PDBsum entry: 1pdq

Structural protein

PDB-id

1pdq


	Asymmetric unit

Contents

Description

Header details

Protein chain

Ligands

LEU-ALA-THR-LYS-
ALA-ALA-ARG-M3L-
SER

Waters ×194

* Residue conservation analysis

Tools

Image Generation

AstexViewer™@PDBe

Run PROCHECK

Clefts Calculation

		Biological unit, dimer (as deduced by PQS)

PDB id:

1pdq

Name:

Structural protein

Title:

Polycomb chromodomain complexed with the histone h3 tail containing trimethyllysine 27.

Structure:

Polycomb protein. Chain: a. Fragment: residues 15-77. Engineered: yes. Histone h3.3. Chain: b. Fragment: residues 15-32. Synonym: h3.A, h3.B, h3.3q. 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: synthetic peptide

Biological unit:

Dimer (from PQS)

UniProt:

P26017 (PC_DROME)

Seq:

Struc:

Seq:

390 a.a.

Struc:

51 a.a.

Key:		PfamA domain
		Secondary structure			CATH domain

Resolution:

1.76Å

R-factor:

0.223

R-free:

0.253

Authors:

W.Fischle,Y.Wang,S.A.Jacobs,Y.Kim,C.D.Allis,S.Khorasanizadeh

Key ref:

W.Fischle et al. (2003). Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains.. Genes Dev, 17, 1870-1881. [PubMed id: 12897054] [DOI: 10.1101/gad.1110503]

Date:

20-May-03

Release date:

26-Aug-03

Related entries:

1kna
1kne
1guw

Quick_links

RCSB

PDBe

SRS

MMDB

JenaLib

OCA

PDBWiki

Proteopedia

CATH

SCOP

FSSP

HSSP

PDBSWS

PDBbind

PQS

ProSAT

Whatcheck

EDS

Procheck

Clefts

Surface

Key reference

DOI no: 10.1101/gad.1110503 Genes Dev 17:1870-1881 (2003)

PubMed id: 12897054

Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains.

W.Fischle, Y.Wang, S.A.Jacobs, Y.Kim, C.D.Allis, S.Khorasanizadeh.

ABSTRACT

On the histone H3 tail, Lys 9 and Lys 27 are both methylation sites associated with epigenetic repression, and reside within a highly related sequence motif ARKS. Here we show that the chromodomain proteins Polycomb (Pc) and HP1 (heterochromatin protein 1) are highly discriminatory for binding to these sites in vivo and in vitro. In Drosophila S2 cells, and on polytene chromosomes, methyl-Lys 27 and Pc are both excluded from areas that are enriched in methyl-Lys 9 and HP1. Swapping of the chromodomain regions of Pc and HP1 is sufficient for switching the nuclear localization patterns of these factors, indicating a role for their chromodomains in both target site binding and discrimination. To better understand the molecular basis for the selection of methyl-lysine binding sites, we solved the 1.8 A structure of the Pc chromodomain in complex with a H3 peptide bearing trimethyl-Lys 27, and compared it with our previously determined structure of the HP1 chromodomain in complex with a H3 peptide bearing trimethyl-Lys 9. The Pc chromodomain distinguishes its methylation target on the H3 tail via an extended recognition groove that binds five additional residues preceding the ARKS motif.

Literature references that cite this PDB file's key reference

PubMed id Reference

19937593 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.

19629595 A.I.Shevchenko, S.V.Pavlova, E.V.Dementyeva, and S.M.Zakian (2009).
Mosaic heterochromatin of the inactive X chromosome in vole Microtus rossiaemeridionalis.

Mamm Genome, 20, 644-653.

19541851 A.N.Scharf, T.K.Barth, and A.Imhof (2009).
Establishment of histone modifications after chromatin assembly.

Nucleic Acids Res, 37, 5032-5040.

19005673 C.Baumann, and R.De La Fuente (2009).
ATRX marks the inactive X chromosome (Xi) in somatic cells and during imprinted X chromosome inactivation in trophoblast stem cells.

Chromosoma, 118, 209-222.

19750210 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.

20003410 D.Dryhurst, T.Ishibashi, K.L.Rose, J.M.Eirín-López, D.McDonald, B.Silva-Moreno, N.Veldhoen, C.C.Helbing, M.J.Hendzel, J.Shabanowitz, D.F.Hunt, and J.Ausió (2009).
Characterization of the histone H2A.Z-1 and H2A.Z-2 isoforms in vertebrates.

BMC Biol, 7, 86.

19956676 D.J.Bua, A.J.Kuo, P.Cheung, C.L.Liu, V.Migliori, A.Espejo, F.Casadio, C.Bassi, B.Amati, M.T.Bedford, E.Guccione, and O.Gozani (2009).
Epigenome microarray platform for proteome-wide dissection of chromatin-signaling networks.

PLoS One, 4, e6789.

19503595 E.M.Kallin, R.Cao, R.Jothi, K.Xia, K.Cui, K.Zhao, and Y.Zhang (2009).
Genome-wide uH2A localization analysis highlights Bmi1-dependent deposition of the mark at repressed genes.

PLoS Genet, 5, e1000506.

18853173 E.de Wit, and B.van Steensel (2009).
Chromatin domains in higher eukaryotes: insights from genome-wide mapping studies.

Chromosoma, 118, 25-36.

19636380 G.N.Maertens, S.El Messaoudi-Aubert, T.Racek, J.K.Stock, J.Nicholls, M.Rodriguez-Niedenführ, J.Gil, and G.Peters (2009).
Several distinct polycomb complexes regulate and co-localize on the INK4a tumor suppressor locus.

PLoS One, 4, e6380.

19270745 H.A.Baskind, L.Na, Q.Ma, M.P.Patel, D.L.Geenen, and Q.T.Wang (2009).
Functional conservation of asxl2, a murine homolog for the Drosophila enhancer of trithorax and polycomb group gene asx.

PLoS ONE, 4, e4750.

19462008 H.Agherbi, A.Gaussmann-Wenger, C.Verthuy, L.Chasson, M.Serrano, and M.Djabali (2009).
Polycomb mediated epigenetic silencing and replication timing at the INK4a/ARF locus during senescence.

PLoS One, 4, e5622.

19451220 H.Boukarabila, A.J.Saurin, E.Batsché, N.Mossadegh, M.van Lohuizen, A.P.Otte, J.Pradel, C.Muchardt, M.Sieweke, and E.Duprez (2009).
The PRC1 Polycomb group complex interacts with PLZF/RARA to mediate leukemic transformation.

Genes Dev, 23, 1195-1206.

19808672 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.

19335899 J.A.Rosenfeld, Z.Wang, D.E.Schones, K.Zhao, R.DeSalle, and M.Q.Zhang (2009).
Determination of enriched histone modifications in non-genic portions of the human genome.

BMC Genomics, 10, 143.

19574378 J.A.Simon (2009).
Transcription. Sweet silencing.

Science, 325, 45-46.

19841675 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: 3feo

18985277 J.K.Kim, M.Samaranayake, and S.Pradhan (2009).
Epigenetic mechanisms in mammals.

Cell Mol Life Sci, 66, 596-612.

19884659 L.B.Song, J.Li, W.T.Liao, Y.Feng, C.P.Yu, L.J.Hu, Q.L.Kong, L.H.Xu, X.Zhang, W.L.Liu, M.Z.Li, L.Zhang, T.B.Kang, L.W.Fu, W.L.Huang, Y.F.Xia, S.W.Tsao, M.Li, V.Band, H.Band, Q.H.Shi, Y.X.Zeng, and M.S.Zeng (2009).
The polycomb group protein Bmi-1 represses the tumor suppressor PTEN and induces epithelial-mesenchymal transition in human nasopharyngeal epithelial cells.

J Clin Invest, 119, 3626-3636.

19158989 N.Omura, and M.Goggins (2009).
Epigenetics and epigenetic alterations in pancreatic cancer.

Int J Clin Exp Pathol, 2, 310-326.

19513271 O.Novikova (2009).
Chromodomains and LTR retrotransposons in plants.

Commun Integr Biol, 2, 158-162.

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.

Magn Reson Chem, 47, 352-358.

19528329 R.B.Emmons, H.Genetti, S.Filandrinos, J.Lokere, and C.T.Wu (2009).
Molecular genetic analysis of Suppressor 2 of zeste identifies key functional domains.

Genetics, 182, 999.

19554611 R.P.Kumar (2009).
Polycomb group proteins: remembering how to catch chromatin during replication.

Bioessays, 31, 822-825.

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.

19322211 T.Neff, and S.A.Armstrong (2009).
Chromatin maps, histone modifications and leukemia.

Leukemia, 23, 1243-1251.

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

18268008 A.Safi, K.A.Wallace, and L.N.Rusche (2008).
Evolution of new function through a single amino acid change in the yeast repressor Sum1p.

Mol Cell Biol, 28, 2567-2578.

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

18568039 D.Egli, G.Birkhoff, and K.Eggan (2008).
Mediators of reprogramming: transcription factors and transitions through mitosis.

Nat Rev Mol Cell Biol, 9, 505-516.

18521949 E.A.Gustafson, and G.M.Wessel (2008).
Polycomb group gene expression in the sea urchin.

Dev Dyn, 237, 1851-1861.

18227505 E.Bernstein, T.L.Muratore-Schroeder, R.L.Diaz, J.C.Chow, L.N.Changolkar, J.Shabanowitz, E.Heard, J.R.Pehrson, D.F.Hunt, and C.D.Allis (2008).
A phosphorylated subpopulation of the histone variant macroH2A1 is excluded from the inactive X chromosome and enriched during mitosis.

Proc Natl Acad Sci U S A, 105, 1533-1538.

18560994 E.Fedorova, N.Sadoni, I.K.Dahlsveen, J.Koch, E.Kremmer, D.Eick, R.Paro, and D.Zink (2008).
The nuclear organization of Polycomb/Trithorax group response elements in larval tissues of Drosophila melanogaster.

Chromosome Res, 16, 649-673.

18039863 E.R.Smith, M.G.Lee, B.Winter, N.M.Droz, J.C.Eissenberg, R.Shiekhattar, and A.Shilatifard (2008).
Drosophila UTX is a histone H3 Lys27 demethylase that colocalizes with the elongating form of RNA polymerase II.

Mol Cell Biol, 28, 1041-1046.

18369463 E.de Wit, U.Braunschweig, F.Greil, H.J.Bussemaker, and B.van Steensel (2008).
Global chromatin domain organization of the Drosophila genome.

PLoS Genet, 4, e1000045.

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.

18381279 J.J.Pesavento, C.R.Bullock, R.D.LeDuc, C.A.Mizzen, and N.L.Kelleher (2008).
Combinatorial modification of human histone H4 quantitated by two-dimensional liquid chromatography coupled with top down mass spectrometry.

J Biol Chem, 283, 14927-14937.

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.

17625597 K.Lee, G.Adhikary, S.Balasubramanian, R.Gopalakrishnan, T.McCormick, G.P.Dimri, R.L.Eckert, and E.A.Rorke (2008).
Expression of Bmi-1 in epidermis enhances cell survival by altering cell cycle regulatory protein expression and inhibiting apoptosis.

J Invest Dermatol, 128, 9.

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.

18375980 M.Lloret-Llinares, C.Carré, A.Vaquero, N.de Olano, and F.Azorín (2008).
Characterization of Drosophila melanogaster JmjC+N histone demethylases.

Nucleic Acids Res, 36, 2852-2863.

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.

18293357 N.Soshnikova, and D.Duboule (2008).
Epigenetic regulation of Hox gene activation: the waltz of methyls.

Bioessays, 30, 199-202.

19072646 P.K.Lo, and S.Sukumar (2008).
Epigenomics and breast cancer.

Pharmacogenomics, 9, 1879-1902.

18493325 P.van der Stoop, E.A.Boutsma, D.Hulsman, S.Noback, M.Heimerikx, R.M.Kerkhoven, J.W.Voncken, L.F.Wessels, and M.van Lohuizen (2008).
Ubiquitin E3 ligase Ring1b/Rnf2 of polycomb repressive complex 1 contributes to stable maintenance of mouse embryonic stem cells.

PLoS ONE, 3, e2235.

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.

18498648 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.

18673494 S.Balasubramanian, K.Lee, G.Adhikary, R.Gopalakrishnan, E.A.Rorke, and R.L.Eckert (2008).
The Bmi-1 polycomb group gene in skin cancer: regulation of function by (-)-epigallocatechin-3-gallate.

Nutr Rev, 66, S65-S68.

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.

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.

18256242 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.

18224410 Y.Takihara (2008).
Role of Polycomb-group genes in sustaining activities of normal and malignant stem cells.

Int J Hematol, 87, 25-34.

18037899 A.J.Ruthenburg, H.Li, D.J.Patel, and C.D.Allis (2007).
Multivalent engagement of chromatin modifications by linked binding modules.

Nat Rev Mol Cell Biol, 8, 983-994.

17470536 A.Smallwood, P.O.Estève, S.Pradhan, and M.Carey (2007).
Functional cooperation between HP1 and DNMT1 mediates gene silencing.

Genes Dev, 21, 1169-1178.

17921257 C.Beisel, A.Buness, I.M.Roustan-Espinosa, B.Koch, S.Schmitt, S.A.Haas, M.Hild, T.Katsuyama, and R.Paro (2007).
Comparing active and repressed expression states of genes controlled by the Polycomb/Trithorax group proteins.

Proc Natl Acad Sci U S A, 104, 16615-16620.

17335352 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.

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.

Mol Cell Biol, 27, 2014-2026.

17542647 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.

17387148 H.Ferreira, J.Somers, R.Webster, A.Flaus, and T.Owen-Hughes (2007).
Histone tails and the H3 alphaN helix regulate nucleosome mobility and stability.

Mol Cell Biol, 27, 4037-4048.

17962312 H.G.Chin, P.O.Estève, M.Pradhan, J.Benner, D.Patnaik, M.F.Carey, and S.Pradhan (2007).
Automethylation of G9a and its implication in wider substrate specificity and HP1 binding.

Nucleic Acids Res, 35, 7313-7323.

17251191 J.A.Casas-Mollano, K.van Dijk, J.Eisenhart, and H.Cerutti (2007).
SET3p monomethylates histone H3 on lysine 9 and is required for the silencing of tandemly repeated transgenes in Chlamydomonas.

Nucleic Acids Res, 35, 939-950.

17589523 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: 2q8c 2q8d 2q8e

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

17277801 L.Corsini, and M.Sattler (2007).
Tudor hooks up with DNA repair.

Nat Struct Mol Biol, 14, 98-99.

17620408 M.Leeb, and A.Wutz (2007).
Ring1B is crucial for the regulation of developmental control genes and PRC1 proteins but not X inactivation in embryonic cells.

J Cell Biol, 178, 219-229.

17332741 N.Dietrich, A.P.Bracken, E.Trinh, C.K.Schjerling, H.Koseki, J.Rappsilber, K.Helin, and K.H.Hansen (2007).
Bypass of senescence by the polycomb group protein CBX8 through direct binding to the INK4A-ARF locus.

EMBO J, 26, 1637-1648.

17409063 P.Neumann, H.Yan, and J.Jiang (2007).
The centromeric retrotransposons of rice are transcribed and differentially processed by RNA interference.

Genetics, 176, 749-761.

18096052 P.Robin, L.Fritsch, O.Philipot, F.Svinarchuk, and S.Ait-Si-Ali (2007).
Post-translational modifications of histones H3 and H4 associated with the histone methyltransferases Suv39h1 and G9a.

Genome Biol, 8, R270.

17023513 Q.Gan, T.Yoshida, O.G.McDonald, and G.K.Owens (2007).
Concise review: epigenetic mechanisms contribute to pluripotency and cell lineage determination of embryonic stem cells.

Stem Cells, 25, 2-9.

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.

17581885 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.

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.

17984971 S.Lall (2007).
Primers on chromatin.

Nat Struct Mol Biol, 14, 1110-1115.

17892444 S.Liu, Y.Yu, Y.Ruan, D.Meyer, M.Wolff, L.Xu, N.Wang, A.Steinmetz, and W.H.Shen (2007).
Plant SET- and RING-associated domain proteins in heterochromatinization.

Plant J, 52, 914-926.

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

17938195 T.H.Kang, D.Y.Park, Y.H.Choi, K.J.Kim, H.S.Yoon, and K.T.Kim (2007).
Mitotic histone H3 phosphorylation by vaccinia-related kinase 1 in mammalian cells.

Mol Cell Biol, 27, 8533-8546.

17173055 Y.B.Schwartz, and V.Pirrotta (2007).
Polycomb silencing mechanisms and the management of genomic programmes.

Nat Rev Genet, 8, 9.

16547465 A.Buscaino, G.Legube, and A.Akhtar (2006).
X-chromosome targeting and dosage compensation are mediated by distinct domains in MSL-3.

EMBO Rep, 7, 531-538.

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.

17224041 G.Lomberk, L.Wallrath, and R.Urrutia (2006).
The Heterochromatin Protein 1 family.

Genome Biol, 7, 228.

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.

16821138 K.Bouazoune, and A.Brehm (2006).
ATP-dependent chromatin remodeling complexes in Drosophila.

Chromosome Res, 14, 433-449.

16551261 K.M.Ansel, I.Djuretic, B.Tanasa, and A.Rao (2006).
Regulation of Th2 differentiation and Il4 locus accessibility.

Annu Rev Immunol, 24, 607-656.

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.

16507439 P.A.Wade, and T.K.Archer (2006).
Epigenetics: environmental instructions for the genome.

Environ Health Perspect, 114, A140-A141.

16506098 P.J.Horn, and C.L.Peterson (2006).
Heterochromatin assembly: a new twist on an old model.

Chromosome Res, 14, 83-94.

17048991 P.Jelinic, J.C.Stehle, and P.Shaw (2006).
The testis-specific factor CTCFL cooperates with the protein methyltransferase PRMT7 in H19 imprinting control region methylation.

PLoS Biol, 4, e355.

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

16759393 R.M.Nissen, A.Amsterdam, and N.Hopkins (2006).
A zebrafish screen for craniofacial mutants identifies wdr68 as a highly conserved gene required for endothelin-1 expression.

BMC Dev Biol, 6, 28.

16506095 S.J.McBryant, V.H.Adams, and J.C.Hansen (2006).
Chromatin architectural proteins.

Chromosome Res, 14, 39-51.

16680199 S.Kalantry, and T.Magnuson (2006).
The Polycomb group protein EED is dispensable for the initiation of random X-chromosome inactivation.

PLoS Genet, 2, e66.

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.

16857008 T.Jenuwein (2006).
The epigenetic magic of histone lysine methylation.

FEBS J, 273, 3121-3135.

16618800 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.

16512904 V.Krauss, A.Fassl, P.Fiebig, I.Patties, and H.Sass (2006).
The evolution of the histone methyltransferase gene Su(var)3-9 in metazoans includes a fusion with and a re-fission from a functionally unrelated gene.

BMC Evol Biol, 6, 18.

16732288 Y.B.Schwartz, T.G.Kahn, D.A.Nix, X.Y.Li, R.Bourgon, M.Biggin, and V.Pirrotta (2006).
Genome-wide analysis of Polycomb targets in Drosophila melanogaster.

Nat Genet, 38, 700-705.

16826231 Y.Zhang (2006).
It takes a PHD to interpret histone methylation.

Nat Struct Mol Biol, 13, 572-574.

15821938 A.A.Gortchakov, H.Eggert, M.Gan, J.Mattow, I.F.Zhimulev, and H.Saumweber (2005).
Chriz, a chromodomain protein specific for the interbands of Drosophila melanogaster polytene chromosomes.

Chromosoma, 114, 54-66.

16261189 C.Martin, and Y.Zhang (2005).
The diverse functions of histone lysine methylation.

Nat Rev Mol Cell Biol, 6, 838-849.

16299514 C.Qian, Q.Zhang, S.Li, L.Zeng, M.J.Walsh, and M.M.Zhou (2005).
Structure and chromosomal DNA binding of the SWIRM domain.

Nat Struct Mol Biol, 12, 1078-1085.

PDB codes: 2aqe 2aqf

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.

15601853 H.G.Yoon, Y.Choi, P.A.Cole, and J.Wong (2005).
Reading and function of a histone code involved in targeting corepressor complexes for repression.

Mol Cell Biol, 25, 324-335.

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.

16285873 J.C.Lucchesi, W.G.Kelly, and B.Panning (2005).
Chromatin remodeling in dosage compensation.

Annu Rev Genet, 39, 615-651.

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

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.

15630020 J.Swaminathan, E.M.Baxter, and V.G.Corces (2005).
The role of histone H2Av variant replacement and histone H4 acetylation in the establishment of Drosophila heterochromatin.

Genes Dev, 19, 65-76.

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.

EMBO J, 24, 108-119.

16244868 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.

15776017 M.Nekrasov, B.Wild, and J.Müller (2005).
Nucleosome binding and histone methyltransferase activity of Drosophila PRC2.

EMBO Rep, 6, 348-353.

15774718 M.Tachibana, J.Ueda, M.Fukuda, N.Takeda, T.Ohta, H.Iwanari, T.Sakihama, T.Kodama, T.Hamakubo, and Y.Shinkai (2005).
Histone methyltransferases G9a and GLP form heteromeric complexes and are both crucial for methylation of euchromatin at H3-K9.

Genes Dev, 19, 815-826.

15892607 N.A.Tchurikov (2005).
Molecular mechanisms of epigenetics.

Biochemistry (Mosc), 70, 406-423.

15899859 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.

16135807 R.T.Utley, N.Lacoste, O.Jobin-Robitaille, S.Allard, and J.Côté (2005).
Regulation of NuA4 histone acetyltransferase activity in transcription and DNA repair by phosphorylation of histone H4.

Mol Cell Biol, 25, 8179-8190.

15741315 S.Schmitt, M.Prestel, and R.Paro (2005).
Intergenic transcription through a polycomb group response element counteracts silencing.

Genes Dev, 19, 697-708.

15862105 S.Sung, and R.M.Amasino (2005).
Remembering winter: toward a molecular understanding of vernalization.

Annu Rev Plant Biol, 56, 491-508.

16222244 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.

16222246 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.

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.

15869391 X.Cheng, R.E.Collins, and X.Zhang (2005).
Structural and sequence motifs of protein (histone) methylation enzymes.

Annu Rev Biophys Biomol Struct, 34, 267-294.

15448640 A.Breiling, L.P.O'Neill, D.D'Eliseo, B.M.Turner, and V.Orlando (2004).
Epigenome changes in active and inactive polycomb-group-controlled regions.

EMBO Rep, 5, 976-982.

14702037 A.Herbert (2004).
The four Rs of RNA-directed evolution.

Nat Genet, 36, 19-25.

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.

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

15105826 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.

15071554 C.Maison, and G.Almouzni (2004).
HP1 and the dynamics of heterochromatin maintenance.

Nat Rev Mol Cell Biol, 5, 296-304.

15169908 C.Rougeulle, J.Chaumeil, K.Sarma, C.D.Allis, D.Reinberg, P.Avner, and E.Heard (2004).
Differential histone H3 Lys-9 and Lys-27 methylation profiles on the X chromosome.

Mol Cell Biol, 24, 5475-5484.

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.

Genetics, 166, 187-200.

15503092 G.L.Buglia, and M.Ferraro (2004).
Germline cyst development and imprinting in male mealybug Planococcus citri.

Chromosoma, 113, 284-294.

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.

J Cell Biol, 167, 1025-1035.

15040448 L.A.Boyer, R.R.Latek, and C.L.Peterson (2004).
The SANT domain: a unique histone-tail-binding module?

Nat Rev Mol Cell Biol, 5, 158-163.

15568982 L.Ringrose, and R.Paro (2004).
Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins.

Annu Rev Genet, 38, 413-443.

15520279 L.Srinivasan, and M.L.Atchison (2004).
YY1 DNA binding and PcG recruitment requires CtBP.

Genes Dev, 18, 2596-2601.

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.

14970850 S.B.Hake, A.Xiao, and C.D.Allis (2004).
Linking the epigenetic 'language' of covalent histone modifications to cancer.

Br J Cancer, 90, 761-769.

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.

16117662 Y.B.Schwartz, T.G.Kahn, G.I.Dellino, and V.Pirrotta (2004).
Polycomb silencing mechanisms in Drosophila.

Cold Spring Harb Symp Quant Biol, 69, 301-308.

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.

14523437 W.Fischle, Y.Wang, and C.D.Allis (2003).
Binary switches and modification cassettes in histone biology and beyond.

Nature, 425, 475-479.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.