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PDBsum entry 1pfb
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Peptide binding protein PDB id
1pfb

 

 

 

 

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Contents
Protein chains
55 a.a. *
11 a.a. *
Ligands
BME
ACY
Metals
_CL ×2
Waters ×147
* Residue conservation analysis
PDB id:
1pfb
Name: Peptide binding protein
Title: Structural basis for specific binding of polycomb chromodomain to histone h3 methylated at k27
Structure: Polycomb protein. Chain: a. Fragment: chromodomain. Engineered: yes. Histone h3, embryonic. Chain: b. Engineered: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: pc or cg7618. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the peptide was chemically synthesized. It is naturally found in strongylocentrotus purpuratus.
Biol. unit: Dimer (from PQS)
Resolution:
1.40Å     R-factor:   0.197     R-free:   0.216
Authors: J.R.Min,Y.Zhang,R.-M.Xu
Key ref: J.Min et al. (2003). Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev, 17, 1823-1828. PubMed id: 12897052
Date:
24-May-03     Release date:   07-Oct-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P26017  (PC_DROME) -  Polycomb group protein Pc from Drosophila melanogaster
Seq:
Struc: 		390 a.a.
55 a.a.
Protein chain
P06352  (H3_STRPU) -  Histone H3, embryonic from Strongylocentrotus purpuratus
Seq:
Struc: 		136 a.a.
11 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
Genes Dev 17:1823-1828 (2003)
PubMed id: 12897052  
 
 
Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27.
J.Min, Y.Zhang, R.M.Xu.
 
  ABSTRACT  
 
The chromodomain of Drosophila Polycomb protein is essential for maintaining the silencing state of homeotic genes during development. Recent studies suggest that Polycomb mediates the assembly of repressive higher-order chromatin structures in conjunction with the methylation of Lys 27 of histone H3 by a Polycomb group repressor complex. A similar mechanism in heterochromatin assembly is mediated by HP1, a chromodomain protein that binds to histone H3 methylated at Lys 9. To understand the molecular mechanism of the methyl-Lys 27 histone code recognition, we have determined a 1.4-A-resolution structure of the chromodomain of Polycomb in complex with a histone H3 peptide trimethylated at Lys 27. The structure reveals a conserved mode of methyl-lysine binding and identifies Polycomb-specific interactions with histone H3. The structure also reveals a dPC dimer in the crystal lattice that is mediated by residues specifically conserved in the Polycomb family of chromodomains. The dimerization of dPC can effectively account for the histone-binding specificity and provides new mechanistic insights into the function of Polycomb. We propose that self-association is functionally important for Polycomb.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23211769 C.A.Musselman, M.E.Lalonde, J.Côté, and T.G.Kutateladze (2012).
Perceiving the epigenetic landscape through histone readers.
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21468892 C.Xu, and J.Min (2011).
Structure and function of WD40 domain proteins.
  Protein Cell, 2, 202-214.
PDB codes: 3e0c 3fm0 3i2n 3ow8
21177970 D.Enderle, C.Beisel, M.B.Stadler, M.Gerstung, P.Athri, and R.Paro (2011).
Polycomb preferentially targets stalled promoters of coding and noncoding transcripts.
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21392507 G.Cavalli (2011).
From Linear Genes to Epigenetic Inheritance of Three-dimensional Epigenomes.
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22081016 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.
  Nat Struct Mol Biol, 18, 1358-1365.  
21047797 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: 2l11 2l12 2l1b 3fdt 3gv6 3h91 3i90 3i91
20974918 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: 3jpx 3jzg 3jzh 3jzn 3k26 3k27
20212086 H.M.Herz, L.D.Madden, Z.Chen, C.Bolduc, E.Buff, R.Gupta, R.Davuluri, A.Shilatifard, I.K.Hariharan, and A.Bergmann (2010).
The H3K27me3 demethylase dUTX is a suppressor of Notch- and Rb-dependent tumors in Drosophila.
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PDB code: 2kvm
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  Cell Stem Cell, 7, 288-298.  
20351181 L.Wang, N.Jahren, E.L.Miller, C.S.Ketel, D.R.Mallin, and J.A.Simon (2010).
Comparative analysis of chromatin binding by Sex Comb on Midleg (SCM) and other polycomb group repressors at a Drosophila Hox gene.
  Mol Cell Biol, 30, 2584-2593.  
21072162 M.A.Adams-Cioaba, Y.Guo, C.Bian, M.F.Amaya, R.Lam, G.A.Wasney, M.Vedadi, C.Xu, and J.Min (2010).
Structural studies of the tandem Tudor domains of fragile X mental retardation related proteins FXR1 and FXR2.
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PDB codes: 3h8z 3o8v
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  Nat Cell Biol, 12, 982-992.  
20123906 M.Leeb, D.Pasini, M.Novatchkova, M.Jaritz, K.Helin, and A.Wutz (2010).
Polycomb complexes act redundantly to repress genomic repeats and genes.
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20975044 N.S.Christophersen, and K.Helin (2010).
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20696397 R.Wang, A.B.Taylor, B.Z.Leal, L.V.Chadwell, U.Ilangovan, A.K.Robinson, V.Schirf, P.J.Hart, E.M.Lafer, B.Demeler, A.P.Hinck, D.G.McEwen, and C.A.Kim (2010).
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PDB codes: 3gs2 3ixs
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19858291 T.B.van Dijk, N.Gillemans, C.Stein, P.Fanis, J.Demmers, M.van de Corput, J.Essers, F.Grosveld, U.M.Bauer, and S.Philipsen (2010).
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  Mol Cell, 38, 191-201.  
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Ezh2 orchestrates gene expression for the stepwise differentiation of tissue-specific stem cells.
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Histones: annotating chromatin.
  Annu Rev Genet, 43, 559-599.  
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19738629 J.A.Simon, and R.E.Kingston (2009).
Mechanisms of polycomb gene silencing: knowns and unknowns.
  Nat Rev Mol Cell Biol, 10, 697-708.  
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Structural studies of a four-MBT repeat protein MBTD1.
  PLoS One, 4, e7274.
PDB code: 3feo
19321450 J.Kim, and P.K.Wong (2009).
Oxidative stress is linked to ERK1/2-p16 signaling-mediated growth defect in ATM-deficient astrocytes.
  J Biol Chem, 284, 14396-14404.  
19345089 J.Müller, and P.Verrijzer (2009).
Biochemical mechanisms of gene regulation by polycomb group protein complexes.
  Curr Opin Genet Dev, 19, 150-158.  
19234526 M.A.Adams-Cioaba, and J.Min (2009).
Structure and function of histone methylation binding proteins.
  Biochem Cell Biol, 87, 93.  
19303136 N.J.Francis, N.E.Follmer, M.D.Simon, G.Aghia, and J.D.Butler (2009).
Polycomb proteins remain bound to chromatin and DNA during DNA replication in vitro.
  Cell, 137, 110-122.  
  19513271 O.Novikova (2009).
Chromodomains and LTR retrotransposons in plants.
  Commun Integr Biol, 2, 158-162.  
19229332 P.Akan, M.Sahlén, and P.Deloukas (2009).
A histone map of human chromosome 20q13.12.
  PLoS ONE, 4, e4479.  
19184981 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.
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Molecular genetic analysis of Suppressor 2 of zeste identifies key functional domains.
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19898523 R.S.Gieni, and M.J.Hendzel (2009).
Polycomb group protein gene silencing, non-coding RNA, stem cells, and cancer.
  Biochem Cell Biol, 87, 711-746.  
19930571 R.Senthilkumar, and R.K.Mishra (2009).
Novel motifs distinguish multiple homologues of Polycomb in vertebrates: expansion and diversification of the epigenetic toolkit.
  BMC Genomics, 10, 549.  
19788421 R.Sharma, R.K.Mohan Singh, G.Malik, P.Deveshwar, A.K.Tyagi, S.Kapoor, and M.Kapoor (2009).
Rice cytosine DNA methyltransferases - gene expression profiling during reproductive development and abiotic stress.
  FEBS J, 276, 6301-6311.  
18718879 S.M.Fuchs, R.N.Laribee, and B.D.Strahl (2009).
Protein modifications in transcription elongation.
  Biochim Biophys Acta, 1789, 26-36.  
18981224 S.M.Lo, N.K.Ahuja, and N.J.Francis (2009).
Polycomb group protein Suppressor 2 of zeste is a functional homolog of Posterior Sex Combs.
  Mol Cell Biol, 29, 515-525.  
19362535 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: 3g7l
19399177 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.  
19233876 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: 3cey 3f70
18598138 B.Delage, and R.H.Dashwood (2008).
Dietary manipulation of histone structure and function.
  Annu Rev Nutr, 28, 347-366.  
18984594 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: 3e9f 3e9g
18689541 D.Garrick, M.De Gobbi, V.Samara, M.Rugless, M.Holland, H.Ayyub, K.Lower, J.Sloane-Stanley, N.Gray, C.Koch, I.Dunham, and D.R.Higgs (2008).
The role of the polycomb complex in silencing alpha-globin gene expression in nonerythroid cells.
  Blood, 112, 3889-3899.  
18560994 E.Fedorova, N.Sadoni, I.K.Dahlsveen, J.Koch, E.Kremmer, D.Eick, R.Paro, and D.Zink (2008).
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  Chromosome Res, 16, 649-673.  
18416604 I.J.Majewski, M.E.Blewitt, C.A.de Graaf, E.J.McManus, M.Bahlo, A.A.Hilton, C.D.Hyland, G.K.Smyth, J.E.Corbin, D.Metcalf, W.S.Alexander, and D.J.Hilton (2008).
Polycomb repressive complex 2 (PRC2) restricts hematopoietic stem cell activity.
  PLoS Biol, 6, e93.  
18474616 J.K.Sims, and J.C.Rice (2008).
PR-Set7 establishes a repressive trans-tail histone code that regulates differentiation.
  Mol Cell Biol, 28, 4459-4468.  
18285464 K.Sarma, R.Margueron, A.Ivanov, V.Pirrotta, and D.Reinberg (2008).
Ezh2 requires PHF1 to efficiently catalyze H3 lysine 27 trimethylation in vivo.
  Mol Cell Biol, 28, 2718-2731.  
19097900 L.Xu, and W.H.Shen (2008).
Polycomb silencing of KNOX genes confines shoot stem cell niches in Arabidopsis.
  Curr Biol, 18, 1966-1971.  
18275833 M.Miyazaki, K.Miyazaki, M.Itoi, Y.Katoh, Y.Guo, R.Kanno, Y.Katoh-Fukui, H.Honda, T.Amagai, M.van Lohuizen, H.Kawamoto, and M.Kanno (2008).
Thymocyte proliferation induced by pre-T cell receptor signaling is maintained through polycomb gene product Bmi-1-mediated Cdkn2a repression.
  Immunity, 28, 231-245.  
18728284 M.Y.Wu, K.W.Eldin, and A.L.Beaudet (2008).
Identification of chromatin remodeling genes Arid4a and Arid4b as leukemia suppressor genes.
  J Natl Cancer Inst, 100, 1247-1259.  
18411339 M.Yamashita, M.Kuwahara, A.Suzuki, K.Hirahara, R.Shinnaksu, H.Hosokawa, A.Hasegawa, S.Motohashi, A.Iwama, and T.Nakayama (2008).
Bmi1 regulates memory CD4 T cell survival via repression of the Noxa gene.
  J Exp Med, 205, 1109-1120.  
18160966 R.A.Laskowski, and J.M.Thornton (2008).
Understanding the molecular machinery of genetics through 3D structures.
  Nat Rev Genet, 9, 141-151.  
18086877 R.Cao, H.Wang, J.He, H.Erdjument-Bromage, P.Tempst, and Y.Zhang (2008).
Role of hPHF1 in H3K27 methylation and Hox gene silencing.
  Mol Cell Biol, 28, 1862-1872.  
18422744 R.Kanno, H.Janakiraman, and M.Kanno (2008).
Epigenetic regulator polycomb group protein complexes control cell fate and cancer.
  Cancer Sci, 99, 1077-1084.  
18034266 S.Chen, A.Birve, and A.Rasmuson-Lestander (2008).
In vivo analysis of Drosophila SU(Z)12 function.
  Mol Genet Genomics, 279, 159-170.  
19160493 S.Mujtaba, K.L.Manzur, J.R.Gurnon, M.Kang, J.L.Van Etten, and M.M.Zhou (2008).
Epigenetic transcriptional repression of cellular genes by a viral SET protein.
  Nat Cell Biol, 10, 1114-1122.  
18450745 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.  
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Chromodomains direct integration of retrotransposons to heterochromatin.
  Genome Res, 18, 359-369.  
18224410 Y.Takihara (2008).
Role of Polycomb-group genes in sustaining activities of normal and malignant stem cells.
  Int J Hematol, 87, 25-34.  
17218268 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.  
17938208 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.
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17350655 C.G.Marfella, and A.N.Imbalzano (2007).
The Chd family of chromatin remodelers.
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17687328 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: 2puy
17210640 F.Tie, C.A.Stratton, R.L.Kurzhals, and P.J.Harte (2007).
The N terminus of Drosophila ESC binds directly to histone H3 and is required for E(Z)-dependent trimethylation of H3 lysine 27.
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17336131 G.Chinnadurai (2007).
Transcriptional regulation by C-terminal binding proteins.
  Int J Biochem Cell Biol, 39, 1593-1607.  
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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: 2rhi 2rhu 2rhx 2rhy 2rhz 2ri2 2ri3 2ri5 2ri7
17304537 J.C.Kiefer (2007).
Epigenetics in development.
  Dev Dyn, 236, 1144-1156.  
18026117 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: 2pqw 2rjc 2rjd 2rje 2rjf
17442611 M.Lohrum, H.G.Stunnenberg, and C.Logie (2007).
The new frontier in cancer research: deciphering cancer epigenetics.
  Int J Biochem Cell Biol, 39, 1450-1461.  
17363975 M.Spivakov, and A.G.Fisher (2007).
Epigenetic signatures of stem-cell identity.
  Nat Rev Genet, 8, 263-271.  
17997413 N.D.Montgomery, D.Yee, S.A.Montgomery, and T.Magnuson (2007).
Molecular and functional mapping of EED motifs required for PRC2-dependent histone methylation.
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17632523 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.  
17868118 R.K.Mishra, T.Yamagishi, D.Vasanthi, C.Ohtsuka, and T.Kondo (2007).
Involvement of polycomb-group genes in establishing HoxD temporal colinearity.
  Genesis, 45, 570-576.  
18282134 S.A.Lavrov, and M.V.Kibanov (2007).
Noncoding RNAs and chromatin structure.
  Biochemistry (Mosc), 72, 1422-1438.  
17984965 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.  
17825942 S.J.Whitcomb, A.Basu, C.D.Allis, and E.Bernstein (2007).
Polycomb Group proteins: an evolutionary perspective.
  Trends Genet, 23, 494-502.  
17984971 S.Lall (2007).
Primers on chromatin.
  Nat Struct Mol Biol, 14, 1110-1115.  
17124606 S.Mendjan, and A.Akhtar (2007).
The right dose for every sex.
  Chromosoma, 116, 95.  
17925232 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.  
18025461 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: 2v83 2v85 2v86 2v87 2v88
17599839 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.  
17374386 X.Cheng, and X.Zhang (2007).
Structural dynamics of protein lysine methylation and demethylation.
  Mutat Res, 618, 102-115.  
17575054 Y.Liu, S.D.Taverna, T.L.Muratore, J.Shabanowitz, D.F.Hunt, and C.D.Allis (2007).
RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena.
  Genes Dev, 21, 1530-1545.  
16946699 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: 2gnq 2h9l 2h9m 2h9n 2h9o 2h9p 2o9k
17060944 A.Sparmann, and M.van Lohuizen (2006).
Polycomb silencers control cell fate, development and cancer.
  Nat Rev Cancer, 6, 846-856.  
16882982 B.Papp, and J.Müller (2006).
Histone trimethylation and the maintenance of transcriptional ON and OFF states by trxG and PcG proteins.
  Genes Dev, 20, 2041-2054.  
16810678 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.
  J Cell Physiol, 209, 162-171.  
16816423 D.Qi, H.Jin, T.Lilja, and M.Mannervik (2006).
Drosophila Reptin and other TIP60 complex components promote generation of silent chromatin.
  Genetics, 174, 241-251.  
16537902 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.  
16728978 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: 2f6j 2f6n 2fsa 2fui 2fuu
16700059 J.C.Eissenberg (2006).
Divided loyalties: transdetermination and the genetics of tissue regeneration.
  Bioessays, 28, 574-577.  
16415788 J.Kim, J.Daniel, A.Espejo, A.Lake, M.Krishna, L.Xia, Y.Zhang, and M.T.Bedford (2006).
Tudor, MBT and chromo domains gauge the degree of lysine methylation.
  EMBO Rep, 7, 397-403.  
16603237 K.Yamane, C.Toumazou, Y.Tsukada, H.Erdjument-Bromage, P.Tempst, J.Wong, and Y.Zhang (2006).
JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor.
  Cell, 125, 483-495.  
16537908 L.Wang, N.Jahren, M.L.Vargas, E.F.Andersen, J.Benes, J.Zhang, E.L.Miller, R.S.Jones, and J.A.Simon (2006).
Alternative ESC and ESC-like subunits of a polycomb group histone methyltransferase complex are differentially deployed during Drosophila development.
  Mol Cell Biol, 26, 2637-2647.  
16613483 N.Nègre, J.Hennetin, L.V.Sun, S.Lavrov, M.Bellis, K.P.White, and G.Cavalli (2006).
Chromosomal distribution of PcG proteins during Drosophila development.
  PLoS Biol, 4, e170.  
17381324 O.Masui, and E.Heard (2006).
RNA and protein actors in X-chromosome inactivation.
  Cold Spring Harb Symp Quant Biol, 71, 419-428.  
16630806 P.Trojer, and D.Reinberg (2006).
Histone lysine demethylases and their impact on epigenetics.
  Cell, 125, 213-217.  
16728977 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: 2g6q
17135209 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: 2f5k
16732292 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.  
17043400 S.Hirose, Y.Komoike, and T.Higashinakagawa (2006).
Identification of a nuclear localization signal in mouse polycomb protein, M33.
  Zoolog Sci, 23, 785-791.  
16506095 S.J.McBryant, V.H.Adams, and J.C.Hansen (2006).
Chromatin architectural proteins.
  Chromosome Res, 14, 39-51.  
16763550 S.Schoeftner, A.K.Sengupta, S.Kubicek, K.Mechtler, L.Spahn, H.Koseki, T.Jenuwein, and A.Wutz (2006).
Recruitment of PRC1 function at the initiation of X inactivation independent of PRC2 and silencing.
  EMBO J, 25, 3110-3122.  
16608399 X.Han, P.Berardi, and K.Riabowol (2006).
Chromatin modification and senescence: linkage by tumor suppressors?
  Rejuvenation Res, 9, 69-76.  
16826231 Y.Zhang (2006).
It takes a PHD to interpret histone methylation.
  Nat Struct Mol Biol, 13, 572-574.  
16600877 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: 2g99 2g9a
16261189 C.Martin, and Y.Zhang (2005).
The diverse functions of histone lysine methylation.
  Nat Rev Mol Cell Biol, 6, 838-849.  
16055700 C.S.Ketel, E.F.Andersen, M.L.Vargas, J.Suh, S.Strome, and J.A.Simon (2005).
Subunit contributions to histone methyltransferase activities of fly and worm polycomb group complexes.
  Mol Cell Biol, 25, 6857-6868.  
15704101 H.W.Brock, and C.L.Fisher (2005).
Maintenance of gene expression patterns.
  Dev Dyn, 232, 633-655.  
16314526 I.Hernández-Muñoz, P.Taghavi, C.Kuijl, J.Neefjes, and M.van Lohuizen (2005).
Association of BMI1 with polycomb bodies is dynamic and requires PRC2/EZH2 and the maintenance DNA methyltransferase DNMT1.
  Mol Cell Biol, 25, 11047-11058.  
16372014 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: 2b2t 2b2u 2b2v 2b2w 2b2y
15699631 J.Gil, D.Bernard, and G.Peters (2005).
Role of polycomb group proteins in stem cell self-renewal and cancer.
  DNA Cell Biol, 24, 117-125.  
16357214 J.M.Goodliffe, E.Wieschaus, and M.D.Cole (2005).
Polycomb mediates Myc autorepression and its transcriptional control of many loci in Drosophila.
  Genes Dev, 19, 2941-2946.  
15952226 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: 2bok
16052488 L.Srinivasan, X.Pan, and M.L.Atchison (2005).
Transient requirements of YY1 expression for PcG transcriptional repression and phenotypic rescue.
  J Cell Biochem, 96, 689-699.  
15647753 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.  
15592428 M.H.Kagey, T.A.Melhuish, S.E.Powers, and D.Wotton (2005).
Multiple activities contribute to Pc2 E3 function.
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15776017 M.Nekrasov, B.Wild, and J.Müller (2005).
Nucleosome binding and histone methyltransferase activity of Drosophila PRC2.
  EMBO Rep, 6, 348-353.  
15959555 P.O.Hassa, and M.O.Hottiger (2005).
An epigenetic code for DNA damage repair pathways?
  Biochem Cell Biol, 83, 270-285.  
16359901 R.Cao, Y.Tsukada, and Y.Zhang (2005).
Role of Bmi-1 and Ring1A in H2A ubiquitylation and Hox gene silencing.
  Mol Cell, 20, 845-854.  
15964809 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.  
15851025 Y.Okada, Q.Feng, Y.Lin, Q.Jiang, Y.Li, V.M.Coffield, L.Su, G.Xu, and Y.Zhang (2005).
hDOT1L links histone methylation to leukemogenesis.
  Cell, 121, 167-178.  
15145347 A.H.Lund, and M.van Lohuizen (2004).
Polycomb complexes and silencing mechanisms.
  Curr Opin Cell Biol, 16, 239-246.  
15280237 A.J.Peterson, D.R.Mallin, N.J.Francis, C.S.Ketel, J.Stamm, R.K.Voeller, R.E.Kingston, and J.A.Simon (2004).
Requirement for sex comb on midleg protein interactions in Drosophila polycomb group repression.
  Genetics, 167, 1225-1239.  
15252442 A.Kohlmaier, F.Savarese, M.Lachner, J.Martens, T.Jenuwein, and A.Wutz (2004).
A chromosomal memory triggered by Xist regulates histone methylation in X inactivation.
  PLoS Biol, 2, E171.  
15099518 A.Kuzmichev, T.Jenuwein, P.Tempst, and D.Reinberg (2004).
Different EZH2-containing complexes target methylation of histone H1 or nucleosomal histone H3.
  Mol Cell, 14, 183-193.  
15457214 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.  
14765118 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: 1s4z
15457212 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.  
16117637 E.Heard, J.Chaumeil, O.Masui, and I.Okamoto (2004).
Mammalian X-chromosome inactivation: an epigenetics paradigm.
  Cold Spring Harb Symp Quant Biol, 69, 89.  
15020417 F.Janody, J.D.Lee, N.Jahren, D.J.Hazelett, A.Benlali, G.I.Miura, I.Draskovic, and J.E.Treisman (2004).
A mosaic genetic screen reveals distinct roles for trithorax and polycomb group genes in Drosophila eye development.
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15337094 J.Bender (2004).
Chromatin-based silencing mechanisms.
  Curr Opin Plant Biol, 7, 521-526.  
14647293 J.Gil, D.Bernard, D.Martínez, and D.Beach (2004).
Polycomb CBX7 has a unifying role in cellular lifespan.
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15596546 K.Plath, D.Talbot, K.M.Hamer, A.P.Otte, T.P.Yang, R.Jaenisch, and B.Panning (2004).
Developmentally regulated alterations in Polycomb repressive complex 1 proteins on the inactive X chromosome.
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15040448 L.A.Boyer, R.R.Latek, and C.L.Peterson (2004).
The SANT domain: a unique histone-tail-binding module?
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15568982 L.Ringrose, and R.Paro (2004).
Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins.
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15520279 L.Srinivasan, and M.L.Atchison (2004).
YY1 DNA binding and PcG recruitment requires CtBP.
  Genes Dev, 18, 2596-2601.  
15175158 L.Wang, J.L.Brown, R.Cao, Y.Zhang, J.A.Kassis, and R.S.Jones (2004).
Hierarchical recruitment of polycomb group silencing complexes.
  Mol Cell, 14, 637-646.  
15184976 M.J.Bottomley (2004).
Structures of protein domains that create or recognize histone modifications.
  EMBO Rep, 5, 464-469.  
16117651 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.  
15225548 R.Cao, and Y.Zhang (2004).
SUZ12 is required for both the histone methyltransferase activity and the silencing function of the EED-EZH2 complex.
  Mol Cell, 15, 57-67.  
15196462 R.Cao, and Y.Zhang (2004).
The functions of E(Z)/EZH2-mediated methylation of lysine 27 in histone H3.
  Curr Opin Genet Dev, 14, 155-164.  
15219397 S.Henikoff, T.Furuyama, and K.Ahmad (2004).
Histone variants, nucleosome assembly and epigenetic inheritance.
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15031712 T.Klymenko, and J.Müller (2004).
The histone methyltransferases Trithorax and Ash1 prevent transcriptional silencing by Polycomb group proteins.
  EMBO Rep, 5, 373-377.  
16117663 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.  
14585615 R.J.Sims, K.Nishioka, and D.Reinberg (2003).
Histone lysine methylation: a signature for chromatin function.
  Trends Genet, 19, 629-639.  
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.

 

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