8/9/2019 Histone Modifications12
1/70
8/9/2019 Histone Modifications12
2/70
Outline
1. Overview of histone modifications:
a. Types of modifications and modifiers
b. General roles of modifications
c. Techniques used to study histone modifications
2. Specific modifications (acetylation, methylation, etc):a. Residues/positions that are frequently modified
b. Enzymes that add/remove the modification
c. Biological roles
3. Cross-tal !etween histone modifications
". S#mmary
$. % histone code&
8/9/2019 Histone Modifications12
3/70
'#ic Overview
• Modifications andmodifiers
• General roles• Techniques
8/9/2019 Histone Modifications12
4/70
Bhaumi! "mith! and "hilati
ypes of istone *odifications
8/9/2019 Histone Modifications12
5/70
8/9/2019 Histone Modifications12
6/70
• "mall vs. arge groups
• ne or up to three groups per residue
+eat#res of istone*odifications
Jason L J M et al. J. Biol. Chem. 2005
-b 0 12.3 )a*4 0 54 )a
8/9/2019 Histone Modifications12
7/70
• riters6 enzymes that add a mar
• eaders6 proteins that bind to and 7interpret8 the mar
•rasers6 enzymes that remove a mar
Tarahovsy! +.! 9ature :mmuno
istone *odifications and*odifers
8/9/2019 Histone Modifications12
8/70
; thers6 "umoylation 'ysine(! +), Ribosylation 'Glutamate(
istone *odifications and*odifers
esid#e *odification *odiyin/ n0yme
ysine+cetylation)eacetylation
*+T*)+&
ysine Methylation)emethylation *MT*)M
ysine-biquitylation)eubiquitylation
-b ligase-b protease
"erine/Threonine
,hosphorylation
)ephosphorylation
8/9/2019 Histone Modifications12
9/70
8/9/2019 Histone Modifications12
10/70
eneral oles of istone*odifications
• 4ntrinsic
– "ingle nucleosome changes
– E>ample6 histone variant specific modifications '*#+?(
• 5trinsic
– &hromatin organization6 nucleosome/nucleosome
interactions
– +lter chromatin pacaging! electrostatic charge
– E>ample6 *4 acetylation
• ffector-mediated
– Recruitment of other proteins to the chromatin via
• Bromodomains bind acetylation
• &hromo=lie royal domains 'chromo! tudor! MBT( and,*) bind methylation
• 54=@=@ proteins bind phosphorylation
8/9/2019 Histone Modifications12
11/70
eneral oles of istone*odifications
Aade , + *um. Mol.
ene e/#lation
Moggs and rphanides! To>icological "cience
% ama/e
8/9/2019 Histone Modifications12
12/70
eneral oles of istone*odifications
Chromatin Condensation Spermato/enesis
8/9/2019 Histone Modifications12
13/70
echni6#es to St#dy istone*odifications
• Chromatin imm#noprecipitation (Ch47): Strate/y forlocali0in/ histone mars
• &h:,=q,&R6 if you noC the target gene
• &h:,=chip! &h:,=seq! or other genome=Cidetechniques6 unbiased
• imitations6
» +ntibody specificity
» :nherent biases of localization methods
• *ass Spectrometry:
• Requires digestion of histones
8/9/2019 Histone Modifications12
14/70
Ch47-chip
8/9/2019 Histone Modifications12
15/70
Massively parallel sequencing
ocal amplification
Ch47-se6
8/9/2019 Histone Modifications12
16/70
Ch47-se6
Genome
7)epth86 thenumber of mappedsequence tags
7&overage86 hoC much of the genome the reads can be
mapped to
8/9/2019 Histone Modifications12
17/70
Ch47-se6 vs. Ch47-chip
Mielsen et al.
8/9/2019 Histone Modifications12
18/70
8/9/2019 Histone Modifications12
19/70
Specific istone
*odifications; ,ositions that are
modified; Modifying enzymes
; Dunctions of the
modification
8/9/2019 Histone Modifications12
20/70
8ysine %cetylation
Bhaumi! "mith! and "hilati
8/9/2019 Histone Modifications12
21/70
%cetylation
• *any lysine resid#es can !e acetylated
; mainly on histone tails 'sometimes in core(
; Can !e part of lar/e acetylation domains
; *odifyin/ en0ymes:
; often multi=enzyme comple>es
; can modify multiple residues
; ell correlated with transcriptional activation
; Other roles (chromatin assem!ly, % repair, etc.)
8/9/2019 Histone Modifications12
22/70
• TCo general types6• ype 9: cytoplasmic 'neCly synthesized
histones(• *+T5
8/9/2019 Histone Modifications12
23/70
5. G9+T
#. M"T
@. ,@$$/&B,'metazoan(
ther *+Ts e>ist as
Cell6e.g. associated Cithnuclear receptors or,ol :::
4. Rtt5$F
% S#perfamiliesype %: n#clear
8/9/2019 Histone Modifications12
24/70
Marmorstein and TrieveG9+T M"T ,@$$/&B, Rtt5$F
% S#perfamilies
• Similarities
• "tructurally conserved central core
• &an acetylate non=histone proteins
• ifferences
• "equence divergence
• &atalytic mechanisms
• :nteracting proteins 'regulate specificity(
8/9/2019 Histone Modifications12
25/70
• Multi=enzyme comple>es
• Targeted by transcriptional repressors
• )eactylate histone tails
istone eacetylases (%Cs)
8/9/2019 Histone Modifications12
26/70
• Class 4 %Cs• R,)@=lie '*)+& 5! #! @(• most cell types• in nucleus
• Class 44 %Cs• *)+5= lie '*)+& 4! 3! ! %! F! 5$(• *)+& and 9=term repressor motif• restricted e>pression• shuttle in/out nucleus
• Class 444 %Cs• "ir=# '9+)=dependent(• sirtuins
%C S#perfamilies
8/9/2019 Histone Modifications12
27/70
%Cs are in Comple5es
Butler and Bates! Nature Reviews
8/9/2019 Histone Modifications12
28/70
5. Opens #p chromatin:
– Reduces charge interactions ofhistones Cith )9+ '< has apositive charge(
– ,revents chromatin compaction
'*4
8/9/2019 Histone Modifications12
29/70
8/9/2019 Histone Modifications12
30/70
3. Correlated with !indin/ of activatin/ transcriptionfactors
i.e. enriched at promoters and enhancers
oles of %cetylation
*eintzman 9 et al.! 9ature Gen
"%c 3%c p3pression6E5IE#IE@%4 enhancers
'distal p@$$ binding sites
8/9/2019 Histone Modifications12
31/70
8ysine *ethylation
Bhaumi! "mith! and "hilati
8/9/2019 Histone Modifications12
32/70
8ysine *ethylation
• *any lysine resid#es can !e methylated
; Mainly on histone tails 'sometimes in core(
; &an be mono=! di=! or tri=methylated
; ependin/ on resid#e and n#m!er of methyl /ro#ps, can!e associated with active or repressive transcription
; ther roles
; Transcriptional elongation
; ,ericentromeric heterochromatin
; ? chromosome inactivationiu et. al! +nnu. Rev. ,la
8/9/2019 Histone Modifications12
33/70
• n0ymes very specific• Target a certain lysine on a certain histone
• ,ut on mono! di! and/or tri methyl 'me! me#! me@(
• Many contain "ET domains 'me=transferase(
• =eado#t> is very specific
• E>. *@
8/9/2019 Histone Modifications12
34/70
*@/"et5!
8/9/2019 Histone Modifications12
35/70
8/9/2019 Histone Modifications12
36/70
8/9/2019 Histone Modifications12
37/70
Bannister and
8/9/2019 Histone Modifications12
38/70
oles of 8ysine *ethylation
iu et. al! +nnu. Rev. ,la
2. ifferent reado#t dependin/ on level of methylation
8/9/2019 Histone Modifications12
39/70
oles of 8ysine *ethylation
#. ifferent reado#t dependin/ on level of methylation
– Methylation status of *@( 0transcription activation
• *@
8/9/2019 Histone Modifications12
40/70
i et al.!
oles of 8ysine *ethylation
3. ranscriptional activation
– *@
8/9/2019 Histone Modifications12
41/70
3. Transcriptional activation
– H3K36me3 marks actively transcribed genes
Guenther et al.!
3;3?me3
oles of 8ysine *ethylation
7ol44
8/9/2019 Histone Modifications12
42/70
". ranscriptional repression• *@
8/9/2019 Histone Modifications12
43/70
Co-occ#rrence of activatin/ andrepressive
lysine methylation
Bivalency mars 7poised8 genes
Mielsen et al.!
8/9/2019 Histone Modifications12
44/70
7osition of histonemodifications
Mielsen et al.!
*@
8/9/2019 Histone Modifications12
45/70
Aysoca et al.! &el
umonHi family6 *@
8/9/2019 Histone Modifications12
46/70
8ysine emethylation
• 8S1
– first histone demethylase
– amine o>idase
– only me5 and me# can serve as substrates
• )ifferent domain structure from other demethylase
• &omple> determines specificity '*@
8/9/2019 Histone Modifications12
47/70
8/9/2019 Histone Modifications12
48/70
Lysine Methylation/Demethylation
"hi! 9ature RevieCs
Individual lysines can be targeted by diferentmethyltranserases/demethylases
8/9/2019 Histone Modifications12
49/70
8/9/2019 Histone Modifications12
50/70
Arginine Methylation
Bhaumi et al.! 9"MB
8/9/2019 Histone Modifications12
51/70
Arginine Methylation
&an be symmetric or asymmetric
Lhang et al.! EMB ournal! #$$$.
7 i % i i
8/9/2019 Histone Modifications12
52/70
7rotein %r/inine*ethyltransferases (7*s)
+rginine methylation can be activating or repressiv
8/9/2019 Histone Modifications12
53/70
+rginine demethylation65. different amino acid
:nvolves a different mechanism thanysine demethylation
ysine demethylation6removal of methyl groups
%r/inine emethylation
Bannister and
8/9/2019 Histone Modifications12
54/70
Serinehreonine 7hosphorylation
Bhaumi et al.! 9"MB
8/9/2019 Histone Modifications12
55/70
Serinehreonine 7hosphorylation
• ample *@"5$, during mitosis
8/9/2019 Histone Modifications12
56/70
oles of Serhr 7hosphorylation
&heung et al.! &el
2%B-p Serhr
8/9/2019 Histone Modifications12
57/70
*irota et al.! 9ature! #$$3.
Dernandez=&apetilly et al.!
%74
aser
-N
Serhr7hosphorylatio
n
8/9/2019 Histone Modifications12
58/70
istone !i6#itination
• -biquitination
– *#+
8/9/2019 Histone Modifications12
59/70
Outline
1. Overview of histone modifications:a. Types of modifications and modifiers
b. General roles of modifications
c. Techniques used to study histone modifications
2. Specific modifications (acetylation, methylation, etc):a. Residues/positions that are frequently modified
b. Enzymes that add/remove the modification
c. Biological roles
3. Cross-tal !etween histone modifications
". S#mmary
$. % histone code&
8/9/2019 Histone Modifications12
60/70
8/9/2019 Histone Modifications12
61/70
8/9/2019 Histone Modifications12
62/70
Crosstal amon/ *odifications
• *#t#ally e5cl#sive: a position can be modified eitherCith an activating or repressive mar 'competitiveantagonism(
– *@
8/9/2019 Histone Modifications12
63/70
Crosstal amon/ *odifications
• *#t#ally e5cl#sive6 a position can be modified either Cithan activating or repressive mar
– *@
8/9/2019 Histone Modifications12
64/70
One comple5 may contain !oth demethylase and methyltransferasetar/etin/ different resid#es with opposin/ f#nctions
Crosstal amon/ *odifications
8/9/2019 Histone Modifications12
65/70
Crosstal amon/ *odifications
One modification affects the /eneration of another
"chotta et al.! Genes and
,ericentric heteroch
*@
8/9/2019 Histone Modifications12
66/70
S#mmary: istone 7*s
• &ovalent and reversible• -sually occur on histone tails• Modifying enzymes6
• Redundancy6 + single position can be modified bymultiple different enzymes
• "pecificity6 "ome enzymes 'lie *MTs( can targetonly one residue and some 'lie *+Ts( can targetmany
• *istone ,TMs recruit other proteins to )9+ via specificdomains
• Bromo '+c(• &hromo/,*) 'Me(
• 54=@=@ ',h(• ,articipate in regulation of many processes
– transcription – )9+ repair – chromatin assembly – long=range pacaging 'heterochromatin formation!
silencing(•
8/9/2019 Histone Modifications12
67/70
8/9/2019 Histone Modifications12
68/70
S i th hi t d &
8/9/2019 Histone Modifications12
69/70
• )iscuss.
SoDis there a histone code&
S#mmary: istone 7*s and
8/9/2019 Histone Modifications12
70/70
5. Type of modification
– Ahich amino=acid
– 9umber of modifications 'me(
#. ,osition in genome
– ,romoter6 *@
Top Related