histone modifications12

8/9/2019 Histone Modifications12

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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&


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'#ic Overview

• Modifications andmodifiers

• General roles• Techniques


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Bhaumi! "mith! and "hilati

ypes of istone *odifications


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• "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


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• 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


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; 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


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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


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Aade , + *um. Mol.

ene e/#lation

Moggs and rphanides! To>icological "cience

% ama/e


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Chromatin Condensation Spermato/enesis


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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


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Ch47-chip


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Massively parallel sequencing

ocal amplification

Ch47-se6


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Ch47-se6

Genome

7)epth86 thenumber of mappedsequence tags

7&overage86 hoC much of the genome the reads can be

mapped to


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Ch47-se6 vs. Ch47-chip

Mielsen et al.


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Specific istone

*odifications; ,ositions that are

modified; Modifying enzymes

; Dunctions of the

modification


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8ysine %cetylation



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%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.)


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• TCo general types6• ype 9: cytoplasmic 'neCly synthesized

histones(• *+T5


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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


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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(


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• Multi=enzyme comple>es

• Targeted by transcriptional repressors

• )eactylate histone tails

istone eacetylases (%Cs)


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• 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


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%Cs are in Comple5es

Butler and Bates! Nature Reviews


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5. Opens #p chromatin:

– Reduces charge interactions ofhistones Cith )9+ '< has apositive charge(

– ,revents chromatin compaction

'*4


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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


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8ysine *ethylation



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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


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• 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>. *@


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*@/"et5!


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Bannister and


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oles of 8ysine *ethylation

iu et. al! +nnu. Rev. ,la

2. ifferent reado#t dependin/ on level of methylation


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#. ifferent reado#t dependin/ on level of methylation

– Methylation status of *@( 0transcription activation

• *@


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i et al.!


3. ranscriptional activation

– *@


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3. Transcriptional activation

– H3K36me3 marks actively transcribed genes

Guenther et al.!

3;3?me3


7ol44


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". ranscriptional repression• *@


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Co-occ#rrence of activatin/ andrepressive

lysine methylation

Bivalency mars 7poised8 genes

Mielsen et al.!


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7osition of histonemodifications

Mielsen et al.!

*@


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Aysoca et al.! &el

umonHi family6 *@


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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 '*@


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Lysine Methylation/Demethylation

"hi! 9ature RevieCs

Individual lysines can be targeted by diferentmethyltranserases/demethylases


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Arginine Methylation

Bhaumi et al.! 9"MB


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Arginine Methylation

&an be symmetric or asymmetric

Lhang et al.! EMB ournal! #$$$.

7 i % i i


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7rotein %r/inine*ethyltransferases (7*s)

+rginine methylation can be activating or repressiv


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+rginine demethylation65. different amino acid

:nvolves a different mechanism thanysine demethylation

ysine demethylation6removal of methyl groups

%r/inine emethylation

Bannister and


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Serinehreonine 7hosphorylation

Bhaumi et al.! 9"MB


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Serinehreonine 7hosphorylation

• ample *@"5$, during mitosis


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oles of Serhr 7hosphorylation

&heung et al.! &el

2%B-p Serhr


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*irota et al.! 9ature! #$$3.

Dernandez=&apetilly et al.!

%74

aser

-N

Serhr7hosphorylatio

n


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istone !i6#itination

• -biquitination

– *#+


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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&


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Crosstal amon/ *odifications

• *#t#ally e5cl#sive: a position can be modified eitherCith an activating or repressive mar 'competitiveantagonism(

– *@


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• *#t#ally e5cl#sive6 a position can be modified either Cithan activating or repressive mar

– *@


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One comple5 may contain !oth demethylase and methyltransferasetar/etin/ different resid#es with opposin/ f#nctions



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One modification affects the /eneration of another

"chotta et al.! Genes and

,ericentric heteroch

*@


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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(•


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S i th hi t d &


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• )iscuss.

SoDis there a histone code&

S#mmary: istone 7*s and


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5. Type of modification

– Ahich amino=acid

– 9umber of modifications 'me(

#. ,osition in genome

– ,romoter6 *@

histone modifications12

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