Shelley BergerThe Wistar InstituteUniversity of Pennsylvania

Overview of Histone Variants

Bio 483October 9, 2012

Shelley BergerBiology; CDB; GeneticsPenn Epigenetics Programbergers@upenn.edu

Lecture OutlineWhat are histone variants?Review nuclesome structure wrt replacement

Consideration of following issues: - sequence variation - nucleosome structure- genome function- location within the genome- physiological function

Discuss H2A: macroH2A, H2A.Bbd, H2Ax, H2AZH3: CENPA, H3.3

testes histone variants

Core vs. variant histonesH3

H4

H2A

H2B

globularN C

Are there additional histones?

H2A

H2B

H3

H4

H1

Luger and Richmond, Nature 1997

H3

H4

H2A

H2B H3 ‘tail’

New nucleosome formation: after replication

H3/H4 tetramer binds to DNA

2 dimers H2A/H2B bind H3/H4 tetramer

How to replace?

1. During replication assemble with variant histones

2. H2A/H2B dimer exchange

3. Disassembly of nucleosome during DNA damage repair, transcription

H2A

H2B

H3

H4

DNA repair

Gene repressionX chrom inact

Gene activation

Centromere identity

Gene activation

H2A

Chromatin compaction by

macroH2A

Chromatin destabilization by

H2A.Bbd

H2AxH2A

Histone H2Axin DNA damage pathway

DNA damage leads to complex repair pathways

Molecular details of DNA repair

H2Ax evolutionary conservation

H2Ax phosphorylation is an early step

in the repair process

Histone H2AZ (= HTZ1):

How does it affect NCP structure and positioning?

What is its localization in the genome?What genomic process does it regulate?

Histone H2AZin gene regulation

Genome-wide view of H2AZ at promotors

TSS

Nuc “Depleted” Region

Gene ORFPromoter

TSS

H2AZ tends to occur in one nuc up- and one nuc down-stream of the TSS

Does it regulate transcription?

H2AZ is released as genes are activated Its release is required for full activation

Association of H2A/H2AZ with chromatin

H2AZ is more loosely bound to chromatin (although NCP structure very similar)

Is there a difference in nucleosome stability?

What is the localization of H2AZaround active/inactive genes?

Active genes less enriched than inactive

H2AZ

How does it affect NCP structure and positioning?

What is its localization in the genome?

What genomic process does it regulate?

Inactive promoters

Poises genes for activation

Destablizes NCP:correlates with depletion of one NCP over the TSS

How is it incorporated?

…a digression

Nucleosomes can be changedin detailed association with DNA,

position, presence

ATP-dependentNucleosome Remodeling

Activities of ATP-dependent chromatin remodeling enzymes

ATP ADP + Pi

ATPRemodeler

Evolutionary Tree of SWI2/SNF2 Remodelers

BRM-HsBRG-1-HsBrahma-DmSWI2-I

STH1-ScCHD-Dm

CHD1-HsCHD2-HsCHD1-ScMI2-DmCHD3-HsCHD4-Hs

CHD5-HsISWI-DmSNF2H-Hs

SNF2L-HsISW2-ScISW1-Sc

ino80-sc

SWI/SNF

ISWI

CHD

INO80

Start with H2A NCPs

ATP dependent remodelersand Histone Variant deposition

Swr1

H2AZ

What do ATP-dependent remodeling complexes do?

2. Exchange histones and histone variants:New paradigm!

1. Directly alter NCP position

Biochem. Cell Biol vol 84 2006

Model for H2AZ

Instability of H2AZ NCPs allows high temp to turn on/off genes in plants

Histone H3 and its Variants

CenpA

ReplicationCoupleddeposition(only S phase)

Replicationindependent Deposition(not strictlyduring S phase)

H3/H3.1

H4

H3.3

Histone H3.1 and H3.3

H3.3 is very similar to H3.1

H3.3 is more ancient

What genomic processes do H3.1/H3.3 regulate?

ReplicationDependent:EitherH3.1 or H3.3

ReplicationIndependent:Only H3.3

H3.3 localizes with RNAPII and K4me

genes

RNAP

K4me2

H3.1

H3.3

H3.1 H3.3

How are H3.1 and H3.3 deposited in RC and RI pathways?

HIRA

IP-WesternTwo different chaperone/

assembly factors

p150

p60

Nucleosome assembly RC or RI

CENPAH3

H4

Histone CENPA

What are centromeres?

Sequ

ence

com

plex

ity

CENPA, an H3 variant, is in a specialized NCP at centromeres in all eukaryotes

Targeting of CENPA to centromeres

Mapping in vitro and in vivo defined a region in the histone fold as “CATD”

Chaperone for Centromeric Localization

Cell line expressingCENPA-TAP

HJURP required for CENPA targeting to centromeres

HJURP Knock Down cell line

No targeting of CENPA in HJURP KD

1. OE CENPA did not restore targeting2. H3-CATD recruited by HJURP

Controversy regarding structure of the centromeric CENPA NCP

Proposed structures:

Is there a distinct structure?

(CENPA-H4)2 is more compact

Structure of CENPA NCP

Structural features map to CATD!

It forms a well behaved octamer

CenpA

HJURPHIRACAF1

Summary: H3 variants and their functions

Spermatogenesis and chromatin compaction: key role for histone variants

Testes-specific histone variants replace core histones following meiosis

All histones (except H4) have testes variants

H2A

H2B

H3

H4

H1

A remarkable variety of histone variants to regulate the genome via location-specific nuclesome funtion

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