 |
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
|
|
|
|
|
|
|
|
|
|
Structural protein
|
PDB id
|
|
|
|
1kne
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
 |
|
 |
|
 |
|
|
Gene Ontology (GO) functional annotation
|
|
|
|
 |
 |
 |
|
 |
 |
 |
 |
|
 |
|
Cellular component
|
nucleus
|
2 terms
|
 |
|
Biological process
|
chromatin assembly or disassembly
|
1 term
|
 |
|
Biochemical function
|
chromatin binding
|
1 term
|
 |
|
|
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
|
|
|
| |
|
DOI no:
|
Science
295:2080-2083
(2002)
|
|
PubMed id:
|
|
|
|
|
| |
|
Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail.
|
|
S.A.Jacobs,
S.Khorasanizadeh.
|
|
|
|
| |
ABSTRACT
|
|
|
| |
|
The chromodomain of the HP1 family of proteins recognizes histone tails with
specifically methylated lysines. Here, we present structural, energetic, and
mutational analyses of the complex between the Drosophila HP1 chromodomain and
the histone H3 tail with a methyllysine at residue 9, a modification associated
with epigenetic silencing. The histone tail inserts as a beta strand, completing
the beta-sandwich architecture of the chromodomain. The methylammonium group is
caged by three aromatic side chains, whereas adjacent residues form discerning
contacts with one face of the chromodomain. Comparison of dimethyl- and
trimethyllysine-containing complexes suggests a role for cation-pi and van der
Waals interactions, with trimethylation slightly improving the binding affinity.
|
|
|
|
|
| |
Selected figure(s)
|
|
|
| |
 |
 |
|
 |
|
 |
Figure 1.
Fig. 1. Structure of the Drosophila HP1 chromodomain in complex
with MeK9 histone H3 peptide. The PDB accession codes are 1kna
(with Me[2]K7 H3) and 1Kne (with Me[3]K7 H3). (A) Stereodiagram
of the |F[o] - F[c]| "omit" map showing the electron density for
the bound Me[2]K9 H3 peptide (magenta). The chromodomain is in
blue. (B) Comparison of the chromodomain-H3 peptide complex
(red) with the free chromodomain (black) (11) and the free
chromo shadow domain (yellow) (20).
|
 |
Figure 2.
Fig. 2. Specific interactions between the chromodomain and MeK9
H3 tail. (A) Stereodiagram showing the Me[2]K9 (yellow) and
Me[3]K9 (orange) H3 in complex with the chromodomain (blue and
green, respectively). The van der Waals representation
corresponds to the Me[3]K complex. (B) Backbone (left) and
side-chain (right) interactions between Me[2]K9 H3 and
chromodomain. (C) Binding of chromodomain mutants to Me[3]K9 H3
tail. (D) Binding of wild-type chromodomain to point mutants of
Me[3]K9 H3 tail.
|
 |
|
|
|
| |
The above figures are
reprinted
by permission from the AAAs:
Science
(2002,
295,
2080-2083)
copyright 2002.
|
|
| |
Figures were
selected
by the author.
|
|
|
|
|
 |
 |
|
 |
 |
 |
 |
 |
 |
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
 |
| |
PubMed id
|
 |
Reference
|
 |
|
|
|
 |
A.Dhayalan,
R.Tamas,
I.Bock,
A.Tattermusch,
E.Dimitrova,
S.Kudithipudi,
S.Ragozin,
and
A.Jeltsch
(2011).
The ATRX-ADD domain binds to H3 tail peptides and reads the combined methylation state of K4 and K9.
|
| |
Hum Mol Genet, 20,
2195-2203.
|
 |
|
|
|
|
 |
D.L.Mendez,
D.Kim,
M.Chruszcz,
G.E.Stephens,
W.Minor,
S.Khorasanizadeh,
and
S.C.Elgin
(2011).
The HP1a disordered C terminus and chromo shadow domain cooperate to select target peptide partners.
|
| |
Chembiochem, 12,
1084-1096.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
F.Erdel,
K.Müller-Ott,
M.Baum,
M.Wachsmuth,
and
K.Rippe
(2011).
Dissecting chromatin interactions in living cells from protein mobility maps.
|
| |
Chromosome Res, 19,
99.
|
 |
|
|
|
|
 |
J.Xu,
B.Wang,
Y.Wu,
P.Du,
J.Wang,
M.Wang,
C.Yi,
M.Gu,
and
G.Liang
(2011).
Fine mapping and candidate gene analysis of ptgms2-1, the photoperiod-thermo-sensitive genic male sterile gene in rice (Oryza sativa L.).
|
| |
Theor Appl Genet, 122,
365-372.
|
 |
|
|
|
|
 |
L.Kaustov,
H.Ouyang,
M.Amaya,
A.Lemak,
N.Nady,
S.Duan,
G.A.Wasney,
Z.Li,
M.Vedadi,
M.Schapira,
J.Min,
and
C.H.Arrowsmith
(2011).
Recognition and specificity determinants of the human cbx chromodomains.
|
| |
J Biol Chem, 286,
521-529.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
M.Park,
S.Jo,
J.K.Kwon,
J.Park,
J.H.Ahn,
S.Kim,
Y.H.Lee,
T.J.Yang,
C.G.Hur,
B.C.Kang,
B.D.Kim,
and
D.Choi
(2011).
Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements.
|
| |
BMC Genomics, 12,
85.
|
 |
|
|
|
|
 |
P.Voigt,
and
D.Reinberg
(2011).
Histone tails: ideal motifs for probing epigenetics through chemical biology approaches.
|
| |
Chembiochem, 12,
236-252.
|
 |
|
|
|
|
 |
R.A.Varier,
and
H.T.Timmers
(2011).
Histone lysine methylation and demethylation pathways in cancer.
|
| |
Biochim Biophys Acta, 1815,
75-89.
|
 |
|
|
|
|
 |
Y.Chang,
J.R.Horton,
M.T.Bedford,
X.Zhang,
and
X.Cheng
(2011).
Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9: potential effect of phosphorylation on methyl-lysine binding.
|
| |
J Mol Biol, 408,
807-814.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
A.M.Quinn,
M.T.Bedford,
A.Espejo,
A.Spannhoff,
C.P.Austin,
U.Oppermann,
and
A.Simeonov
(2010).
A homogeneous method for investigation of methylation-dependent protein-protein interactions in epigenetics.
|
| |
Nucleic Acids Res, 38,
e11.
|
 |
|
|
|
|
 |
A.Rottach,
C.Frauer,
G.Pichler,
I.M.Bonapace,
F.Spada,
and
H.Leonhardt
(2010).
The multi-domain protein Np95 connects DNA methylation and histone modification.
|
| |
Nucleic Acids Res, 38,
1796-1804.
|
 |
|
|
|
|
 |
B.Xhemalce,
and
T.Kouzarides
(2010).
A chromodomain switch mediated by histone H3 Lys 4 acetylation regulates heterochromatin assembly.
|
| |
Genes Dev, 24,
647-652.
|
 |
|
|
|
|
 |
C.L.Woodcock,
and
R.P.Ghosh
(2010).
Chromatin higher-order structure and dynamics.
|
| |
Cold Spring Harb Perspect Biol, 2,
a000596.
|
 |
|
|
|
|
 |
C.M.Santiveri,
and
M.A.Jiménez
(2010).
Tryptophan residues: Scarce in proteins but strong stabilizers of β-hairpin peptides.
|
| |
Biopolymers, 94,
779-790.
|
 |
|
|
|
|
 |
C.S.Beshara,
C.E.Jones,
K.D.Daze,
B.J.Lilgert,
and
F.Hof
(2010).
A simple calixarene recognizes post-translationally methylated lysine.
|
| |
Chembiochem, 11,
63-66.
|
 |
|
|
|
|
 |
C.Xu,
C.Bian,
W.Yang,
M.Galka,
H.Ouyang,
C.Chen,
W.Qiu,
H.Liu,
A.E.Jones,
F.MacKenzie,
P.Pan,
S.S.Li,
H.Wang,
and
J.Min
(2010).
Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2).
|
| |
Proc Natl Acad Sci U S A, 107,
19266-19271.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
D.Kim,
B.J.Blus,
V.Chandra,
P.Huang,
F.Rastinejad,
and
S.Khorasanizadeh
(2010).
Corecognition of DNA and a methylated histone tail by the MSL3 chromodomain.
|
| |
Nat Struct Mol Biol, 17,
1027-1029.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
D.P.Gavin,
and
R.P.Sharma
(2010).
Histone modifications, DNA methylation, and schizophrenia.
|
| |
Neurosci Biobehav Rev, 34,
882-888.
|
 |
|
|
|
|
 |
J.C.Merrill,
M.H.Kagey,
T.A.Melhuish,
S.E.Powers,
B.J.Zerlanko,
and
D.Wotton
(2010).
Inhibition of CtBP1 activity by Akt-mediated phosphorylation.
|
| |
J Mol Biol, 398,
657-671.
|
 |
|
|
|
|
 |
K.Baar
(2010).
Epigenetic control of skeletal muscle fibre type.
|
| |
Acta Physiol (Oxf), 199,
477-487.
|
 |
|
|
|
|
 |
K.L.Yap,
and
M.M.Zhou
(2010).
Keeping it in the family: diverse histone recognition by conserved structural folds.
|
| |
Crit Rev Biochem Mol Biol, 45,
488-505.
|
 |
|
|
|
|
 |
K.L.Yap,
S.Li,
A.M.Muñoz-Cabello,
S.Raguz,
L.Zeng,
S.Mujtaba,
J.Gil,
M.J.Walsh,
and
M.M.Zhou
(2010).
Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a.
|
| |
Mol Cell, 38,
662-674.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
L.A.Ingerman,
M.E.Cuellar,
and
M.L.Waters
(2010).
A small molecule receptor that selectively recognizes trimethyl lysine in a histone peptide with native protein-like affinity.
|
| |
Chem Commun (Camb), 46,
1839-1841.
|
 |
|
|
|
|
 |
M.Billur,
H.D.Bartunik,
and
P.B.Singh
(2010).
The essential function of HP1 beta: a case of the tail wagging the dog?
|
| |
Trends Biochem Sci, 35,
115-123.
|
 |
|
|
|
|
 |
M.R.Machado,
P.D.Dans,
and
S.Pantano
(2010).
Isoform-specific determinants in the HP1 binding to histone 3: insights from molecular simulations.
|
| |
Amino Acids, 38,
1571-1581.
|
 |
|
|
|
|
 |
M.T.Cooper,
A.W.Conant,
and
J.A.Kennison
(2010).
Molecular genetic analysis of Chd3 and polytene chromosome region 76B-D in Drosophila melanogaster.
|
| |
Genetics, 185,
811-822.
|
 |
|
|
|
|
 |
S.Falk,
S.Ravaud,
J.Koch,
and
I.Sinning
(2010).
The C terminus of the Alb3 membrane insertase recruits cpSRP43 to the thylakoid membrane.
|
| |
J Biol Chem, 285,
5954-5962.
|
 |
|
|
|
|
 |
T.K.Barth,
and
A.Imhof
(2010).
Fast signals and slow marks: the dynamics of histone modifications.
|
| |
Trends Biochem Sci, 35,
618-626.
|
 |
|
|
|
|
 |
X.Lu,
and
S.J.Triezenberg
(2010).
Chromatin assembly on herpes simplex virus genomes during lytic infection.
|
| |
Biochim Biophys Acta, 1799,
217-222.
|
 |
|
|
|
|
 |
Y.Sun,
X.Jiang,
and
B.D.Price
(2010).
Tip60: connecting chromatin to DNA damage signaling.
|
| |
Cell Cycle, 9,
930-936.
|
 |
|
|
|
|
 |
A.G.Chatterjee,
Y.E.Leem,
F.D.Kelly,
and
H.L.Levin
(2009).
The chromodomain of Tf1 integrase promotes binding to cDNA and mediates target site selection.
|
| |
J Virol, 83,
2675-2685.
|
 |
|
|
|
|
 |
A.G.Muntean,
and
J.L.Hess
(2009).
Epigenetic dysregulation in cancer.
|
| |
Am J Pathol, 175,
1353-1361.
|
 |
|
|
|
|
 |
A.J.Riemen,
and
M.L.Waters
(2009).
Design of highly stabilized beta-hairpin peptides through cation-pi interactions of lysine and n-methyllysine with an aromatic pocket.
|
| |
Biochemistry, 48,
1525-1531.
|
 |
|
|
|
|
 |
B.Weber,
and
T.Schmidt
(2009).
Nested Ty3-gypsy retrotransposons of a single Beta procumbens centromere contain a putative chromodomain.
|
| |
Chromosome Res, 17,
379-396.
|
 |
|
|
|
|
 |
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.
|
| |
Biochem J, 423,
179-187.
|
 |
|
|
|
|
 |
C.A.Musselman,
and
T.G.Kutateladze
(2009).
PHD fingers: epigenetic effectors and potential drug targets.
|
| |
Mol Interv, 9,
314-323.
|
 |
|
|
|
|
 |
C.M.Koch,
M.Honemann-Capito,
D.Egger-Adam,
and
A.Wodarz
(2009).
Windei, the Drosophila homolog of mAM/MCAF1, is an essential cofactor of the H3K9 methyl transferase dSETDB1/Eggless in germ line development.
|
| |
PLoS Genet, 5,
e1000644.
|
 |
|
|
|
|
 |
D.Vermaak,
and
H.S.Malik
(2009).
Multiple roles for heterochromatin protein 1 genes in Drosophila.
|
| |
Annu Rev Genet, 43,
467-492.
|
 |
|
|
|
|
 |
E.Hallacli,
and
A.Akhtar
(2009).
X chromosomal regulation in flies: when less is more.
|
| |
Chromosome Res, 17,
603-619.
|
 |
|
|
|
|
 |
E.I.Campos,
and
D.Reinberg
(2009).
Histones: annotating chromatin.
|
| |
Annu Rev Genet, 43,
559-599.
|
 |
|
|
|
|
 |
G.LeRoy,
J.T.Weston,
B.M.Zee,
N.L.Young,
M.D.Plazas-Mayorca,
and
B.A.Garcia
(2009).
Heterochromatin protein 1 is extensively decorated with histone code-like post-translational modifications.
|
| |
Mol Cell Proteomics, 8,
2432-2442.
|
 |
|
|
|
|
 |
H.Franz,
K.Mosch,
S.Soeroes,
H.Urlaub,
and
W.Fischle
(2009).
Multimerization and H3K9me3 binding are required for CDYL1b heterochromatin association.
|
| |
J Biol Chem, 284,
35049-35059.
|
 |
|
|
|
|
 |
H.R.Salzler,
J.M.Davidson,
N.D.Montgomery,
and
R.J.Duronio
(2009).
Loss of the histone pre-mRNA processing factor stem-loop binding protein in Drosophila causes genomic instability and impaired cellular proliferation.
|
| |
PLoS One, 4,
e8168.
|
 |
|
|
|
|
 |
J.Abel,
R.Eskeland,
G.D.Raffa,
E.Kremmer,
and
A.Imhof
(2009).
Drosophila HP1c is regulated by an auto-regulatory feedback loop through its binding partner Woc.
|
| |
PLoS ONE, 4,
e5089.
|
 |
|
|
|
|
 |
J.Eryilmaz,
P.Pan,
M.F.Amaya,
A.Allali-Hassani,
A.Dong,
M.A.Adams-Cioaba,
F.Mackenzie,
M.Vedadi,
and
J.Min
(2009).
Structural studies of a four-MBT repeat protein MBTD1.
|
| |
PLoS One, 4,
e7274.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
J.K.Kim,
M.Samaranayake,
and
S.Pradhan
(2009).
Epigenetic mechanisms in mammals.
|
| |
Cell Mol Life Sci, 66,
596-612.
|
 |
|
|
|
|
 |
J.M.Gottesfeld,
and
M.Pandolfo
(2009).
Development of histone deacetylase inhibitors as therapeutics for neurological disease.
|
| |
Future Neurol, 4,
775-784.
|
 |
|
|
|
|
 |
K.Pérez-Toledo,
A.P.Rojas-Meza,
L.Mancio-Silva,
N.A.Hernández-Cuevas,
D.M.Delgadillo,
M.Vargas,
S.Martínez-Calvillo,
A.Scherf,
and
R.Hernandez-Rivas
(2009).
Plasmodium falciparum heterochromatin protein 1 binds to tri-methylated histone 3 lysine 9 and is linked to mutually exclusive expression of var genes.
|
| |
Nucleic Acids Res, 37,
2596-2606.
|
 |
|
|
|
|
 |
K.P.Müller,
F.Erdel,
M.Caudron-Herger,
C.Marth,
B.D.Fodor,
M.Richter,
M.Scaranaro,
J.Beaudouin,
M.Wachsmuth,
and
K.Rippe
(2009).
Multiscale analysis of dynamics and interactions of heterochromatin protein 1 by fluorescence fluctuation microscopy.
|
| |
Biophys J, 97,
2876-2885.
|
 |
|
|
|
|
 |
K.S.Champagne,
and
T.G.Kutateladze
(2009).
Structural insight into histone recognition by the ING PHD fingers.
|
| |
Curr Drug Targets, 10,
432-441.
|
 |
|
|
|
|
 |
M.A.Adams-Cioaba,
and
J.Min
(2009).
Structure and function of histone methylation binding proteins.
|
| |
Biochem Cell Biol, 87,
93.
|
 |
|
|
|
|
 |
M.Bühler,
and
S.M.Gasser
(2009).
Silent chromatin at the middle and ends: lessons from yeasts.
|
| |
EMBO J, 28,
2149-2161.
|
 |
|
|
|
|
 |
M.S.Luijsterburg,
C.Dinant,
H.Lans,
J.Stap,
E.Wiernasz,
S.Lagerwerf,
D.O.Warmerdam,
M.Lindh,
M.C.Brink,
J.W.Dobrucki,
J.A.Aten,
M.I.Fousteri,
G.Jansen,
N.P.Dantuma,
W.Vermeulen,
L.H.Mullenders,
A.B.Houtsmuller,
P.J.Verschure,
and
R.van Driel
(2009).
Heterochromatin protein 1 is recruited to various types of DNA damage.
|
| |
J Cell Biol, 185,
577-586.
|
 |
|
|
|
|
 |
M.Sinha,
and
C.L.Peterson
(2009).
Chromatin dynamics during repair of chromosomal DNA double-strand breaks.
|
| |
Epigenomics, 1,
371-385.
|
 |
|
|
|
|
 |
M.T.Hayashi,
T.S.Takahashi,
T.Nakagawa,
J.Nakayama,
and
H.Masukata
(2009).
The heterochromatin protein Swi6/HP1 activates replication origins at the pericentromeric region and silent mating-type locus.
|
| |
Nat Cell Biol, 11,
357-362.
|
 |
|
|
|
|
 |
O.Novikova
(2009).
Chromodomains and LTR retrotransposons in plants.
|
| |
Commun Integr Biol, 2,
158-162.
|
 |
|
|
|
|
 |
P.G.Greciano,
M.F.Ruiz,
L.Kremer,
and
C.Goday
(2009).
Two new chromodomain-containing proteins that associate with heterochromatin in Sciara coprophila chromosomes.
|
| |
Chromosoma, 118,
361-376.
|
 |
|
|
|
|
 |
P.V.Peña,
C.A.Musselman,
A.J.Kuo,
O.Gozani,
and
T.G.Kutateladze
(2009).
NMR assignments and histone specificity of the ING2 PHD finger.
|
| |
Magn Reson Chem, 47,
352-358.
|
 |
|
|
|
|
 |
R.Sanchez,
and
M.M.Zhou
(2009).
The role of human bromodomains in chromatin biology and gene transcription.
|
| |
Curr Opin Drug Discov Devel, 12,
659-665.
|
 |
|
|
|
|
 |
S.M.Fuchs,
R.N.Laribee,
and
B.D.Strahl
(2009).
Protein modifications in transcription elongation.
|
| |
Biochim Biophys Acta, 1789,
26-36.
|
 |
|
|
|
|
 |
T.Gao,
R.E.Collins,
J.R.Horton,
X.Zhang,
R.Zhang,
A.Dhayalan,
R.Tamas,
A.Jeltsch,
and
X.Cheng
(2009).
The ankyrin repeat domain of Huntingtin interacting protein 14 contains a surface aromatic cage, a potential site for methyl-lysine binding.
|
| |
Proteins, 76,
772-777.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
T.M.Spektor,
and
J.C.Rice
(2009).
Identification and characterization of posttranslational modification-specific binding proteins in vivo by mammalian tethered catalysis.
|
| |
Proc Natl Acad Sci U S A, 106,
14808-14813.
|
 |
|
|
|
|
 |
T.Neff,
and
S.A.Armstrong
(2009).
Chromatin maps, histone modifications and leukemia.
|
| |
Leukemia, 23,
1243-1251.
|
 |
|
|
|
|
 |
T.S.Kang,
and
R.M.Kini
(2009).
Structural determinants of protein folding.
|
| |
Cell Mol Life Sci, 66,
2341-2361.
|
 |
|
|
|
|
 |
T.Schalch,
G.Job,
V.J.Noffsinger,
S.Shanker,
C.Kuscu,
L.Joshua-Tor,
and
J.F.Partridge
(2009).
High-affinity binding of Chp1 chromodomain to K9 methylated histone H3 is required to establish centromeric heterochromatin.
|
| |
Mol Cell, 34,
36-46.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
V.Exner,
E.Aichinger,
H.Shu,
T.Wildhaber,
P.Alfarano,
A.Caflisch,
W.Gruissem,
C.Köhler,
and
L.Hennig
(2009).
The chromodomain of LIKE HETEROCHROMATIN PROTEIN 1 is essential for H3K27me3 binding and function during Arabidopsis development.
|
| |
PLoS ONE, 4,
e5335.
|
 |
|
|
|
|
 |
Y.Guo,
N.Nady,
C.Qi,
A.Allali-Hassani,
H.Zhu,
P.Pan,
M.A.Adams-Cioaba,
M.F.Amaya,
A.Dong,
M.Vedadi,
M.Schapira,
R.J.Read,
C.H.Arrowsmith,
and
J.Min
(2009).
Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2.
|
| |
Nucleic Acids Res, 37,
2204-2210.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
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.
|
| |
Genes Cells, 14,
789-806.
|
 |
|
|
|
|
 |
Y.Sun,
X.Jiang,
Y.Xu,
M.K.Ayrapetov,
L.A.Moreau,
J.R.Whetstine,
and
B.D.Price
(2009).
Histone H3 methylation links DNA damage detection to activation of the tumour suppressor Tip60.
|
| |
Nat Cell Biol, 11,
1376-1382.
|
 |
|
|
|
|
 |
Z.Lu,
J.Lai,
and
Y.Zhang
(2009).
Importance of charge independent effects in readout of the trimethyllysine mark by HP1 chromodomain.
|
| |
J Am Chem Soc, 131,
14928-14931.
|
 |
|
|
|
|
 |
B.Sun,
J.Hong,
P.Zhang,
X.Dong,
X.Shen,
D.Lin,
and
J.Ding
(2008).
Molecular basis of the interaction of Saccharomyces cerevisiae Eaf3 chromo domain with methylated H3K36.
|
| |
J Biol Chem, 283,
36504-36512.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
G.LeRoy,
B.Rickards,
and
S.J.Flint
(2008).
The double bromodomain proteins Brd2 and Brd3 couple histone acetylation to transcription.
|
| |
Mol Cell, 30,
51-60.
|
 |
|
|
|
|
 |
H.van Ingen,
F.M.van Schaik,
H.Wienk,
J.Ballering,
H.Rehmann,
A.C.Dechesne,
J.A.Kruijzer,
R.M.Liskamp,
H.T.Timmers,
and
R.Boelens
(2008).
Structural insight into the recognition of the H3K4me3 mark by the TFIID subunit TAF3.
|
| |
Structure, 16,
1245-1256.
|
 |
|
|
|
|
 |
J.Lee,
J.R.Thompson,
M.V.Botuyan,
and
G.Mer
(2008).
Distinct binding modes specify the recognition of methylated histones H3K4 and H4K20 by JMJD2A-tudor.
|
| |
Nat Struct Mol Biol, 15,
109-111.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
J.Lukas,
and
J.Bartek
(2008).
DNA damage: a histone-code mediator leaves the stage.
|
| |
Nat Struct Mol Biol, 15,
430-432.
|
 |
|
|
|
|
 |
J.Zlatanova,
C.Seebart,
and
M.Tomschik
(2008).
The linker-protein network: control of nucleosomal DNA accessibility.
|
| |
Trends Biochem Sci, 33,
247-253.
|
 |
|
|
|
|
 |
K.Zhang,
K.Mosch,
W.Fischle,
and
S.I.Grewal
(2008).
Roles of the Clr4 methyltransferase complex in nucleation, spreading and maintenance of heterochromatin.
|
| |
Nat Struct Mol Biol, 15,
381-388.
|
 |
|
|
|
|
 |
M.C.Shun,
Y.Botbol,
X.Li,
F.Di Nunzio,
J.E.Daigle,
N.Yan,
J.Lieberman,
M.Lavigne,
and
A.Engelman
(2008).
Identification and characterization of PWWP domain residues critical for LEDGF/p75 chromatin binding and human immunodeficiency virus type 1 infectivity.
|
| |
J Virol, 82,
11555-11567.
|
 |
|
|
|
|
 |
M.El Gazzar,
B.K.Yoza,
X.Chen,
J.Hu,
G.A.Hawkins,
and
C.E.McCall
(2008).
G9a and HP1 couple histone and DNA methylation to TNFalpha transcription silencing during endotoxin tolerance.
|
| |
J Biol Chem, 283,
32198-32208.
|
 |
|
|
|
|
 |
M.M.Brent,
and
R.Marmorstein
(2008).
Ankyrin for methylated lysines.
|
| |
Nat Struct Mol Biol, 15,
221-222.
|
 |
|
|
|
|
 |
M.R.Motamedi,
E.J.Hong,
X.Li,
S.Gerber,
C.Denison,
S.Gygi,
and
D.Moazed
(2008).
HP1 proteins form distinct complexes and mediate heterochromatic gene silencing by nonoverlapping mechanisms.
|
| |
Mol Cell, 32,
778-790.
|
 |
|
|
|
|
 |
M.Sadaie,
R.Kawaguchi,
Y.Ohtani,
F.Arisaka,
K.Tanaka,
K.Shirahige,
and
J.Nakayama
(2008).
Balance between distinct HP1 family proteins controls heterochromatin assembly in fission yeast.
|
| |
Mol Cell Biol, 28,
6973-6988.
|
 |
|
|
|
|
 |
N.Ayoub,
A.D.Jeyasekharan,
J.A.Bernal,
and
A.R.Venkitaraman
(2008).
HP1-beta mobilization promotes chromatin changes that initiate the DNA damage response.
|
| |
Nature, 453,
682-686.
|
 |
|
|
|
|
 |
N.Kalakonda,
W.Fischle,
P.Boccuni,
N.Gurvich,
R.Hoya-Arias,
X.Zhao,
Y.Miyata,
D.Macgrogan,
J.Zhang,
J.K.Sims,
J.C.Rice,
and
S.D.Nimer
(2008).
Histone H4 lysine 20 monomethylation promotes transcriptional repression by L3MBTL1.
|
| |
Oncogene, 27,
4293-4304.
|
 |
|
|
|
|
 |
N.Nady,
J.Min,
M.S.Kareta,
F.Chédin,
and
C.H.Arrowsmith
(2008).
A SPOT on the chromatin landscape? Histone peptide arrays as a tool for epigenetic research.
|
| |
Trends Biochem Sci, 33,
305-313.
|
 |
|
|
|
|
 |
P.Hu,
S.Wang,
and
Y.Zhang
(2008).
How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by Ab initio QM/MM molecular dynamics simulations.
|
| |
J Am Chem Soc, 130,
3806-3813.
|
 |
|
|
|
|
 |
P.Karagianni,
L.Amazit,
J.Qin,
and
J.Wong
(2008).
ICBP90, a novel methyl K9 H3 binding protein linking protein ubiquitination with heterochromatin formation.
|
| |
Mol Cell Biol, 28,
705-717.
|
 |
|
|
|
|
 |
P.Rathert,
A.Dhayalan,
M.Murakami,
X.Zhang,
R.Tamas,
R.Jurkowska,
Y.Komatsu,
Y.Shinkai,
X.Cheng,
and
A.Jeltsch
(2008).
Protein lysine methyltransferase G9a acts on non-histone targets.
|
| |
Nat Chem Biol, 4,
344-346.
|
 |
|
|
|
|
 |
R.A.Laskowski,
and
J.M.Thornton
(2008).
Understanding the molecular machinery of genetics through 3D structures.
|
| |
Nat Rev Genet, 9,
141-151.
|
 |
|
|
|
|
 |
R.Van Duyne,
R.Easley,
W.Wu,
R.Berro,
C.Pedati,
Z.Klase,
K.Kehn-Hall,
E.K.Flynn,
D.E.Symer,
and
F.Kashanchi
(2008).
Lysine methylation of HIV-1 Tat regulates transcriptional activity of the viral LTR.
|
| |
Retrovirology, 5,
40.
|
 |
|
|
|
|
 |
T.Iida,
J.Nakayama,
and
D.Moazed
(2008).
siRNA-mediated heterochromatin establishment requires HP1 and is associated with antisense transcription.
|
| |
Mol Cell, 31,
178-189.
|
 |
|
|
|
|
 |
T.J.Kang,
S.Yuzawa,
and
H.Suga
(2008).
Expression of histone H3 tails with combinatorial lysine modifications under the reprogrammed genetic code for the investigation on epigenetic markers.
|
| |
Chem Biol, 15,
1166-1174.
|
 |
|
|
|
|
 |
W.Fischle,
H.Franz,
S.A.Jacobs,
C.D.Allis,
and
S.Khorasanizadeh
(2008).
Specificity of the chromodomain Y chromosome family of chromodomains for lysine-methylated ARK(S/T) motifs.
|
| |
J Biol Chem, 283,
19626-19635.
|
 |
|
|
|
|
 |
X.Gao,
Y.Hou,
H.Ebina,
H.L.Levin,
and
D.F.Voytas
(2008).
Chromodomains direct integration of retrotransposons to heterochromatin.
|
| |
Genome Res, 18,
359-369.
|
 |
|
|
|
|
 |
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.
|
| |
Mol Cell, 25,
15-30.
|
 |
|
|
|
|
 |
A.M.Johansson,
P.Stenberg,
F.Pettersson,
and
J.Larsson
(2007).
POF and HP1 Bind Expressed Exons, Suggesting a Balancing Mechanism for Gene Regulation.
|
| |
PLoS Genet, 3,
e209.
|
 |
|
|
|
|
 |
C.C.Yuan,
X.Zhao,
L.Florens,
S.K.Swanson,
M.P.Washburn,
and
N.Hernandez
(2007).
CHD8 associates with human Staf and contributes to efficient U6 RNA polymerase III transcription.
|
| |
Mol Cell Biol, 27,
8729-8738.
|
 |
|
|
|
|
 |
C.Grimm,
A.G.de Ayala Alonso,
V.Rybin,
U.Steuerwald,
N.Ly-Hartig,
W.Fischle,
J.Müller,
and
C.W.Müller
(2007).
Structural and functional analyses of methyl-lysine binding by the malignant brain tumour repeat protein Sex comb on midleg.
|
| |
EMBO Rep, 8,
1031-1037.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
E.Bártová,
J.Pacherník,
A.Kozubík,
and
S.Kozubek
(2007).
Differentiation-specific association of HP1alpha and HP1beta with chromocentres is correlated with clustering of TIF1beta at these sites.
|
| |
Histochem Cell Biol, 127,
375-388.
|
 |
|
|
|
|
 |
E.de Wit,
F.Greil,
and
B.van Steensel
(2007).
High-resolution mapping reveals links of HP1 with active and inactive chromatin components.
|
| |
PLoS Genet, 3,
e38.
|
 |
|
|
|
|
 |
F.Greil,
E.de Wit,
H.J.Bussemaker,
and
B.van Steensel
(2007).
HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila.
|
| |
EMBO J, 26,
741-751.
|
 |
|
|
|
|
 |
F.Lan,
R.E.Collins,
R.De Cegli,
R.Alpatov,
J.R.Horton,
X.Shi,
O.Gozani,
X.Cheng,
and
Y.Shi
(2007).
Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression.
|
| |
Nature, 448,
718-722.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
F.Turck,
F.Roudier,
S.Farrona,
M.L.Martin-Magniette,
E.Guillaume,
N.Buisine,
S.Gagnot,
R.A.Martienssen,
G.Coupland,
and
V.Colot
(2007).
Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27.
|
| |
PLoS Genet, 3,
e86.
|
 |
|
|
|
|
 |
H.Li,
W.Fischle,
W.Wang,
E.M.Duncan,
L.Liang,
S.Murakami-Ishibe,
C.D.Allis,
and
D.J.Patel
(2007).
Structural basis for lower lysine methylation state-specific readout by MBT repeats of L3MBTL1 and an engineered PHD finger.
|
| |
Mol Cell, 28,
677-691.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
J.Dai,
W.Xie,
T.L.Brady,
J.Gao,
and
D.F.Voytas
(2007).
Phosphorylation regulates integration of the yeast Ty5 retrotransposon into heterochromatin.
|
| |
Mol Cell, 27,
289-299.
|
 |
|
|
|
|
 |
J.F.Couture,
E.Collazo,
P.A.Ortiz-Tello,
J.S.Brunzelle,
and
R.C.Trievel
(2007).
Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase.
|
| |
Nat Struct Mol Biol, 14,
689-695.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
J.M.Holaska,
and
K.L.Wilson
(2007).
An emerin "proteome": purification of distinct emerin-containing complexes from HeLa cells suggests molecular basis for diverse roles including gene regulation, mRNA splicing, signaling, mechanosensing, and nuclear architecture.
|
| |
Biochemistry, 46,
8897-8908.
|
 |
|
|
|
|
 |
J.Mateos-Langerak,
M.C.Brink,
M.S.Luijsterburg,
I.van der Kraan,
R.van Driel,
and
P.J.Verschure
(2007).
Pericentromeric heterochromatin domains are maintained without accumulation of HP1.
|
| |
Mol Biol Cell, 18,
1464-1471.
|
 |
|
|
|
|
 |
J.Min,
A.Allali-Hassani,
N.Nady,
C.Qi,
H.Ouyang,
Y.Liu,
F.MacKenzie,
M.Vedadi,
and
C.H.Arrowsmith
(2007).
L3MBTL1 recognition of mono- and dimethylated histones.
|
| |
Nat Struct Mol Biol, 14,
1229-1230.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
K.K.Lee,
and
J.L.Workman
(2007).
Histone acetyltransferase complexes: one size doesn't fit all.
|
| |
Nat Rev Mol Cell Biol, 8,
284-295.
|
 |
|
|
|
|
 |
M.Kato,
Y.Kato,
M.Nishida,
T.Hayakawa,
T.Haraguchi,
Y.Hiraoka,
Y.H Inoue,
and
M.Yamaguchi
(2007).
Functional domain analysis of human HP1 isoforms in Drosophila.
|
| |
Cell Struct Funct, 32,
57-67.
|
 |
|
|
|
|
 |
N.Shaw,
M.Zhao,
C.Cheng,
H.Xu,
J.Saarikettu,
Y.Li,
Y.Da,
Z.Yao,
O.Silvennoinen,
J.Yang,
Z.J.Liu,
B.C.Wang,
and
Z.Rao
(2007).
The multifunctional human p100 protein 'hooks' methylated ligands.
|
| |
Nat Struct Mol Biol, 14,
779-784.
|
 |
|
|
|
|
 |
P.Sabbattini,
C.Canzonetta,
M.Sjoberg,
S.Nikic,
A.Georgiou,
G.Kemball-Cook,
H.W.Auner,
and
N.Dillon
(2007).
A novel role for the Aurora B kinase in epigenetic marking of silent chromatin in differentiated postmitotic cells.
|
| |
EMBO J, 26,
4657-4669.
|
 |
|
|
|
|
 |
P.Trojer,
G.Li,
R.J.Sims,
A.Vaquero,
N.Kalakonda,
P.Boccuni,
D.Lee,
H.Erdjument-Bromage,
P.Tempst,
S.D.Nimer,
Y.H.Wang,
and
D.Reinberg
(2007).
L3MBTL1, a histone-methylation-dependent chromatin lock.
|
| |
Cell, 129,
915-928.
|
 |
|
|
|
|
 |
R.Eskeland,
A.Eberharter,
and
A.Imhof
(2007).
HP1 binding to chromatin methylated at H3K9 is enhanced by auxiliary factors.
|
| |
Mol Cell Biol, 27,
453-465.
|
 |
|
|
|
|
 |
R.K.Dunn,
and
R.E.Kingston
(2007).
Gene regulation in the postgenomic era: technology takes the wheel.
|
| |
Mol Cell, 28,
708-714.
|
 |
|
|
|
|
 |
R.M.Hughes,
K.R.Wiggins,
S.Khorasanizadeh,
and
M.L.Waters
(2007).
Recognition of trimethyllysine by a chromodomain is not driven by the hydrophobic effect.
|
| |
Proc Natl Acad Sci U S A, 104,
11184-11188.
|
 |
|
|
|
|
 |
S.C.Sampath,
I.Marazzi,
K.L.Yap,
S.C.Sampath,
A.N.Krutchinsky,
I.Mecklenbräuker,
A.Viale,
E.Rudensky,
M.M.Zhou,
B.T.Chait,
and
A.Tarakhovsky
(2007).
Methylation of a histone mimic within the histone methyltransferase G9a regulates protein complex assembly.
|
| |
Mol Cell, 27,
596-608.
|
 |
|
|
|
|
 |
S.D.Taverna,
H.Li,
A.J.Ruthenburg,
C.D.Allis,
and
D.J.Patel
(2007).
How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers.
|
| |
Nat Struct Mol Biol, 14,
1025-1040.
|
 |
|
|
|
|
 |
S.Lall
(2007).
Primers on chromatin.
|
| |
Nat Struct Mol Biol, 14,
1110-1115.
|
 |
|
|
|
|
 |
S.M.Biros,
and
J.Rebek
(2007).
Structure and binding properties of water-soluble cavitands and capsules.
|
| |
Chem Soc Rev, 36,
93.
|
 |
|
|
|
|
 |
S.R.Patel,
D.Kim,
I.Levitan,
and
G.R.Dressler
(2007).
The BRCT-domain containing protein PTIP links PAX2 to a histone H3, lysine 4 methyltransferase complex.
|
| |
Dev Cell, 13,
580-592.
|
 |
|
|
|
|
 |
S.R.Schulze,
and
L.L.Wallrath
(2007).
Gene regulation by chromatin structure: paradigms established in Drosophila melanogaster.
|
| |
Annu Rev Entomol, 52,
171-192.
|
 |
|
|
|
|
 |
S.Ramón-Maiques,
A.J.Kuo,
D.Carney,
A.G.Matthews,
M.A.Oettinger,
O.Gozani,
and
W.Yang
(2007).
The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2.
|
| |
Proc Natl Acad Sci U S A, 104,
18993-18998.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
S.Rana,
B.Kundu,
and
S.Durani
(2007).
A mixed-alpha,beta miniprotein stereochemically reprogrammed to high-binding affinity for acetylcholine.
|
| |
Biopolymers, 87,
231-243.
|
 |
|
|
|
|
 |
S.Wu,
R.C.Trievel,
and
J.C.Rice
(2007).
Human SFMBT is a transcriptional repressor protein that selectively binds the N-terminal tail of histone H3.
|
| |
FEBS Lett, 581,
3289-3296.
|
 |
|
|
|
|
 |
X.Cheng,
and
X.Zhang
(2007).
Structural dynamics of protein lysine methylation and demethylation.
|
| |
Mutat Res, 618,
102-115.
|
 |
|
|
|
|
 |
Z.Chen,
J.Zang,
J.Kappler,
X.Hong,
F.Crawford,
Q.Wang,
F.Lan,
C.Jiang,
J.Whetstine,
S.Dai,
K.Hansen,
Y.Shi,
and
G.Zhang
(2007).
Structural basis of the recognition of a methylated histone tail by JMJD2A.
|
| |
Proc Natl Acad Sci U S A, 104,
10818-10823.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
A.J.Ruthenburg,
W.Wang,
D.M.Graybosch,
H.Li,
C.D.Allis,
D.J.Patel,
and
G.L.Verdine
(2006).
Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex.
|
| |
Nat Struct Mol Biol, 13,
704-712.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
A.Morillon
(2006).
Is histone loss a common feature of DNA metabolism regulation?
|
| |
Biochem Cell Biol, 84,
450-462.
|
 |
|
|
|
|
 |
A.Schuetz,
A.Allali-Hassani,
F.Martín,
P.Loppnau,
M.Vedadi,
A.Bochkarev,
A.N.Plotnikov,
C.H.Arrowsmith,
and
J.Min
(2006).
Structural basis for molecular recognition and presentation of histone H3 by WDR5.
|
| |
EMBO J, 25,
4245-4252.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
A.Shilatifard
(2006).
Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression.
|
| |
Annu Rev Biochem, 75,
243-269.
|
 |
|
|
|
|
 |
B.T.Seet,
I.Dikic,
M.M.Zhou,
and
T.Pawson
(2006).
Reading protein modifications with interaction domains.
|
| |
Nat Rev Mol Cell Biol, 7,
473-483.
|
 |
|
|
|
|
 |
C.L.Woodcock
(2006).
Chromatin architecture.
|
| |
Curr Opin Struct Biol, 16,
213-220.
|
 |
|
|
|
|
 |
E.Bernstein,
E.M.Duncan,
O.Masui,
J.Gil,
E.Heard,
and
C.D.Allis
(2006).
Mouse polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin.
|
| |
Mol Cell Biol, 26,
2560-2569.
|
 |
|
|
|
|
 |
G.Lomberk,
L.Wallrath,
and
R.Urrutia
(2006).
The Heterochromatin Protein 1 family.
|
| |
Genome Biol, 7,
228.
|
 |
|
|
|
|
 |
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:
|
 |
|
|
|
|
|
 |
J.C.Eissenberg,
and
A.Shilatifard
(2006).
Leaving a mark: the many footprints of the elongating RNA polymerase II.
|
| |
Curr Opin Genet Dev, 16,
184-190.
|
 |
|
|
|
|
 |
J.C.Eissenberg,
and
S.C.Elgin
(2006).
Marking time.
|
| |
Nat Genet, 38,
276-277.
|
 |
|
|
|
|
 |
J.F.Couture,
E.Collazo,
and
R.C.Trievel
(2006).
Molecular recognition of histone H3 by the WD40 protein WDR5.
|
| |
Nat Struct Mol Biol, 13,
698-703.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
J.Perry
(2006).
The Epc-N domain: a predicted protein-protein interaction domain found in select chromatin associated proteins.
|
| |
BMC Genomics, 7,
6.
|
 |
|
|
|
|
 |
K.Luger
(2006).
Dynamic nucleosomes.
|
| |
Chromosome Res, 14,
5.
|
 |
|
|
|
|
 |
M.C.Brink,
Y.van der Velden,
W.de Leeuw,
J.Mateos-Langerak,
A.S.Belmont,
R.van Driel,
and
P.J.Verschure
(2006).
Truncated HP1 lacking a functional chromodomain induces heterochromatinization upon in vivo targeting.
|
| |
Histochem Cell Biol, 125,
53-61.
|
 |
|
|
|
|
 |
M.S.Cosgrove
(2006).
PHinDing a new histone "effector" domain.
|
| |
Structure, 14,
1096-1098.
|
 |
|
|
|
|
 |
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.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
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:
|
 |
|
|
|
|
|
 |
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:
|
 |
|
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
S.A.Grigoryev,
Y.A.Bulynko,
and
E.Y.Popova
(2006).
The end adjusts the means: heterochromatin remodelling during terminal cell differentiation.
|
| |
Chromosome Res, 14,
53-69.
|
 |
|
|
|
|
 |
S.Sung,
R.J.Schmitz,
and
R.M.Amasino
(2006).
A PHD finger protein involved in both the vernalization and photoperiod pathways in Arabidopsis.
|
| |
Genes Dev, 20,
3244-3248.
|
 |
|
|
|
|
 |
T.Klymenko,
B.Papp,
W.Fischle,
T.Köcher,
M.Schelder,
C.Fritsch,
B.Wild,
M.Wilm,
and
J.Müller
(2006).
A Polycomb group protein complex with sequence-specific DNA-binding and selective methyl-lysine-binding activities.
|
| |
Genes Dev, 20,
1110-1122.
|
 |
|
|
|
|
 |
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:
|
 |
|
|
|
|
|
 |
D.E.Cryderman,
S.K.Grade,
Y.Li,
L.Fanti,
S.Pimpinelli,
and
L.L.Wallrath
(2005).
Role of Drosophila HP1 in euchromatic gene expression.
|
| |
Dev Dyn, 232,
767-774.
|
 |
|
|
|
|
 |
D.Vermaak,
S.Henikoff,
and
H.S.Malik
(2005).
Positive selection drives the evolution of rhino, a member of the heterochromatin protein 1 family in Drosophila.
|
| |
PLoS Genet, 1,
96.
|
 |
|
|
|
|
 |
E.R.Smith,
C.Cayrou,
R.Huang,
W.S.Lane,
J.Côté,
and
J.C.Lucchesi
(2005).
A human protein complex homologous to the Drosophila MSL complex is responsible for the majority of histone H4 acetylation at lysine 16.
|
| |
Mol Cell Biol, 25,
9175-9188.
|
 |
|
|
|
|
 |
E.de Wit,
F.Greil,
and
B.van Steensel
(2005).
Genome-wide HP1 binding in Drosophila: developmental plasticity and genomic targeting signals.
|
| |
Genome Res, 15,
1265-1273.
|
 |
|
|
|
|
 |
F.B.Berry,
M.A.O'Neill,
M.Coca-Prados,
and
M.A.Walter
(2005).
FOXC1 transcriptional regulatory activity is impaired by PBX1 in a filamin A-mediated manner.
|
| |
Mol Cell Biol, 25,
1415-1424.
|
 |
|
|
|
|
 |
H.Chen,
and
H.X.Zhou
(2005).
Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data.
|
| |
Proteins, 61,
21-35.
|
 |
|
|
|
|
 |
J.C.Eissenberg,
and
S.C.Elgin
(2005).
Molecular biology: antagonizing the neighbours.
|
| |
Nature, 438,
1090-1091.
|
 |
|
|
|
|
 |
J.F.Flanagan,
L.Z.Mi,
M.Chruszcz,
M.Cymborowski,
K.L.Clines,
Y.Kim,
W.Minor,
F.Rastinejad,
and
S.Khorasanizadeh
(2005).
Double chromodomains cooperate to recognize the methylated histone H3 tail.
|
| |
Nature, 438,
1181-1185.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
K.Schärer,
M.Morgenthaler,
R.Paulini,
U.Obst-Sander,
D.W.Banner,
D.Schlatter,
J.Benz,
M.Stihle,
and
F.Diederich
(2005).
Quantification of cation-pi interactions in protein-ligand complexes: crystal-structure analysis of Factor Xa bound to a quaternary ammonium ion ligand.
|
| |
Angew Chem Int Ed Engl, 44,
4400-4404.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
M.C.Keogh,
S.K.Kurdistani,
S.A.Morris,
S.H.Ahn,
V.Podolny,
S.R.Collins,
M.Schuldiner,
K.Chin,
T.Punna,
N.J.Thompson,
C.Boone,
A.Emili,
J.S.Weissman,
T.R.Hughes,
B.D.Strahl,
M.Grunstein,
J.F.Greenblatt,
S.Buratowski,
and
N.J.Krogan
(2005).
Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex.
|
| |
Cell, 123,
593-605.
|
 |
|
|
|
|
 |
M.D.Stewart,
J.Li,
and
J.Wong
(2005).
Relationship between histone H3 lysine 9 methylation, transcription repression, and heterochromatin protein 1 recruitment.
|
| |
Mol Cell Biol, 25,
2525-2538.
|
 |
|
|
|
|
 |
M.G.Pray-Grant,
J.A.Daniel,
D.Schieltz,
J.R.Yates,
and
P.A.Grant
(2005).
Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation.
|
| |
Nature, 433,
434-438.
|
 |
|
|
|
|
 |
M.Libault,
F.Tessadori,
S.Germann,
B.Snijder,
P.Fransz,
and
V.Gaudin
(2005).
The Arabidopsis LHP1 protein is a component of euchromatin.
|
| |
Planta, 222,
910-925.
|
 |
|
|
|
|
 |
N.Macdonald,
J.P.Welburn,
M.E.Noble,
A.Nguyen,
M.B.Yaffe,
D.Clynes,
J.G.Moggs,
G.Orphanides,
S.Thomson,
J.W.Edmunds,
A.L.Clayton,
J.A.Endicott,
and
L.C.Mahadevan
(2005).
Molecular basis for the recognition of phosphorylated and phosphoacetylated histone h3 by 14-3-3.
|
| |
Mol Cell, 20,
199-211.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
N.Nameki,
N.Tochio,
S.Koshiba,
M.Inoue,
T.Yabuki,
M.Aoki,
E.Seki,
T.Matsuda,
Y.Fujikura,
M.Saito,
M.Ikari,
M.Watanabe,
T.Terada,
M.Shirouzu,
M.Yoshida,
H.Hirota,
A.Tanaka,
Y.Hayashizaki,
P.Güntert,
T.Kigawa,
and
S.Yokoyama
(2005).
Solution structure of the PWWP domain of the hepatoma-derived growth factor family.
|
| |
Protein Sci, 14,
756-764.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
P.J.Verschure,
I.van der Kraan,
W.de Leeuw,
J.van der Vlag,
A.E.Carpenter,
A.S.Belmont,
and
R.van Driel
(2005).
In vivo HP1 targeting causes large-scale chromatin condensation and enhanced histone lysine methylation.
|
| |
Mol Cell Biol, 25,
4552-4564.
|
 |
|
|
|
|
 |
P.O.Hassa,
and
M.O.Hottiger
(2005).
An epigenetic code for DNA damage repair pathways?
|
| |
Biochem Cell Biol, 83,
270-285.
|
 |
|
|
|
|
 |
R.E.Collins,
M.Tachibana,
H.Tamaru,
K.M.Smith,
D.Jia,
X.Zhang,
E.U.Selker,
Y.Shinkai,
and
X.Cheng
(2005).
In vitro and in vivo analyses of a Phe/Tyr switch controlling product specificity of histone lysine methyltransferases.
|
| |
J Biol Chem, 280,
5563-5570.
|
 |
|
|
|
|
 |
R.J.Sims,
C.F.Chen,
H.Santos-Rosa,
T.Kouzarides,
S.S.Patel,
and
D.Reinberg
(2005).
Human but not yeast CHD1 binds directly and selectively to histone H3 methylated at lysine 4 via its tandem chromodomains.
|
| |
J Biol Chem, 280,
41789-41792.
|
 |
|
|
|
|
 |
R.Margueron,
P.Trojer,
and
D.Reinberg
(2005).
The key to development: interpreting the histone code?
|
| |
Curr Opin Genet Dev, 15,
163-176.
|
 |
|
|
|
|
 |
S.Sung,
and
R.M.Amasino
(2005).
Remembering winter: toward a molecular understanding of vernalization.
|
| |
Annu Rev Plant Biol, 56,
491-508.
|
 |
|
|
|
|
 |
T.Hirota,
J.J.Lipp,
B.H.Toh,
and
J.M.Peters
(2005).
Histone H3 serine 10 phosphorylation by Aurora B causes HP1 dissociation from heterochromatin.
|
| |
Nature, 438,
1176-1180.
|
 |
|
|
|
|
 |
W.Fischle,
B.S.Tseng,
H.L.Dormann,
B.M.Ueberheide,
B.A.Garcia,
J.Shabanowitz,
D.F.Hunt,
H.Funabiki,
and
C.D.Allis
(2005).
Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation.
|
| |
Nature, 438,
1116-1122.
|
 |
|
|
|
|
 |
W.Selleck,
I.Fortin,
D.Sermwittayawong,
J.Côté,
and
S.Tan
(2005).
The Saccharomyces cerevisiae Piccolo NuA4 histone acetyltransferase complex requires the Enhancer of Polycomb A domain and chromodomain to acetylate nucleosomes.
|
| |
Mol Cell Biol, 25,
5535-5542.
|
 |
|
|
|
|
 |
X.de la Cruz,
S.Lois,
S.Sánchez-Molina,
and
M.A.Martínez-Balbás
(2005).
Do protein motifs read the histone code?
|
| |
Bioessays, 27,
164-175.
|
 |
|
|
|
|
 |
A.Brehm,
K.R.Tufteland,
R.Aasland,
and
P.B.Becker
(2004).
The many colours of chromodomains.
|
| |
Bioessays, 26,
133-140.
|
 |
|
|
|
|
 |
A.M.Lindroth,
D.Shultis,
Z.Jasencakova,
J.Fuchs,
L.Johnson,
D.Schubert,
D.Patnaik,
S.Pradhan,
J.Goodrich,
I.Schubert,
T.Jenuwein,
S.Khorasanizadeh,
and
S.E.Jacobsen
(2004).
Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3.
|
| |
EMBO J, 23,
4286-4296.
|
 |
|
|
|
|
 |
A.Thiru,
D.Nietlispach,
H.R.Mott,
M.Okuwaki,
D.Lyon,
P.R.Nielsen,
M.Hirshberg,
A.Verreault,
N.V.Murzina,
and
E.D.Laue
(2004).
Structural basis of HP1/PXVXL motif peptide interactions and HP1 localisation to heterochromatin.
|
| |
EMBO J, 23,
489-499.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
B.Mateescu,
P.England,
F.Halgand,
M.Yaniv,
and
C.Muchardt
(2004).
Tethering of HP1 proteins to chromatin is relieved by phosphoacetylation of histone H3.
|
| |
EMBO Rep, 5,
490-496.
|
 |
|
|
|
|
 |
C.Maison,
and
G.Almouzni
(2004).
HP1 and the dynamics of heterochromatin maintenance.
|
| |
Nat Rev Mol Cell Biol, 5,
296-304.
|
 |
|
|
|
|
 |
E.Futai,
S.Hamamoto,
L.Orci,
and
R.Schekman
(2004).
GTP/GDP exchange by Sec12p enables COPII vesicle bud formation on synthetic liposomes.
|
| |
EMBO J, 23,
4146-4155.
|
 |
|
|
|
|
 |
G.Jiang,
F.Yang,
C.Sanchez,
and
M.Ehrlich
(2004).
Histone modification in constitutive heterochromatin versus unexpressed euchromatin in human cells.
|
| |
J Cell Biochem, 93,
286-300.
|
 |
|
|
|
|
 |
H.Cam,
and
S.I.Grewal
(2004).
RNA interference and epigenetic control of heterochromatin assembly in fission yeast.
|
| |
Cold Spring Harb Symp Quant Biol, 69,
419-427.
|
 |
|
|
|
|
 |
J.Bender
(2004).
DNA methylation of the endogenous PAI genes in Arabidopsis.
|
| |
Cold Spring Harb Symp Quant Biol, 69,
145-153.
|
 |
|
|
|
|
 |
J.Bender
(2004).
Chromatin-based silencing mechanisms.
|
| |
Curr Opin Plant Biol, 7,
521-526.
|
 |
|
|
|
|
 |
M.Freitag,
P.C.Hickey,
T.K.Khlafallah,
N.D.Read,
and
E.U.Selker
(2004).
HP1 is essential for DNA methylation in neurospora.
|
| |
Mol Cell, 13,
427-434.
|
 |
|
|
|
|
 |
M.J.Bottomley
(2004).
Structures of protein domains that create or recognize histone modifications.
|
| |
EMBO Rep, 5,
464-469.
|
 |
|
|
|
|
 |
M.L.Waters
(2004).
Aromatic interactions in peptides: impact on structure and function.
|
| |
Biopolymers, 76,
435-445.
|
 |
|
|
|
|
 |
M.Lachner,
R.Sengupta,
G.Schotta,
and
T.Jenuwein
(2004).
Trilogies of histone lysine methylation as epigenetic landmarks of the eukaryotic genome.
|
| |
Cold Spring Harb Symp Quant Biol, 69,
209-218.
|
 |
|
|
|
|
 |
S.M.Janicki,
T.Tsukamoto,
S.E.Salghetti,
W.P.Tansey,
R.Sachidanandam,
K.V.Prasanth,
T.Ried,
Y.Shav-Tal,
E.Bertrand,
R.H.Singer,
and
D.L.Spector
(2004).
From silencing to gene expression: real-time analysis in single cells.
|
| |
Cell, 116,
683-698.
|
 |
|
|
|
|
 |
T.Cheutin,
S.A.Gorski,
K.M.May,
P.B.Singh,
and
T.Misteli
(2004).
In vivo dynamics of Swi6 in yeast: evidence for a stochastic model of heterochromatin.
|
| |
Mol Cell Biol, 24,
3157-3167.
|
 |
|
|
|
|
 |
U.Rath,
D.Wang,
Y.Ding,
Y.Z.Xu,
H.Qi,
M.J.Blacketer,
J.Girton,
J.Johansen,
and
K.M.Johansen
(2004).
Chromator, a novel and essential chromodomain protein interacts directly with the putative spindle matrix protein skeletor.
|
| |
J Cell Biochem, 93,
1033-1047.
|
 |
|
|
|
|
 |
Y.Zhang,
R.Cao,
L.Wang,
and
R.S.Jones
(2004).
Mechanism of Polycomb group gene silencing.
|
| |
Cold Spring Harb Symp Quant Biol, 69,
309-317.
|
 |
|
|
|
|
 |
Z.Lippman,
and
R.Martienssen
(2004).
The role of RNA interference in heterochromatic silencing.
|
| |
Nature, 431,
364-370.
|
 |
|
|
|
|
 |
B.G.Mellone,
L.Ball,
N.Suka,
M.R.Grunstein,
J.F.Partridge,
and
R.C.Allshire
(2003).
Centromere silencing and function in fission yeast is governed by the amino terminus of histone H3.
|
| |
Curr Biol, 13,
1748-1757.
|
 |
|
|
|
|
 |
C.Pivot-Pajot,
C.Caron,
J.Govin,
A.Vion,
S.Rousseaux,
and
S.Khochbin
(2003).
Acetylation-dependent chromatin reorganization by BRDT, a testis-specific bromodomain-containing protein.
|
| |
Mol Cell Biol, 23,
5354-5365.
|
 |
|
|
|
|
 |
F.Greil,
I.van der Kraan,
J.Delrow,
J.F.Smothers,
E.de Wit,
H.J.Bussemaker,
R.van Driel,
S.Henikoff,
and
B.van Steensel
(2003).
Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location.
|
| |
Genes Dev, 17,
2825-2838.
|
 |
|
|
|
|
 |
J.Min,
Y.Zhang,
and
R.M.Xu
(2003).
Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27.
|
| |
Genes Dev, 17,
1823-1828.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
L.Hughes-Davies,
D.Huntsman,
M.Ruas,
F.Fuks,
J.Bye,
S.F.Chin,
J.Milner,
L.A.Brown,
F.Hsu,
B.Gilks,
T.Nielsen,
M.Schulzer,
S.Chia,
J.Ragaz,
A.Cahn,
L.Linger,
H.Ozdag,
E.Cattaneo,
E.S.Jordanova,
E.Schuuring,
D.S.Yu,
A.Venkitaraman,
B.Ponder,
A.Doherty,
S.Aparicio,
D.Bentley,
C.Theillet,
C.P.Ponting,
C.Caldas,
and
T.Kouzarides
(2003).
EMSY links the BRCA2 pathway to sporadic breast and ovarian cancer.
|
| |
Cell, 115,
523-535.
|
 |
|
|
|
|
 |
M.Iizuka,
and
M.M.Smith
(2003).
Functional consequences of histone modifications.
|
| |
Curr Opin Genet Dev, 13,
154-160.
|
 |
|
|
|
|
 |
M.M.van Noesel,
S.van Bezouw,
P.A.Voûte,
J.G.Herman,
R.Pieters,
and
R.Versteeg
(2003).
Clustering of hypermethylated genes in neuroblastoma.
|
| |
Genes Chromosomes Cancer, 38,
226-233.
|
 |
|
|
|
|
 |
N.Gilbert,
S.Boyle,
H.Sutherland,
J.de Las Heras,
J.Allan,
T.Jenuwein,
and
W.A.Bickmore
(2003).
Formation of facultative heterochromatin in the absence of HP1.
|
| |
EMBO J, 22,
5540-5550.
|
 |
|
|
|
|
 |
R.J.Sims,
K.Nishioka,
and
D.Reinberg
(2003).
Histone lysine methylation: a signature for chromatin function.
|
| |
Trends Genet, 19,
629-639.
|
 |
|
|
|
|
 |
R.R.Meehan,
C.F.Kao,
and
S.Pennings
(2003).
HP1 binding to native chromatin in vitro is determined by the hinge region and not by the chromodomain.
|
| |
EMBO J, 22,
3164-3174.
|
 |
|
|
|
|
 |
T.C.Fleischer,
U.J.Yun,
and
D.E.Ayer
(2003).
Identification and characterization of three new components of the mSin3A corepressor complex.
|
| |
Mol Cell Biol, 23,
3456-3467.
|
 |
|
|
|
|
 |
T.P.Rasmussen
(2003).
Embryonic stem cell differentiation: a chromatin perspective.
|
| |
Reprod Biol Endocrinol, 1,
100.
|
 |
|
|
|
|
 |
W.Fischle,
Y.Wang,
and
C.D.Allis
(2003).
Binary switches and modification cassettes in histone biology and beyond.
|
| |
Nature, 425,
475-479.
|
 |
|
|
|
|
 |
W.Fischle,
Y.Wang,
and
C.D.Allis
(2003).
Histone and chromatin cross-talk.
|
| |
Curr Opin Cell Biol, 15,
172-183.
|
 |
|
|
|
|
 |
W.Fischle,
Y.Wang,
S.A.Jacobs,
Y.Kim,
C.D.Allis,
and
S.Khorasanizadeh
(2003).
Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains.
|
| |
Genes Dev, 17,
1870-1881.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
W.K.Wang,
V.Tereshko,
P.Boccuni,
D.MacGrogan,
S.D.Nimer,
and
D.J.Patel
(2003).
Malignant brain tumor repeats: a three-leaved propeller architecture with ligand/peptide binding pockets.
|
| |
Structure, 11,
775-789.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
X.Zhang,
Z.Yang,
S.I.Khan,
J.R.Horton,
H.Tamaru,
E.U.Selker,
and
X.Cheng
(2003).
Structural basis for the product specificity of histone lysine methyltransferases.
|
| |
Mol Cell, 12,
177-185.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
B.Czermin,
R.Melfi,
D.McCabe,
V.Seitz,
A.Imhof,
and
V.Pirrotta
(2002).
Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites.
|
| |
Cell, 111,
185-196.
|
 |
|
|
|
|
 |
B.M.Turner
(2002).
Cellular memory and the histone code.
|
| |
Cell, 111,
285-291.
|
 |
|
|
|
|
 |
D.C.Schultz,
K.Ayyanathan,
D.Negorev,
G.G.Maul,
and
F.J.Rauscher
(2002).
SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins.
|
| |
Genes Dev, 16,
919-932.
|
 |
|
|
|
|
 |
H.T.Spotswood,
and
B.M.Turner
(2002).
An increasingly complex code.
|
| |
J Clin Invest, 110,
577-582.
|
 |
|
|
|
|
 |
K.Bouazoune,
A.Mitterweger,
G.Längst,
A.Imhof,
A.Akhtar,
P.B.Becker,
and
A.Brehm
(2002).
The dMi-2 chromodomains are DNA binding modules important for ATP-dependent nucleosome mobilization.
|
| |
EMBO J, 21,
2430-2440.
|
 |
|
|
|
|
 |
L.Aravind,
and
L.M.Iyer
(2002).
The SWIRM domain: a conserved module found in chromosomal proteins points to novel chromatin-modifying activities.
|
| |