!+~$
E)i$
E. Heard, February 11 th , 2013
Probst et al. (2009) Nat. Rev. Mol. Cell Biol. (

1. Passive loss (absence of maintenance mechanisms)
2. Active loss (enzymatic removal of histone modifications, histone
exchange, nucleosome eviction, chromatin remodelling, etc)
Chromatin is highly dynamic
Yet states of gene activity can be stably propagated over hundreds of cell divisions in many cases
!
!
Synergy between chromatin, RNA-based, DNA methylationbased, nuclear organization and other mechanisms?
Reprogramming may involve both active and passive removal.
“Accidental” loss may occur sporadically, or after DNA damage, or with ageing– and may lead to epimutation and disease.
E. Heard, February 11 th , 2013

RNA Pol II
"
Ac
"
Ac
"
Ac
" g$
Xist RNA
!
g$ g$ y#)+50.-#(.$,*$E)i$),-12#3#/f$
~0/.$yWNg$
R"+,-%8($/.%.#g$ y#)+50.-#(.$*%).,+g$
Histone variant
MacroH2A
"
"
PRC2
Suz12
"
Ezh2
" Eed
"
"
PRC1-like
Mel18
"
"
Ring1
"
Bmi1
"
Pc?
" Ring1
"
H3K27me3
"
H2A Ub
"
H4K20
" me1
"
H2A Ub
"
H3K27
" " me3
"
H2A
"
Ub
"
H3K9
" me2
"
H3K4
" me3
"
Ac
"
?
"
H3K4
" me2
" y#-,'%2$,*$#5)"+,-%8)$-%+9/f$
@0/.,(#$#3)"%(6#g$
@0/.,(#$j#+%/#+/kg$
R"+,-%8($+#-,&#220(6g$
$
@0/.,(#$&#6+%&%8,(g$
H4K20
" me1
"
H3K9
" me2
"
?
" ?
"
E+^B#.K$ @T!%/#$
H3K27
" me3
"
H3K9
" me2
"
H4K20
" me1
"
2%.#$+#120)%8,($8-0(6$
E+,6+#//0'#$6#(#$/02#()0(6$
B-)@QH$
B1%8%2$+#,+6%(0/%8,($,*$."#$)"+,-,/,-#$
QWN$-#."<2%8,($
Dnmt
"
H3K9
" me2
"
&%<$H$ &%<$U$ &%<$M$
?B$)#22$&07#+#(8%8,($
&%<$d$ &%<$J$ $&%<$K$
E. Heard, February 11 th , 2013

Identical DNA sequences
Opposite gene activity states
~0/.$yWN$$
RNA Pol II
"
Ac
"
Ac
"
Ac
"
H3K27
" " me3
"
H2A
"
Ub
"
H3K9
" me2
" m--5(,l5,+#/)#()#$l5,+#/)#(.#$%'#)$&07p+#(./$$%(8),+1/$$
E,5+$&#/$-,&0`)0%8,(/$/1p)0`Z5#/$&_"0/.,(#/$
H3K4
" me3
"
Ac
"
H3K4
" me2
"
H3K9
" me2
"
Active X chromosome Inactive X chromosome
Synergy of epigenetic marks provides extremely stable heritable silencingover hundreds of cell divisions.
Fully reversible in the germ line and in iPS
@Mod-#U$ @dN)$ @Moc-#U$
E. Heard, February 11 th , 2013

Heterochromatin Assembly and Replication at Pericentromeric DNA Repeats in Fission Yeast
Cohesin
!
Swi6
!
H3K9me2
!
F*U.!
K(A.!
S'$4!
complex targets a nascent noncoding RNA, transcribed from pericentromeric (cen)
DNA repeats by base-pairing interactions. The RITS complex recruits the
RNA-dependent RNA polymerase complex (RDRC) and the
Dicer (Dcr1) ribonuclease, which generate additional siRNAs. RITS also directly recruits the
CLRC complex, containing the Clr4/Suv39h H3 lysine 9
(H3K9) methyltransferase.
The methylation of H3K9 (red) allows efficient association of RITS with chromatin.
Moazed D. (2011) Cell 146.
E. Heard, February 11 th , 2013
During replication of heterochromatin, the silent state is efficiently re-established as RITS complex can bind cooperatively via siRNA-mediated base pairing and association with H3K9 methylation. RITS-mediated recruitment of CLRC then results in methylation of newly deposited histones and re-establishment of silencing.
S,).!
M#A:!
T+(.!
S*9.0!
K%$.!
F9$.!
J$$.!
S
!
G2
!
G1/S
!
M
!
P P P P P
P
!
P P P P P
P
!

When and how are epigenetic mechanisms important in development ?
How are epigenetic states perpetuated across the cell cycle?
(RNAi /HP1; PcG/TrX; DNA methylation; TFs…)
And in non-dividing cells?
How is reprogramming achieved?
(whether in vivo or experimentally)
How are epigenetic processes affected by:
Ageing
Disease (eg cancer)
Environmentally induced changes
Nutritionally induced changes
Which epigenetic marks can be perpetuated across generations and how?
E. Heard, February 11 th , 2013

M,&!?)*+&@(8*%A!?$#!

M,&!?)*+&@(8*%A!?$#!
!
V&@(8&W7*9&!#@#'XA*A!(Q!%,$(8#N@!8#$UA=!Y*@9*@+!)$(B&*@A=!FZTA[!
HC !
R"+,-%8(4$1+,.#0($%(&$QWN$
-#."<2%.50($-%110(6f$
$$
$R"mE^B#Z4$T#QmE$B#Z$#.)$$
$GR"+,-%8($0--5(,1+#)010.%8,($
,($-0),+%++%</$,+$/#Z5#()0(6$
UC !
T%110(6$,*$2,(6$+%(6#$98&$
%(&$*",.&$0(.#+%)8,(/$0($."#$
$$
(5)2#5/$f$
$ R"+,-,/,-#$),(*,+-%8,($
)%1.5+# $
MC $m&#(8`)%8,($,*$/-%22$ yWN/$G-0yWN/4$/0yWN/4$
$$
10yWN/nL$=<$&##1$
/#Z5#()0(6$
E. Heard, February 11 th , 2013

M,&!?)*+&@(8*%A!?$#!
Combined with the power of genetics and biochemistry, the identification of the epigenomic changes during development, reprogramming and disease, as well as across generations, should help us understand the underlying epigenetic mechanisms;
And to what extent, if at all, agiven epigenomic change can be considered epigenetic in the heritable sense. iPS
?-=+<,(0)$B.#-$
R#22/$
E. Heard, February 11 th , 2013

The study of the mechanisms of development through which genes bring about phenotypic effects. Conrad H. Waddington 1942
The study of mitotically or meiotically heritable changes in gene expression that are not accompanied by changes in the DNA sequence. Robin Holliday, 1994, Art Riggs, 1996
All the weird and wonderful things that cannot be explained by genetics” Denise Barlow, Epigenome Network of Excellence (website)
Everything we do—everything we eat or smoke—can affect our gene expression and that of future generations. Epigenetics introduces the concept of free will into our idea of genetics. Randy Jirtle , 2007
Epigenetic events correspond to the structural adaptation of chromosomal regions so as to register, signal, or perpetuate altered activity states. Adrian Bird, 2007
E. Heard, February 11 th , 2013