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DNA compactioncompaction in a human nucleus
1bp (0.3nm)
10,000 nm
30nm
11 nm
Compaction of DNA by histones Compaction by chromosome scaffold / nuclear matrix
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HISTONESare
highly conserved,small, basic proteins
H1
H2B
H2A
H3
H4
helix
variable
conserved
Histone acetylationis a reversible modificationof lysines in the N-terminiof the core histones. Result:• reduced binding to DNA• destabilization of chromatin
Linker histone
Core histones
N
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Core Histones
The basic structure of ALL core histones is the same:• 1 long hydrophobic alpha-helix, bordered by• 2 short hydrophobic alpha helices that form pairs• H2A - H2B and H3 - H4 which interact.
References: Moudrianakis et al. PNAS 88, 10138 (1991); PNAS 90, 10489 (1993); PNAS 92, 11170 (1995)
The histone-fold
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Histone octamer assembly
H3-H4tetramer H2A-H2B
dimer
Histoneoctamer
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The Nucleosome as the fundamental chromatin unit
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• 146-149 bp DNA in a 1.65 turns of a flat, left-handed superhelix• one pseudo twofold axis centered at the “dyad” (reference: 0 helical turns)• one base-pair precisely at the dyad• sharp bends at + 1.5 and + 4-5 turns• Histone-fold domains organize 121 bp of DNA. The DNA is bound at 10 bp intervals through many contacts, including penetration of arginines at all 14 minor grooves facing the protein core• The grooves from neighboring DNA turns line up; forming channels• H3 and H2B N-termini exit one of these channels every 20bp.• The H4 tail establishes contacts with the next core particle.
Nucleosome features
H2B H4H3H2A
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Chromatosome
5 mM
1 mM
Linker Histone and histone terminicontrol linker DNA entry/exit of
chromatosome in chromatin fiber.
Core histone octamer + 1 Linker Histone + 2 full turns of DNA (168 bp)
H3
H1
N
C
H3
Zhou, Gerchman, Ramakrishnan, Travers,Muyldermans Nature 395, 402 (1998)
An, Leuba, van Holde, ZlatanovaPNAS 95, 3396 (1998)
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Chromatinfibers
+ charged N termini(bind DNA on neigboringnucleosomes)
highly acetylatedcore histones
(especially H3 and H4)
30 nmchromatin fiber
11 nm(beads)
• HIGH level of histone H1 • Reduced level of histone H1
• NO gene transcription • Gene transcription possible
Alternative chromatin fiber models
Zigzag fiber
Histone modifications
Cell (2002) 111, 285-91
27
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Acetylation of conserved lysines
H4 N-terminus
H3 N-terminus
Ac-S-G-R-G-K-G-G-K-G-L-G-K-G-G-A-K-R-H-R-K-V-L-R-D-+ + + + + ++ + + +
Ac or MeAcAcAcAc
5 8 12 16 20
A-R-T-K-Q-T-A-R-K-S-T-G-G-K-A-P-R-K-Q-L-A-T-K-A-A-R-K-S-A-P-
MeAc or Me
Ac Ac Ac Ac
++ + + + + + ++
4 9 14 18 23 27
The N-termini of histones H4 and H3, and their acetylation patterns, are absolutely conserved.
Lysine
-N-Acetyl-Lysine
HAT (HistoneAcetyl-Transferase)
HistoneDeacetylase
reversible reactions
O
N
C
C C
C
C
CN+
P
OO
OP
O
-DNAbackbonebinding
no DNAbindingO
N
C
C C
C
C
C
N
O
C
C
Acetyl-CoA
CoAP-
--
--
---
--
--
--
--
--
-
-
-
-
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Acetylation of Chromatin Domains: analysis by the technique of Chromatin Immunoprecipitation (ChIP)
Hebbes, Clayton, Thorne, Crane-Robinson EMBO J. 13, 1823 (1994)
Example: the chicken -globin gene domain
l High levels of chromatin acetylation, across complete chromatin domains(DNA loops), induces chromatin changes detected as “general DNase I sensitivity”
l Within these chromatin domains, at functional genes or transcription factors, the chromatin structure is interrupted by small “DNase I hypersensitive sites”
domainboundary
domainboundary
H A
0 10 20 30 kb
DNase I hyper-sensitive site
= -globin genes:
(Ac-Lys) antibody nucleosome ppt
DNA loop domain
General DNase I sensitivity
Control:inactive gene
chickenovalbumin
0 1 2 DNase I(U/ml)
DN
A r
em
ain
ing
DNase I
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Acetylation at Promoters leads to transcriptional activation
Thyroid Hormone Receptorexample of DNA-binding
Transcription Factor
TAF 250II
TBP
HAT
TATA
pol.II
HATGCN5
ACGGTC
ADA2ADA3
TranscriptionalACTIVATION
co-activator
HistoneAcetylTransferases
TH
ho
rmo
ne
+
HAT
P/CAF
p300CPB
HAT
TACCCG
TH
Hyper-acetylateddecondensed
Chromatin fiber
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TranscriptionalREPRESSION
co-repressor
TAF 250II
TBP
HAT
TATA
TACCCG
N-CoRSin3
RPD3
HistoneDeacetylase
Without Thyroid Hormone
Deacetylation at Promoters leads to Transcriptional repression
Hypo-acetylatedcondensed
Chromatin fiber
X
Acétylationdes histones
Chromatine décondensée:Etat transcriptionnel
actif
Déacetylationdes histones
Chromatine condensée:Etat transcriptionnel
réprimé
Acétylation vs déacetylation des histones
C C
Histone Methylation
Lysine
-N-monomethyl-Lysine
HMT (HistoneMethyl-Transferase)
Histonedemethylase
O
N
C
C C
C
C
CN+
O
N
C
C C
C
C
C
C
HMT (HistoneMethyl-Transferase)
S-adenosylmethyionine
O
N
C
C C
C
C
C
C
C
HMT (HistoneMethyl-Transferase)
O
N
C C
C
C
C
C
-N-dimethyl-Lysine
C-N-trimethyl-Lysine
DNA backbonebinding may not be strongly affected, but specific proteins may recognize these modifications
N+
N+
N+
S-adenosylmethyionine
S-adenosylmethyionine
Histones can be methylated at lysines or arginines. Example: H3 K4 methylation
Histonedemethylase
Histonedemethylase
Histone demethylases found for K4, K9, K27 and K36
Histone methylation : Histone methyltransferases
Enhancer of Zeste H3 K27Enhancer of Zeste
Dm Trx, Ash1Mammalian MLL1-3
Euchromatin methylation, PcG-dependent gene silencing
Euchromatin methylation, gene activationtrxG-dependent gene silencing
Histone demethylases
2 classes:
LSD1
JmjC domain proteins
Histone demethylasesLSD1 demethylases target mono or dimethyl K4 and K9 of histone H3, depending
on their interacting cofactor
Histone demethylasesJmjC domain demethylases target many different lysines and are conserved
Histone methylationA reversible phenomenon with many dedicated components
Utx
JMJD3
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