A High Density Map for Navigating the Human Polycomb Complexome
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R. Aebersold | R. Paro | M. Gerstung | C. Beisel | M. Gstaiger | Timo Glatter | K. Hansen | Simon Hauri | F. Comoglio | M. Seimiya
[1] R. Paro,et al. Polycomb purification by in vivo biotinylation tagging reveals cohesin and Trithorax group proteins as interaction partners , 2011, Proceedings of the National Academy of Sciences.
[2] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[3] A I Saeed,et al. TM4: a free, open-source system for microarray data management and analysis. , 2003, BioTechniques.
[4] J. Min,et al. Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. , 2003, Genes & development.
[5] David M. Livingston,et al. A Complex with Chromatin Modifiers That Occupies E2F- and Myc-Responsive Genes in G0 Cells , 2002, Science.
[6] P. Angrand,et al. Interaction Proteomics Analysis of Polycomb Proteins Defines Distinct PRC1 Complexes in Mammalian Cells* , 2011, Molecular & Cellular Proteomics.
[7] Jeroen A. A. Demmers,et al. dKDM2 couples histone H2A ubiquitylation to histone H3 demethylation during Polycomb group silencing. , 2008, Genes & development.
[8] Jianmin Wu,et al. Integrated network analysis platform for protein-protein interactions , 2009, Nature Methods.
[9] Thomas A Milne,et al. Regulation of MLL1 H3K4 methyltransferase activity by its core components , 2006, Nature Structural &Molecular Biology.
[10] Juri Rappsilber,et al. JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells , 2010, Nature.
[11] M. Wilm,et al. Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB , 2010, Nature.
[12] Giulio Superti-Furga,et al. Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS , 2013, Nature Methods.
[13] D. Zheng,et al. An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting. , 2013, Molecular cell.
[14] Guo-Cheng Yuan,et al. EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. , 2008, Molecular cell.
[15] D. Reinberg,et al. The Polycomb complex PRC2 and its mark in life , 2011, Nature.
[16] Robertson Craig,et al. TANDEM: matching proteins with tandem mass spectra. , 2004, Bioinformatics.
[17] Kristian Helin,et al. Tet proteins connect the O-linked N-acetylglucosamine transferase Ogt to chromatin in embryonic stem cells. , 2013, Molecular cell.
[18] Juri Rappsilber,et al. A model for transmission of the H3K27me3 epigenetic mark , 2008, Nature Cell Biology.
[19] Hao Wu,et al. Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes , 2013, Nature Cell Biology.
[20] R. Kingston,et al. A Drosophila Polycomb group complex includes Zeste and dTAFII proteins , 2001, Nature.
[21] R. Young,et al. The polycomb group protein L3mbtl2 assembles an atypical PRC1-family complex that is essential in pluripotent stem cells and early development. , 2012, Cell stem cell.
[22] P. Farnham,et al. Functional Analysis of KAP1 Genomic Recruitment , 2011, Molecular and Cellular Biology.
[23] Jacob D. Jaffe,et al. Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator* , 2015, Molecular & Cellular Proteomics.
[24] G. Peters,et al. Role for the MOV10 RNA helicase in Polycomb-mediated repression of the INK4a tumor suppressor , 2010, Nature Structural &Molecular Biology.
[25] Amos Tanay,et al. Functional Anatomy of Polycomb and Trithorax Chromatin Landscapes in Drosophila Embryos , 2009, PLoS biology.
[26] Paul Tempst,et al. PRC2 Complexes with JARID2, MTF2, and esPRC2p48 in ES Cells to Modulate ES Cell Pluripotency and Somatic Cell Reprograming , 2011, Stem cells.
[27] S. Orkin,et al. Jumonji Modulates Polycomb Activity and Self-Renewal versus Differentiation of Stem Cells , 2009, Cell.
[28] Cory Y. McLean,et al. GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.
[29] Brigitte Wild,et al. Histone Methyltransferase Activity of a Drosophila Polycomb Group Repressor Complex , 2002, Cell.
[30] Kristian Vlahovicek,et al. Genomation: a Toolkit to Summarize, Annotate and Visualize Genomic Intervals , 2015, Bioinform..
[31] Jürg Müller,et al. Essential Role of the Glycosyltransferase Sxc/Ogt in Polycomb Repression , 2009, Science.
[32] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.
[33] Anke Sparmann,et al. Polycomb silencers control cell fate, development and cancer , 2006, Nature Reviews Cancer.
[34] A. Yasui,et al. Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1 , 2012, Nature Structural &Molecular Biology.
[35] P. Defossez,et al. MBD5 and MBD6 interact with the human PR‐DUB complex through their methyl‐CpG‐binding domain , 2014, Proteomics.
[36] R. Paro,et al. Analysis of chromatin structure by in vivo formaldehyde cross-linking. , 1997, Methods.
[37] S. Gygi,et al. Network organization of the human autophagy system , 2010, Nature.
[38] M. Vidal,et al. Role of histone H2A ubiquitination in Polycomb silencing , 2004, Nature.
[39] M. Vermeulen,et al. Histone H2A monoubiquitination promotes histone H3 methylation in Polycomb repression , 2014, Nature Structural &Molecular Biology.
[40] Yuval Kluger,et al. PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. , 2012, Molecular cell.
[41] H. Stunnenberg,et al. Non-canonical PRC1.1 Targets Active Genes Independent of H3K27me3 and Is Essential for Leukemogenesis. , 2016, Cell reports.
[42] L. Cozzuto,et al. RYBP and Cbx7 define specific biological functions of polycomb complexes in mouse embryonic stem cells. , 2013, Cell reports.
[43] R. Aebersold,et al. An integrated workflow for charting the human interaction proteome: insights into the PP2A system , 2009, Molecular systems biology.
[44] RYBP-PRC1 Complexes Mediate H2A Ubiquitylation at Polycomb Target Sites Independently of PRC2 and H3K27me3 , 2012, Cell.
[45] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[46] Xiaoyong Yang,et al. Disrupting the enzyme complex regulating O-GlcNAcylation blocks signaling and development. , 2006, Glycobiology.
[47] G. Viglietto,et al. Nonredundant and locus-specific gene repression functions of PRC1 paralog family members in human hematopoietic stem/progenitor cells. , 2013, Blood.
[48] Yang Shi,et al. Coordinated histone modifications mediated by a CtBP co-repressor complex , 2003, Nature.
[49] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[50] Natalie I. Tasman,et al. A guided tour of the Trans‐Proteomic Pipeline , 2010, Proteomics.
[51] Ezh2 Requires PHF1 To Efficiently Catalyze H3 Lysine 27 Trimethylation In Vivo , 2008, Molecular and Cellular Biology.
[52] Mary Anne Wheeler,et al. Stem , 1985 .
[53] C. Allis,et al. Mouse Polycomb Proteins Bind Differentially to Methylated Histone H3 and RNA and Are Enriched in Facultative Heterochromatin , 2006, Molecular and Cellular Biology.
[54] Haruhiko Koseki,et al. Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation. , 2004, Developmental cell.
[55] B. Spencer‐Dene,et al. HAN11 binds mDia1 and controls GLI1 transcriptional activity. , 2006, Journal of dermatological science.
[56] Raphael Gottardo,et al. Orchestrating high-throughput genomic analysis with Bioconductor , 2015, Nature Methods.
[57] T. Furuyama,et al. SIR2 Is Required for Polycomb Silencing and Is Associated with an E(Z) Histone Methyltransferase Complex , 2004, Current Biology.
[58] John H. White,et al. Ligand-dependent nuclear receptor corepressor LCoR functions by histone deacetylase-dependent and -independent mechanisms. , 2003, Molecular cell.
[59] Prashanth Athri,et al. Polycomb preferentially targets stalled promoters of coding and noncoding transcripts. , 2011, Genome research.
[60] G. Hart,et al. Cross talk between O-GlcNAcylation and phosphorylation: roles in signaling, transcription, and chronic disease. , 2011, Annual review of biochemistry.
[61] Renato Paro,et al. Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data , 2015, BMC Bioinformatics.
[62] C. Ponting,et al. KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands , 2012, eLife.
[63] M. Cole,et al. Subunit Composition and Substrate Specificity of a MOF-containing Histone Acetyltransferase Distinct from the Male-specific Lethal (MSL) Complex* , 2009, The Journal of Biological Chemistry.
[64] Anthony A. Hyman,et al. Stoichiometry of chromatin-associated protein complexes revealed by label-free quantitative mass spectrometry-based proteomics , 2012, Nucleic acids research.
[65] Anping Li,et al. Cell fate determination factor DACH1 inhibits c-Jun-induced contact-independent growth. , 2007, Molecular biology of the cell.
[66] Malgorzata Schelder,et al. A Polycomb group protein complex with sequence-specific DNA-binding and selective methyl-lysine-binding activities. , 2006, Genes & development.
[67] Hengbin Wang,et al. Role of Histone H3 Lysine 27 Methylation in Polycomb-Group Silencing , 2002, Science.
[68] J. Sale,et al. Cellular epigenetic stability and cancer. , 2012, Trends in genetics : TIG.
[69] P. Hart,et al. Structure of the polycomb group protein PCGF1 in complex with BCOR reveals basis for binding selectivity of PCGF homologs. , 2013, Structure.
[70] K. Helin,et al. Supplemental Information Fbxl 10 / Kdm 2 b Recruits Polycomb Repressive Complex 1 to CpG Islands and Regulates H 2 A Ubiquitylation , 2013 .
[71] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[72] Michael K. Coleman,et al. Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. , 2006, Journal of proteome research.
[73] M. Washburn,et al. Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors , 2006, Proceedings of the National Academy of Sciences.
[74] Youngchang Kim,et al. Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. , 2003, Genes & development.
[75] K. Helin,et al. Fbxl10/Kdm2b recruits polycomb repressive complex 1 to CpG islands and regulates H2A ubiquitylation. , 2013, Molecular cell.
[76] Robert Tibshirani,et al. The Elements of Statistical Learning: Data Mining, Inference, and Prediction, 2nd Edition , 2001, Springer Series in Statistics.
[77] Haruhiko Koseki,et al. Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells , 2007, Nature Cell Biology.
[78] Rafael C. Jimenez,et al. The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases , 2013, Nucleic Acids Res..
[79] Arend Sidow,et al. Jarid2/Jumonji Coordinates Control of PRC2 Enzymatic Activity and Target Gene Occupancy in Pluripotent Cells , 2009, Cell.
[80] D. Reinberg,et al. An AUTS2–Polycomb complex activates gene expression in the CNS , 2014, Nature.
[81] Thomas A. Milne,et al. A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling , 2006, Nature.
[82] W. Liang,et al. 9) TM4 Microarray Software Suite , 2006 .
[83] Hana Kim,et al. AEBP2 as a potential targeting protein for Polycomb Repression Complex PRC2 , 2009 .
[84] Somasekar Seshagiri,et al. Loss of the Tumor Suppressor BAP1 Causes Myeloid Transformation , 2012, Science.
[85] R. Paro,et al. Signaling meets chromatin during tissue regeneration in Drosophila. , 2006, Current opinion in genetics & development.
[86] Renato Paro,et al. Silencing chromatin: comparing modes and mechanisms , 2011, Nature Reviews Genetics.
[87] L. Sánchez-Pulido,et al. RAWUL: A new ubiquitin-like domain in PRC1 Ring finger proteins that unveils putative plant and worm PRC1 orthologs , 2008, BMC Genomics.
[88] L. Cozzuto,et al. Nonoverlapping functions of the Polycomb group Cbx family of proteins in embryonic stem cells. , 2012, Cell stem cell.
[89] M. Hild,et al. Comparing active and repressed expression states of genes controlled by the Polycomb/Trithorax group proteins , 2007, Proceedings of the National Academy of Sciences.
[90] Julien Gagneur,et al. Dynamic regulation by polycomb group protein complexes controls pattern formation and the cell cycle in Drosophila. , 2008, Developmental cell.
[91] N. Tommerup,et al. REST–Mediated Recruitment of Polycomb Repressor Complexes in Mammalian Cells , 2012, PLoS genetics.
[92] Youngsook Lee,et al. JUMONJI, a Critical Factor for Cardiac Development, Functions as a Transcriptional Repressor* , 2003, Journal of Biological Chemistry.
[93] J. Couture,et al. The plasticity of WDR5 peptide-binding cleft enables the binding of the SET1 family of histone methyltransferases , 2012, Nucleic acids research.
[94] Jun S. Song,et al. Polycomb-Like 3 Promotes Polycomb Repressive Complex 2 Binding to CpG Islands and Embryonic Stem Cell Self-Renewal , 2012, PLoS genetics.
[95] D. Reinberg,et al. Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms. , 2008, Molecular cell.
[96] Y. Miyata,et al. DYRK1A binds to an evolutionarily conserved WD40-repeat protein WDR68 and induces its nuclear translocation. , 2011, Biochimica et biophysica acta.
[97] R. Santoro. Analysis of chromatin composition of repetitive sequences: the ChIP-Chop assay. , 2014, Methods in molecular biology.
[98] C. Sánchez,et al. Proteomics Analysis of Ring1B/Rnf2 Interactors Identifies a Novel Complex with the Fbxl10/Jhdm1B Histone Demethylase and the Bcl6 Interacting Corepressor*S , 2007, Molecular & Cellular Proteomics.
[99] L. Ringrose. Polycomb comes of age: genome-wide profiling of target sites. , 2007, Current opinion in cell biology.
[100] D. Reinberg,et al. L3MBTL2 protein acts in concert with PcG protein-mediated monoubiquitination of H2A to establish a repressive chromatin structure. , 2011, Molecular cell.
[101] U. Rüther,et al. Mouse Dac, a novel nuclear factor with homology to Drosophila dachshund shows a dynamic expression in the neural crest, the eye, the neocortex, and the limb bud , 1999, Developmental dynamics : an official publication of the American Association of Anatomists.
[102] Alexey I Nesvizhskii,et al. Abacus: A computational tool for extracting and pre‐processing spectral count data for label‐free quantitative proteomic analysis , 2011, Proteomics.
[103] J. Carroll,et al. The forkhead transcription factor FOXK2 acts as a chromatin targeting factor for the BAP1-containing histone deubiquitinase complex , 2014, Nucleic acids research.
[104] P. Kharchenko,et al. Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL cross-linking and affinity purification , 2014, Proceedings of the National Academy of Sciences.
[105] R. Young,et al. Stem Cells, the Molecular Circuitry of Pluripotency and Nuclear Reprogramming , 2008, Cell.
[106] E. Guccione,et al. On WD40 proteins: Propelling our knowledge of transcriptional control? , 2012, Epigenetics.