epigenetics in cancer carcinogenesis 2009

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Epigenetics in Cancer

Shikhar Sharma1, 2, Theresa K. Kelly1 and Peter A. Jones1*

1Department of Urology, io!hemistry and "ole!#lar iology, 2 Department of $eneti!s,

"ole!#lar and %ell#lar iology, US%&'orris %omprehensi(e %an!er %enter Ke!k S!hool

of "edi!ine, Uni(ersity of So#thern %alifornia, )os Angeles, %A++-11, USA

#nning title/ 0pigeneti!s in %an!er

Keyords/ 0pigeneti!s, %an!er, D'A methylation, istone "odifi!ations, '#!leosome

Positioning, mi!ro'As

*To hom !orresponden!e sho#ld 3e addressed/ 0-mail/4ones5p6!!nt.#s!.ed#

Carcinogenesis Advance Access published September 13, 2009



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ABSTRACT

0pigeneti! me!hanisms are essential for normal de(elopment and maintenan!e of

tiss#e spe!ifi! gene e7pression patterns in mammals. Disr#ption of epigeneti! pro!esses

!an lead to altered gene f#n!tion and malignant !ell#lar transformation. $lo3al !hanges

in the epigeneti! lands!ape are a hallmark of !an!er. The initiation and progression of

!an!er, traditionally seen as a geneti! disease, is no reali8ed to in(ol(e epigeneti!

a3normalities along ith geneti! alterations. e!ent ad(an!ements in the rapidly

e(ol(ing field of !an!er epigeneti!s ha(e shon e7tensi(e reprogramming of e(ery

!omponent of the epigeneti! ma!hinery in !an!er in!l#ding D'A methylation, histone

modifi!ations, n#!leosome positioning and non-!oding 'As, spe!ifi!ally mi!ro'A

e7pression. The re(ersi3le nat#re of epigeneti! a3errations has led to the emergen!e of

the promising field of epigeneti! therapy, hi!h is already making progress ith the

re!ent 9DA appro(al of three epigeneti! dr#gs for !an!er treatment. :n this re(ie, e

dis!#ss the !#rrent #nderstanding of alterations in the epigeneti! lands!ape that o!!#r in

!an!er !ompared to normal !ells, the roles of these !hanges in !an!er initiation and

progression, in!l#ding the !an!er stem !ell model, and the potential #se of this

knoledge in designing more effe!ti(e treatment strategies.



;

INTRODUCTION

%hromatin str#!t#re defines the state in hi!h geneti! information in the form of

D'A is organi8ed ithin a !ell. This organi8ation of the genome into a pre!ise !ompa!t

str#!t#re greatly infl#en!es the a3ilities of genes to 3e a!ti(ated or silen!ed. 0pigeneti!s,

originally defined 3y %. . <addington as =the !a#sal intera!tions 3eteen genes and

their prod#!ts, hi!h 3ring the phenotype into 3eing> ?1@, in(ol(es #nderstanding

!hromatin str#!t#re and its impa!t on gene f#n!tion. <addingtons definition initially

referred to the role of epigeneti!s in em3ryoni! de(elopment, hoe(er, the definition of

epigeneti!s has e(ol(ed o(er time as it is impli!ated in a ide (ariety of 3iologi!al

pro!esses. The !#rrent definition of epigeneti!s is =the st#dy of herita3le !hanges in gene

e7pression that o!!#r independent of !hanges in the primary D'A seB#en!e.> "ost of

these herita3le !hanges are esta3lished d#ring differentiation and are sta3ly maintained

thro#gh m#ltiple !y!les of !ell di(ision, ena3ling !ells to ha(e distin!t identities hile

!ontaining the same geneti! information. This herita3ility of gene e7pression patterns is

mediated 3y epigeneti! modifi!ations, hi!h in!l#de methylation of !ytosine 3ases in

D'A, post-translational modifi!ations of histone proteins as ell as the positioning of

n#!leosomes along the D'A. The !omplement of these modifi!ations, !olle!ti(ely

referred to as the epigenome, pro(ides a me!hanism for !ell#lar di(ersity 3y reg#lating

hat geneti! information !an 3e a!!essed 3y !ell#lar ma!hinery. 9ail#re of the proper

maintenan!e of herita3le epigeneti! marks !an res#lt in inappropriate a!ti(ation or

inhi3ition of (ario#s signaling pathays and lead to disease states s#!h as !an!er ?2,;@.

e!ent ad(an!es in the field of epigeneti!s ha(e shon that h#man !an!er !ells

har3or glo3al epigeneti! a3normalities, in addition to n#mero#s geneti! alterations ?;,C@.



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These geneti! and epigeneti! alterations intera!t at all stages of !an!er de(elopment,

orking together to promote !an!er progression ?@. The geneti! origin of !an!er is

idely a!!epted, hoe(er re!ent st#dies s#ggest that epigeneti! alterations may 3e the

key initiating e(ents in some forms of !an!er ?E@. These findings ha(e led to a glo3al

initiati(e to #nderstand the role of epigeneti!s in the initiation and propagation of !an!er

?F@. The fa!t that epigeneti! a3errations, #nlike geneti! m#tations, are potentially

re(ersi3le and !an 3e restored to their normal state 3y epigeneti! therapy makes s#!h

initiati(es promising and therape#ti!ally rele(ant ?@.

:n this re(ie e take a !omprehensi(e look at the !#rrent #nderstanding of the

epigeneti! me!hanisms at ork in normal mammalian !ells and their !omparati(e

a3errations that o!!#r d#ring !ar!inogenesis. <e also dis!#ss the idea of !an!er stem

!ells as the originators of !an!er and the prospe!t of epigeneti! therapy in designing

effi!ient strategies for !an!er treatment.

EPIGENETIC MECHANISMS IN NORMAL CELLS

%hromatin is made of repeating #nits of n#!leosomes, hi!h !onsist of G1CE 3ase

pairs of D'A rapped aro#nd an o!tamer of fo#r !ore histone proteins H;, C, 2A

and 2I ?@. 0pigeneti! me!hanisms that modify !hromatin str#!t#re !an 3e di(ided

into fo#r main !ategories/ D'A methylation, !o(alent histone modifi!ations, non-

!o(alent me!hanisms s#!h as in!orporation of histone (ariants and n#!leosome

remodeling and non-!oding 'As in!l#ding mi!ro'As. These modifi!ations ork

together to reg#late the f#n!tioning of the genome 3y altering the lo!al str#!t#ral

dynami!s of !hromatin, primarily reg#lating its a!!essi3ility and !ompa!tness. The



interplay of these modifi!ations !reates an =epigeneti! lands!ape> hi!h reg#lates the

ay the mammalian genome manifests itself in different !ell types, de(elopmental stages

and disease states, in!l#ding !an!er ?C,1+-1C@. The distin!t patterns of these modifi!ations

present in different !ell#lar states ser(e as a g#ardian of !ell#lar identity HTa3le :I. ere

e ill dis!#ss the important aspe!ts of the key epigeneti! me!hanisms present in normal

!ells.

DNA Methylatin

D'A methylation is perhaps the most e7tensi(ely st#died epigeneti! modifi!ation

in mammals. :t pro(ides a sta3le gene silen!ing me!hanism hi!h plays an important role

in reg#lating gene e7pression and !hromatin ar!hite!t#re, in asso!iation ith histone

modifi!ations and other !hromatin asso!iated proteins. :n mammals, D'A methylation

primarily o!!#rs 3y the !o(alent modifi!ation of !ytosine resid#es in %p$ din#!leotides.

%p$ din#!leotides are not e(enly distri3#ted a!ross the h#man genome 3#t are instead

!on!entrated in short %p$-ri!h D'A stret!hes !alled =%p$ islands> and regions of large

repetiti(e seB#en!es He.g. !entromeri! repeats, retrotransposon elements, rD'A et!.I

?1,1E@. %p$ islands are preferentially lo!ated at the end of genes and o!!#py GE+ of

h#man gene promoters ?1F@. <hile most of the %p$ sites in the genome are methylated,

the ma4ority of %p$ islands #s#ally remain #nmethylated d#ring de(elopment and in

differentiated tiss#es ?11@. oe(er, some %p$ island promoters 3e!ome methylated

d#ring de(elopment, hi!h res#lts in long-term trans!riptional silen!ing. -!hromosome

ina!ti(ation and imprinted genes are !lassi! e7amples of s#!h nat#rally o!!#rring %p$

island methylation d#ring de(elopment ?1@. Some tiss#e-spe!ifi! %p$ island



E

methylation has also 3een reported to o!!#r in a (ariety of somati! tiss#es, primarily at

de(elopmentally important genes ?1,1@. :n !ontrast, the repetiti(e genomi! seB#en!es

that are s!attered all o(er the h#man genome are hea(ily methylated hi!h pre(ents

!hromosomal insta3ility 3y silen!ing non-!oding D'A and transposa3le D'A elements

?11@. D'A methylation !an lead to gene silen!ing 3y either pre(enting or promoting the

re!r#itment of reg#latory proteins to D'A. 9or e7ample, :t !an inhi3it trans!riptional

a!ti(ation 3y 3lo!king trans!ription fa!tors from a!!essing target 3inding sites e.g. !-my!

and ")T9 ?2+,21@. Alternati(ely, it !an pro(ide 3inding sites for methyl-3inding domain

H"DI proteins, hi!h !an mediate gene repression thro#gh intera!tions ith histone

dea!etylases HDA%sI ?22,2;@. Th#s, D'A methylation #ses a (ariety of me!hanisms to

herita3ly silen!e genes and non-!oding genomi! regions.

The pre!ise D'A methylation patterns fo#nd in the mammalian genome are

generated and herita3ly maintained 3y the !ooperati(e a!ti(ity of the de novo

methyltransferases - D'"T;A and D'"T;, hi!h a!t independent of repli!ation and

sho eB#al preferen!e for 3oth #nmethylated and hemimethylated D'A and the

maintenan!e D'A methyltransferases - D'"T1, hi!h a!ts d#ring repli!ation

preferentially methylating hemimethylated D'A ?2C,2@.

<hile the role of %p$ island promoter methylation in gene silen!ing is ell

esta3lished, m#!h less is knon a3o#t the role of methylation of non-%p$ island

promoters. e!ent st#dies ha(e shon that D'A methylation is also important for the

reg#lation of non-%p$ island promoters. 9or e7ample, tiss#e-spe!ifi! e7pression of

"ASP:', hi!h does not !ontain a %p$ island ithin its promoter, is reg#lated 3y D'A

methylation ?2E@. Similarly, methylation of the non-%p$ island L!t-C promoter, strongly



F

infl#en!es its e7pression le(el ?2F@. Sin!e %p$ islands o!!#py only GE+ of h#man gene

promoters, it is essential to el#!idate the role of non-%p$ island methylation in order to

f#lly #nderstand the glo3al role of D'A methylation in normal tiss#e ?1F@.

C!alent Histne M"i#icatins

istone proteins, hi!h !omprise the n#!leosome !ore, !ontain a glo3#lar %-

terminal domain and an #nstr#!t#red '-terminal tail ?@. The amino terminal tails of

n#!leosomes !an #ndergo a (ariety of post-translational !o(alent modifi!ations in!l#ding

methylation, a!etylation, #3iB#itylation, s#moylation, and phosphorylation on spe!ifi!

resid#es ?12@. These modifi!ations reg#late key !ell#lar pro!esses s#!h as trans!ription,

repli!ation and repair ?12@. The !omplement of modifi!ations is proposed to store the

epigeneti! memory inside a !ell in the form of a =histone !ode> hi!h determines the

str#!t#re and a!ti(ity of different !hromatin regions ?2@. istone modifi!ations ork 3y

either !hanging the a!!essi3ility of !hromatin or 3y re!r#iting and&or o!!l#ding non-

histone effe!tor proteins, hi!h de!ode the message en!oded 3y the modifi!ation

patterns. The me!hanism of inheritan!e of this =histone !ode> hoe(er, is still not f#lly

#nderstood.

Unlike D'A methylation, histone modifi!ations !an lead to either a!ti(ation or

repression depending #pon hi!h resid#es are modified and the type of modifi!ations

present. 9or e7ample, lysine a!etylation !orrelates ith trans!riptional a!ti(ation ?12,2@

hile lysine methylation leads to trans!riptional a!ti(ation or repression depending #pon

hi!h resid#e is modified and the degree of methylation. 9or e7ample, trimethylation of

lysine C on histone ; H;KCme;I is enri!hed at trans!riptionally a!ti(e gene promoters



?;+@ hile trimethylation of ;K H;Kme;I and ;K2F H;K2Fme;I is present at

gene promoters that are trans!riptionally repressed ?12@. These to modifi!ations

together !onstit#te the to main silen!ing me!hanisms in mammalian !ells, ;Kme;

orking in !on!ert ith D'A methylation and ;K2Fme; largely orking e7!l#si(e of

D'A methylation H9ig#re 1I. A (ast array of a!ti(e and repressi(e histone modifi!ations

ha(e 3een identified, hi!h !onstit#te a !omple7 gene reg#latory netork essential for

the physiologi! a!ti(ities of !ells ?1+,12@. $enome-ide st#dies shoing distin!t

lo!ali8ation and !om3inatorial patterns of these histone marks in the genome ha(e

signifi!antly in!reased o#r #nderstanding of ho these di(erse modifi!ations a!t in a

!ooperati(e manner to reg#late glo3al gene e7pression patterns ?;1,;2@.

Spe!ifi! patterns of histone modifi!ations are present ithin distin!t !ell types

and are proposed to play a key role in determining !ell#lar identity ?;;,;C@. 9or e7ample,

em3ryoni! stem H0SI !ells possess =3i(alent domains> hi!h !ontain !oe7isting a!ti(e

H;KCme;I and repressi(e H;K2Fme;I marks at promoters of de(elopmentally

important genes ?;,;E@. S#!h 3i(alent domains are esta3lished 3y the a!ti(ity of to

!riti!al reg#lators of de(elopment in mammals/ the poly!om3 gro#p HP!$I hi!h

!ataly8es the repressi(e ;K2F trimethylation mark and is essential for maintaining 0S

!ell pl#ripoten!y thro#gh silen!ing !ell-fate spe!ifi! genesM and potentially the trithora7

gro#p Htr7$I hi!h !ataly8es the a!ti(ating ;KC trimethylation mark and is reB#ired for

maintaining a!ti(e !hromatin states d#ring de(elopment ?;C@. This 3i(alen!y is

hypothesi8ed to add to phenotypi! plasti!ity, ena3ling 0S !ells to tightly reg#late gene

e7pression d#ring different de(elopmental pro!esses. Differentiated !ells lose this

3i(alen!y and a!B#ire a more rigid !hromatin str#!t#re, hi!h may 3e important for



maintaining !ell fate d#ring !ell#lar e7pansion ?;;@. This hypothesis is s#pported 3y the

re!ent dis!o(ery of large !ondensed !hromatin regions !ontaining the repressi(e

;Kme2 mark, termed =)L%Ks> Hlarge organi8ed !hromatin K modifi!ationsI, in

differentiated 0S !ells hi!h !an maintain silen!ing of large genomi! regions in

differentiated tiss#es ?;F@.

istone modifi!ation patterns are dynami!ally reg#lated 3y en8ymes that add and

remo(e !o(alent modifi!ations to histone proteins. istone a!etyltransferases HATsI

and histone methyltransferases H"TsI, add a!etyl and methyl gro#ps, respe!ti(ely hile

histone dea!etylases HDA%sI and histone demethylases HD"sI remo(e a!etyl and

methyl gro#ps, respe!ti(ely ?;,;@. A n#m3er of histone modifying en8ymes in!l#ding

(ario#s ATs, "Ts, DA%s and D"s ha(e 3een identified in the past de!ade ?12@.

These histone modifying en8ymes intera!t ith ea!h other as ell as other D'A

reg#latory me!hanisms to tightly link !hromatin state and trans!ription.

Interplay # DNA Methylatin an" Histne M"i#icatins

:n addition to performing their indi(id#al roles, histone modifi!ations and D'A

methylation intera!t ith ea!h other at m#ltiple le(els, to determine gene e7pression

stat#s, !hromatin organi8ation and !ell#lar identity ?C+@. Se(eral histone

methyltransferases in!l#ding $a, SUN;1 and P"T, !an dire!t D'A methylation

to spe!ifi! genomi! targets 3y dire!tly re!r#iting D'"Ts to sta3ly silen!ed genes ?C1-

C;@. :n addition to the dire!t re!r#itment of D'"Ts, histone methyltransferases and

demethylases also infl#en!e D'A methylation le(els 3y reg#lating the sta3ility of

D'"T proteins ?CC,C@. D'"Ts !an in t#rn re!r#it DA%s and methyl 3inding proteins



1+

H"PsI to a!hie(e gene silen!ing and !hromatin !ondensation ?22,2;@. D'A methylation

!an also dire!t ;K methylation thro#gh effe!tor proteins, s#!h as "e%P2, there3y

esta3lishing a repressi(e !hromatin state ?CE@. The intera!tions 3eteen D'A

methylation ma!hinery and histone modifying en8ymes f#rther enhan!e the !omple7ity

of epigeneti! reg#lation of gene e7pression, hi!h determines and maintains !ell#lar

identity and f#n!tion.

N$cles%e Psitining & Histne 'ariants

'on-!o(alent me!hanisms, s#!h as n#!leosome remodeling and repla!ement of

!anoni!al histone proteins ith spe!iali8ed histone (ariants, also play an important role in

ho !hromatin str#!t#re reg#lates gene a!ti(ity. :n addition to ser(ing as the 3asi!

mod#les for D'A pa!kaging ithin a !ell, n#!leosomes reg#late gene e7pression 3y

altering the a!!essi3ility of reg#latory D'A seB#en!es to trans!ription fa!tors ?1C@.

$enome-ide n#!leosome mapping data for (ario#s e#karyoti! organisms re(eal a

!ommon organi8ational theme ith pre!ise positioning of n#!leosomes aro#nd gene

promoters, !ompared to the relati(ely random pattern fo#nd in gene 3odies ?CF@.

'#!leosome 9ree egions H'9sI present at the and ; ends of genes are tho#ght to

pro(ide the sites for assem3ly and disassem3ly of the trans!ription ma!hinery ?C@. The

loss of a n#!leosome dire!tly #pstream of the TSS is tightly !orrelated ith gene

a!ti(ation ?C,+@. 9#rthermore, the presen!e of an '9 at gene promoters ith 3asal

le(el of trans!ription !orrelates ith their a3ility for rapid a!ti(ation #pon stim#lation

?1@. :n !ontrast, o!!l#sion of the trans!ription start site HTSSI ithin the '9 3y a

n#!leosome is asso!iated ith gene repression ?2@. "od#lation of the '9s is



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or!hestrated 3y ATP-dependent !hromatin remodeling !omple7es, hi!h modify the

a!!essi3ility of D'A reg#latory sites thro#gh 3oth sliding and e4e!tion of n#!leosomes

?;@. The intera!tion of n#!leosome remodeling ma!hinery ith D'A methylation and

histone modifi!ations plays a pi(otal role in esta3lishing glo3al gene e7pression patterns

and !hromatin ar!hite!t#re H9ig#re 1 and 2I ?C,@.

:n addition to physi!al alterations in n#!leosomal positioning (ia n#!leosome

remodelers, the in!orporation of histone (ariants e.g. ;.; and 2A.O, into n#!leosomes

also infl#en!es n#!leosome o!!#pan!y and th#s gene a!ti(ity ?E,F@. Unlike the ma4or

histone s#3types hose synthesis and in!orporation is !o#pled to D'A repli!ation in S

phase, these (ariants are synthesi8ed and in!orporated into !hromatin thro#gho#t the !ell

!y!le ?E@. ;.; and 2A.O are preferentially enri!hed at promoters of a!ti(e genes or

genes poised for a!ti(ation and !an mediate gene a!ti(ation 3y altering the sta3ility of

n#!leosomes ?@. 2A.O in!orporation may also !ontri3#te to gene a!ti(ation 3y

prote!ting genes against D'A methylation ?@. :n 0S !ells, 2A.O !o-lo!ali8es ith

3i(alent domains here it may assist in maintaining key de(elopmental genes in a poised

state ?E+@. )ike !anoni!al histones, histone (ariants #ndergo (ario#s post-translational

modifi!ations, hi!h determine their n#!lear lo!ali8ation and f#n!tion. 9or e7ample,

a!etylated 2A.O primarily asso!iates ith a!ti(e genes in e#!hromatin hile

#3iB#itylated 2A.O asso!iates ith fa!#ltati(e hetero!hromatin ?E1,E2@. Taken together,

the in!l#sion of histone (ariants ithin n#!leosomes pro(ides an additional epigeneti!

me!hanism #tili8ed 3y !ells to modify !hromatin str#!t#re a!!ording to the needs of

di(erse !ell#lar pro!esses.



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%iRNAs

"i!ro'As Hmi'AsI are small, G22 n#!leotide, non-!oding 'As that reg#late

gene e7pression thro#gh post-trans!riptional silen!ing of target genes. SeB#en!e-spe!ifi!

3ase pairing of mi'As ith ; #ntranslated regions of target m'A ithin the :S%

!omple7 H'A-ind#!ed silen!ing !omple7I res#lts in target m'A degradation or

inhi3ition of translation ?E;@. mi'As are e7pressed in a tiss#e spe!ifi! manner and

!ontrol a ide array of 3iologi!al pro!esses in!l#ding !ell proliferation, apoptosis and

differentiation. The list of mi'As identified in the h#man genome and their potential

target genes is groing rapidly, demonstrating their e7tensi(e role in maintaining glo3al

gene e7pression patterns ?1;@. )ike normal genes, the e7pression of mi'As !an 3e

reg#lated 3y epigeneti! me!hanisms ?EC@. :n addition, mi'As !an also mod#late

epigeneti! reg#latory me!hanisms inside a !ell 3y targeting en8ymes responsi3le for

D'A methylation HD'"T;A and D'"T;I and histone modifi!ations H0O2I ?E,EE@.

S#!h intera!tion among the (ario#s !omponents of the epigeneti! ma!hinery re-

emphasi8es the integrated nat#re of epigeneti! me!hanisms in(ol(ed in the maintenan!e

of glo3al gene e7pression patterns.

ABERRANT REPROGRAMMING O( THE EPIGENOME IN CANCER

The pre!ise epigenomi! lands!ape present in normal !ells #ndergoes e7tensi(e

distortion in !an!er ?C@. These epim#tations, along ith idespread geneti! alterations,

play an important role in !an!er initiation and progression ?;@. The !an!er epigenome is

!hara!teri8ed 3y glo3al !hanges in D'A methylation and histone modifi!ation patterns as

ell as altered e7pression profiles of !hromatin modifying en8ymes. These epigeneti!



1;

!hanges res#lt in glo3al dysreg#lation of gene e7pression profiles leading to the

de(elopment and progression of disease states ?2@. 0pim#tations !an lead to silen!ing of

t#mor s#ppressor genes independently and also in !on4#n!tion ith deleterio#s geneti!

m#tations or deletions, th#s ser(ing as the se!ond hit reB#ired for !an!er initiation

a!!ording to the =to-hit> model proposed 3y Alfred Kn#dson ?@. :n addition to

ina!ti(ating t#mor s#ppressors, epim#tations !an also promote t#morigenesis 3y

a!ti(ating on!ogenes. The e(ents that lead to initiation of these epigeneti! a3normalities

are still not f#lly #nderstood. 'e(ertheless, sin!e epigeneti! alterations, like geneti!

m#tations, are mitoti!ally herita3le, they are sele!ted for in a rapidly groing !an!er !ell

pop#lation and !onfer a groth ad(antage to t#mor !ells res#lting in their #n!ontrolled

groth.

DNA Methylatin A)erratins in Cancer

%an!er initiation and progression are a!!ompanied 3y profo#nd !hanges in D'A

methylation hi!h ere the first epigeneti! alterations identified in !an!er ?EF,E@. A

!an!er epigenome is marked 3y genome-ide hypomethylation and site-spe!ifi! %p$

island promoter hypermethylation H9ig#re 2I ?;@. <hile the #nderlying me!hanisms

hi!h initiate these glo3al !hanges are still #nder in(estigation, re!ent st#dies indi!ate

that some !hanges o!!#r (ery early in !an!er de(elopment and may !ontri3#te to !an!er

initiation ?E@.

$lo3al D'A hypomethylation plays a signifi!ant role in t#morigenesis and o!!#rs

at (ario#s genomi! seB#en!es in!l#ding repetiti(e elements, retrotransposons, %p$ poor

promoters, introns and gene deserts ?E@. D'A hypomethylation at repeat seB#en!es



1C

leads to in!reased genomi! insta3ility 3y promoting !hromosomal rearrangements ?;,F+@.

ypomethylation of retrotransposons !an res#lt in their a!ti(ation and translo!ation to

other genomi! regions, th#s in!reasing genomi! insta3ility ?F1@. :nd#!tion of genomi!

insta3ility 3y hypomethylation is 3est e7emplified in patients ith the :%9

Himm#nodefi!ien!y, !entromeri! region insta3ility and fa!ial anomaliesI syndrome,

hi!h ha(e a germ-line m#tation in the D'"T; en8yme res#lting in hypomethylation

and s#3seB#ent !hromosomal insta3ility ?F2@. Similar loss of D'A methylation and

genomi! insta3ility is impli!ated in a (ariety of h#man !an!ers ?F1@. :n addition, D'A

hypomethylation !an lead to the a!ti(ation of groth-promoting genes, s#!h as R-Ras

and MAPSIN in gastri! !an!er, S-100 in !olon !an!er and MAGE Hmelanoma-asso!iated

antigenI in melanoma ?F;@ and a loss of imprinting H)L:I in t#mors ?FC@. :n <ilms

t#mor, hypomethylation ind#!ed )L: of IGF2, an important a#to!rine groth fa!tor,

res#lts in its pathologi!al 3ialleli! e7pression ?F@. )L: of :$92 has also 3een linked ith

an in!reased risk of !olore!tal !an!er ?FE@. Th#s, D'A hypomethylation leads to a3errant

a!ti(ation of genes and non-!oding regions thro#gh a (ariety of me!hanisms hi!h

!ontri3#tes to !an!er de(elopment and progression.

:n !ontrast to hypomethylation, hi!h in!reases genomi! insta3ility and a!ti(ates

proto-on!ogenes, site-spe!ifi! hypermethylation !ontri3#tes to t#morigenesis 3y silen!ing

t#mor s#ppressor genes. Sin!e the initial dis!o(ery of %p$ island hypermethylation of

the Rb promoter Ha t#mor s#ppressor gene asso!iated ith retino3lastomaI ?FF@, (ario#s

other t#mor s#ppressor genes in!l#ding p16 , MLH1 and BRCA1, ha(e also 3een shon to

#ndergo t#mor-spe!ifi! silen!ing 3y hypermethylation ?;,C,F@. These genes are in(ol(ed

in !ell#lar pro!esses, hi!h are integral to !an!er de(elopment and progression,



1

in!l#ding D'A repair, !ell !y!le, !ell adhesion, apoptosis and angiogenesis. 0pigeneti!

silen!ing of s#!h t#mor s#ppressor genes !an also lead to t#mor initiation 3y ser(ing as

the se!ond hit in the Kn#dsons =to-hit> model ?@. :n addition to dire!t ina!ti(ation of

t#mor s#ppressor genes, D'A hypermethylation !an also indire!tly silen!e additional

!lasses of genes 3y silen!ing trans!ription fa!tors and D'A-repair genes. Promoter

hypermethylation ind#!ed silen!ing of trans!ription fa!tors s#!h as RUNX in esophageal

!an!er ?F@, and GA!A-" and GA!A-# in !olore!tal and gastri! !an!ers ?+@, leads to

ina!ti(ation of their donstream targets. Silen!ing of D'A-repair genes He.g. MLH1,

BRCA1 et!.I ena3les !ells to a!!#m#late f#rther geneti! lesions leading to the rapid

progression of !an!er.

<hile the a3ility of D'A hypermethylation to silen!e t#mor s#ppressor genes in

!an!er is ell esta3lished, ho genes are targeted for this a3errant D'A methylation is

still #n!lear. Lne possi3ility is that silen!ing spe!ifi! genes 3y hypermethylation pro(ides

a groth ad(antage to !ells res#lting in their !lonal sele!tion and proliferation. T#mor-

spe!ifi! %p$ island methylation !an o!!#r thro#gh a seB#en!e spe!ifi! instr#!ti(e

me!hanism 3y hi!h D'"Ts are targeted to spe!ifi! genes 3y their asso!iation ith

on!ogeni! trans!ription fa!tors. A3errant hypermethylation and silen!ing of spe!ifi!

target gene promoters 3y the P")-A f#sion protein in a!#te promyelo!yti! le#kemia

is an e7ample of s#!h a me!hanism ?1@. )arge stret!hes of D'A !an 3e!ome a3normally

methylated in !an!er ?2@ !a#sing some %p$ islands to 3e hypermethylated as a res#lt of

their lo!ation inside s#!h genomi! regions hi!h ha(e #ndergone large-s!ale epigeneti!

reprogramming. Another interesting me!hanism proposes a role of histone marks in the

t#mor-spe!ifi! targeting of de novo methylation and ill 3e dis!#ssed in detail in the ne7t



1E

se!tion. :nterestingly, regions that are hypermethylated in !an!er are often pre-marked

ith ;K2Fme; poly!om3 mark in em3ryoni! stem H0SI !ells H9ig#re ;I ?;-@

s#ggesting a link 3eteen the reg#lation of de(elopment and t#morigenesis. This

o3ser(ation also partially e7plains the theory of =%p$ island methylator phenotype> or

%:"P hi!h hypothesi8es that there is !oordinated methylation of a s#3set of %p$

islands in t#mors sin!e many of these %:"P lo!i are knon poly!om3 targets ?C,E@.

9#rther #nderstanding of ho spe!ifi! genomi! regions are targeted for D'A

hypermethylation in !an!er ill potentially lead to additional therape#ti! targets.

Changes in Histne M"i#icatins in Cancer

e!ent ad(an!es in high thro#ghp#t seB#en!ing ha(e ena3led genome ide

mapping of !hromatin !hanges o!!#rring d#ring t#morigenesis. These st#dies ha(e

re(ealed a glo3al loss of a!etylated C-lysine 1E HCK1Ea!I and C-lysine 2+

trimethylation HCK2+me;I ?F@. S#!h loss of histone a!etylation, hi!h is mediated 3y

histone dea!etylases HDA%sI res#lts in gene repression. DA%s are often fo#nd

o(ere7pressed in (ario#s types of !an!er ?,@ and th#s, ha(e 3e!ome a ma4or target for

epigeneti! therapy. istone a!etyltransferases HATsI, hi!h ork in !on!ert ith

DA%s to maintain histone a!etylation le(els, !an also 3e altered in !an!er. A3errant

formation of f#sion proteins thro#gh !hromosomal translo!ations of AT and AT-

related genes He.g. "LO, "L9, %P and p;++I o!!#rs in le#kemia ?+@. "istargeting

of s#!h deleterio#s f#sion proteins !ontri3#tes to glo3al alterations in histone a!etylation

patterns in !an!er.



1F

:n addition to !hanges in histone a!etylation, !an!er !ells also display idespread

!hanges in histone methylation patterns. Alterations in ;K and ;K2F methylation

patterns are asso!iated ith a3errant gene silen!ing in (ario#s forms of !an!er ?1,2@.

Dysreg#lation of histone methyltransferases responsi3le for repressi(e marks res#lts in

altered distri3#tion of these marks in !an!er and leads to a3errant silen!ing of t#mor

s#ppressor genes. 9or e7ample, 0O2, hi!h is the ;K2F histone methyltransferase, is

o(ere7pressed in 3reast and prostate !an!er ?2@. :n!reased le(els of $a, the ;K

histone methyltransferase, has 3een fo#nd in li(er !an!er, and is impli!ated in

perpet#ating malignant phenotype possi3ly thro#gh mod#lation of !hromatin str#!t#re

?;,C@ . %hromosomal translo!ations of ")), the ;KC histone methyltransferase,

leads to e!topi! e7pression of (ario#s homeoti! Ho7I genes and plays a key role in

le#kemi! progression ?@.

:n addition to histone methyltransferases, lysine spe!ifi!-demethylases hi!h

ork in !oordination ith "Ts to maintain glo3al histone methylation patterns, are also

impli!ated in !an!er progression ?E@. )SD1, the first identified lysine-demethylase, !an

effe!ti(ely remo(e 3oth a!ti(ating and repressing marks H;KC and ;K methylation,

respe!ti(elyI depending on its spe!ifi! 3inding partners ?F,@, th#s, a!ting as either a

!o-repressor or a !o-a!ti(ator. After )SD1, se(eral other histone lysine demethylases

ha(e 3een dis!o(ered in!l#ding J#mon4i % domain HJm4%I proteins. Se(eral of these

histone demethylases are #preg#lated in prostate !an!er, th#s making them potential

therape#ti! targets ?;@. oe(er, sin!e histone demethylases, like )SD1, !an perform

3oth a!ti(ating and repressi(e f#n!tions, it is essential to first #nderstand their pre!ise

!onte7t-dependent roles 3efore their therape#ti! inhi3ition !an 3e #sed as an effe!ti(e



1

!an!er treatment strategy. Despite these !hallenges, targeting histone demethylases is a

promising treatment option for the f#t#re as re(ealed 3y a re!ent st#dy hi!h shoed that

inhi3ition of )SD1 in ne#ro3lastoma, !a#ses de!reased proliferation $n v$%&o and

inhi3ition of 7enograft groth ?@.

Epigenetic S*itching in Cancer

As mentioned pre(io#sly, D'A methylation and histone modifi!ations ork

independently and in !on!ert to alter gene e7pression d#ring t#morigenesis. A key fa!et

of s#!h silen!ing me!hanisms is the formation of a rigid repressi(e !hromatin state hi!h

res#lts in red#!ed !ell#lar plasti!ity. The re!ent dis!o(ery of t#mor-spe!ifi! de novo

methylation of poly!om3 target genes, hi!h are silen!ed 3y ;K2Fme; in normal !ells,

is another e7ample of this phenomenon ?;-@. :n 0S !ells, de(elopmentally important

genes are re(ersi3ly silen!ed 3y poly!om3 proteins thro#gh the esta3lishment of the

repressi(e ;K2Fme; mark. After differentiation, these genes !ontin#e to 3e repressed

thro#gh the maintenan!e of the poly!om3 mark on #nmethylated promoters 3y 0O2. :n

!an!er, the poly!om3 mark is repla!ed 3y de novo D'A methylation possi3ly thro#gh the

re!r#itment of D'"Ts (ia the poly!om3 !omple7 ?1++@. This t#mor-spe!ifi! =epigeneti!

sit!hing> of the plasti! poly!om3 mark ith more sta3le D'A methylation res#lts in

the permanent silen!ing of key reg#latory genes hi!h may !ontri3#te to !ell

proliferation and t#morigenesis H9ig#re ;I ?1+1@. oe(er, hi!h transformation-

asso!iated fa!tors trigger this sit!h is still #n!lear.



1

Rle # N$cles%e Psitining in Cancer

The roles of D'A methylation and histone modifi!ations in !an!er initiation and

progression are ell esta3lished, hoe(er the !hanges in !hromatin str#!t#re that

a!!ompany D'A methylation and histone modifi!ation !hanges are less ell #nderstood.

0merging data has re(ealed that n#!leosome remodeling orks in !on!ert ith D'A

methylation and histone modifi!ations, and plays a !entral role in t#mor-spe!ifi! gene

silen!ing. D'A methylation ind#!ed silen!ing of t#mor s#ppressor genes in !an!er

in(ol(es distin!t !hanges in n#!leosome positioning res#lting in n#!leosome o!!#pan!y

at TSS H9ig#re 2I. ea!ti(ation of s#!h silen!ed genes #sing D'"T inhi3itors is

a!!ompanied 3y a loss of n#!leosomes from the promoter region ?+@. :n addition,

n#!leosome remodeling !an lead to a3errant gene silen!ing (ia the transmission of

repressi(e epigeneti! marks to t#mor s#ppressor gene promoters. e!ent ork 3y "orey

et al. H2++I demonstrated that n#!leosome remodeling and dea!etylase !orepressor

!omple7 H'#DI plays a !entral role in a3errant gene silen!ing in le#kemia (ia the

on!ogeni! trans!ription fa!tor, P")-Aa. The '#D !omple7 fa!ilitates re!r#itment

of the poly!om3 repressi(e !omple7 2 HP%2I and D'"T;A to P")-Aa target gene

promoters leading to their permanent silen!ing 3y esta3lishing a repressi(e !hromatin

state ?1+2@. '#D !an also 3e re!r#ited to methylated promoters thro#gh its intera!tion

ith the "D2 protein ?1+;@. S#stained 3inding of '#D to s#!h promoters may assist

in preser(ing their repressi(e state thro#gh maintenan!e of D'A methylation.

Alterations in the S<:&S'9 !omple7, an ATP-dependent !hromatin remodeling

!omple7, are also asso!iated ith !an!er de(elopment ?1+C@. A3rogation of S<:&S'9

f#n!tion thro#gh alterations in its (ario#s s#3#nits !an res#lt in malignant transformation.



2+

The A9CF HhS'9I s#3#nit of the S<:&S'9 !omple7 is a bona '$de t#mor s#ppressor

and its inhi3ition in rha3doid t#mors !a#ses ina!ti(ation of the p21 and p1E pathays

leading to on!ogeni! transformation ?1+@. 9#rthermore, $1 and ", the !atalyti!

s#3#nits of S<:&S'9, are silen!ed in a3o#t 1-2+ of primary non-small-!ell l#ng

!an!ers ?1+E@. Treatment of " n#ll !ell lines ith DA% inhi3itors has 3een shon

to restore its e7pression th#s making it a promising target for epigeneti! therapy.

oe(er, s#!h treatment also res#lted in a!etylation of " protein hi!h a3rogated its

f#n!tion ?1+C@. De(elopment of spe!ifi! DA% inhi3itors, hi!h !an !ir!#m(ent "

a!etylation, is essential for s#!!essf#l ind#!tion of f#n!tional " in t#mors, hi!h !an

3e #sed as a prospe!ti(e therape#ti! target in the f#t#re.

:nterestingly, a !onte7t dependent on!ogeni! role of $1 has also 3een

proposed. <ork 3y 'aid# et al. H2++I re(eals that $1 !ontri3#tes to !an!er

de(elopment 3y !onstraining p; a!ti(ity thro#gh the desta3ili8ation of the p; protein.

Lpposing roles of S<:&S'9 s#3#nits highlights the reB#irement for a deeper

#nderstanding of the role of n#!leosome remodeling in !an!er de(elopment in order to

de(elop effe!ti(e t#mor-spe!ifi! therapies ?1+F@.

:n addition to remodeling !omple7es, the histone (ariant 2A.O has also 3een

impli!ated in t#morigenesis. 2A.O is o(ere7pressed in se(eral types of !an!er and has

3een asso!iated ith the promotion of !ell !y!le progression ?E2@. :nterestingly, loss of

2A.O has also 3een impli!ated in t#mor progression thro#gh possi3le desta3ili8ation of

!hromosomal 3o#ndaries res#lting in spreading of repressi(e !hromatin domains and de

novo hypermethylation of t#mor-s#ppressor gene promoters ?1+@.



21

Dereg$latin # %iRNAs in Cancer

A!!#m#lating e(iden!e from st#dies !omparing mi'A e7pression profiles in

t#mors and !orresponding normal tiss#es indi!ate idespread !hanges in mi'A

e7pression d#ring t#morigenesis ?1+@. Sin!e mi'As reg#late genes in(ol(ed in

trans!riptional reg#lation, !ell proliferation and apoptosis Hthe most !ommon pro!esses

dereg#lated in !an!erI, alteration in their e7pression !an promote t#morigenesis. mi'As

!an f#n!tion as either t#mor s#ppressors or on!ogenes depending #pon their target genes.

"any t#mor s#ppressor mi'As that target groth promoting genes are repressed in

!an!er. 9or e7ample, ($R-1 and 16 hi!h target BCL2, an anti-apoptoti! gene, are

donreg#lated in !hroni! lympho!yti! le#kemia, hile )e% -F hi!h targets the on!ogene,

RAS* is donreg#lated in l#ng !an!er ?1;,11+@. 9#rthermore, ($R-12+ , hi!h targets

%)E, is signifi!antly donreg#lated in prostate and 3ladder t#mors ?111@ and ($&-101,

hi!h targets poly!om3 gro#p protein 0O2, is donreg#lated in 3ladder transitional

!ell !ar!inoma ?EE@. :n !ontrast to t#mor s#ppressor mi'As, on!ogeni! mi'As, hi!h

target groth inhi3itory pathays, are often #preg#lated in !an!er. 9or e7ample, ($R-21*

hi!h targets P!EN* is #preg#lated in h#man glio3lastoma ?112@. ($RNA-1## is

#preg#lated in 3reast, l#ng and se(eral hematopoieti! malignan!ies ?11;@. <hile the

e7a!t me!hanism of a!tion of ($R-1## is still #n!lear, there are s#ggestions that it may

play a role in !lass sit!h re!om3ination pro!ess 3y targeting A:D Ha!ti(ation-ind#!ed

!ytidine deaminaseI ?11C@. The on!ogeni! ($R-1+,2 !l#ster, hi!h targets pro-

apoptoti! gene B$(, is fo#nd o(ere7pressed in se(eral kinds of !an!er ?11@.

%hanges in mi'A e7pression !an 3e a!hie(ed thro#gh (ario#s me!hanisms

in!l#ding !hromosomal a3normalities, trans!ription fa!tor 3inding and epigeneti!



22

alterations ?11E@. The initial report 3y Saito et al. H2++EI, hi!h demonstrated that ($R-

12+ , a t#mor s#ppressor mi'A em3edded in a %p$ island, as silen!ed in !an!er 3y

D'A methylation, has led to s#3seB#ent dis!o(ery of se(eral other mi'As hi!h are

also silen!ed 3y epigeneti! me!hanisms in !an!er ?11F, Toyota, 2++ ;+1,11@. Sin!e

s#!h epigeneti! repression of t#mor s#ppressor mi'As !an 3e potentially re(ersed 3y

treatment ith !hromatin modifying dr#gs, they !an ser(e as promising targets for

epigeneti! therapy. Saito et al. s#!!essf#lly demonstrated re-a!ti(ation of ($R-12+ in T2C

3ladder !an!er !ells folloing treatment ith !hromatin modifying dr#gs in!l#ding D'A

methylation and DA% inhi3itors ?EC,111@. S#!h dr#g ind#!ed a!ti(ation of t#mor

s#ppressor mi'As holds great promise for the f#t#re of !an!er therape#ti!s.

The Cancer Ste% Cell M"el

e!ent ork s#ggests that the glo3al epigeneti! !hanges in !an!er, may in(ol(e

the dysreg#lation of h#ndreds of genes d#ring t#morigenesis. The me!hanism 3y hi!h a

t#mor !ell a!!#m#lates s#!h idespread epigeneti! a3normalities d#ring !an!er

de(elopment is still not f#lly #nderstood. The sele!ti(e ad(antage of these epim#tations

d#ring t#mor progression is possi3le, 3#t it is #nlikely that the m#ltit#de of epigeneti!

alterations that reside in a !an!er epigenome o!!#r in a random fashion and then

a!!#m#late inside the t#mor d#e to !lonal sele!tion. A more pla#si3le e7planation o#ld

3e that the a!!#m#lation of s#!h glo3al epigenomi! a3normalities arises from initial

alterations in the !entral epigeneti! !ontrol ma!hinery, hi!h o!!#r at a (ery early stage

of neoplasti! e(ol#tion. S#!h initiating e(ents !an predispose t#mor !ells to gain f#rther

epim#tations d#ring t#mor progression in a fashion similar to a!!#m#lation of the geneti!



2;

alterations that o!!#rs folloing defe!ts in D'A repair ma!hinery in !an!er. The =!an!er

stem !ell> model s#ggests that the epigeneti! !hanges, hi!h o!!#r in normal stem or

progenitor !ells, are the earliest e(ents in !an!er initiation ?E@. The idea that these initial

e(ents o!!#r in stem !ell pop#lations is s#pported 3y the !ommon finding that epigeneti!

a3errations are some of the earliest e(ents that o!!#r in (ario#s types of !an!er and also

3y the dis!o(ery that normal tiss#es ha(e altered progenitor !ells in !an!er patients

?FE,11,12+@. This stem !ell 3ased !an!er initiation model is !onsistent ith the

o3ser(ation that t#mors !ontain a heterogeneo#s pop#lation of !ells ith di(erse

t#morigeni! properties ?121@. Sin!e epigeneti! me!hanisms are !entral to maintenan!e of

stem !ell identity ?;;,122@, it is reasona3le to spe!#late that their disr#ption may gi(e rise

to a high risk a3errant progenitor !ell pop#lation hi!h !an #ndergo transformation on

gain of s#3seB#ent geneti! gatekeeper m#tations. This epigeneti! disr#ption !an lead to

an o(erall in!rease in n#m3er of progenitor !ells along ith an in!rease in their a3ility to

maintain their stem !ell state, forming a high risk s#3strate pop#lation hi!h !an readily

3e!ome neoplasti! on gain of additional geneti! m#tations ?C@.

Se(eral findings ha(e re!ently emerged in s#pport of the =!an!er stem !ell>

model. "i!e ith a loss of imprinting H)L:I at the IGF2 lo!#s and an Ap. m#tation sho

an e7pansion in the progenitor !ell pop#lation of the intestinal epitheli#m, ith the

epithelial !ells shoing higher e7pression of progenitor !ell markers and shifting toards

a less-differentiated state ?12;@. These mi!e ere also at a higher risk for intestinal

t#mors relati(e to !ontrol mi!e ?12;@. :nterestingly, h#mans ith )L: of IGF2 also sho

a similar de-differentiation of normal !oloni! m#!osa !ells along ith a higher risk for

!olore!tal !an!er ?FE@. Also, stem !ell-like !hara!teristi!s of t#mor !ells ere displayed



2C

thro#gh s#!!essf#l !loning of mo#se melanoma and med#llo3lastoma n#!lei to form

3lasto!ysts and !himeri! mi!e ?12C@.

D'A methylation ind#!ed silen!ing of genes in(ol(ed in the reg#lation of stem&

pre!#rsor !ells self reneal !apa!ity, s#!h as p16* APC* SFRPs et!., is !ommonly

o3ser(ed in the early stages of !olon and other !an!ers ?C@. A3errant silen!ing of these so

!alled =epigeneti! gatekeeper> genes in !onditions of !hroni! stress, s#!h as

inflammation, ena3les stem&pre!#rsor !ells to gain infinite reneal !apa!ity there3y

3e!oming immortal. These pre-in(asi(e immortal stem !ells are sele!ted for and then

form a pool of a3normal pre!#rsor !ells that !an #ndergo f#rther geneti! m#tations

leading to t#morigenesis ?C,12@ . #man 0S !ells ith !an!er-!ell !hara!teristi!s

in!l#ding higher freB#en!y of teratoma-initiating !ells HT:%sI, groth fa!tor and ni!he

independen!e ha(e also 3een fo#nd ?12E@. These partially transformed stem !ells display

a higher e7pression of pl#ripoten!y markers s#ggesting their enhan!ed =stemness> along

ith high proliferati(e !apa!ity ?12E@.

Poly!om3 proteins, hi!h !ontrol the silen!ing of de(elopmental reg#lators in 0S

!ells, pro(ide another link 3eteen stem !ell 3iology and !an!er initiation. Poly!om3

proteins are !ommonly #preg#lated in (ario#s forms of !an!er ?2@. :n addition, genes

that are marked 3y poly!om3 repressi(e mark ;K2Fme; in 0S !ells are often

methylated in !an!er s#ggesting the presen!e of a shared reg#latory frameork, hi!h

!onne!ts !an!er !ells ith stem&progenitor !ell pop#lations. S#!h findings s#pport the

hypothesis of epigeneti!s playing a !entral role in early neoplasia and !an!er stem !ells

3eing the key perpet#ators of !an!er ?;,C@.



2

Epigenetic Therapy # Cancer

The re(ersi3le nat#re of the profo#nd epigeneti! !hanges that o!!#r in !an!er has

led to the possi3ility of =epigeneti! therapy> as a treatment option. The aim of epigeneti!

therapy is to re(erse the !a#sal epigeneti! a3errations that o!!#r in !an!er, leading to the

restoration of a =normal epigenome>. "any epigeneti! dr#gs ha(e 3een dis!o(ered in the

re!ent past that !an effe!ti(ely re(erse D'A methylation and histone modifi!ation

a3errations that o!!#r in !an!er ?@. D'A methylation inhi3itors ere among the first

epigeneti! dr#gs proposed for #se as !an!er therape#ti!s. The remarka3le dis!o(ery that

treatment ith !ytoto7i! agents, -a8a!ytidine H-a8a-%I and -a8a-2-deo7y!ytidine H-

a8a-%dI lead to the inhi3ition of D'A methylation hi!h ind#!ed gene e7pression and

!a#sed differentiation in !#lt#red !ells led to the reali8ation of the potential #se of these

dr#gs in !an!er therapy ?12F@. These n#!leoside analogs get in!orporated into the D'A

of rapidly groing t#mor !ells d#ring repli!ation and inhi3it D'A methylation 3y

trapping D'A methyltransferases onto the D'A, leading to their depletion inside the !ell

?2@. This dr#g ind#!ed red#!tion of D'A methylation !a#ses groth inhi3ition in !an!er

!ells 3y a!ti(ating t#mor s#ppressor genes a3errantly silen!ed in !an!er ?@. -a8a-%

Ha8a!itidineI and -a8a-%d Hde!ita3ineI ha(e no 3een 9DA appro(ed for #se in the

treatment of myelodysplasti! syndromes H"DSI and promising res#lts ha(e also emerged

from the treatment of other hematologi!al malignan!ies s#!h as a!#te myeloid le#kemia

HA")I and !hroni! myeloid le#kemia H%")I #sing these dr#gs ?12@. The possi3le

!lini!al #se of other impro(ed D'A methylation inhi3itors s#!h as 8e3#larine, hi!h !an

3e orally administered, is !#rrently #nder in(estigation ?12@.



2E

The a3ility of these dr#gs to 3e in!orporated into D'A raises !on!erns regarding

their potential to7i! effe!t on normal !ells. oe(er, sin!e these dr#gs only a!t on

di(iding !ells, one !an arg#e that treatment ith these dr#gs sho#ld mainly target rapidly

di(iding t#mor !ells and sho#ld ha(e minimal effe!ts on sloly di(iding normal !ells.

This arg#ment has 3een s#pported 3y st#dies demonstrating minimal side effe!ts of long-

term treatment ith D'A methylation inhi3itors ?1;+@. 'e(ertheless, an alternati(e

approa!h in(ol(ing the de(elopment of non-n#!leoside !ompo#nds, hi!h !an

effe!ti(ely inhi3it D'A methylation itho#t 3eing in!orporated into D'A, is also 3eing

a!ti(ely p#rs#ed. De(elopment of se(eral small mole!#le inhi3itors s#!h as S$:-1+2F,

$1+ and "$ is a step in that dire!tion ?1;1,1;2@. These mole!#les !an a!hie(e their

inhi3itory effe!ts 3y either 3lo!king !atalyti!&!ofa!tor 3inding sites of D'"Ts or 3y

targeting their reg#latory m'A seB#en!esM hoe(er, the eak inhi3itory potential of

these dr#gs indi!ates a need for the de(elopment of more potent inhi3itory !ompo#nds in

f#t#re.

A3errant gene silen!ing in !an!er is also asso!iated ith a !on!omitant loss of

histone a!etylation. e-esta3lishing normal histone a!etylation patterns thro#gh treatment

ith DA% inhi3itors has 3een shon to ha(e anti-t#morigeni! effe!ts in!l#ding groth

arrest, apoptosis and the ind#!tion of differentiation. These anti-proliferati(e effe!ts of

DA% inhi3itors are mediated 3y their a3ility to rea!ti(ate silen!ed t#mor s#ppressor

genes ?1;;@. SAA Hs#3eroylanilide hydro7ami! a!idI, hi!h is an DA% inhi3itor, has

no 3een appro(ed for #se in !lini! for treatment of T !ell !#taneo#s lymphoma. Se(eral

other DA% inhi3itors s#!h as depsipeptide and phenyl3#tyrate are !#rrently #nder

!lini!al trials ?1;1@.



2F

The intera!tion 3eteen different !omponents of the epigeneti! ma!hinery has led

to the e7ploration of effe!ti(e !om3inatorial !an!er treatment strategies, hi!h in(ol(e

#se of 3oth D'A methylation and DA% inhi3itors together. S#!h !om3ination

treatment strategies ha(e 3een fo#nd to 3e more effe!ti(e than indi(id#al treatment

approa!hes. 9or e7ample, the de-repression of !ertain p#tati(e t#mor s#ppressor genes

as only seen hen -A8a-%d and tri!hostatin A ere !om3ined ?1;C@. Anti-

t#morigeni! effe!ts of depsipeptide ere enhan!ed hen le#kemi! !ells ere

sim#ltaneo#sly treated ith -A8a-%d ?1;@. Synergisti! a!ti(ities of D'A methylation

and DA% inhi3itors ere also demonstrated in a st#dy shoing greater red#!tion of

l#ng t#mor formation in mi!e hen treated ith phenyl3#tyrate and -A8a-%d together

?1;E@.

Apart from D'A methylation and DA% inhi3itors, histone methyltransferase

inhi3itors ha(e also 3een a!ti(ely e7plored re!ently. Lne s#!h inhi3itor !ompo#nd,

DO'ep, as shon to s#!!essf#lly ind#!e apoptosis in !an!er !ells 3y sele!ti(ely

targeting poly!om3 repressi(e !omple7 2 HP%2I proteins, hi!h are generally

o(ere7pressed in !an!er ?1;F@. <hile the spe!ifi!ity of DO'ep as !hallenged in a

s#3seB#ent st#dy ?1;@, these findings reinfor!e the potential of "T inhi3itors and the

need for f#rther de(elopment of spe!ifi! histone methylation inhi3itors.

mi'As also represent promising targets for epigeneti! therapy. The finding 3y

Saito et al. H2++EI that donreg#lation of the on!ogene %)E (ia re-a!ti(ation of ($R-

12+ folloing treatment ith -A8a-%d and C-phenyl3#tyri! a!id strongly ad(o!ates in

fa(or of the potential of a mi'A 3ased treatment strategy ?111@. :n addition, the

introd#!tion of syntheti! mi'As, hi!h mimi! t#mor s#ppressor mi'As, !an 3e #sed



2

to sele!ti(ely repress on!ogenes in t#mors. mi'As, s#!h as ($R-101 hi!h targets

0O2 ?EE@, !an 3e #sed to reg#late the a3errant epigeneti! ma!hinery in !an!er hi!h

may assist in restoring of the normal epigenome. oe(er, the la!k of effi!ient deli(ery

methods is a ma4or h#rdle in the effe!ti(e #se of this strategy. De(elopment of effi!ient

(ehi!le mole!#les for targeted deli(ery of syntheti! mi'As to t#mor !ells is of prime

importan!e in f#t#re.

($t$re Prspects an" Challenges

The epigeneti! re(ol#tion that has !ome a3o#t in the field of 3iology d#ring the

last fe de!ades has !hallenged the long-held traditional (ie of the geneti! !ode 3eing

the key determinant of !ell#lar gene f#n!tion and its alteration 3eing the ma4or !a#se of

h#man diseases. Ad(an!es made in the field of !an!er epigeneti!s ha(e led to the

reali8ation that the pa!kaging of the genome is potentially as important as the genome

itself, in reg#lating the essential !ell#lar pro!esses reB#ired for preser(ing !ell#lar

identity and also in gi(ing rise to disease states like !an!er. Deeper #nderstandings of the

glo3al patterns of these epigeneti! modifi!ations and their !orresponding !hanges in

!an!er ha(e ena3led the design of 3etter treatment strategies. A !om3inatorial approa!h

#tili8ing different epigeneti! therape#ti! approa!hes along ith standard !hemotherapy

holds signifi!ant promise for s#!!essf#l treatment of !an!er in f#t#re. S#!h approa!hes

might also help in sensiti8ing !an!er !ells, espe!ially !an!er stem !ells, hi!h are

refra!tory to standard !hemotherapy. 9#rther #nderstanding of !an!er stem !ells, along

ith de(elopment of more spe!ifi! epigeneti! dr#gs may hold the key to o#r a3ility to

s#!!essf#lly reset the a3normal !an!er epigenome.



2

RE(ERENCES

1. <addington, %.. H1C2I The epigenotype. Endeavo/& +, 1-2+.

2. 0gger, $., )iang, $., Apari!io, A. and Jones, P.A. H2++CI 0pigeneti!s in h#man

disease and prospe!ts for epigeneti! therapy. Na%/&e, ,-., CF-E;.

;. Jones, P.A. and aylin, S.. H2++2I The f#ndamental role of epigeneti! e(ents in

!an!er. Na% Rev Gene% , /, C1-2.

C. Jones, P.A. and aylin, S.. H2++FI The epigenomi!s of !an!er. Ce)) , +-0, E;-

2.

. Jones, P.A. and )aird, P.<. H1I %an!er epigeneti!s !omes of age. Na% Gene% ,

-+, 1E;-F.

E. 9ein3erg, A.P., Lhlsson, . and enikoff, S. H2++EI The epigeneti! progenitor

origin of h#man !an!er. Na% Rev Gene% , 1, 21-;;.

F. Jones, P.A. and "artienssen, . H2++I A 3l#eprint for a #man 0pigenome

Pro4e!t/ the AA% #man 0pigenome <orkshop. Can.e& Res, 23, 112C1-E.

. Qoo, %.. and Jones, P.A. H2++EI 0pigeneti! therapy of !an!er/ past, present and

f#t#re. Na% Rev &/ $s.ov, 3, ;F-+.

. )#ger, K., "ader, A.<., i!hmond, .K., Sargent, D.9. and i!hmond, T.J.

H1FI %rystal str#!t#re of the n#!leosome !ore parti!le at 2. A resol#tion.

Na%/&e, /0., 21-E+.

1+. ernstein, .0., "eissner, A. and )ander, 0.S. H2++FI The mammalian

epigenome. Ce)) , +-0, EE-1.

11. S#8#ki, ".". and ird, A. H2++I D'A methylation lands!apes/ pro(o!ati(e

insights from epigenomi!s. Na% Rev Gene% , ., CE-FE.



;+

12. Ko#8arides, T. H2++FI %hromatin modifi!ations and their f#n!tion. Ce)) , +-0, E;-

F+.

1;. Ohang, ., Pan, ., %o33, $.P. and Anderson, T.A. H2++FI mi!ro'As as

on!ogenes and t#mor s#ppressors. ev B$o) , /4-, 1-12.

1C. Jiang, %. and P#gh, .9. H2++I '#!leosome positioning and gene reg#lation/

ad(an!es thro#gh genomi!s. Na% Rev Gene% , +4, 1E1-F2.

1. ird, A. H2++2I D'A methylation patterns and epigeneti! memory. Genes ev,

+2, E-21.

1E. Takai, D. and Jones, P.A. H2++2I %omprehensi(e analysis of %p$ islands in

h#man !hromosomes 21 and 22. P&o. Na%) A.ad S.$ U S A, .., ;FC+-.

1F. <ang, Q. and )e#ng, 9.%. H2++CI An e(al#ation of ne !riteria for %p$ islands

in the h#man genome as gene markers. B$o$n'o&(a%$.s, -4, 11F+-F.

1. 0!khardt, 9., )ein, J., %ortese, ., akyan, N.K., Attood, J., #rger, ".,

#rton, J., %o7, T.N., Da(ies, ., Don, T.A., aefliger, %., orton, ., oe,

K., Ja!kson, D.K., K#nde, J., Koenig, %., )iddle, J., 'i3lett, D., Ltto, T., Pettett,

., Seemann, S., Thompson, %., <est, T., ogers, J., Llek, A., erlin, K. and

e!k, S. H2++EI D'A methylation profiling of h#man !hromosomes E, 2+ and 22.

Na% Gene% , /0, 1;F-.

1. :llingorth, ., Kerr, A., Deso#sa, D., Jorgensen, ., 0llis, P., Stalker, J.,

Ja!kson, D., %lee, %., Pl#m3, ., ogers, J., #mphray, S., %o7, T., )angford, %.

and ird, A. H2++I A no(el %p$ island set identifies tiss#e-spe!ifi! methylation

at de(elopmental gene lo!i. PLoS B$o) , 2, e22.



;1

2+. Prendergast, $.%. and Oiff, 0.. H11I "ethylation-sensiti(e seB#en!e-spe!ifi!

D'A 3inding 3y the !-"y! 3asi! region. S.$en.e, -3+, 1E-.

21. <att, 9. and "olloy, P.). H1I %ytosine methylation pre(ents 3inding to D'A

of a e)a !ell trans!ription fa!tor reB#ired for optimal e7pression of the

adeno(ir#s ma4or late promoter. Genes ev, -, 11;E-C;.

22. Jones, P.)., Neenstra, $.J., <ade, P.A., Nermaak, D., Kass, S.U., )ands3erger,

'., Stro#3o#lis, J. and <olffe, A.P. H1I "ethylated D'A and "e%P2 re!r#it

histone dea!etylase to repress trans!ription. Na% Gene% , +., 1F-1.

2;. 'an, ., 'g, .., Johnson, %.A., )aherty, %.D., T#rner, ."., 0isenman, .'.

and ird, A. H1I Trans!riptional repression 3y the methyl-%p$-3inding

protein "e%P2 in(ol(es a histone dea!etylase !omple7. Na%/&e, /./, ;E-.

2C. Kim, $.D., 'i, J., Kelesogl#, '., o3erts, .J. and Pradhan, S. H2++2I %o-

operation and !omm#ni!ation 3eteen the h#man maintenan!e and de no(o D'A

H!ytosine-I methyltransferases. E(bo , -+, C1;-.

2. Lkano, "., ell, D.<., a3er, D.A. and )i, 0. H1I D'A methyltransferases

Dnmt;a and Dnmt;3 are essential for de no(o methylation and mammalian

de(elopment. Ce)) , .., 2CF-F.

2E. 9#ts!her, .<., Lshiro, "."., <o8niak, .J., oltan, '., anigan, %.)., D#an,

. and Domann, 9.0. H2++2I ole for D'A methylation in the !ontrol of !ell type

spe!ifi! maspin e7pression. Na% Gene% , /+, 1F-.

2F. attori, '., 'ishino, K., Ko, Q.$., attori, '., Lhgane, J., Tanaka, S. and Shiota,

K. H2++CI 0pigeneti! !ontrol of mo#se L!t-C gene e7pression in em3ryoni! stem

!ells and tropho3last stem !ells. B$o) C3e(, -1., 1F+E;-.



;2

2. Jen#ein, T. and Allis, %.D. H2++1I Translating the histone !ode. S.$en.e, -./,

1+FC-+.

2. e33es, T.., Thorne, A.<. and %rane-o3inson, %. H1I A dire!t link

3eteen !ore histone a!etylation and trans!riptionally a!ti(e !hromatin. E(bo ,

1, 1;-C+2.

;+. )iang, $., )in, J.%., <ei, N., Qoo, %., %heng, J.%., 'g#yen, %.T., <eisen3erger,

D.J., 0gger, $., Takai, D., $on8ales, 9.A. and Jones, P.A. H2++CI Distin!t

lo!ali8ation of histone ; a!etylation and ;-KC methylation to the trans!ription

start sites in the h#man genome. P&o. Na%) A.ad S.$ U S A, +4+, F;F-E2.

;1. arski, A., %#ddapah, S., %#i, K., oh, T.Q., S!hones, D.0., <ang, O., <ei, $.,

%hepele(, :. and Ohao, K. H2++FI igh-resol#tion profiling of histone

methylations in the h#man genome. Ce)) , +-., 2;-;F.

;2. <ang, O., Oang, %., osenfeld, J.A., S!hones, D.0., arski, A., %#ddapah, S.,

%#i, K., oh, T.Q., Peng, <., Ohang, ".R. and Ohao, K. H2++I %om3inatorial

patterns of histone a!etylations and methylations in the h#man genome. Na%

Gene% , ,4, F-+;.

;;. "ikkelsen, T.S., K#, "., Jaffe, D.., :ssa!, ., )ie3erman, 0., $ianno#kos, $.,

Al(are8, P., ro!kman, <., Kim, T.K., Ko!he, .P., )ee, <., "endenhall, 0.,

LDono(an, A., Presser, A., #ss, %., ie, ., "eissner, A., <ernig, ".,

Jaenis!h, ., '#s3a#m, %., )ander, 0.S. and ernstein, .0. H2++FI $enome-ide

maps of !hromatin state in pl#ripotent and lineage-!ommitted !ells. Na%/&e, ,,0,

;-E+.



;;

;C. ingrose, ). and Paro, . H2++FI Poly!om3&Trithora7 response elements and

epigeneti! memory of !ell identity. eve)op(en% , +/,, 22;-;2.

;. ernstein, .0., "ikkelsen, T.S., ie, ., Kamal, "., #e3ert, D.J., %#ff, J., 9ry,

., "eissner, A., <ernig, "., Plath, K., Jaenis!h, ., <ags!hal, A., 9eil, .,

S!hrei3er, S.). and )ander, 0.S. H2++EI A 3i(alent !hromatin str#!t#re marks key

de(elopmental genes in em3ryoni! stem !ells. Ce)) , +-3, ;1-2E.

;E. A8#ara, N., Perry, P., Sa#er, S., Spi(ako(, "., Jorgensen, .9., John, .".,

$o#ti, "., %asano(a, "., <arnes, $., "erkens!hlager, ". and 9isher, A.$.

H2++EI %hromatin signat#res of pl#ripotent !ell lines. Na% Ce)) B$o) , 0, ;2-.

;F. <en, ., <#, ., Shinkai, Q., :ri8arry, .A. and 9ein3erg, A.P. H2++I )arge

histone ; lysine dimethylated !hromatin 3lo!ks disting#ish differentiated from

em3ryoni! stem !ells. Na% Gene% , ,+, 2CE-+.

;. a3erland, "., "ontgomery, .). and Llson, 0.'. H2++I The many roles of

histone dea!etylases in de(elopment and physiology/ impli!ations for disease and

therapy. Na% Rev Gene% , +4, ;2-C2.

;. Shi, Q. H2++FI istone lysine demethylases/ emerging roles in de(elopment,

physiology and disease. Na% Rev Gene% , 0, 2-;;.

C+. %edar, . and ergman, Q. H2++I )inking D'A methylation and histone

modifi!ation/ patterns and paradigms. Na% Rev Gene% , +4, 2-;+C.

C1. Ta!hi3ana, "., "ats#m#ra, Q., 9#k#da, "., Kim#ra, . and Shinkai, Q. H2++I

$a&$)P !omple7es independently mediate ;K and D'A methylation to

silen!e trans!ription. E(bo , -1, 2E1-+.



;C

C2. )ehnert8, ., Ueda, Q., Deri4!k, A.A., ra#ns!heig, U., Pere8-#rgos, ).,

K#3i!ek, S., %hen, T., )i, 0., Jen#ein, T. and Peters, A.. H2++;I S#(;h-

mediated histone ; lysine methylation dire!ts D'A methylation to ma4or

satellite repeats at peri!entri! hetero!hromatin. C/&& B$o) , +/, 112-2++.

C;. Ohao, R., ank, $., Tan, Q.T., )i, ., "orit8, .)., Simpson, .J., %err#ti, ).,

%#rtis, D.J., Patel, D.J., Allis, %.D., %#nningham, J.". and Jane, S.". H2++I

P"T-mediated methylation of histone C; re!r#its D'"T;A, !o#pling

histone and D'A methylation in gene silen!ing. Na% S%&/.% Mo) B$o) , +2, ;+C-11.

CC. 0ste(e, P.L., %hin, .$., enner, J., 9eehery, $.., Samaranayake, "., orit8,

$.A., Ja!o3sen, S.0. and Pradhan, S. H2++I eg#lation of D'"T1 sta3ility

thro#gh S0TF-mediated lysine methylation in mammalian !ells. P&o. Na%) A.ad

S.$ U S A, +42, +FE-1.

C. <ang, J., e(i, S., K#rash, J.K., )ei, ., $ay, 9., a4ko, J., S#, ., S#n, <.,

%hang, ., #, $., $a#det, 9., )i, 0. and %hen, T. H2++I The lysine demethylase

)SD1 HKD"1I is reB#ired for maintenan!e of glo3al D'A methylation. Na%

Gene% , ,+, 12-.

CE. 9#ks, 9., #rd, P.J., <olf, D., 'an, ., ird, A.P. and Ko#8arides, T. H2++;I The

methyl-%p$-3inding protein "e%P2 links D'A methylation to histone

methylation. B$o) C3e(, -10, C+;-C+.

CF. "a(ri!h, T.'., :oshikhes, :.P., Nenters, .J., Jiang, %., Tomsho, ).P., Ri, J.,

S!h#ster, S.%., Al3ert, :. and P#gh, .9. H2++I A 3arrier n#!leosome model for

statisti!al positioning of n#!leosomes thro#gho#t the yeast genome. Geno(e Res,

+0, 1+F;-;.



;

C. Q#an, $.%., )i#, Q.J., Dion, ".9., Sla!k, ".D., <#, ).9., Alts!h#ler, S.J. and

ando, L.J. H2++I $enome-s!ale identifi!ation of n#!leosome positions in S.

!ere(isiae. S.$en.e, /4., E2E-;+.

C. Shi(asamy, S., hinge, A., Ohao, Q., Jones, S., irst, ". and :yer, N.. H2++I

Dynami! remodeling of indi(id#al n#!leosomes a!ross a e#karyoti! genome in

response to trans!riptional pert#r3ation. PLoS B$o) , 2, eE.

+. )in, J.%., Jeong, S., )iang, $., Takai, D., 9atemi, "., Tsai, Q.%., 0gger, $., $al-

Qam, 0.'. and Jones, P.A. H2++FI ole of n#!leosomal o!!#pan!y in the

epigeneti! silen!ing of the ")1 %p$ island. Can.e& Ce)) , +-, C;2-CC.

1. $al-Qam, 0.'., Jeong, S.,Tanay A., 0gger, 0., )ee, A.s., and Jones, P.A. H2++EI

%onstit#ti(e '#!leosome Depletion and Lrdered 9a!tor Assem3ly at the GRP F

Promoter e(ealed 3y Single "ole!#le 9ootprinting. P)os Gene%$.s, -, e1E+.

2. S!hones, D.0., %#i, K., %#ddapah, S., oh, T.Q., arski, A., <ang, O., <ei, $.

and Ohao, K. H2++I Dynami! reg#lation of n#!leosome positioning in the h#man

genome. Ce)) , +/-, F-.

;. Smith, %.). and Peterson, %.). H2++I ATP-dependent !hromatin remodeling.

C/&& !op ev B$o) , 23, 11-C.

C. arikrishnan, K.'., %ho, ".O., aker, 0.K., Pal, S., assal, S., rasa!!hio, D.,

<ang, )., %raig, J."., Jones, P.)., Sif, S. and 0l-Lsta, A. H2++I rahma links

the S<:&S'9 !hromatin-remodeling !omple7 ith "e%P2-dependent

trans!riptional silen!ing. Na% Gene% , /1, 2C-EC.

. <yso!ka, J., Sig#t, T., iao, ., "ilne, T.A., Kon, S.Q., )andry, J., Ka#er,

"., Ta!kett, A.J., %hait, .T., adenhorst, P., <#, %. and Allis, %.D. H2++EI A



;E

PD finger of 'U9 !o#ples histone ; lysine C trimethylation ith !hromatin

remodelling. Na%/&e, ,,-, E-+.

E. Santenard, A. and Torres-Padilla, ".0. H2++I 0pigeneti! reprogramming in

mammalian reprod#!tion/ !ontri3#tion from histone (ariants. Ep$ene%$.s, ,, +-C.

F. Sarma, K. and ein3erg, D. H2++I istone (ariants meet their mat!h. Na% Rev

Mo) Ce)) B$o) , 2, 1;-C.

. Jin, %. and 9elsenfeld, $. H2++FI '#!leosome sta3ility mediated 3y histone

(ariants ;.; and 2A.O. Genes ev, -+, 11-2.

. Oil3erman, D., %oleman-Derr, D., allinger, T. and enikoff, S. H2++I istone

2A.O and D'A methylation are m#t#ally antagonisti! !hromatin marks. Na%/&e,

,32, 12-.

E+. %reyghton, ".P., "arko#laki, S., )e(ine, S.S., anna, J., )odato, ".A., Sha, K.,

Qo#ng, .A., Jaenis!h, . and oyer, ).A. H2++I 2AO is enri!hed at poly!om3

!omple7 target genes in 0S !ells and is ne!essary for lineage !ommitment. Ce)) ,

+/3, EC-E1.

E1. Olatano(a, J. and Thakar, A. H2++I 2A.O/ (ie from the top. S%&/.%/&e, +2,

1EE-F.

E2. S(otelis, A., $e(ry, '. and $a#drea#, ). H2++I eg#lation of gene e7pression

and !ell#lar proliferation 3y histone 2A.O. B$o.3e( Ce)) B$o) , 01, 1F-.

E;. e, ). and annon, $.J. H2++CI "i!ro'As/ small 'As ith a 3ig role in gene

reg#lation. Na% Rev Gene% , 3, 22-;1.

EC. Saito, Q. and Jones, P.A. H2++EI 0pigeneti! a!ti(ation of t#mor s#ppressor

mi!ro'As in h#man !an!er !ells. Ce)) C4.)e, 3, 222+-2.



;F

E. 9a33ri, "., $ar8on, ., %immino, A., )i#, O., Oanesi, '., %allegari, 0., )i#, S.,

Alder, ., %ostinean, S., 9ernande8-%ymering, %., Nolinia, S., $#ler, $.,

"orrison, %.D., %han, K.K., "ar!#!!i, $., %alin, $.A., #e3ner, K. and %ro!e,

%.". H2++FI "i!ro'A-2 family re(erts a3errant methylation in l#ng !an!er 3y

targeting D'A methyltransferases ;A and ;. P&o. Na%) A.ad S.$ U S A, +4,,

1+-1+.

EE. 9riedman, J."., )iang, $., )i#, %.%., <olff, 0."., Tsai, Q.%., Qe, <., Oho#, .

and Jones, P.A. H2++I The p#tati(e t#mor s#ppressor mi!ro'A-1+1 mod#lates

the !an!er epigenome 3y repressing the poly!om3 gro#p protein 0O2. Can.e&

Res, 2., 2E2;-.

EF. 9ein3erg, A.P. and Nogelstein, . H1;I ypomethylation disting#ishes genes of

some h#man !an!ers from their normal !o#nterparts. Na%/&e, /4+, -2.

E. iggs, A.D. and Jones, P.A. H1;I -methyl!ytosine, gene reg#lation, and

!an!er. Adv Can.e& Res, ,4, 1-;+.

E. odrig#e8, J., 9rigola, J., Nendrell, 0., isB#es, .A., 9raga, ".9., "orales, %.,

"oreno, N., 0steller, "., %apella, $., i3as, ". and Peinado, ".A. H2++EI

%hromosomal insta3ility !orrelates ith genome-ide D'A demethylation in

h#man primary !olore!tal !an!ers. Can.e& Res, 22, CE2-CE.

F+. 0den, A., $a#det, 9., <aghmare, A. and Jaenis!h, . H2++;I %hromosomal

insta3ility and t#mors promoted 3y D'A hypomethylation. S.$en.e, /44, C.

F1. oard, $., 0iges, ., $a#det, 9., Jaenis!h, . and 0den, A. H2++I A!ti(ation

and transposition of endogeno#s retro(iral elements in hypomethylation ind#!ed

t#mors in mi!e. 5n.oene, -1, C+C-.



;

F2. 0hrli!h, ". H2++;I The :%9 syndrome, a D'A methyltransferase ; defi!ien!y

and imm#nodefi!ien!y disease. C)$n I((/no) , +4., 1F-2.

F;. <ilson, A.S., Poer, .0. and "olloy, P.). H2++FI D'A hypomethylation and

h#man diseases. B$o.3$( B$op34s A.%a, +113, 1;-E2.

FC. ainier, S., Johnson, ).A., Do3ry, %.J., Ping, A.J., $r#ndy, P.0. and 9ein3erg,

A.P. H1;I ela7ation of imprinted genes in h#man !an!er. Na%/&e, /2-, FCF-.

F. Lgaa, L., 0!!les, ".., S8eto, J., "!'oe, ).A., Q#n, K., "a, ".A., Smith,

P.J. and ee(e, A.0. H1;I ela7ation of ins#lin-like groth fa!tor :: gene

imprinting impli!ated in <ilms t#mo#r. Na%/&e, /2-, FC-1.

FE. %#i, ., %r#8-%orrea, "., $iardiello, 9."., #t!heon, D.9., Kafonek, D..,

randen3#rg, S., <#, Q., e, ., Poe, '.. and 9ein3erg, A.P. H2++;I )oss of

:$92 imprinting/ a potential marker of !olore!tal !an!er risk. S.$en.e, -.., 1F;-

.

FF. $reger, N., Passarge, 0., opping, <., "essmer, 0. and orsthemke, . H1I

0pigeneti! !hanges may !ontri3#te to the formation and spontaneo#s regression

of retino3lastoma. H/( Gene% , 0/, 1-.

F. aylin, S.. H2++I D'A methylation and gene silen!ing in !an!er. Na% C)$n

P&a.% 5n.o) , - S$ppl +, SC-11.

F. )ong, %., Qin, ., )#, R., Oho#, ., #, J., Qang, Q., Q#, 9. and Q#an, Q. H2++FI

Promoter hypermethylation of the U'; gene in esophageal sB#amo#s !ell

!ar!inoma. Can.e& Inves% , -3, E-+.

+. Akiyama, Q., <atkins, '., S#8#ki, ., Jair, K.<., (an 0ngeland, "., 0steller, ".,

Sakai, ., en, %.Q., Q#asa, Q., erman, J.$. and aylin, S.. H2++;I $ATA-C



;

and $ATA- trans!ription fa!tor genes and potential donstream antit#mor target

genes are epigeneti!ally silen!ed in !olore!tal and gastri! !an!er. Mo) Ce)) B$o) ,

-/, C2-;.

1. Di %ro!e, )., aker, N.A., %orsaro, "., 9a8i, 9., 9anelli, "., 9aretta, "., 9#ks, 9.,

)o %o!o, 9., Ko#8arides, T., 'er(i, %., "in#!!i, S. and Peli!!i, P.$. H2++2I

"ethyltransferase re!r#itment and D'A hypermethylation of target promoters 3y

an on!ogeni! trans!ription fa!tor. S.$en.e, -.3, 1+F-2.

2. 9rigola, J., Song, J., Stir8aker, %., inshelood, .A., Peinado, ".A. and %lark,

S.J. H2++EI 0pigeneti! remodeling in !olore!tal !an!er res#lts in !oordinate gene

s#ppression a!ross an entire !hromosome 3and. Na% Gene% , /0, C+-.

;. S!hlesinger, Q., Stra#ssman, ., Keshet, :., 9arkash, S., e!ht, "., Oimmerman,

J., 0den, 0., Qakhini, O., en-Sh#shan, 0., e#3inoff, .0., ergman, Q., Simon,

:. and %edar, . H2++FI Poly!om3-mediated methylation on )ys2F of histone ;

pre-marks genes for de no(o methylation in !an!er. Na% Gene% , /., 2;2-E.

C. <ids!hendter, "., 9iegl, ., 0gle, D., "#eller-ol8ner, 0., Spi88o, $., "arth,

%., <eisen3erger, D.J., %ampan, "., Qo#ng, J., Ja!o3s, :. and )aird, P.<. H2++FI

0pigeneti! stem !ell signat#re in !an!er. Na% Gene% , /., 1F-.

. Lhm, J.0., "!$ar(ey, K."., Q#, ., %heng, )., S!h#e3el, K.0., %ope, ).,

"ohammad, .P., %hen, <., Daniel, N.%., Q#, <., erman, D."., Jen#ein, T.,

Pr#itt, K., Sharkis, S.J., <atkins, D.'., erman, J.$. and aylin, S.. H2++FI A

stem !ell-like !hromatin pattern may predispose t#mor s#ppressor genes to D'A

hypermethylation and herita3le silen!ing. Na% Gene% , /., 2;F-C2.



C+

E. <eisen3erger, D.J., Siegm#nd, K.D., %ampan, "., Qo#ng, J., )ong, T.:., 9aasse,

".A., Kang, $.., <ids!hendter, "., <eener, D., #!hanan, D., Koh, .,

Simms, )., arker, "., )eggett, ., )e(ine, J., Kim, "., 9ren!h, A.J., Thi3odea#,

S.'., Jass, J., aile, . and )aird, P.<. H2++EI %p$ island methylator phenotype

#nderlies sporadi! mi!rosatellite insta3ility and is tightly asso!iated ith A9

m#tation in !olore!tal !an!er. Na% Gene% , /0, FF-;.

F. 9raga, ".9., allestar, 0., Nillar-$area, A., oi7-%hornet, "., 0spada, J.,

S!hotta, $., onaldi, T., aydon, %., opero, S., Petrie, K., :yer, '.$., Pere8-

osado, A., %al(o, 0., )ope8, J.A., %ano, A., %alasan8, ".J., %olomer, D., Piris,

".A., Ahn, '., :mhof, A., %aldas, %., Jen#ein, T. and 0steller, ". H2++I )oss

of a!etylation at )ys1E and trimethylation at )ys2+ of histone C is a !ommon

hallmark of h#man !an!er. Na% Gene% , /1, ;1-C++.

. alkido#, K., $a#ghan, )., %ook, S., )e#ng, .Q., 'eal, D.0. and o3son, %.'.

H2++CI Upreg#lation and n#!lear re!r#itment of DA%1 in hormone refra!tory

prostate !an!er. P&os%a%e, 3., 1FF-.

. Song, J., 'oh, J.., )ee, J.., 0#n, J.<., Ahn, Q."., Kim, S.Q., )ee, S.., Park,

<.S., Qoo, '.J., )ee, J.Q. and 'am, S.<. H2++I :n!reased e7pression of histone

dea!etylase 2 is fo#nd in h#man gastri! !an!er. Ap($s, ++/, 2EC-.

+. Qang, .J. H2++CI The di(erse s#perfamily of lysine a!etyltransferases and their

roles in le#kemia and other diseases. N/.)e$. A.$ds Res, /-, -FE.

1. 'g#yen, %.T., <eisen3erger, D.J., Neli!es!#, "., $on8ales, 9.A., )in, J.%.,

)iang, $. and Jones, P.A. H2++2I istone ;-lysine methylation is asso!iated



C1

ith a3errant gene silen!ing in !an!er !ells and is rapidly re(ersed 3y -a8a-2-

deo7y!ytidine. Can.e& Res, 2-, ECE-E1.

2. Nalk-)ing3eek, ".0., r#ggeman, S.<. and (an )oh#i8en, ". H2++CI Stem !ells

and !an!erM the poly!om3 !onne!tion. Ce)) , ++0, C+-1.

;. Kondo, Q., Shen, )., Ahmed, S., o#m3er, Q., Sekido, Q., addad, .. and :ssa,

J.P. H2++I Donreg#lation of histone ; lysine methyltransferase $a ind#!es

!entrosome disr#ption and !hromosome insta3ility in !an!er !ells. PLoS 5ne, /,

e2+;F.

C. Kondo, Q., Shen, )., S#8#ki, S., K#rokaa, T., "as#ko, K., Tanaka, Q., Kato, .,

"i8#no, Q., Qokoe, "., S#ga#!hi, 9., irashima, '., Lrito, 0., Lsada, ., Ueda,

., $#o, Q., %hen, ., :ssa, J.P. and Sekido, Q. H2++FI Alterations of D'A

methylation and histone modifi!ations !ontri3#te to gene silen!ing in

hepato!ell#lar !ar!inomas. Hepa%o) Res, /1, FC-;.

. Kri(tso(, A.N. and Armstrong, S.A. H2++FI ")) translo!ations, histone

modifi!ations and le#kaemia stem-!ell de(elopment. Na% Rev Can.e& , 1, 2;-;;.

E. %loos, P.A., %hristensen, J., Agger, K. and elin, K. H2++I 0rasing the methyl

mark/ histone demethylases at the !enter of !ell#lar differentiation and disease.

Genes ev, --, 111-C+.

F. Shi, Q., )an, 9., "atson, %., "#lligan, P., <hetstine, J.., %ole, P.A., %asero,

.A. and Shi, Q. H2++CI istone demethylation mediated 3y the n#!lear amine

o7idase homolog )SD1. Ce)) , ++., C1-;.

. "et8ger, 0., <issmann, "., Qin, '., "#ller, J."., S!hneider, ., Peters, A..,

$#nther, T., #ettner, . and S!h#le, . H2++I )SD1 demethylates repressi(e



C2

histone marks to promote androgen-re!eptor-dependent trans!ription. Na%/&e,

,/1, C;E-.

. S!h#lte, J.., )im, S., S!hramm, A., 9riedri!hs, '., Koster, J., Nersteeg, ., Lra,

:., Pa4tler, K., Klein-itpass, )., K#hfittig-K#lle, S., "et8ger, 0., S!h#le, .,

0ggert, A., #ettner, . and Kirfel, J. H2++I )ysine-spe!ifi! demethylase 1 is

strongly e7pressed in poorly differentiated ne#ro3lastoma/ impli!ations for

therapy. Can.e& Res, 2., 2+E-F1.

1++. Nire, 0., renner, %., Depl#s, ., lan!hon, )., 9raga, "., Didelot, %., "orey, ).,

Nan 0ynde, A., ernard, D., Nanderinden, J."., ollen, "., 0steller, "., Di

%ro!e, )., de )a#noit, Q. and 9#ks, 9. H2++EI The Poly!om3 gro#p protein 0O2

dire!tly !ontrols D'A methylation. Na%/&e, ,/., F1-C.

1+1. $al-Qam, 0.'., 0gger, $., :nig#e8, )., olster, ., 0inarsson, S., Ohang, ., )in,

J.%., )iang, $., Jones, P.A. and Tanay, A. H2++I 9reB#ent sit!hing of

Poly!om3 repressi(e marks and D'A hypermethylation in the P%; prostate

!an!er !ell line. P&o. Na%) A.ad S.$ U S A, +43, 12F-C.

1+2. "orey, )., renner, %., 9a8i, 9., Nilla, ., $#tierre8, A., #s!h3e!k, "., 'er(i,

%., "in#!!i, S., 9#ks, 9. and Di %ro!e, ). H2++I "D;, a !omponent of the

'#D !omple7, fa!ilitates !hromatin alteration and deposition of epigeneti!

marks. Mo) Ce)) B$o) , -0, 12-2;.

1+;. 9eng, R. and Ohang, Q. H2++1I The "e%P1 !omple7 represses trans!ription

thro#gh preferential 3inding, remodeling, and dea!etylating methylated

n#!leosomes. Genes ev, +3, 2F-;2.



C;

1+C. eisman, D., $laros, S. and Thompson, 0.A. H2++I The S<:&S'9 !omple7 and

!an!er. 5n.oene, -0, 1E;-E.

1+. %hai, J., %har3onea#, A.)., et8, .). and <eissman, .0. H2++I )oss of the

hS'9 gene !on!omitantly ina!ti(ates p21%:P&<A91 and p1E:'KCa a!ti(ity

asso!iated ith repli!ati(e senes!en!e in A2+C rha3doid t#mor !ells. Can.e& Res,

23, 1+12-.

1+E. eisman, D.'., S!iarrotta, J., <ang, <., 9#nkho#ser, <.K. and <eissman, .0.

H2++;I )oss of $1&" in h#man l#ng !an!er !ell lines and primary l#ng

!an!ers/ !orrelation ith poor prognosis. Can.e& Res, 2/, E+-E.

1+F. 'aid#, S.., )o(e, :."., :m3al8ano, A.'., $rossman, S.. and Androphy, 0.J.

H2++I The S<:&S'9 !hromatin remodeling s#3#nit $1 is a !riti!al reg#lator

of p; ne!essary for proliferation of malignant !ells. 5n.oene, -0, 2C2-+1.

1+. <it!her, ". and 0merson, .". H2++I 0pigeneti! silen!ing of the p1EH:'KCaI

t#mor s#ppressor is asso!iated ith loss of %T%9 3inding and a !hromatin

3o#ndary. Mo) Ce)) , /,, 2F1-C.

1+. )#, J., $et8, $., "iska, 0.A., Al(are8-Saa(edra, 0., )am3, J., Pe!k, D., Seet-

%ordero, A., 03ert, .)., "ak, .., 9errando, A.A., Doning, J.., Ja!ks, T.,

or(it8, .. and $ol#3, T.. H2++I "i!ro'A e7pression profiles !lassify

h#man !an!ers. Na%/&e, ,/3, ;C-.

11+. Nent#ra, A. and Ja!ks, T. H2++I "i!ro'As and !an!er/ short 'As go a long

ay. Ce)) , +/2, E-1.

111. Saito, Q., )iang, $., 0gger, $., 9riedman, J."., %h#ang, J.%., %oet8ee, $.A. and

Jones, P.A. H2++EI Spe!ifi! a!ti(ation of mi!ro'A-12F ith donreg#lation of



CC

the proto-on!ogene %)E 3y !hromatin-modifying dr#gs in h#man !an!er !ells.

Can.e& Ce)) , ., C;-C;.

112. %han, J.A., Kri!he(sky, A.". and Kosik, K.S. H2++I "i!ro'A-21 is an

antiapoptoti! fa!tor in h#man glio3lastoma !ells. Can.e& Res, 23, E+2-;;.

11;. Kl#i(er, J., Kroesen, .J., Poppema, S. and (an den erg, A. H2++EI The role of

mi!ro'As in normal hematopoiesis and hematopoieti! malignan!ies. Le/e($a,

-4, 1;1-E.

11C. Dorsett, Q., "!ride, K."., Janko(i!, "., $a8#myan, A., Thai, T.., o33iani,

D.9., Di Nirgilio, "., San-"artin, .., eidkamp, $., S!hi!kert, T.A.,

0isenrei!h, T., a4esky, K. and '#ssen8eig, ".%. H2++I "i!ro'A-1

s#ppresses a!ti(ation-ind#!ed !ytidine deaminase-mediated "y!-:gh

translo!ation. I((/n$%4, -0, E;+-.

11. "endell, J.T. H2++I miiad roles for the mi-1F-2 !l#ster in de(elopment and

disease. Ce)) , +//, 21F-22.

11E. Deng, S., %alin, $.A., %ro!e, %."., %o#kos, $. and Ohang, ). H2++I

"e!hanisms of mi!ro'A dereg#lation in h#man !an!er. Ce)) C4.)e, 1, 2EC;-E.

11F. )#4am3io, A., %alin, $.A., Nillan#e(a, A., opero, S., San!he8-%espedes, ".,

lan!o, D., "ont#enga, )."., ossi, S., 'i!oloso, ".S., 9aller, <.J., $allagher,

<."., 0!!les, S.A., %ro!e, %.". and 0steller, ". H2++I A mi!ro'A D'A

methylation signat#re for h#man !an!er metastasis. P&o. Na%) A.ad S.$ U S A,

+43, 1;E-E1.

11. Toyota, "., S#8#ki, ., Sasaki, Q., "ar#yama, ., :mai, K., Shinom#ra, Q. and

Tokino, T. H2++I 0pigeneti! silen!ing of mi!ro'A-;C3&! and -!ell



C

translo!ation gene C is asso!iated ith %p$ island methylation in !olore!tal

!an!er. Can.e& Res, 20, C12;-;2.

11. "ats#3ayashi, ., Sato, '., 9#k#shima, '., Qeo, %.J., <alter, K."., r#ne, K.,

Sahin, 9., r#3an, .. and $oggins, ". H2++;I "ethylation of !y!lin D2 is

o3ser(ed freB#ently in pan!reati! !an!er 3#t is also an age-related phenomenon in

gastrointestinal tiss#es. C)$n Can.e& Res, ., 1CCE-2.

12+. Peters, :., Naske, ., Al3re!ht, K., K#!8yk, ".A., Jonas, U. and Serth, J. H2++FI

Adiposity and age are statisti!ally related to enhan!ed ASS91A t#mor

s#ppressor gene promoter methylation in normal a#topsy kidney tiss#e. Can.e&

Ep$de($o) B$o(a&e&s P&ev, +2, 22E-;2.

121. Al-a44, "., <i!ha, ".S., enito-ernande8, A., "orrison, S.J. and %larke, ".9.

H2++;I Prospe!ti(e identifi!ation of t#morigeni! 3reast !an!er !ells. P&o. Na%)

A.ad S.$ U S A, +44, ;;-.

122. S#rani, ".A., ayashi, K. and a4ko(a, P. H2++FI $eneti! and epigeneti!

reg#lators of pl#ripoten!y. Ce)) , +-0, FCF-E2.

12;. Sakatani, T., Kaneda, A., :a!o3#8io-Donah#e, %.A., %arter, ".$., de oom

<it8el, S., Lkano, ., Ko, ".S., Lhlsson, ., )ongo, D.). and 9ein3erg, A.P.

H2++I )oss of imprinting of :gf2 alters intestinal mat#ration and t#morigenesis in

mi!e. S.$en.e, /41, 1FE-.

12C. o!hedlinger, K., lello!h, ., rennan, %., Qamada, Q., Kim, "., %hin, ). and

Jaenis!h, . H2++CI eprogramming of a melanoma genome 3y n#!lear

transplantation. Genes ev, +0, 1F-.



CE

12. aylin, S.. and Lhm, J.0. H2++EI 0pigeneti! gene silen!ing in !an!er - a

me!hanism for early on!ogeni! pathay addi!tion Na% Rev Can.e& , 2, 1+F-1E.

12E. <er3oetski-Lgil(ie, T.0., osse, "., Steart, "., S!hner!h, A., amos-"e4ia,

N., o#lea#, A., <ynder, T., Smith, ".J., Dingall, S., %arter, T., <illiams, %.,

arris, %., Dolling, J., <ynder, %., oreham, D. and hatia, ". H2++I

%hara!teri8ation of h#man em3ryoni! stem !ells ith feat#res of neoplasti!

progression. Na% B$o%e.3no) , -1, 1-F.

12F. %onstantinides, P.$., Jones, P.A. and $e(ers, <. H1FFI 9#n!tional striated

m#s!le !ells from non-myo3last pre!#rsors folloing -a8a!ytidine treatment.

Na%/&e, -21, ;EC-E.

12. Plima!k, 0.., Kantar4ian, .". and :ssa, J.P. H2++FI De!ita3ine and its role in

the treatment of hematopoieti! malignan!ies. Le/ L4(p3o(a, ,0, 1CF2-1.

12. %heng, J.%., Qoo, %.., <eisen3erger, D.J., %h#ang, J., <o8niak, %., )iang, $.,

"arB#e8, N.0., $reer, S., Lrntoft, T.9., Thyk4aer, T. and Jones, P.A. H2++CI

Preferential response of !an!er !ells to 8e3#larine. Can.e& Ce)) , 2, 11-.

1;+. Qang, A.S., 0ste!io, ".., $ar!ia-"anero, $., Kantar4ian, .". and :ssa, J.P.

H2++;I %omment on %hromosomal insta3ility and t#mors promoted 3y D'A

hypomethylation and :nd#!tion of t#mors in ni!e 3y genomi!

hypomethylation. S.$en.e, /4-, 11;M a#thor reply 11;.

1;1. %orte8, %.%. and Jones, P.A. H2++I %hromatin, !an!er and dr#g therapies. M/%a%

Res, 2,1, CC-1.

1;2. Datta, J., $hoshal, K., Denny, <.A., $amage, S.A., rooke, D.$., Phiasi(ongsa,

P., edkar, S. and Ja!o3, S.T. H2++I A ne !lass of B#inoline-3ased D'A



CF

hypomethylating agents rea!ti(ates t#mor s#ppressor genes 3y 3lo!king D'A

methyltransferase 1 a!ti(ity and ind#!ing its degradation. Can.e& Res, 2., C2FF-

.

1;;. %are, J.S., $iles, 9.J. and 'aro!ki, S.T. H2++I istone dea!etylase inhi3itors/

me!hanisms of !ell death and promise in !om3ination !an!er therapy. Can.e&

Le%% , -2., F-1F.

1;C. %ameron, 0.0., a!hman, K.0., "yohanen, S., erman, J.$. and aylin, S..

H1I Synergy of demethylation and histone dea!etylase inhi3ition in the re-

e7pression of genes silen!ed in !an!er. Na% Gene% , -+, 1+;-F.

1;. Kliso(i!, ".:., "aghra3y, 0.A., Parth#n, ".., $#imond, "., Sklenar, A..,

<hitman, S.P., %han, K.K., "#rphy, T., Anon, J., Ar!her, K.J., #sh, ).J., Plass,

%., $re(er, ".., yrd, J.%. and "ar!#!!i, $. H2++;I Depsipeptide H9 +122I

promotes histone a!etylation, gene trans!ription, apoptosis and its a!ti(ity is

enhan!ed 3y D'A methyltransferase inhi3itors in A")1&0TL-positi(e le#kemi!

!ells. Le/e($a, +1, ;+-.

1;E. elinsky, S.A., Klinge, D."., Stidley, %.A., :ssa, J.P., erman, J.$., "ar!h, T..

and aylin, S.. H2++;I :nhi3ition of D'A methylation and histone dea!etylation

pre(ents m#rine l#ng !an!er. Can.e& Res, 2/, F+-;.

1;F. Tan, J., Qang, ., Oh#ang, )., Jiang, ., %hen, <., )ee, P.)., Kar#t#ri, .K., Tan,

P.., )i#, 0.T. and Q#, R. H2++FI Pharma!ologi! disr#ption of Poly!om3-

repressi(e !omple7 2-mediated gene repression sele!ti(ely ind#!es apoptosis in

!an!er !ells. Genes ev, -+, 1++-E;.



C

1;. "iranda, T.., %orte8, %.%., Qoo, %.., )iang, $., A3e, "., Kelly, T.K.,

"arB#e8, N.0. and Jones, P.A. H2++I DO'ep is a glo3al histone methylation

inhi3itor that rea!ti(ates de(elopmental genes not silen!ed 3y D'A methylation.

Mo) Can.e& !3e& , 0, 1F-.



C

TABLE LEGEND

Ta)le I5 Epigenetic %echanis%s in!l!e" in reg$lating gene e6pressin an"

chr%atin str$ct$re in nr%al %a%%alian cells5 0pigeneti! me!hanisms in!l#ding

D'A methylation, !o(alent histone modifi!ations, n#!leososme positioning and

mi!ro'As are essential for normal mammalian de(elopment and reg#lation of gene

e7pression. These epigeneti! modifi!ations display #niB#e properties and distri3#tion

patterns in different mammalian !ells. The distin!t !om3inatorial patterns of these

modifi!ations, !olle!ti(ely termed the epigenome, are key determinants of !ell fate and

gene a!ti(ity. 0m3ryoni! stem !ells maintain a more plasti! epigenome reB#ired for

de(elopmental pro!esses. :n !ontrast, the epigenome of differentiated tiss#e displays a

relati(ely restri!ted str#!t#re hi!h is sta3ly maintained thro#gh m#ltiple !ell di(isions.



+

(IGURE LEGENDS

(ig5 +5 Epigenetic gene silencing %echanis%s in %a%%als5 HAI An a!ti(e gene shos

an open !hromatin str#!t#re !onsisting of an #nmethylated promoter region Hsmall hite

!ir!les on D'A strandsI, ith no n#!leosome #pstream of the trans!ription start site

HTSS, thi!k 3la!k arroI, an enri!hment of a!ti(e histone marks s#!h as a!etylation

Hgreen triangle, A!I and ;KC methylation Hgreen !ir!les, CI and high le(els of 2A.O on

n#!leosomes HorangeI s#rro#nding the TSS. The open !hromatin str#!t#re is permissi3le

for 3inding of trans!ription fa!tors and 'A Pol-::, hi!h mediate a!ti(e trans!ription

on s#!h promoters. epression of s#!h a!ti(e genes Hindi!ated 3y red arrosI !an 3e

a!hie(ed in normal !ells 3y to main me!hanisms/ HI $ene repression 3y the a!tion of

Poly!om3 epressi(e $ro#p HP%1 and P%2I hi!h mediate the repressi(e ;K2F

methylation Hred !ir!les, 2FI, is a!!ompanied 3y the remo(al of a!etylation 3y histone

dea!etylases, loss of ;KC methylation, !hromatin !ompa!tion and n#!leosome

o!!#pan!y in the '9 and #3iB#itylation of 2A.OM H%I )ong-term silen!ing thro#gh

D'A methylation is performed 3y D'A methyltransferases. D'A methylation Hsmall red

!ir!les on D'A strandsI is often a!!ompanied 3y the repressi(e ;K methylation Hred

!ir!les, I, on promoters, hi!h leads to !hromatin !ompa!tion 3y re!r#itment of P1.

D'A "ethylated silen!ed promoters sho a depletion of 2A.O, loss of ;KC

methylation and histone de-a!etylation. A!/ a!etylation, U3/ #3iB#itination, KC-"T/

istone ; lysine C histone methyltransferase, K-"T/ istone ; lysine histone

methyltransferase, AT/ histone a!etyltransferase, DA%/ histone dea!etylase, P%1

and P%2/ poly!om3 repressi(e !omple7 1 and 2, 0O2/ enhan!er of 8este homolog#e 2,

P1/ hetero!hromatin protein 1, Pol-::/ 'A polymerase ::.



1

(ig5 -5 DNA %ethylatin changes in cancer5 :n normal !ells, %p$ island promoters are

generally #nmethylated and hen a!ti(e, as in the !ase of t#mor s#ppressor genes, are

a!!ompanied 3y a!ti(e histone marks s#!h as a!etylation and ;KC methylation Hgreen

!ir!les, CI alloing for a trans!riptionally a!ti(e open !hromatin str#!t#re. oe(er,

repetiti(e regions, transposons, %p$ poor intergeni! regions and imprinted gene

promoters are hea(ily methylated and a!!ompanied 3y repressi(e histone marks s#!h as

;K methylation Hred !ir!les, I hi!h together form a silent !hromatin state. D#ring

t#morigenesis, t#mor s#ppressor gene promoters ith %p$ islands 3e!ome methylated,

res#lting in the formation of silent !hromatin str#!t#re and a3errant silen!ing Hindi!ated

3y the red arroI. :n !ontrast, the repetiti(e seB#en!es, transposons and imprinted gene

promoters 3e!ome hypomethylated res#lting in a3errant a!ti(ation Hindi!ated 3y the

green arroI.

(ig5 /5 Reprgra%%ing # the epigen%e "$ring "e!elp%ent an" t$%rigenesis.

HAI :n em3ryoni! stem !ells, de(elopmentally important genes are marked 3y a #niB#e

=3i(alent domain> str#!t#re, !onsisting of the a!ti(e ;KC methylation Hgreen !ir!les, CI

and repressi(e ;K2F methylation Hred !ir!les, 2FI marks together ith 2A.O. S#!h

3i(alent domains are important for maintaining epigenomi! plasti!ity that is reB#ired

d#ring de(elopment. D#ring differentiation, the =3i(alent domains> are lost, gi(ing ay

to the esta3lishment of a more rigid =mono(alent domain> str#!t#re hi!h is either a!ti(e

Hindi!ated 3y the green arroI or repressi(e Hindi!ated 3y the red arroI depending #pon

hi!h mark is maintained. HI :n !an!er, !ells #ndergo a3errant somati! reprogramming

hi!h res#lts in gene silen!ing thro#gh formation of a !ompa!t !hromatin str#!t#re.



2

Silen!ing !an o!!#r thro#gh P% HPoly!om3 epressi(e %omple7I reprogramming V

silen!ing of a!ti(e genes 3y the poly!om3 gro#pM D'A methylation reprogramming V

silen!ing thro#gh de novo hypermethylation Hsmall red !ir!les on D'A strandsI

a!!ompanied 3y ;K methylation Hred !ir!les, IM or epigeneti! sit!hing V

repla!ement of gene repression 3y the poly!om3 mark ith long-term silen!ing thro#gh

D'A methylation. U3/ #3iB#itylation.



DNA

Methylation

All Cell Types

- Stable Heritable Modification- Gene Silencing- Chromatin Organization- Imprinting, X-Chromosome Inactivation, Silencing of

Repetitive lements- Mediated b! "#M$s

ES Cells

- %imodal "istrib&tion 'attern

Global CpG Meth!lation

CpG Islands (nmeth!lated

- 'l&ripotenc! Gene 'romoters (nmeth!lated

Somatic Cells

- $iss&e Specific Meth!lation of some CpG Islands and mostnon-CpG Island 'romoters

- 'l&ripotenc! Gene 'romoters Meth!lated

Covalent

Histone

Modifications

All Cell Types

- )abile Heritable Modification- %oth Gene Silencing *H+me, H+./me etc01 2 Gene

3ctivation *H+4me, 3cet!lation etc01- Specific "istrib&tion 'atterns of Histone Mar5s contrib&te to

Chromatin Organization- Mediated b! HM$s, H"Ms, H3$s 2 H"3Cs etc0

ES Cells

- %ivalent "omains - Coe6istence of 3ctive and Repressive

Mar5s *H+4me 2 H+./me1 at promoters of developmentall!

important genes

- 'lastic pigenome

Somatic Cells

- )oss of %ivalenc! and Restricted pigenome- stablishment of $iss&e Specific Monovalent H+./me and

H+4me "omains- 'resence of )arge Organized Chromatin Modifications

*)OCs1

Nucleosome

Positioning

& Histone

a!iants

All Cell Types

- )abile pigenetic Reg&lator! Mechanism- %oth Gene Silencing and Gene 3ctivation b! mod&lating

chromatin accessibilit!- Mediated b! 3$' dependent Chromatin Remodeling

Comple6es- %oth sliding of e6isting and incorporation of ne7 n&cleosomes

- H.308 and H+0+ preferentiall! localized to gene promoters7hich are active or poised for activation

- 3cet!lated H.308 associates 7ith &chromatin and

&bi9&it!lated H.308 7ith :ac&ltative Heterochromatin

mic!o"NAsAll Cell Types

- )abile pigenetic Reg&lator! Mechanism

- Gene Silencing- $iss&e-specific e6pression- Can be pigeneticall! Reg&lated

epigenetics in cancer carcinogenesis 2009

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