E.E. Furlong, Tissue-speci c analysis of chromatin state identi es temporal signatures of enhancer activity during embryonic development, Nat. Genet. 44 (2012)148 e 156.

[30] A. Rada-Iglesias, R. Bajpai, T. Swigut, S.A. Brugmann, R.A. Flynn, J. Wysocka,A unique chromatin signature uncovers early developmental enhancers inhumans, Nature 470 (2011) 279 e 283.

M.R. Hassler, G. Egger / Biochimie 94 (2012) 2219 e 22302226

7/27/2019 EPI EXAM

http://slidepdf.com/reader/full/epi-exam 9/12

[31] N.D. Heintzman, G.C. Hon, R.D. Hawkins, P. Kheradpour, A. Stark, L.F. Harp,Z. Ye, L.K. Lee, R.K. Stuart, C.W. Ching, K.A. Ching, J.E. Antosiewicz-Bourget,H. Liu, X. Zhang, R.D. Green, V.V. Lobanenkov, R. Stewart, J.A. Thomson,G.E. Crawford, M. Kellis, B. Ren, Histone modi cations at human enhancersre ect global cell-type-speci c gene expression, Nature 459 (2009)108 e 112.

[32] P.C. Taberlay, T.K. Kelly, C.C. Liu, J.S. You, D.D. De Carvalho, T.B. Miranda,X.J. Zhou, G. Liang, P.A. Jones, Polycomb-repressed genes have permissiveenhancers that initiate reprogramming, Cell 147 (2011) 1283 e 1294.

[33] B.E. Bernstein, T.S. Mikkelsen, X. Xie, M. Kamal, D.J. Huebert, J. Cuff, B. Fry,

A. Meissner, M. Wernig, K. Plath, R. Jaenisch, A. Wagschal, R. Feil,S.L. Schreiber, E.S. Lander, A bivalent chromatin structure marks key devel-opmental genes in embryonic stem cells, Cell 125 (2006) 315 e 326.

[34] B. Schuettengruber, G. Cavalli, Recruitment of polycomb group complexesand their role in the dynamic regulation of cell fate choice, Development 136(2009) 3531 e 3542.

[35] J.T. Lee, Gracefully ageing at 50, X-chromosome inactivation becomesa paradigm for RNA and chromatin control, Nat. Rev. Mol. Cell Biol. 12 (2011)815 e 826.

[36] F.M. Pauler, M.A. Sloane, R. Huang, K. Regha, M.V. Koerner, I. Tamir,A. Sommer, A. Aszodi, T. Jenuwein, D.P. Barlow, H3K27me3 forms BLOCs oversilent genes and intergenic regions and speci es a histone banding patternon a mouse autosomal chromosome, Genome Res. 19 (2009) 221 e 233.

[37] B. Wen, H. Wu, Y. Shinkai, R.A. Irizarry, A.P. Feinberg, Large histone H3 lysine9 dimethylated chromatin blocks distinguish differentiated from embryonicstem cells, Nat. Genet. 41 (2009) 246 e 250.

[38] A. Wutz, X inactivation: a histone protects from reprogramming by the frog,Embo J. 30 (2011) 2310 e 2311.

[39] J.S. Verdaasdonk, K. Bloom, Centromeres: unique chromatin structures thatdrive chromosome segregation, Nat. Rev. Mol. Cell Biol. 12 (2011) 320 e 332.

[40] J. Lukas, C. Lukas, J. Bartek, More than just a focus: the chromatin response toDNA damage and its role in genome integrity maintenance, Nat. Cell Biol. 13(2011) 1161 e 1169.

[41] Y. Mito, J.G. Henikoff, S. Henikoff, Genome-scale pro ling of histone H3.3replacement patterns, Nat. Genet. 37 (2005) 1090 e 1097.

[42] C. Jin, C. Zang, G. Wei, K. Cui, W. Peng, K. Zhao, G. Felsenfeld, H3.3/H2A.Zdouble variant-containing nucleosomes mark ‘ nucleosome-free regions ’ of active promoters and other regulatory regions, Nat. Genet. 41 (2009)941 e 945.

[43] A.D. Goldberg, L.A. Banaszynski, K.M. Noh, P.W. Lewis, S.J. Elsaesser,S. Stadler, S. Dewell, M. Law, X. Guo, X. Li, D. Wen, A. Chapgier, R.C. DeKelver, J.C. Miller, Y.L. Lee, E.A. Boydston, M.C. Holmes, P.D. Gregory, J.M. Greally,S. Ra i, C. Yang, P.J. Scambler, D. Garrick, R.J. Gibbons, D.R. Higgs, I.M. Cristea,F.D. Urnov, D. Zheng, C.D. Allis, Distinct factors control histone variant H3.3localization at speci c genomic regions, Cell 140 (2010) 678 e 691.

[44] L.H. Wong, H. Ren, E. Williams, J. McGhie, S. Ahn, M. Sim, A. Tam, E. Earle,M.A. Anderson, J. Mann, K.H. Choo, Histone H3.3 incorporation provides

a unique and functionally essential telomeric chromatin in embryonic stemcells, Genome Res. 19 (2009) 404 e 414.[45] P. Drane, K. Ouararhni, A. Depaux, M. Shuaib, A. Hamiche, The death-

associated protein DAXX is a novel histone chaperone involved in thereplication-independent deposition of H3.3, Genes Dev. 24 (2010)1253 e 1265.

[46] D. Ray-Gallet, A. Woolfe, I. Vassias, C. Pellentz, N. Lacoste, A. Puri,D.C. Schultz, N.A. Pchelintsev, P.D. Adams, L.E. Jansen, G. Almouzni, Dynamicsof histone H3 deposition in vivo reveal a nucleosome gap- lling mechanismfor H3.3 to maintain chromatin integrity, Mol. Cell 44 (2011) 928 e 941.

[47] E. Segal, Y. Fondufe-Mittendorf, L. Chen, A. Thastrom, Y. Field, I.K. Moore, J.P. Wang, J. Widom, A genomic code for nucleosome positioning, Nature 442(2006) 772 e 778.

[48] O. Bell, V.K. Tiwari, N.H. Thoma, D. Schubeler, Determinants and dynamics of genome accessibility, Nat. Rev. Genet. 12 (2011) 554 e 564.

[49] P. Bertone, V. Stolc, T.E. Royce, J.S. Rozowsky, A.E. Urban, X. Zhu, J.L. Rinn,W. Tongprasit, M. Samanta, S. Weissman, M. Gerstein, M. Snyder, Globalidenti cation of human transcribed sequences with genome tiling arrays,Science 306 (2004) 2242 e 2246.

[50] P. Carninci, T. Kasukawa, S. Katayama, J. Gough, M.C. Frith, N. Maeda,R. Oyama, T. Ravasi, B. Lenhard, C. Wells, R. Kodzius, K. Shimokawa, V.B. Bajic,S.E. Brenner, S. Batalov, A.R. Forrest, M. Zavolan, M.J. Davis, L.G. Wilming,V. Aidinis, J.E. Allen, A. Ambesi-Impiombato, R. Apweiler, R.N. Aturaliya,T.L. Bailey, M. Bansal, L. Baxter, K.W. Beisel, T. Bersano, H. Bono, A.M. Chalk,K.P. Chiu, V. Choudhary, A. Christoffels, D.R. Clutterbuck, M.L. Crowe, E. Dalla,B.P. Dalrymple, B. de Bono, G. Della Gatta, D. di Bernardo, T. Down,P. Engstrom, M. Fagiolini, G. Faulkner, C.F. Fletcher, T. Fukushima, M. Furuno,S. Futaki, M. Gariboldi, P. Georgii-Hemming, T.R. Gingeras, T. Gojobori,R.E. Green, S. Gustincich, M. Harbers, Y. Hayashi, T.K. Hensch, N. Hirokawa,D. Hill, L. Huminiecki, M. Iacono, K. Ikeo, A. Iwama, T. Ishikawa, M. Jakt,A. Kanapin, M. Katoh, Y. Kawasawa, J. Kelso, H. Kitamura, H. Kitano,G. Kollias, S.P. Krishnan, A. Kruger, S.K. Kummerfeld, I.V. Kurochkin,L.F. Lareau, D. Lazarevic, L. Lipovich, J. Liu, S. Liuni, S. McWilliam, M. MadanBabu, M. Madera, L. Marchionni, H. Matsuda, S. Matsuzawa, H. Miki,F. Mignone, S. Miyake, K. Morris, S. Mottagui-Tabar, N. Mulder, N. Nakano,H. Nakauchi, P. Ng, R. Nilsson, S. Nishiguchi, S. Nishikawa, F. Nori, O. Ohara,Y. Okazaki, V. Orlando, K.C. Pang, W.J. Pavan, G. Pavesi, G. Pesole,N. Petrovsky, S. Piazza, J. Reed, J.F. Reid, B.Z. Ring, M. Ringwald, B. Rost,

Y. Ruan, S.L. Salzberg, A. Sandelin, C. Schneider, C. Schonbach, K. Sekiguchi,C.A. Semple, S. Seno, L. Sessa, Y. Sheng, Y. Shibata, H. Shimada, K. Shimada,D. Silva, B. Sinclair, S. Sperling, E. Stupka, K. Sugiura, R. Sultana, Y. Takenaka,K. Taki, K. Tammoja, S.L. Tan, S. Tang, M.S. Taylor, J. Tegner, S.A. Teichmann,H.R. Ueda, E. van Nimwegen, R. Verardo, C.L. Wei, K. Yagi, H. Yamanishi,E. Zabarovsky, S. Zhu, A. Zimmer, W. Hide, C. Bult, S.M. Grimmond,R.D. Teasdale, E.T. Liu, V. Brusic, J. Quackenbush, C. Wahlestedt, J.S. Mattick,D.A. Hume, C. Kai, D. Sasaki, Y. Tomaru, S. Fukuda, M. Kanamori-Katayama,M. Suzuki, J. Aoki, T. Arakawa, J. Iida, K. Imamura, M. Itoh, T. Kato, H. Kawaji,N. Kawagashira, T. Kawashima, M. Kojima, S. Kondo, H. Konno, K. Nakano,N. Ninomiya, T. Nishio, M. Okada, C. Plessy, K. Shibata, T. Shiraki, S. Suzuki,M. Tagami, K. Waki, A. Watahiki, Y. Okamura-Oho, H. Suzuki, J. Kawai,Y. Hayashizaki, The transcriptional landscape of the mammalian genome,Science 309 (2005) 1559 e 1563.

[51] B.T. Wilhelm, S. Marguerat, S. Watt, F. Schubert, V. Wood, I. Goodhead,C.J. Penkett, J. Rogers, J. Bahler, Dynamic repertoire of a eukaryotic tran-scriptome surveyed at single-nucleotide resolution, Nature 453 (2008)1239 e 1243.

[52] P. Kapranov, A.T. Willingham, T.R. Gingeras, Genome-wide transcription andthe implications for genomic organization, Nat. Rev. Genet. 8 (2007)413 e 423.

[53] C.A. Brosnan, O. Voinnet, The long and the short of noncoding RNAs, Curr.Opin. Cell Biol. 21 (2009) 416 e 425.

[54] M. Esteller, Non-coding RNAs in human disease, Nat. Rev. Genet. 12 (2011)861 e 874.

[55] S. Knowling, K.V. Morris, Non-coding RNA and antisense RNA. Nature ’ s trashor treasure? Biochimie 93 (2011) 1922 e 1927.

[56] C.P. Ponting, P.L. Oliver, W. Reik, Evolution and functions of long noncodingRNAs, Cell 136 (2009) 629 e 641.

[57] P. Kapranov, G. St Laurent, T. Raz, F. Ozsolak, C.P. Reynolds, P.H. Sorensen,G. Reaman, P. Milos, R.J. Arceci, J.F. Thompson, T.J. Triche, The majority of total nuclear-encoded non-ribosomal RNA in a human cell is ‘ dark matter ’

un-annotated RNA, BMC Biol. 8 (2010) 149.[58] L. Yang, M.O. Duff, B.R. Graveley, G.G. Carmichael, L.L. Chen, Genomewide

characterization of non-polyadenylated RNAs, Genome Biol. 12 (2011) R16.[59] M. Guttman, J.L. Rinn, Modular regulatory principles of large non-coding

RNAs, Nature 482 (2012) 339 e 346.[60] M. Guttman, I. Amit, M. Garber, C. French, M.F. Lin, D. Feldser, M. Huarte,

O. Zuk, B.W. Carey, J.P. Cassady, M.N. Cabili, R. Jaenisch, T.S. Mikkelsen,T. Jacks, N. Hacohen, B.E. Bernstein, M. Kellis, A. Regev, J.L. Rinn, E.S. Lander,Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals, Nature 458 (2009) 223 e 227.

[61] A.M. Khalil, M. Guttman, M. Huarte, M. Garber, A. Raj, D. Rivea Morales,K. Thomas, A. Presser, B.E. Bernstein, A. van Oudenaarden, A. Regev,E.S. Lander, J.L. Rinn, Many human large intergenic noncoding RNAs asso-ciate with chromatin-modifying complexes and affect gene expression, Proc.Natl. Acad. Sci. U S A 106 (2009) 11667 e 11672.

[62] M. Guttman, J. Donaghey, B.W. Carey, M. Garber, J.K. Grenier, G. Munson,G. Young, A.B. Lucas, R. Ach, L. Bruhn, X. Yang, I. Amit, A. Meissner, A. Regev, J.L. Rinn, D.E. Root, E.S. Lander, LincRNAs act in the circuitry controllingpluripotency and differentiation, Nature 477 (2011) 295 e 300.

[63] G. Bejerano, M. Pheasant, I. Makunin, S. Stephen, W.J. Kent, J.S. Mattick,D. Haussler, Ultraconserved elements in the human genome, Science 304(2004) 1321 e 1325.

[64] G.A. Calin, C.G. Liu, M. Ferracin, T. Hyslop, R. Spizzo, C. Sevignani, M. Fabbri,A. Cimmino, E.J. Lee, S.E. Wojcik, M. Shimizu, E. Tili, S. Rossi, C. Taccioli,F. Pichiorri, X. Liu, S. Zupo, V. Herlea, L. Gramantieri, G. Lanza, H. Alder,L. Rassenti, S. Volinia, T.D. Schmittgen, T.J. Kipps, M. Negrini, C.M. Croce,Ultraconserved regions encoding ncRNAs are altered in human leukemiasand carcinomas, Cancer Cell 12 (2007) 215 e 229.

[65] P. Scaruf , The transcribed-ultraconserved regions: a novel class of longnoncoding RNAs involved in cancer susceptibility, Scienti cWorldJournal 11(2011) 340 e 352.

[66] P. Mestdagh, E. Fredlund, F. Pattyn, A. Rihani, T. Van Maerken, J. Vermeulen,C. Kumps, B. Menten, K. De Preter, A. Schramm, J. Schulte, R. Noguera,G. Schleiermacher, I. Janoueix-Lerosey, G. Laureys, R. Powel, D. Nittner, J.C. Marine, M. Ringner, F. Speleman, J. Vandesompele, An integrativegenomics screen uncovers ncRNA T-UCR functions in neuroblastomatumours, Oncogene 29 (2010) 3583 e 3592.

[67] C. Chu, K. Qu, F.L. Zhong, S.E. Artandi, H.Y. Chang, Genomic maps of longnoncoding RNA occupancy reveal principles of RNA-chromatin interactions,Mol. Cell 44 (2011) 667 e 678.

[68] B. Lehnertz, Y. Ueda, A.A. Derijck, U. Braunschweig, L. Perez-Burgos,S. Kubicek, T. Chen, E. Li, T. Jenuwein, A.H. Peters, Suv39h-mediated histoneH3 lysine 9 methylation directs DNA methylation to major satellite repeatsat pericentric heterochromatin, Curr. Biol. 13 (2003) 1192 e 1200.

[69] M. Tachibana, Y. Matsumura, M. Fukuda, H. Kimura, Y. Shinkai, G9a/GLPcomplexes independently mediate H3K9 and DNA methylation to silencetranscription, Embo J. 27 (2008) 2681 e 2690.

[70] E. Vire, C. Brenner, R. Deplus, L. Blanchon, M. Fraga, C. Didelot, L. Morey,A. Van Eynde, D. Bernard, J.M. Vanderwinden, M. Bollen, M. Esteller, L. DiCroce, Y. de Launoit, F. Fuks, The polycomb group protein EZH2 directlycontrols DNA methylation, Nature 439 (2006) 871 e 874.

[71] S. Sharma, D.S. Gerke, H.F. Han, S. Jeong, M.R. Stallcup, P.A. Jones, G. Liang,Lysine methyltransferase G9a is not required for DNMT3A/3B anchoring to

M.R. Hassler, G. Egger / Biochimie 94 (2012) 2219 e 2230 2227

7/27/2019 EPI EXAM

http://slidepdf.com/reader/full/epi-exam 10/12

methylated nucleosomes and maintenance of DNA methylation in somaticcells, Epigenetics Chromatin 5 (2012) 3.

[72] J. Sharif, M. Muto, S. Takebayashi, I. Suetake, A. Iwamatsu, T.A. Endo, J. Shinga,Y. Mizutani-Koseki, T. Toyoda, K. Okamura, S. Tajima, K. Mitsuya, M. Okano,H. Koseki, The SRA protein Np95 mediates epigenetic inheritance byrecruiting Dnmt1 to methylated DNA, Nature 450 (2007) 908 e 912.

[73] M. Bostick, J.K. Kim, P.O. Esteve, A. Clark, S. Pradhan, S.E. Jacobsen, UHRF1plays a role in maintaining DNA methylation in mammalian cells, Science317 (2007) 1760 e 1764.

[74] N. Nady, A. Lemak, J.R. Walker, G.V. Avvakumov, M.S. Kareta, M. Achour,

S. Xue, S. Duan, A. Allali-Hassani, X. Zuo, Y.X. Wang, C. Bronner, F. Chedin,C.H. Arrowsmith, S. Dhe-Paganon, Recognition of multivalent histone statesassociated with heterochromatin by UHRF1 protein, J. Biol. Chem. 286 (2011)24300 e 24311.

[75] D. Meilinger, K. Fellinger, S. Bultmann, U. Rothbauer, I.M. Bonapace,W.E. Klinkert, F. Spada, H. Leonhardt, Np95 interacts with de novo DNAmethyltransferases, Dnmt3a and Dnmt3b, and mediates epigenetic silencingof the viral CMV promoter in embryonic stem cells, EMBO Rep. 10 (2009)1259 e 1264.

[76] J.K. Kim, P.O. Esteve, S.E. Jacobsen, S. Pradhan, UHRF1 binds G9a andparticipates in p21 transcriptional regulation in mammalian cells, NucleicAcids Res. 37 (2009) 493 e 505.

[77] M. Unoki, T. Nishidate, Y. Nakamura, ICBP90, an E2F-1 target, recruits HDAC1and binds to methyl-CpG through its SRA domain, Oncogene 23 (2004)7601 e 7610.

[78] M. Achour, G. Fuhrmann, M. Alhosin, P. Ronde, T. Chataigneau, M. Mousli,V.B. Schini-Kerth, C. Bronner, UHRF1 recruits the histone acetyltransferaseTip60 and controls its expression and activity, Biochem. Biophys. Res.Commun. 390 (2009) 523 e 528.

[79] F. Fuks, P.J. Hurd, D. Wolf, X. Nan, A.P. Bird, T. Kouzarides, The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation, J. Biol.Chem. 278 (2003) 4035 e 4040.

[80] R.J. Klose, A.P. Bird, Genomic DNA methylation: the mark and its mediators,Trends Biochem. Sci. 31 (2006) 89 e 97.

[81] T. Watanabe, S. Tomizawa, K. Mitsuya, Y. Totoki, Y. Yamamoto, S. Kuramochi-Miyagawa, N. Iida, Y. Hoki, P.J. Murphy, A. Toyoda, K. Gotoh, H. Hiura,T. Arima, A. Fujiyama, T. Sado, T. Shibata, T. Nakano, H. Lin, K. Ichiyanagi,P.D. Soloway, H. Sasaki, Role for piRNAs and noncoding RNA in de novo DNAmethylation of the imprinted mouse Rasgrf1 locus, Science 332 (2011)848 e 852.

[82] N. Kaplan, I. Moore, Y. Fondufe-Mittendorf, A.J. Gossett, D. Tillo, Y. Field,T.R. Hughes, J.D. Lieb, J. Widom, E. Segal, Nucleosome sequence preferencesin uence in vivo nucleosome organization author reply 920 e 912, Nat.Struct. Mol. Biol. 17 (2010) 918 e 920.

[83] F. Lienert, C. Wirbelauer, I. Som, A. Dean, F. Mohn, D. Schubeler, Identi cationof genetic elements that autonomously determine DNA methylation states,Nat. Genet. 43 (2011) 1091 e 1097.

[84] J. Zhao, B.K. Sun, J.A. Erwin, J.J. Song, J.T. Lee, Polycomb proteins targeted bya short repeat RNA to the mouse X chromosome, Science 322 (2008)750 e 756.

[85] J.T. Lee, L.S. Davidow, D. Warshawsky, Tsix, a gene antisense to Xist at the X-inactivation centre, Nat. Genet. 21 (1999) 400 e 404.

[86] F. Sleutels, R. Zwart, D.P. Barlow, The non-coding air RNA is required forsilencing autosomal imprinted genes, Nature 415 (2002) 810 e 813.

[87] T. Nagano, J.A. Mitchell, L.A. Sanz, F.M. Pauler, A.C. Ferguson-Smith, R. Feil,P. Fraser, The air noncoding RNA epigenetically silences transcription bytargeting G9a to chromatin, Science 322 (2008) 1717 e 1720.

[88] R.R. Pandey, T. Mondal, F. Mohammad, S. Enroth, L. Redrup, J. Komorowski,T. Nagano, D. Mancini-Dinardo, C. Kanduri, Kcnq1ot1 antisense noncodingRNA mediates lineage-speci c transcriptional silencing through chromatin-level regulation, Mol. Cell 32 (2008) 232 e 246.

[89] S.Y. Ng, R. Johnson, L.W. Stanton, Human long non-coding RNAs promotepluripotency and neuronal differentiation by association with chromatinmodi ers and transcription factors, Embo J. 31 (2011) 522 e 533.

[90] M. Huarte, M. Guttman, D. Feldser, M. Garber, M.J. Koziol, D. Kenzelmann-Broz, A.M. Khalil, O. Zuk, I. Amit, M. Rabani, L.D. Attardi, A. Regev, E.S. Lander,T. Jacks, J.L. Rinn, A large intergenic noncoding RNA induced by p53 mediatesglobal gene repression in the p53 response, Cell 142 (2010) 409 e 419.

[91] T. Hung, Y. Wang, M.F. Lin, A.K. Koegel, Y. Kotake, G.D. Grant, H.M. Horlings,N. Shah, C. Umbricht, P. Wang, B. Kong, A. Langerod, A.L. Borresen-Dale,S.K. Kim, M. van de Vijver, S. Sukumar, M.L. Whit eld, M. Kellis, Y. Xiong,D.J. Wong, H.Y. Chang, Extensive and coordinated transcription of noncodingRNAs within cell-cycle promoters, Nat. Genet. 43 (2011) 621 e 629.

[92] Y. Zhou, Y. Zhong, Y. Wang, X. Zhang, D.L. Batista, R. Gejman, P.J. Ansell, J. Zhao, C. Weng, A. Klibanski, Activation of p53 by MEG3 non-coding RNA, J. Biol. Chem. 282 (2007) 24731 e 24742.

[93] A. Feber, G.A. Wilson, L. Zhang, N. Presneau, B. Idowu, T.A. Down, V.K. Rakyan,L.A. Noon, A.C. Lloyd, E. Stupka, V. Schiza, A.E. Teschendorff, G.P. Schroth,A.Flanagan,S. Beck, Comparativemethylomeanalysisof benignand malignantperipheral nerve sheath tumors, Genome Res. 21 (2011) 515 e 524.

[94] M. Toyota, N. Ahuja, M. Ohe-Toyota, J.G. Herman, S.B. Baylin, J.P. Issa, CpGisland methylator phenotype in colorectal cancer, Proc. Natl. Acad. Sci. USA96 (1999) 8681 e 8686.

[95] D.J. Weisenberger, K.D. Siegmund, M. Campan, J. Young, T.I. Long,M.A. Faasse, G.H. Kang, M. Widschwendter, D. Weener, D. Buchanan, H. Koh,

L. Simms, M. Barker, B. Leggett, J. Levine, M. Kim, A.J. French, S.N. Thibodeau, J. Jass, R. Haile, P.W. Laird, CpG island methylator phenotype underliessporadic microsatellite instability and is tightly associated with BRAFmutation in colorectal cancer, Nat. Genet. 38 (2006) 787 e 793.

[96] H. Noushmehr, D.J. Weisenberger, K. Diefes, H.S. Phillips, K. Pujara,B.P. Berman, F. Pan, C.E. Pelloski, E.P. Sulman, K.P. Bhat, R.G. Verhaak,K.A. Hoadley, D.N. Hayes, C.M. Perou, H.K. Schmidt, L. Ding, R.K. Wilson,D. Van Den Berg, H. Shen, H. Bengtsson, P. Neuvial, L.M. Cope, J. Buckley, J.G. Herman, S.B. Baylin, P.W. Laird, K. Aldape, Identi cation of a CpG islandmethylator phenotype that de nes a distinct subgroup of glioma, Cancer Cell17 (2010) 510 e 522.

[97] F. Fang, S. Turcan, A. Rimner, A. Kaufman, D. Giri, L.G. Morris, R. Shen,V. Seshan, Q. Mo, A. Heguy, S.B. Baylin, N. Ahuja, A. Viale, J. Massague,L. Norton, L.T. Vahdat, M.E. Moynahan, T.A. Chan, Breast cancer methylomesestablish an epigenomic foundation for metastasis, Sci. Transl Med. 3 (2011)75ra25.

[98] S. Dedeurwaerder, D. Fumagalli, F. Fuks, Unravelling the epigenomicdimension of breast cancers, Curr. Opin. Oncol. 23 (2011) 559 e 565.

[99] T. Hinoue, D.J. Weisenberger, C.P. Lange, H. Shen, H.M. Byun, D. Van DenBerg, S. Malik, F. Pan, H. Noushmehr, C.M. van Dijk, R.A. Tollenaar, P.W. Laird,Genome-scale analysis of aberrant DNA methylation in colorectal cancer,Genome Res. 22 (2012) 271 e 282.

[100] Integrated genomic analyses of ovarian carcinoma, Nature 474 (2011)609 e 615.

[101] G. Egger, M. Wielscher, W. Pulverer, A. Kriegner, A. Weinhausel, DNAmethylation testing and marker validation using PCR: diagnostic applica-tions, Expert Rev. Mol. Diagn. 12 (2012) 75 e 92.

[102] R.A. Irizarry, C. Ladd-Acosta, B. Wen, Z. Wu, C. Montano, P. Onyango, H. Cui,K. Gabo, M. Rongione, M. Webster, H. Ji, J.B. Potash, S. Sabunciyan,A.P. Feinberg, The human colon cancer methylome shows similar hypo- andhypermethylation at conserved tissue-speci c CpG island shores, Nat. Genet.41 (2009) 178 e 186.

[103] K. Ogoshi, S. Hashimoto, Y. Nakatani, W. Qu, K. Oshima, K. Tokunaga,S. Sugano, M. Hattori, S. Morishita, K. Matsushima, Genome-wide pro ling of DNA methylation in human cancer cells, Genomics 98 (2011) 280 e 287.

[104] A.M. Deaton, S. Webb, A.R. Kerr, R.S. Illingworth, J. Guy, R. Andrews, A. Bird,Cell type-speci c DNA methylation at intragenic CpG islands in the immunesystem, Genome Res. 21 (2011) 1074 e 1086.

[105] K.D. Hansen, W. Timp, H.C. Bravo, S. Sabunciyan, B. Langmead,O.G. McDonald, B. Wen, H. Wu, Y. Liu, D. Diep, E. Briem, K. Zhang,R.A. Irizarry, A.P. Feinberg, Increased methylation variation in epigeneticdomains across cancer types, Nat. Genet. 43 (2011) 768 e 775.

[106] J.P. Issa, Epigenetic variation and cellular Darwinism, Nat. Genet. 43 (2011)724 e 726.

[107] B.P. Berman, D.J. Weisenberger, J.F. Aman, T. Hinoue, Z. Ramjan, Y. Liu,H. Noushmehr, C.P. Lange, C.M. van Dijk, R.A. Tollenaar, D. Van Den Berg,P.W. Laird, Regions of focal DNA hypermethylation and long-range hypo-

methylation in colorectal cancer coincide with nuclear lamina-associateddomains, Nat. Genet. 44 (2011) 40 e 46.[108] M. Witcher, B.M. Emerson, Epigenetic silencing of the p16(INK4a) tumor

suppressor is associated with loss of CTCF binding and a chromatinboundary, Mol. Cell 34 (2009) 271 e 284.

[109] J. Fullgrabe, E. Kavanagh, B. Joseph, Histone onco-modi cations, Oncogene30 (2011) 3391 e 3403.

[110] M.F. Fraga, E. Ballestar, A. Villar-Garea, M. Boix-Chornet, J. Espada, G. Schotta,T. Bonaldi, C. Haydon, S. Ropero, K. Petrie, N.G. Iyer, A. Perez-Rosado, E. Calvo, J.A. Lopez, A. Cano, M.J. Calasanz, D. Colomer, M.A. Piris, N. Ahn, A. Imhof,C. Caldas, T. Jenuwein, M. Esteller, Loss of acetylation at Lys16 and trime-thylation at Lys20 of histone H4 is a common hallmark of human cancer, Nat.Genet. 37 (2005) 391 e 400.

[111] Y. Kondo, L. Shen, A.S. Cheng, S. Ahmed, Y. Boumber, C. Charo, T. Yamochi,T. Urano, K. Furukawa, B. Kwabi-Addo, D.L. Gold, Y. Sekido, T.H. Huang, J.P. Issa, Gene silencing in cancer by histone H3 lysine 27 trimethylationindependent of promoter DNA methylation, Nat. Genet. 40 (2008) 741 e 750.

[112] J.E. Ohm, K.M. McGarvey, X. Yu, L. Cheng, K.E. Schuebel, L. Cope,H.P. Mohammad, W. Chen, V.C. Daniel, W. Yu, D.M. Berman, T. Jenuwein,K. Pruitt, S.J. Sharkis, D.N. Watkins, J.G. Herman, S.B. Baylin, A stem cell-likechromatin pattern may predispose tumor suppressor genes to DNA hyper-methylation and heritable silencing, Nat. Genet. 39 (2007) 237 e 242.

[113] Y. Schlesinger, R. Straussman, I. Keshet, S. Farkash, M. Hecht, J. Zimmerman,E. Eden, Z. Yakhini, E. Ben-Shushan, B.E. Reubinoff, Y. Bergman, I. Simon,H. Cedar, Polycomb-mediated methylation on Lys27 of histone H3 pre-marksgenes for de novo methylation in cancer, Nat. Genet. 39 (2007) 232 e 236.

[114] M. Widschwendter, H. Fiegl, D. Egle, E. Mueller-Holzner, G. Spizzo, C. Marth,D.J. Weisenberger, M. Campan, J. Young, I. Jacobs, P.W. Laird, Epigenetic stemcell signature in cancer, Nat. Genet. 39 (2007) 157 e 158.

[115] G. Lagger, D. O ’ Carroll, M. Rembold, H. Khier, J. Tischler, G. Weitzer,B. Schuettengruber, C. Hauser, R. Brunmeir, T. Jenuwein, C. Seiser, Essentialfunction of histone deacetylase 1 in proliferation control and CDK inhibitorrepression, Embo J. 21 (2002) 2672 e 2681.

[116] S. Lagger, D. Meunier, M. Mikula, R. Brunmeir, M. Schlederer, M. Artaker,O. Pusch, G. Egger, A. Hagelkruys, W. Mikulits, G. Weitzer, E.W. Muellner,M. Susani, L. Kenner, C. Seiser, Crucial function of histone deacetylase 1 fordifferentiation of teratomas in mice and humans, Embo J. 29 (2011)3992 e 4007.

M.R. Hassler, G. Egger / Biochimie 94 (2012) 2219 e 22302228

7/27/2019 EPI EXAM

http://slidepdf.com/reader/full/epi-exam 11/12

7/27/2019 EPI EXAM

http://slidepdf.com/reader/full/epi-exam 12/12

[156] B. Deng, S. Melnik, P.R. Cook, Transcription factories, chromatin loops, andthe dysregulation of gene expression in malignancy, Semin. Cancer Biol.(2012).

[157] G. Li, X. Ruan, R.K. Auerbach, K.S. Sandhu, M. Zheng, P. Wang, H.M. Poh,Y. Goh, J. Lim, J. Zhang, H.S. Sim, S.Q. Peh, F.H. Mulawadi, C.T. Ong, Y.L. Orlov,S. Hong, Z. Zhang, S. Landt, D. Raha, G. Euskirchen, C.L. Wei, W. Ge, H. Wang,C. Davis, K.I. Fisher-Aylor, A. Mortazavi, M. Gerstein, T. Gingeras, B. Wold,Y. Sun, M.J. Fullwood, E. Cheung, E. Liu, W.K. Sung, M. Snyder, Y. Ruan,Extensive promoter-centered chromatin interactions provide a topologicalbasis for transcription regulation, Cell 148 (2012) 84 e 98.

[158] L. Handoko, H. Xu, G. Li, C.Y. Ngan, E. Chew, M. Schnapp, C.W. Lee, C. Ye, J.L. Ping, F. Mulawadi, E. Wong, J. Sheng, Y. Zhang, T. Poh, C.S. Chan,G. Kunarso, A. Shahab, G. Bourque, V. Cacheux-Rataboul, W.K. Sung, Y. Ruan,C.L. Wei, CTCF-mediated functional chromatin interactome in pluripotentcells, Nat. Genet. 43 (2011) 630 e 638.

[159] M.H. Kagey, J.J. Newman, S. Bilodeau, Y. Zhan, D.A. Orlando, N.L. van Berkum,C.C. Ebmeier, J. Goossens, P.B. Rahl, S.S. Levine, D.J. Taatjes, J. Dekker,R.A. Young, Mediator and cohesin connect gene expression and chromatinarchitecture, Nature 467 (2010) 430 e 435.

[160] G.M. Euskirchen, R.K. Auerbach, E. Davidov, T.A. Gianoulis, G. Zhong, J. Rozowsky, N. Bhardwaj, M.B. Gerstein, M. Snyder, Diverse roles andinteractions of the SWI/SNF chromatin remodeling complex revealed usingglobal approaches, PLoS Genet. 7 (2011) e1002008.

[161] H.P. Easwaran, S.B. Baylin, Role of nuclear architecture in epigenetic alter-ations in cancer, Cold Spring Harb Symp. Quant Biol. 75 (2010) 507 e 515.

[162] H.M. O ’ Hagan, W. Wang, S. Sen, C. Destefano Shields, S.S. Lee, Y.W. Zhang,E.G. Clements, Y. Cai, L. Van Neste, H. Easwaran, R.A. Casero, C.L. Sears,S.B. Baylin, Oxidative damage targets complexes containing DNA methyl-transferases, SIRT1, and polycomb members to promoter CpG Islands, CancerCell 20 (2011) 606 e 619.

[163] F. Bantignies, G. Cavalli, Cellular memory and dynamic regulation of poly-comb group proteins, Curr. Opin. Cell Biol. 18 (2006) 275 e 283.

[164] N. Lee, C. Maurange, L. Ringrose, R. Paro, Suppression of Polycomb groupproteins by JNK signalling induces transdetermination in Drosophila imag-inal discs, Nature 438 (2005) 234 e 237.

[165] G. Caretti, D. Palacios, V. Sartorelli, P.L. Puri, Phosphoryl-EZH-ion, Cell StemCell 8 (2011) 262 e 265.

[166] V.K. Tiwari, M.B. Stadler, C. Wirbelauer, R. Paro, D. Schubeler, C. Beisel,A chromatin-modifying function of JNK during stem cell differentiation, Nat.Genet. 44 (2012) 94 e 100.

[167] S.H. Baek, When signaling kinases meet histones and histone modi ers inthe nucleus, Mol. Cell 42 (2011) 274 e 284.

[168] S.B. Baylin, P.A. Jones, A decade of exploring the cancer epigenome e bio-logical and translational implications, Nat. Rev. Cancer 11 (2011) 726 e 734.

[169] D. Zink, A.H. Fischer, J.A. Nickerson, Nuclear structure in cancer cells, Nat.Rev. Cancer 4 (2004) 677 e 687.

[170] K.C. Wang, Y.W. Yang, B. Liu, A. Sanyal, R. Corces-Zimmerman, Y. Chen,B.R. Lajoie, A. Protacio, R.A. Flynn, R.A. Gupta, J. Wysocka, M. Lei, J. Dekker, J.A. Helms, H.Y. Chang, A long noncoding RNA maintains active chromatin tocoordinate homeotic gene expression, Nature 472 (2010) 120 e 124.

[171] M.C. Tsai, O. Manor, Y. Wan, N. Mosammaparast, J.K. Wang, F. Lan, Y. Shi,E. Segal, H.Y. Chang, Long noncoding RNA as modular scaffold of histonemodi cation complexes, Science 329 (2010) 689 e 693.

[172] A.T. Willingham, A.P. Orth, S. Batalov, E.C. Peters, B.G. Wen, P. Aza-Blanc, J.B. Hogenesch, P.G. Schultz, A strategy for probing the function of noncodingRNAs nds a repressor of NFAT, Science 309 (2005) 1570 e 1573.

[173] M. Cesana, D. Cacchiarelli, I. Legnini, T. Santini, O. Sthandier, M. Chinappi,A. Tramontano, I. Bozzoni, A long noncoding RNA controls muscle differen-tiation by functioning as a competing endogenous RNA, Cell 147 (2011)358 e 369.

M.R. Hassler, G. Egger / Biochimie 94 (2012) 2219 e 22302230