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Histone modifications
Nucleosomes Are Complexes of DNA and Histones
Eukaryotic DNA is not naked; chromatin, DNA plus histones (50%)
Five major histones; H2A, H2B, H3, H4 and H1 highly basic (Arg and Lys >25%)
Roger Kornberg in 1974; Chromatin is made up of repeating units called
nucleosomes, each containing 200 bp of DNA and two copies each of H2A, H2B, H3,
H4 (histone octamer); beads on a string, nucleosome core particle plus linker DNA
(H1 binds to this DNA)
Figure 31.19 Chromatin structure. An electron micrograph of chromatin showing
its “beads on a string” character.
Nucleosome core particle (~100Å in diameter); ~145 bp DNA wrapped around histone
octamer
Figure 31.20 Nucleosome core particle. The structure consists of a core of eight
histone proteins surrounded by DNA. (A) A view showing the DNA wrapping around
the histone core. (B) A view related to that in part A by a 90-degree rotation. Notice
that the DNA forms a left-handed superhelix as it wraps around the core. (C) A
schematic view..
Eukaryotic DNA is packaged in
nucleosomes
Approximately 147 base pa
irs of DNA wrapped around
a histone octamer
~ 147 bp DNA
+
8 histones:
2 each H2A
H2B
H3
H4
Eukaryotic DNA Is Wrapped Around Histones to Form
Nucleosomes
The four types of histone are homologous and similar in structure
An histone octomer consists of a (H3)2(H4)2 tetramer and a pair of H2A-H2B dimers to form
a left-handed superhelical ramp around which the DNA wraps.
Each histone has an flexible N-terminal tail rich in Lys and Arg that extends out from the
core structure.
Covalent modification of these tails play an essential role in modulating the affinity of the
histones for DNA and other proteins.
Figure 31.21 Homologous histones. Histones H2A, H2B, H3, and H4 adopt a
similar three-dimensional structure as a consequence of common ancestry.
Some parts of the tails at the termini of the proteins are not shown.
Chromatin Structure Is Modulated Through Covalent
Modifications of Histone Tails
How do the coactivator modulate transcription
activity?
Some p160 coactivators are histone
acetyltransferases (HATs); transfer acetyl
group from acetyl CoA to the e amino group
of specific lysine residues in the N-terminal
tail of histones.
1. Changes in affinity to DNA; the acetylated
histone tail or the entire histone complex
2. Recruitment of the bromodomain
(acetyllysine-binding domain) proteins
a. TAFs (TATA-box binding protein (TBP)
associated factors). TAF1 contains two
bromodomains for positions 5 and 12 in the
H4 tail
b. the chromatin remodeling factor to
reorganize chromatin structure
Figure 31.30 Structure of histone acetyltransferase. The amino-terminal tail of histone
H3 extends into a pocket in which a lysine side chain can acceptor an acetyl group
from acetyl CoA bound in an adjacent site.
Histone proteins can be modified to
affect chromatin structure
DNA
Histone octamer
NUCLEOSOME
The amino terminal regions
of the histone monomers ex
tend beyond the nucleosom
e and are accessible for mo
dification.
The Histone Code
• Histones can be modified by
–
–
–
–
–
Acetylation (Ac)
Ubiquitination (Ub)
Methylation (Me)
Phosphorylation (P)
Sumoylation (Su)
• Depending on their position, these can
contribute to transcriptional activation or
inactivation.
Example – H3 modifications
Me
H3
Me
P
Ac
Me Ac
Ac
Me
Me
P
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
4
9 10
14
1718
23
262728
The amino terminus of H3 is often modified at one or more positions,
which can contribute to an activation or inhibition of transcription.
Example – H3 modifications
Me
H3
Me
P
Ac
Me Ac
Ac
Me
Me
P
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
4
9 10
14
1718
23
262728
The amino terminus of H3 is often modified at one or more positions,
which can contribute to an activation or inhibition of transcription.
Lysine can be acetylated, or mono-, di-, or tri-methylated
Methylated lysine
Mono (Kme1)
+
NH3
Lysine (K)
N
Di (Kme2)
CH3
O
Acetylated lysine
(KAc)
Tri (Kme3)
+
NH2
+
N
H
+
N
CH3
CH3
CH3
CH3
CH3
CH3
Histone modification affects
chromatin structure
Open configuration
H3
Me
P
Ac
K4 S10
K14
Closed configuration
H3
Me
Me
P
K9
K27
S28
H3K27me3 is associated with genes
BLUE = Gene density
RED = Repetitive
element density
GREEN = H3K27me3
PURPLE = methylcytosine
H3K27me3 in Arabidopsis
is present within the generich region, not the repeat
-rich region.
epigenetic marks
DNA demethylation
DNA methylation
Histone acetylation
Histone deacetylation
Histone (de) methylation
Histone (de) methylation
Histone variants
Fig 7-48.
An order of events leading to
transcription initiation
at a specific promoter
Eucaryotic gene activator proteins modify
local chromatin structure
Fig 7-45 Local alterations in chromatin structure
directed by eucaryotic gene activator proteins
Fig 7-46 Two specific ways that local histone acetylation stimulate
transcription initiation
Figure 31.31 Structure of a bromodomain. This four-helix-bundle domain binds
peptides containing acetyllysine. An acetylated peptide of histone H4 is shown
bound in the structure.
Figure 31.32 Chromatin remodeling. Eukaryotic gene regulation begins with an activated
transcription factor bound to a specific site on DNA. One scheme for the initiation of
transcription by RNA polymerase ll requires five steps: (1) recruitment of coactivator, (2)
acetylation of lysine residues in the histone tails, (3) binding of a remodeling-engine complex
to the acetylated lysine residues, (4) ATP-dependent remodeling of the chromatin structure to
expose a binding site for RNA polymerase or for other factors, and (5) recruitment of RNA
polymerase. Only two subunits are shown for each complex, although the actual complexes are
much larger. Other schemes are possible. .
Fig 7-49. (continued)