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PDBsum entry 2jmj
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Protein binding
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PDB id
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2jmj
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Contents |
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* Residue conservation analysis
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PDB id:
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Protein binding
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Title:
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Nmr solution structure of the phd domain from the yeast yng1 protein in complex with h3(1-9)k4me3 peptide
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Structure:
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Protein yng1. Chain: a. Fragment: phd finger. Synonym: ing1 homolog 1. Engineered: yes. Histone h3. Chain: p. Engineered: yes
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Source:
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Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: yng1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the peptide h3(1-9)k4me3 is naturally found in saccharomyces cerevisiae (locus aas64341 to aas64341).
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NMR struc:
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20 models
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Authors:
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S.Ilin,S.D.Taverna,R.S.Rogers,J.C.Tanny,H.Lavender,H.Li,L.Baker, J.Boyle,L.P.Blair,B.T.Chait,D.J.Patel,J.D.Aitchison,A.J.Tackett, C.D.Allis
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Key ref:
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S.D.Taverna
et al.
(2006).
Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs.
Mol Cell,
24,
785-796.
PubMed id:
DOI:
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Date:
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15-Nov-06
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Release date:
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03-Jul-07
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PROCHECK
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Headers
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References
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Q08465
(YNG1_YEAST) -
Protein YNG1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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Seq:
Struc:
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219 a.a.
60 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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DOI no:
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Mol Cell
24:785-796
(2006)
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PubMed id:
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Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs.
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S.D.Taverna,
S.Ilin,
R.S.Rogers,
J.C.Tanny,
H.Lavender,
H.Li,
L.Baker,
J.Boyle,
L.P.Blair,
B.T.Chait,
D.J.Patel,
J.D.Aitchison,
A.J.Tackett,
C.D.Allis.
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ABSTRACT
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Posttranslational histone modifications participate in modulating the structure
and function of chromatin. Promoters of transcribed genes are enriched with K4
trimethylation and hyperacetylation on the N-terminal tail of histone H3.
Recently, PHD finger proteins, like Yng1 in the NuA3 HAT complex, were shown to
interact with H3K4me3, indicating a biochemical link between K4 methylation and
hyperacetylation. By using a combination of mass spectrometry, biochemistry, and
NMR, we detail the Yng1 PHD-H3K4me3 interaction and the importance of
NuA3-dependent acetylation at K14. Furthermore, genome-wide ChIP-Chip analysis
demonstrates colocalization of Yng1 and H3K4me3 in vivo. Disrupting the K4me3
binding of Yng1 altered K14ac and transcription at certain genes, thereby
demonstrating direct in vivo evidence of sequential trimethyl binding,
acetyltransferase activity, and gene regulation by NuA3. Our data support a
general mechanism of transcriptional control through which histone acetylation
upstream of gene activation is promoted partially through availability of
H3K4me3, "read" by binding modules in select subunits.
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Selected figure(s)
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Figure 4.
Figure 4. NMR Structure of the Yng1 PHD Interaction with
Trimethylated H3 K4
NMR-derived structure of the PHD finger
(152–212) in the free form. For clarity, residues 152–154
and 208–212 in the unstructured regions were omitted.
(A)
Backbone superposition of 20 energy-minimized structures of the
PHD finger.
(B) Aromatically rich surface that shows
extensive chemical shift changes upon peptide binding (Y157 and
W180).
(C) Backbone superposition of 20 energy-minimized
structures of the PHD finger in complex with H3[1–9]K4me3
peptide.
(D) Aromatically rich surface that shows extensive
interactions with trimethylated lysine K4 (Y157 and W180).
(E) Surface representation of the YNG1 PHD complex with
H3[1–9]K4me3 peptide. Surface residues that undergo the
largest chemical shift upon binding are highlighted in pink.
(F) An ensemble of 20 structures with side chains involved
in complex formation colored in purple (D172 and E179 for H3 R2,
Y157 and W180 for H3K4).
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Figure 7.
Figure 7. Model for H3K4me3-Directed Activity of NuA3
(A) Set1, the H3K4 HMT, is recruited to promoter-proximal
nucleosomes at the ORF to be activated, resulting in H3K4me3.
(B) NuA3 is targeted to and/or retained at sites of H3K4me3
through interactions with the PHD finger of Yng1, promoting
H3K14ac via the Sas3 HAT, positively regulating downstream
transcription events.
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The above figures are
reprinted
by permission from Cell Press:
Mol Cell
(2006,
24,
785-796)
copyright 2006.
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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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A.J.Bannister,
and
T.Kouzarides
(2011).
Regulation of chromatin by histone modifications.
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Cell Res,
21,
381-395.
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K.E.Gardner,
L.Zhou,
M.A.Parra,
X.Chen,
and
B.D.Strahl
(2011).
Identification of lysine 37 of histone H2B as a novel site of methylation.
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PLoS One,
6,
e16244.
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P.Slama,
and
D.Geman
(2011).
Identification of family-determining residues in PHD fingers.
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Nucleic Acids Res,
39,
1666-1679.
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Q.Jin,
L.R.Yu,
L.Wang,
Z.Zhang,
L.H.Kasper,
J.E.Lee,
C.Wang,
P.K.Brindle,
S.Y.Dent,
and
K.Ge
(2011).
Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation.
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EMBO J,
30,
249-262.
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R.T.Taniguchi,
and
M.S.Anderson
(2011).
The role of Aire in clonal selection.
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Immunol Cell Biol,
89,
40-44.
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S.M.Fuchs,
K.Krajewski,
R.W.Baker,
V.L.Miller,
and
B.D.Strahl
(2011).
Influence of combinatorial histone modifications on antibody and effector protein recognition.
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Curr Biol,
21,
53-58.
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V.Sapountzi,
and
J.Côté
(2011).
MYST-family histone acetyltransferases: beyond chromatin.
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Cell Mol Life Sci,
68,
1147-1156.
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A.Bettegowda,
and
M.F.Wilkinson
(2010).
Transcription and post-transcriptional regulation of spermatogenesis.
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Philos Trans R Soc Lond B Biol Sci,
365,
1637-1651.
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A.Chruscicki,
V.E.Macdonald,
B.P.Young,
C.J.Loewen,
and
L.J.Howe
(2010).
Critical determinants for chromatin binding by Saccharomyces cerevisiae Yng1 exist outside of the plant homeodomain finger.
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Genetics,
185,
469-477.
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A.S.Koh,
R.E.Kingston,
C.Benoist,
and
D.Mathis
(2010).
Global relevance of Aire binding to hypomethylated lysine-4 of histone-3.
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Proc Natl Acad Sci U S A,
107,
13016-13021.
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H.Furuhashi,
and
W.G.Kelly
(2010).
The epigenetics of germ-line immortality: lessons from an elegant model system.
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Dev Growth Differ,
52,
527-532.
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H.Lin,
Y.Wang,
Y.Wang,
F.Tian,
P.Pu,
Y.Yu,
H.Mao,
Y.Yang,
P.Wang,
L.Hu,
Y.Lin,
Y.Liu,
Y.Xu,
and
C.D.Chen
(2010).
Coordinated regulation of active and repressive histone methylations by a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans.
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Cell Res,
20,
899-907.
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J.E.Halley,
T.Kaplan,
A.Y.Wang,
M.S.Kobor,
and
J.Rine
(2010).
Roles for H2A.Z and its acetylation in GAL1 transcription and gene induction, but not GAL1-transcriptional memory.
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PLoS Biol,
8,
e1000401.
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J.S.Lee,
E.Smith,
and
A.Shilatifard
(2010).
The language of histone crosstalk.
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Cell,
142,
682-685.
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K.Baar
(2010).
Epigenetic control of skeletal muscle fibre type.
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Acta Physiol (Oxf),
199,
477-487.
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K.L.Yap,
and
M.M.Zhou
(2010).
Keeping it in the family: diverse histone recognition by conserved structural folds.
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Crit Rev Biochem Mol Biol,
45,
488-505.
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N.L.Young,
P.A.Dimaggio,
and
B.A.Garcia
(2010).
The significance, development and progress of high-throughput combinatorial histone code analysis.
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Cell Mol Life Sci,
67,
3983-4000.
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S.Desiderio
(2010).
Temporal and spatial regulatory functions of the V(D)J recombinase.
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Semin Immunol,
22,
362-369.
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S.Park,
U.Osmers,
G.Raman,
R.H.Schwantes,
M.O.Diaz,
and
J.H.Bushweller
(2010).
The PHD3 domain of MLL acts as a CYP33-regulated switch between MLL-mediated activation and repression .
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Biochemistry,
49,
6576-6586.
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PDB codes:
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S.Zheng,
J.J.Wyrick,
and
J.C.Reese
(2010).
Novel trans-tail regulation of H2B ubiquitylation and H3K4 methylation by the N terminus of histone H2A.
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Mol Cell Biol,
30,
3635-3645.
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A.Gradolatto,
S.K.Smart,
S.Byrum,
L.P.Blair,
R.S.Rogers,
E.A.Kolar,
H.Lavender,
S.K.Larson,
J.D.Aitchison,
S.D.Taverna,
and
A.J.Tackett
(2009).
A noncanonical bromodomain in the AAA ATPase protein Yta7 directs chromosomal positioning and barrier chromatin activity.
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Mol Cell Biol,
29,
4604-4611.
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B.Gu,
P.Sun,
Y.Yuan,
R.C.Moraes,
A.Li,
A.Teng,
A.Agrawal,
C.Rhéaume,
V.Bilanchone,
J.M.Veltmaat,
K.Takemaru,
S.Millar,
E.Y.Lee,
M.T.Lewis,
B.Li,
and
X.Dai
(2009).
Pygo2 expands mammary progenitor cells by facilitating histone H3 K4 methylation.
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J Cell Biol,
185,
811-826.
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C.A.Musselman,
R.E.Mansfield,
A.L.Garske,
F.Davrazou,
A.H.Kwan,
S.S.Oliver,
H.O'Leary,
J.M.Denu,
J.P.Mackay,
and
T.G.Kutateladze
(2009).
Binding of the CHD4 PHD2 finger to histone H3 is modulated by covalent modifications.
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Biochem J,
423,
179-187.
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D.Mathis,
and
C.Benoist
(2009).
Aire.
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Annu Rev Immunol,
27,
287-312.
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D.W.Chan,
Y.Wang,
M.Wu,
J.Wong,
J.Qin,
and
Y.Zhao
(2009).
Unbiased proteomic screen for binding proteins to modified lysines on histone H3.
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Proteomics,
9,
2343-2354.
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F.Chignola,
M.Gaetani,
A.Rebane,
T.Org,
L.Mollica,
C.Zucchelli,
A.Spitaleri,
V.Mannella,
P.Peterson,
and
G.Musco
(2009).
The solution structure of the first PHD finger of autoimmune regulator in complex with non-modified histone H3 tail reveals the antagonistic role of H3R2 methylation.
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Nucleic Acids Res,
37,
2951-2961.
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PDB code:
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F.Pryde,
D.Jain,
A.Kerr,
R.Curley,
F.R.Mariotti,
and
M.Vogelauer
(2009).
H3 k36 methylation helps determine the timing of cdc45 association with replication origins.
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PLoS One,
4,
e5882.
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G.G.Wang,
J.Song,
Z.Wang,
H.L.Dormann,
F.Casadio,
H.Li,
J.L.Luo,
D.J.Patel,
and
C.D.Allis
(2009).
Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger.
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Nature,
459,
847-851.
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PDB codes:
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J.K.Choi,
and
L.J.Howe
(2009).
Histone acetylation: truth of consequences?
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Biochem Cell Biol,
87,
139-150.
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J.Sebastian,
M.Ravi,
S.Andreuzza,
A.P.Panoli,
M.P.Marimuthu,
and
I.Siddiqi
(2009).
The plant adherin AtSCC2 is required for embryogenesis and sister-chromatid cohesion during meiosis in Arabidopsis.
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Plant J,
59,
1.
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K.S.Champagne,
and
T.G.Kutateladze
(2009).
Structural insight into histone recognition by the ING PHD fingers.
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Curr Drug Targets,
10,
432-441.
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L.Wang,
R.Wuerffel,
S.Feldman,
A.A.Khamlichi,
and
A.L.Kenter
(2009).
S region sequence, RNA polymerase II, and histone modifications create chromatin accessibility during class switch recombination.
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J Exp Med,
206,
1817-1830.
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M.A.Adams-Cioaba,
and
J.Min
(2009).
Structure and function of histone methylation binding proteins.
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Biochem Cell Biol,
87,
93.
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M.Pinskaya,
S.Gourvennec,
and
A.Morillon
(2009).
H3 lysine 4 di- and tri-methylation deposited by cryptic transcription attenuates promoter activation.
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EMBO J,
28,
1697-1707.
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N.L.Young,
P.A.DiMaggio,
M.D.Plazas-Mayorca,
R.C.Baliban,
C.A.Floudas,
and
B.A.Garcia
(2009).
High throughput characterization of combinatorial histone codes.
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Mol Cell Proteomics,
8,
2266-2284.
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O.J.Rando,
and
H.Y.Chang
(2009).
Genome-wide views of chromatin structure.
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Annu Rev Biochem,
78,
245-271.
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S.B.Kremer,
and
D.S.Gross
(2009).
SAGA and Rpd3 chromatin modification complexes dynamically regulate heat shock gene structure and expression.
|
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J Biol Chem,
284,
32914-32931.
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S.K.Smart,
S.G.Mackintosh,
R.D.Edmondson,
S.D.Taverna,
and
A.J.Tackett
(2009).
Mapping the local protein interactome of the NuA3 histone acetyltransferase.
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Protein Sci,
18,
1987-1997.
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S.M.Fuchs,
R.N.Laribee,
and
B.D.Strahl
(2009).
Protein modifications in transcription elongation.
|
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Biochim Biophys Acta,
1789,
26-36.
|
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S.Qin,
Q.Wang,
A.Ray,
G.Wani,
Q.Zhao,
S.R.Bhaumik,
and
A.A.Wani
(2009).
Sem1p and Ubp6p orchestrate telomeric silencing by modulating histone H2B ubiquitination and H3 acetylation.
|
| |
Nucleic Acids Res,
37,
1843-1853.
|
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T.Hung,
O.Binda,
K.S.Champagne,
A.J.Kuo,
K.Johnson,
H.Y.Chang,
M.D.Simon,
T.G.Kutateladze,
and
O.Gozani
(2009).
ING4 mediates crosstalk between histone H3 K4 trimethylation and H3 acetylation to attenuate cellular transformation.
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Mol Cell,
33,
248-256.
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PDB code:
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T.Kim,
and
S.Buratowski
(2009).
Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5' transcribed regions.
|
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Cell,
137,
259-272.
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W.Y.Lee,
D.Lee,
W.I.Chung,
and
C.S.Kwon
(2009).
Arabidopsis ING and Alfin1-like protein families localize to the nucleus and bind to H3K4me3/2 via plant homeodomain fingers.
|
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Plant J,
58,
511-524.
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Y.Hayashi,
T.Senda,
N.Sano,
and
M.Horikoshi
(2009).
Theoretical framework for the histone modification network: modifications in the unstructured histone tails form a robust scale-free network.
|
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Genes Cells,
14,
789-806.
|
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Y.Jin,
A.M.Rodriguez,
and
J.J.Wyrick
(2009).
Genetic and genomewide analysis of simultaneous mutations in acetylated and methylated lysine residues in histone H3 in Saccharomyces cerevisiae.
|
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Genetics,
181,
461-472.
|
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Y.Liu,
L.Zhang,
and
S.Desiderio
(2009).
Temporal and spatial regulation of V(D)J recombination: interactions of extrinsic factors with the RAG complex.
|
| |
Adv Exp Med Biol,
650,
157-165.
|
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A.Gradolatto,
R.S.Rogers,
H.Lavender,
S.D.Taverna,
C.D.Allis,
J.D.Aitchison,
and
A.J.Tackett
(2008).
Saccharomyces cerevisiae Yta7 regulates histone gene expression.
|
| |
Genetics,
179,
291-304.
|
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A.Rada-Iglesias,
A.Ameur,
P.Kapranov,
S.Enroth,
J.Komorowski,
T.R.Gingeras,
and
C.Wadelius
(2008).
Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders.
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Genome Res,
18,
380-392.
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B.A.Garcia,
C.E.Thomas,
N.L.Kelleher,
and
C.A.Mizzen
(2008).
Tissue-specific expression and post-translational modification of histone H3 variants.
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| |
J Proteome Res,
7,
4225-4236.
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E.Borrelli,
E.J.Nestler,
C.D.Allis,
and
P.Sassone-Corsi
(2008).
Decoding the epigenetic language of neuronal plasticity.
|
| |
Neuron,
60,
961-974.
|
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MYSTs mark chromatin for chromosomal functions.
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Aging Cell,
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Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex.
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Mol Cell,
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PDB codes:
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M.Nair,
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D.P.Mishra,
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Nuclear regulator Pygo2 controls spermiogenesis and histone H3 acetylation.
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Dev Biol,
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Molecular architecture of quartet MOZ/MORF histone acetyltransferase complexes.
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Mol Cell Biol,
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ICBP90, a novel methyl K9 H3 binding protein linking protein ubiquitination with heterochromatin formation.
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Histone H3K4me3 binding is required for the DNA repair and apoptotic activities of ING1 tumor suppressor.
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J Mol Biol,
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PDB code:
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J Biol Chem,
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Bioessays,
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A comprehensive library of histone mutants identifies nucleosomal residues required for H3K4 methylation.
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Nat Struct Mol Biol,
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The ING4 tumor suppressor attenuates NF-kappaB activity at the promoters of target genes.
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Mol Cell Biol,
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Cell cycle- and chaperone-mediated regulation of H3K56ac incorporation in yeast.
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PLoS Genet,
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Tethering by lamin A stabilizes and targets the ING1 tumour suppressor.
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Nat Cell Biol,
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RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination.
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Nature,
450,
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PDB code:
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A.J.Ruthenburg,
C.D.Allis,
and
J.Wysocka
(2007).
Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark.
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Mol Cell,
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A.Lafon,
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MYST opportunities for growth control: yeast genes illuminate human cancer gene functions.
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Oncogene,
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Infrequently transcribed long genes depend on the Set2/Rpd3S pathway for accurate transcription.
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Genes Dev,
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Structural basis for lower lysine methylation state-specific readout by MBT repeats of L3MBTL1 and an engineered PHD finger.
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Mol Cell,
28,
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PDB codes:
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I.Abarrategui,
and
M.S.Krangel
(2007).
Noncoding transcription controls downstream promoters to regulate T-cell receptor alpha recombination.
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EMBO J,
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J.A.Latham,
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Nat Struct Mol Biol,
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Ubiquitylation of histone H2B controls RNA polymerase II transcription elongation independently of histone H3 methylation.
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Genes Dev,
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K.Ingvarsdottir,
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Histone H3 K4 demethylation during activation and attenuation of GAL1 transcription in Saccharomyces cerevisiae.
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Mol Cell Biol,
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L.E.Rosaleny,
A.B.Ruiz-García,
J.García-Martínez,
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The Sas3p and Gcn5p histone acetyltransferases are recruited to similar genes.
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Genome Biol,
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Global assessment of combinatorial post-translational modification of core histones in yeast using contemporary mass spectrometry. LYS4 trimethylation correlates with degree of acetylation on the same H3 tail.
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J Biol Chem,
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After a decade of study-ING, a PHD for a versatile family of proteins.
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The fission yeast Jmj2 reverses histone H3 Lysine 4 trimethylation.
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Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing.
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Mol Cell,
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Long-distance combinatorial linkage between methylation and acetylation on histone H3 N termini.
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The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2.
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PDB codes:
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S.Venkatasubrahmanyam,
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Genome-wide, as opposed to local, antisilencing is mediated redundantly by the euchromatic factors Set1 and H2A.Z.
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MOZ and MORF, two large MYSTic HATs in normal and cancer stem cells.
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Oncogene,
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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
codes are
shown on the right.
|
|
Links
