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Contents |
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* Residue conservation analysis
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PDB id:
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Peptide binding protein
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Title:
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Tandem chromodomains of human chd1 complexed with histone h3 tail containing trimethyllysine 4 and dimethylarginine 2
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Structure:
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Chromodomain-helicase-DNA-binding protein 1. Chain: a, b. Fragment: residues 268-443. Synonym: chd-1. Engineered: yes. Chromodomain-helicase-DNA-binding protein 1. Chain: c. Fragment: residues 268-373. Synonym: chd-1.
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: chd1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: this sequence occurs naturally in homo sapiens (humans).
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Biol. unit:
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Tetramer (from
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Resolution:
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2.95Å
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R-factor:
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0.238
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R-free:
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0.290
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Authors:
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J.F.Flanagan Iv,L.-Z.Mi,M.Chruszcz,M.Cymborowski,K.L.Clines,Y.Kim, W.Minor,F.Rastinejad,S.Khorasanizadeh
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Key ref:
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J.F.Flanagan
et al.
(2005).
Double chromodomains cooperate to recognize the methylated histone H3 tail.
Nature,
438,
1181-1185.
PubMed id:
DOI:
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Date:
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19-Sep-05
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Release date:
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27-Dec-05
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PROCHECK
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Headers
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References
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Enzyme class:
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Chains A, B, C:
E.C.3.6.4.12
- Dna helicase.
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Reaction:
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ATP + H2O = ADP + phosphate + H+
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ATP
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+
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H2O
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=
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ADP
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+
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phosphate
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+
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H(+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Nature
438:1181-1185
(2005)
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PubMed id:
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Double chromodomains cooperate to recognize the methylated histone H3 tail.
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J.F.Flanagan,
L.Z.Mi,
M.Chruszcz,
M.Cymborowski,
K.L.Clines,
Y.Kim,
W.Minor,
F.Rastinejad,
S.Khorasanizadeh.
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ABSTRACT
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Chromodomains are modules implicated in the recognition of lysine-methylated
histone tails and nucleic acids. CHD (for chromo-ATPase/helicase-DNA-binding)
proteins regulate ATP-dependent nucleosome assembly and mobilization through
their conserved double chromodomains and SWI2/SNF2 helicase/ATPase domain. The
Drosophila CHD1 localizes to the interbands and puffs of the polytene
chromosomes, which are classic sites of transcriptional activity. Other CHD
isoforms (CHD3/4 or Mi-2) are important for nucleosome remodelling in histone
deacetylase complexes. Deletion of chromodomains impairs nucleosome binding and
remodelling by CHD proteins. Here we describe the structure of the tandem
arrangement of the human CHD1 chromodomains, and its interactions with histone
tails. Unlike HP1 and Polycomb proteins that use single chromodomains to bind to
their respective methylated histone H3 tails, the two chromodomains of CHD1
cooperate to interact with one methylated H3 tail. We show that the human CHD1
double chromodomains target the lysine 4-methylated histone H3 tail (H3K4me), a
hallmark of active chromatin. Methylammonium recognition involves two aromatic
residues, not the three-residue aromatic cage used by chromodomains of HP1 and
Polycomb proteins. Furthermore, unique inserts within chromodomain 1 of CHD1
block the expected site of H3 tail binding seen in HP1 and Polycomb, instead
directing H3 binding to a groove at the inter-chromodomain junction.
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Selected figure(s)
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Figure 3.
Figure 3: Methyllysine binding by human CHD1. a, The
bound-peptide structure of H3K4me3 (green), H3K4me1 (yellow),
H3K4me3R2me2a (cyan) and H3K4me3T3ph (red). b, The aromatic
cages from HP1 (blue) and Polycomb (cyan) with methyllysines 9
and 27. c, Fluorescence polarization peptide binding assays
using human or yeast CHD1. Using H3K4me3 peptide, human CHD1
(black) binds with a K[d] of 5  M,
W67L-human CHD1 (cyan) does not bind, W64L-human CHD1 (yellow)
binds with a K[d] of 290 M,
and budding yeast CHD1 (red) does not bind. W64L and W67L-human
CHD1 do not allow binding to H3K4me1 or the unmodified peptide.
d, Effect of adjacent peptide modifications. Black, H3K4me3;
cyan, H3K4me3R2me2a; red, H3K4me3T3ph.
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Figure 4.
Figure 4: Comparison of CHD1 with HP1 and Polycomb. a, HP1
chromodomain (blue) in complex with H3K9me3 (brown) superimposed
on CHD1 chromodomain 1 (cyan and yellow) in complex with H3K4me3
(green). b, Polycomb chromodomain (blue) in complex with
H3K27me3 (brown) superimposed on CHD1 chromodomain 1 (cyan and
yellow) in complex with H3K4me3 (green).
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2005,
438,
1181-1185)
copyright 2005.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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C.A.Musselman,
M.E.Lalonde,
J.Côté,
and
T.G.Kutateladze
(2012).
Perceiving the epigenetic landscape through histone readers.
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Nat Struct Mol Biol,
19,
1218-1227.
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C.Ballaré,
M.Lange,
A.Lapinaite,
G.M.Martin,
L.Morey,
G.Pascual,
R.Liefke,
B.Simon,
Y.Shi,
O.Gozani,
T.Carlomagno,
S.A.Benitah,
and
L.Di Croce
(2012).
Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity.
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Nat Struct Mol Biol,
19,
1257-1265.
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PDB code:
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E.L.Greer,
and
Y.Shi
(2012).
Histone methylation: a dynamic mark in health, disease and inheritance.
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Nat Rev Genet,
13,
343-357.
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B.Schuettengruber,
A.M.Martinez,
N.Iovino,
and
G.Cavalli
(2011).
Trithorax group proteins: switching genes on and keeping them active.
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Nat Rev Mol Cell Biol,
12,
799-814.
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D.C.Hargreaves,
and
G.R.Crabtree
(2011).
ATP-dependent chromatin remodeling: genetics, genomics and mechanisms.
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Cell Res,
21,
396-420.
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K.W.Jeong,
K.Kim,
A.J.Situ,
T.S.Ulmer,
W.An,
and
M.R.Stallcup
(2011).
Recognition of enhancer element-specific histone methylation by TIP60 in transcriptional activation.
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Nat Struct Mol Biol,
18,
1358-1365.
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and
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(2011).
Analysis of the coding genome of diffuse large B-cell lymphoma.
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| |
Nat Genet,
43,
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P.Voigt,
and
D.Reinberg
(2011).
Histone tails: ideal motifs for probing epigenetics through chemical biology approaches.
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Chembiochem,
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S.M.Fuchs,
K.Krajewski,
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and
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(2011).
Influence of combinatorial histone modifications on antibody and effector protein recognition.
|
| |
Curr Biol,
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S.Morettini,
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G.Scheran,
H.Wörle,
V.Podhraski,
D.V.Fyodorov,
and
A.Lusser
(2011).
The chromodomains of CHD1 are critical for enzymatic activity but less important for chromatin localization.
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Nucleic Acids Res,
39,
3103-3115.
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S.S.Oliver,
and
J.M.Denu
(2011).
Dynamic interplay between histone H3 modifications and protein interpreters: emerging evidence for a "histone language".
|
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Chembiochem,
12,
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T.G.Kutateladze,
and
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(2010).
Combinatorial profiling of chromatin binding modules reveals multisite discrimination.
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and
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(2010).
A homogeneous method for investigation of methylation-dependent protein-protein interactions in epigenetics.
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Nucleic Acids Res,
38,
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and
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(2010).
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| |
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and
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|
| |
Biopolymers,
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|
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D.Kim,
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F.Rastinejad,
and
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(2010).
Corecognition of DNA and a methylated histone tail by the MSL3 chromodomain.
|
| |
Nat Struct Mol Biol,
17,
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PDB codes:
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F.He,
T.Umehara,
K.Saito,
T.Harada,
S.Watanabe,
T.Yabuki,
T.Kigawa,
M.Takahashi,
K.Kuwasako,
K.Tsuda,
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M.Aoki,
E.Seki,
N.Kobayashi,
P.Güntert,
S.Yokoyama,
and
Y.Muto
(2010).
Structural insight into the zinc finger CW domain as a histone modification reader.
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Structure,
18,
1127-1139.
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PDB codes:
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G.E.Zentner,
W.S.Layman,
D.M.Martin,
and
P.C.Scacheri
(2010).
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(2010).
The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor.
|
| |
Mol Cell,
39,
711-723.
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PDB code:
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J.M.Higgins
(2010).
Haspin: a newly discovered regulator of mitotic chromosome behavior.
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| |
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and
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(2010).
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and
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(2010).
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| |
Nature,
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(2010).
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| |
Nature,
466,
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PDB codes:
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M.N.Cruickshank,
P.Besant,
and
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| |
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and
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CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression.
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PLoS Genet,
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Genetics,
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and
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and
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H.G.Kim,
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PDB code:
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PDB code:
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PDB codes:
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I.Garcia-Bassets,
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Mol Genet Genomics,
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PDB code:
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J.Min,
A.Allali-Hassani,
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PDB codes:
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L.Corsini,
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PDB codes:
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T.Pawson
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PDB codes:
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A.Schuetz,
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25,
4245-4252.
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PDB codes:
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C.G.Marfella,
Y.Ohkawa,
A.H.Coles,
D.S.Garlick,
S.N.Jones,
and
A.N.Imbalzano
(2006).
Mutation of the SNF2 family member Chd2 affects mouse development and survival.
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J Cell Physiol,
209,
162-171.
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D.Reinberg,
and
R.J.Sims
(2006).
de FACTo nucleosome dynamics.
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| |
J Biol Chem,
281,
23297-23301.
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G.P.Vicent,
C.Ballaré,
R.Zaurin,
P.Saragüeta,
and
M.Beato
(2006).
Chromatin remodeling and control of cell proliferation by progestins via cross talk of progesterone receptor with the estrogen receptors and kinase signaling pathways.
|
| |
Ann N Y Acad Sci,
1089,
59-72.
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H.Li,
S.Ilin,
W.Wang,
E.M.Duncan,
J.Wysocka,
C.D.Allis,
and
D.J.Patel
(2006).
Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF.
|
| |
Nature,
442,
91-95.
|
|
|
PDB codes:
|
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|
I.L.de la Serna,
Y.Ohkawa,
and
A.N.Imbalzano
(2006).
Chromatin remodelling in mammalian differentiation: lessons from ATP-dependent remodellers.
|
| |
Nat Rev Genet,
7,
461-473.
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J.C.Eissenberg,
and
S.C.Elgin
(2006).
Marking time.
|
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Nat Genet,
38,
276-277.
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J.Mellor
(2006).
It takes a PHD to read the histone code.
|
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Cell,
126,
22-24.
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K.Bouazoune,
and
A.Brehm
(2006).
ATP-dependent chromatin remodeling complexes in Drosophila.
|
| |
Chromosome Res,
14,
433-449.
|
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|
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|
|
M.S.Cosgrove
(2006).
PHinDing a new histone "effector" domain.
|
| |
Structure,
14,
1096-1098.
|
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M.V.Botuyan,
J.Lee,
I.M.Ward,
J.E.Kim,
J.R.Thompson,
J.Chen,
and
G.Mer
(2006).
Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair.
|
| |
Cell,
127,
1361-1373.
|
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|
PDB codes:
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|
P.B.Becker
(2006).
Gene regulation: a finger on the mark.
|
| |
Nature,
442,
31-32.
|
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P.V.Peña,
F.Davrazou,
X.Shi,
K.L.Walter,
V.V.Verkhusha,
O.Gozani,
R.Zhao,
and
T.G.Kutateladze
(2006).
Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2.
|
| |
Nature,
442,
100-103.
|
|
|
PDB code:
|
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|
P.Zhang,
J.Du,
B.Sun,
X.Dong,
G.Xu,
J.Zhou,
Q.Huang,
Q.Liu,
Q.Hao,
and
J.Ding
(2006).
Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3.
|
| |
Nucleic Acids Res,
34,
6621-6628.
|
|
|
PDB code:
|
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|
R.J.Klose,
K.Yamane,
Y.Bae,
D.Zhang,
H.Erdjument-Bromage,
P.Tempst,
J.Wong,
and
Y.Zhang
(2006).
The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36.
|
| |
Nature,
442,
312-316.
|
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R.Pavri,
B.Zhu,
G.Li,
P.Trojer,
S.Mandal,
A.Shilatifard,
and
D.Reinberg
(2006).
Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II.
|
| |
Cell,
125,
703-717.
|
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|
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|
|
S.Lee,
D.K.Lee,
Y.Dou,
J.Lee,
B.Lee,
E.Kwak,
Y.Y.Kong,
S.K.Lee,
R.G.Roeder,
and
J.W.Lee
(2006).
Coactivator as a target gene specificity determinant for histone H3 lysine 4 methyltransferases.
|
| |
Proc Natl Acad Sci U S A,
103,
15392-15397.
|
|
|
|
|
|
|
T.S.Walter,
C.Meier,
R.Assenberg,
K.F.Au,
J.Ren,
A.Verma,
J.E.Nettleship,
R.J.Owens,
D.I.Stuart,
and
J.M.Grimes
(2006).
Lysine methylation as a routine rescue strategy for protein crystallization.
|
| |
Structure,
14,
1617-1622.
|
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|
|
|
Y.Chu,
A.Sutton,
R.Sternglanz,
and
G.Prelich
(2006).
The BUR1 cyclin-dependent protein kinase is required for the normal pattern of histone methylation by SET2.
|
| |
Mol Cell Biol,
26,
3029-3038.
|
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|
|
Y.Dou,
T.A.Milne,
A.J.Ruthenburg,
S.Lee,
J.W.Lee,
G.L.Verdine,
C.D.Allis,
and
R.G.Roeder
(2006).
Regulation of MLL1 H3K4 methyltransferase activity by its core components.
|
| |
Nat Struct Mol Biol,
13,
713-719.
|
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|
|
Y.Ho,
F.Elefant,
S.A.Liebhaber,
and
N.E.Cooke
(2006).
Locus control region transcription plays an active role in long-range gene activation.
|
| |
Mol Cell,
23,
365-375.
|
|
|
|
|
|
|
Y.Huang,
J.Fang,
M.T.Bedford,
Y.Zhang,
and
R.M.Xu
(2006).
Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A.
|
| |
Science,
312,
748-751.
|
|
|
PDB codes:
|
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Y.Zhang
(2006).
It takes a PHD to interpret histone methylation.
|
| |
Nat Struct Mol Biol,
13,
572-574.
|
|
|
|
|
|
|
Z.Han,
L.Guo,
H.Wang,
Y.Shen,
X.W.Deng,
and
J.Chai
(2006).
Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5.
|
| |
Mol Cell,
22,
137-144.
|
|
|
PDB codes:
|
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|
|
J.C.Eissenberg,
and
S.C.Elgin
(2005).
Molecular biology: antagonizing the neighbours.
|
| |
Nature,
438,
1090-1091.
|
|
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|
|
|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
|
 |
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