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Volumn 23, Issue 7, 2016, Pages 682-690

The dynamic interactome and genomic targets of Polycomb complexes during stem-cell differentiation

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H3; POLYCOMB GROUP PROTEIN; CHROMATIN; HISTONE;

EID: 84977650406     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.3248     Document Type: Article
Times cited : (152)

References (50)
  • 1
    • 84902185617 scopus 로고    scopus 로고
    • Chromatin repressive complexes in stem cells, development, and cancer
    • Laugesen, A. & Helin, K. Chromatin repressive complexes in stem cells, development, and cancer. Cell Stem Cell 14, 735-751 (2014).
    • (2014) Cell Stem Cell , vol.14 , pp. 735-751
    • Laugesen, A.1    Helin, K.2
  • 2
    • 84891478098 scopus 로고    scopus 로고
    • Chromatin organization and global regulation of Hox gene clusters
    • Montavon, T. & Duboule, D. Chromatin organization and global regulation of Hox gene clusters. Phil. Trans. R. Soc. Lond. B 368, 20120367 (2013).
    • (2013) Phil. Trans. R. Soc. Lond. B , vol.368 , pp. 20120367
    • Montavon, T.1    Duboule, D.2
  • 3
    • 84876871047 scopus 로고    scopus 로고
    • Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put
    • Simon, J.A. & Kingston, R.E. Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. Mol. Cell 49, 808-824 (2013).
    • (2013) Mol. Cell , vol.49 , pp. 808-824
    • Simon, J.A.1    Kingston, R.E.2
  • 4
    • 84885393469 scopus 로고    scopus 로고
    • Transcriptional regulation by Polycomb group proteins
    • Di Croce, L. & Helin, K. Transcriptional regulation by Polycomb group proteins. Nat. Struct. Mol. Biol. 20, 1147-1155 (2013).
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 1147-1155
    • Di Croce, L.1    Helin, K.2
  • 5
    • 7244234099 scopus 로고    scopus 로고
    • Role of histone H2A ubiquitination in Polycomb silencing
    • Wang, H. et al. Role of histone H2A ubiquitination in Polycomb silencing. Nature 431, 873-878 (2004).
    • (2004) Nature , vol.431 , pp. 873-878
    • Wang, H.1
  • 6
    • 7744228427 scopus 로고    scopus 로고
    • Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation
    • de Napoles, M. et al. Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation. Dev. Cell 7, 663-676 (2004).
    • (2004) Dev. Cell , vol.7 , pp. 663-676
    • De Napoles, M.1
  • 7
    • 0036830642 scopus 로고    scopus 로고
    • Role of histone H3 lysine 27 methylation in Polycomb-group silencing
    • Cao, R. et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039-1043 (2002).
    • (2002) Science , vol.298 , pp. 1039-1043
    • Cao, R.1
  • 8
    • 18644383738 scopus 로고    scopus 로고
    • Histone methyltransferase activity of a Drosophila Polycomb group repressor complex
    • Müller, J. et al. Histone methyltransferase activity of a Drosophila Polycomb group repressor complex. Cell 111, 197-208 (2002).
    • (2002) Cell , vol.111 , pp. 197-208
    • Müller, J.1
  • 9
    • 77952429798 scopus 로고    scopus 로고
    • Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB
    • Scheuermann, J.C. et al. Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB. Nature 465, 243-247 (2010).
    • (2010) Nature , vol.465 , pp. 243-247
    • Scheuermann, J.C.1
  • 10
    • 84888001513 scopus 로고    scopus 로고
    • A new world of Polycombs: Unexpected partnerships and emerging functions
    • Schwartz, Y.B. & Pirrotta, V. A new world of Polycombs: unexpected partnerships and emerging functions. Nat. Rev. Genet. 14, 853-864 (2013).
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 853-864
    • Schwartz, Y.B.1    Pirrotta, V.2
  • 11
    • 84863011309 scopus 로고    scopus 로고
    • PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes
    • Gao, Z. et al. PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Mol. Cell 45, 344-356 (2012).
    • (2012) Mol. Cell , vol.45 , pp. 344-356
    • Gao, Z.1
  • 12
    • 84871740411 scopus 로고    scopus 로고
    • Stoichiometry of chromatin-associated protein complexes revealed by label-free quantitative mass spectrometry-based proteomics
    • Smits, A.H., Jansen, P.W., Poser, I., Hyman, A.A. & Vermeulen, M. Stoichiometry of chromatin-associated protein complexes revealed by label-free quantitative mass spectrometry-based proteomics. Nucleic Acids Res. 41, e28 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. e28
    • Smits, A.H.1    Jansen, P.W.2    Poser, I.3    Hyman, A.A.4    Vermeulen, M.5
  • 13
    • 84922217833 scopus 로고    scopus 로고
    • An AUTS2-Polycomb complex activates gene expression in the CNS
    • Gao, Z. et al. An AUTS2-Polycomb complex activates gene expression in the CNS. Nature 516, 349-354 (2014).
    • (2014) Nature , vol.516 , pp. 349-354
    • Gao, Z.1
  • 14
    • 84941000940 scopus 로고    scopus 로고
    • Polycomb regulates mesoderm cell fate-specification in embryonic stem cells through activation and repression mechanisms
    • Morey, L. et al. Polycomb regulates mesoderm cell fate-specification in embryonic stem cells through activation and repression mechanisms. Cell Stem Cell 17, 300-315 (2015).
    • (2015) Cell Stem Cell , vol.17 , pp. 300-315
    • Morey, L.1
  • 15
    • 84887460647 scopus 로고    scopus 로고
    • PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells
    • Kaneko, S., Son, J., Shen, S.S., Reinberg, D. & Bonasio, R. PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells. Nat. Struct. Mol. Biol. 20, 1258-1264 (2013).
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 1258-1264
    • Kaneko, S.1    Son, J.2    Shen, S.S.3    Reinberg, D.4    Bonasio, R.5
  • 16
    • 84955387038 scopus 로고    scopus 로고
    • Non-canonical PRC1.1 targets active genes independent of H3K27me3 and is essential for leukemogenesis
    • van den Boom, V. et al. Non-canonical PRC1.1 targets active genes independent of H3K27me3 and is essential for leukemogenesis. Cell Rep. 14, 332-346 (2016).
    • (2016) Cell Rep. , vol.14 , pp. 332-346
    • Van Den Boom, V.1
  • 17
    • 0043127085 scopus 로고    scopus 로고
    • Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains
    • Fischle, W. et al. Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev. 17, 1870-1881 (2003).
    • (2003) Genes Dev. , vol.17 , pp. 1870-1881
    • Fischle, W.1
  • 18
    • 0041624288 scopus 로고    scopus 로고
    • Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27
    • Min, J., Zhang, Y. & Xu, R.M. Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev. 17, 1823-1828 (2003).
    • (2003) Genes Dev. , vol.17 , pp. 1823-1828
    • Min, J.1    Zhang, Y.2    Xu, R.M.3
  • 19
    • 84902127230 scopus 로고    scopus 로고
    • Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation
    • Blackledge, N.P. et al. Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation. Cell 157, 1445-1459 (2014).
    • (2014) Cell , vol.157 , pp. 1445-1459
    • Blackledge, N.P.1
  • 20
    • 84901987800 scopus 로고    scopus 로고
    • Histone H2A monoubiquitination promotes histone H3 methylation in Polycomb repression
    • Kalb, R. et al. Histone H2A monoubiquitination promotes histone H3 methylation in Polycomb repression. Nat. Struct. Mol. Biol. 21, 569-571 (2014).
    • (2014) Nat. Struct. Mol. Biol. , vol.21 , pp. 569-571
    • Kalb, R.1
  • 21
    • 84941956299 scopus 로고    scopus 로고
    • The E3 ubiquitin ligase activity of RING1B is not essential for early mouse development
    • Illingworth, R.S. et al. The E3 ubiquitin ligase activity of RING1B is not essential for early mouse development. Genes Dev. 29, 1897-1902 (2015).
    • (2015) Genes Dev. , vol.29 , pp. 1897-1902
    • Illingworth, R.S.1
  • 22
    • 84938149171 scopus 로고    scopus 로고
    • Transcriptional repression by PRC1 in the absence of H2A monoubiquitylation
    • Pengelly, A.R., Kalb, R., Finkl, K. & Müller, J. Transcriptional repression by PRC1 in the absence of H2A monoubiquitylation. Genes Dev. 29, 1487-1492 (2015).
    • (2015) Genes Dev. , vol.29 , pp. 1487-1492
    • Pengelly, A.R.1    Kalb, R.2    Finkl, K.3    Müller, J.4
  • 23
    • 42949095911 scopus 로고    scopus 로고
    • BAC TransgeneOmics: A high-throughput method for exploration of protein function in mammals
    • Poser, I. et al. BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat. Methods 5, 409-415 (2008).
    • (2008) Nat. Methods , vol.5 , pp. 409-415
    • Poser, I.1
  • 24
    • 84874771985 scopus 로고    scopus 로고
    • Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives
    • Spruijt, C.G. et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 152, 1146-1159 (2013).
    • (2013) Cell , vol.152 , pp. 1146-1159
    • Spruijt, C.G.1
  • 25
    • 84894302147 scopus 로고    scopus 로고
    • Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL cross-linking and affinity purification
    • Alekseyenko, A.A., Gorchakov, A.A., Kharchenko, P.V. & Kuroda, M.I. Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL cross-linking and affinity purification. Proc. Natl. Acad. Sci. USA 111, 2488-2493 (2014).
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. 2488-2493
    • Alekseyenko, A.A.1    Gorchakov, A.A.2    Kharchenko, P.V.3    Kuroda, M.I.4
  • 26
    • 84930432382 scopus 로고    scopus 로고
    • Functional proteomic analysis of repressive histone methyltransferase complexes reveals ZNF518B as a G9A regulator
    • Maier, V.K. et al. Functional proteomic analysis of repressive histone methyltransferase complexes reveals ZNF518B as a G9A regulator. Mol. Cell. Proteomics 14, 1435-1446 (2015).
    • (2015) Mol. Cell. Proteomics , vol.14 , pp. 1435-1446
    • Maier, V.K.1
  • 27
    • 79956322553 scopus 로고    scopus 로고
    • Global quantification of mammalian gene expression control
    • Schwanhäusser, B. et al. Global quantification of mammalian gene expression control. Nature 473, 337-342 (2011).
    • (2011) Nature , vol.473 , pp. 337-342
    • Schwanhäusser, B.1
  • 28
    • 84866117936 scopus 로고    scopus 로고
    • Identification of cross-linked peptides from complex samples
    • Yang, B. et al. Identification of cross-linked peptides from complex samples. Nat. Methods 9, 904-906 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 904-906
    • Yang, B.1
  • 29
    • 84881497258 scopus 로고    scopus 로고
    • Molecular architecture of human polycomb repressive complex 2
    • Ciferri, C. et al. Molecular architecture of human polycomb repressive complex 2. eLife 1, e00005 (2012).
    • (2012) ELife , vol.1
    • Ciferri, C.1
  • 30
    • 72249104107 scopus 로고    scopus 로고
    • Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells
    • Shen, X. et al. Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells. Cell 139, 1303-1314 (2009).
    • (2009) Cell , vol.139 , pp. 1303-1314
    • Shen, X.1
  • 31
    • 84903215772 scopus 로고    scopus 로고
    • MBD5 and MBD6 interact with the human PR-DUB complex through their methyl-CpG-binding domain
    • Baymaz, H.I. et al. MBD5 and MBD6 interact with the human PR-DUB complex through their methyl-CpG-binding domain. Proteomics 14, 2179-2189 (2014).
    • (2014) Proteomics , vol.14 , pp. 2179-2189
    • Baymaz, H.I.1
  • 32
    • 84941313604 scopus 로고    scopus 로고
    • Investigation of genes important in neurodevelopment disorders in adult human brain
    • Maussion, G. et al. Investigation of genes important in neurodevelopment disorders in adult human brain. Hum. Genet. 134, 1037-1053 (2015).
    • (2015) Hum. Genet. , vol.134 , pp. 1037-1053
    • Maussion, G.1
  • 33
    • 84855516244 scopus 로고    scopus 로고
    • Nonoverlapping functions of the Polycomb group Cbx family of proteins in embryonic stem cells
    • Morey, L. et al. Nonoverlapping functions of the Polycomb group Cbx family of proteins in embryonic stem cells. Cell Stem Cell 10, 47-62 (2012).
    • (2012) Cell Stem Cell , vol.10 , pp. 47-62
    • Morey, L.1
  • 34
    • 84862908896 scopus 로고    scopus 로고
    • MicroRNA regulation of Cbx7 mediates a switch of Polycomb orthologs during ESC differentiation
    • O'Loghlen, A. et al. MicroRNA regulation of Cbx7 mediates a switch of Polycomb orthologs during ESC differentiation. Cell Stem Cell 10, 33-46 (2012).
    • (2012) Cell Stem Cell , vol.10 , pp. 33-46
    • O'Loghlen, A.1
  • 35
    • 84961226693 scopus 로고    scopus 로고
    • Characterizing protein-protein interactions using mass spectrometry: Challenges and opportunities
    • Smits, A.H. & Vermeulen, M. Characterizing protein-protein interactions using mass spectrometry: challenges and opportunities. Trends Biotechnol. http://dx.doi.org/10.1016/j.tibtech.2016.02.014 (2016).
    • (2016) Trends Biotechnol
    • Smits, A.H.1    Vermeulen, M.2
  • 36
    • 55549103314 scopus 로고    scopus 로고
    • A model for transmission of the H3K27me3 epigenetic mark
    • Hansen, K.H. et al. A model for transmission of the H3K27me3 epigenetic mark. Nat. Cell Biol. 10, 1291-1300 (2008).
    • (2008) Nat. Cell Biol. , vol.10 , pp. 1291-1300
    • Hansen, K.H.1
  • 37
    • 0028157458 scopus 로고
    • Contrasting patterns of retinoblastoma protein expression in mouse embryonic stem cells and embryonic fibroblasts
    • Savatier, P., Huang, S., Szekely, L., Wiman, K.G. & Samarut, J. Contrasting patterns of retinoblastoma protein expression in mouse embryonic stem cells and embryonic fibroblasts. Oncogene 9, 809-818 (1994).
    • (1994) Oncogene , vol.9 , pp. 809-818
    • Savatier, P.1    Huang, S.2    Szekely, L.3    Wiman, K.G.4    Samarut, J.5
  • 38
    • 24944484633 scopus 로고    scopus 로고
    • Niche-independent symmetrical self-renewal of a mammalian tissue stem cell
    • Conti, L. et al. Niche-independent symmetrical self-renewal of a mammalian tissue stem cell. PLoS Biol. 3, e283 (2005).
    • (2005) PLoS Biol. , vol.3 , pp. e283
    • Conti, L.1
  • 39
    • 84884626274 scopus 로고    scopus 로고
    • Chromatin sampling: An emerging perspective on targeting polycomb repressor proteins
    • Klose, R.J., Cooper, S., Farcas, A.M., Blackledge, N.P. & Brockdorff, N. Chromatin sampling: an emerging perspective on targeting polycomb repressor proteins. PLoS Genet. 9, e1003717 (2013).
    • (2013) PLoS Genet. , vol.9
    • Klose, R.J.1    Cooper, S.2    Farcas, A.M.3    Blackledge, N.P.4    Brockdorff, N.5
  • 40
    • 0021100690 scopus 로고
    • Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei
    • Dignam, J.D., Lebovitz, R.M. & Roeder, R.G. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11, 1475-1489 (1983).
    • (1983) Nucleic Acids Res. , vol.11 , pp. 1475-1489
    • Dignam, J.D.1    Lebovitz, R.M.2    Roeder, R.G.3
  • 41
    • 34548183872 scopus 로고    scopus 로고
    • Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips
    • Rappsilber, J., Mann, M. & Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc. 2, 1896-1906 (2007).
    • (2007) Nat. Protoc. , vol.2 , pp. 1896-1906
    • Rappsilber, J.1    Mann, M.2    Ishihama, Y.3
  • 42
    • 84962576477 scopus 로고    scopus 로고
    • Cross-linking immunoprecipitation-MS (xIP-MS): Topological analysis of chromatin-associated protein complexes using single affinity purification
    • Makowski, M.M., Willems, E., Jansen, P.W. & Vermeulen, M. Cross-linking immunoprecipitation-MS (xIP-MS): topological analysis of chromatin-associated protein complexes using single affinity purification. Mol. Cell. Proteomics 15, 854-865 (2016).
    • (2016) Mol. Cell. Proteomics , vol.15 , pp. 854-865
    • Makowski, M.M.1    Willems, E.2    Jansen, P.W.3    Vermeulen, M.4
  • 43
    • 84867345063 scopus 로고    scopus 로고
    • A cross-platform toolkit for mass spectrometry and proteomics
    • Chambers, M.C. et al. A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 30, 918-920 (2012).
    • (2012) Nat. Biotechnol. , vol.30 , pp. 918-920
    • Chambers, M.C.1
  • 44
    • 84926486138 scopus 로고    scopus 로고
    • XiNET: Cross-link network maps with residue resolution
    • Combe, C.W., Fischer, L. & Rappsilber, J. xiNET: cross-link network maps with residue resolution. Mol. Cell. Proteomics 14, 1137-1147 (2015).
    • (2015) Mol. Cell. Proteomics , vol.14 , pp. 1137-1147
    • Combe, C.W.1    Fischer, L.2    Rappsilber, J.3
  • 45
    • 34547624303 scopus 로고    scopus 로고
    • Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    • Mikkelsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553-560 (2007).
    • (2007) Nature , vol.448 , pp. 553-560
    • Mikkelsen, T.S.1
  • 46
    • 84655167578 scopus 로고    scopus 로고
    • A chromatin-modifying function of JNK during stem cell differentiation
    • Tiwari, V.K. et al. A chromatin-modifying function of JNK during stem cell differentiation. Nat. Genet. 44, 94-100 (2012).
    • (2012) Nat. Genet. , vol.44 , pp. 94-100
    • Tiwari, V.K.1
  • 47
    • 84905572005 scopus 로고    scopus 로고
    • Gene silencing triggers polycomb repressive complex 2 recruitment to CpG islands genome wide
    • Riising, E.M. et al. Gene silencing triggers polycomb repressive complex 2 recruitment to CpG islands genome wide. Mol. Cell 55, 347-360 (2014).
    • (2014) Mol. Cell , vol.55 , pp. 347-360
    • Riising, E.M.1
  • 48
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
    • (2012) Nature , vol.489 , pp. 57-74
    • ENCODE Project Consortium1
  • 49
    • 77952148742 scopus 로고    scopus 로고
    • Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    • Guttman, M. et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28, 503-510 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 503-510
    • Guttman, M.1
  • 50
    • 77952214662 scopus 로고    scopus 로고
    • GREAT improves functional interpretation of cis-regulatory regions
    • McLean, C.Y. et al. GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol. 28, 495-501 (2010).
    • (2010) Nat. Biotechnol. , vol.28 , pp. 495-501
    • McLean, C.Y.1


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