Di Croce L, Helin K. Transcriptional regulation by Polycomb group proteins. Nat Struct Mol Biol. Nature Publishing Group. 2013;20(10):1147–55. https://doi.org/10.1038/nsmb.2669.
Article
CAS
PubMed
Google Scholar
Schwartz YB, Pirrotta V. A new world of Polycombs: unexpected partnerships and emerging functions. Nat Rev Genet. Nature Publishing Group. 2013;14(12):853–64. https://doi.org/10.1038/nrg3603.
Article
CAS
PubMed
Google Scholar
Mozgova I, Hennig L. The Polycomb Group Protein Regulatory Network. Annu Rev Plant Biol. Annual Reviews. 2015;66(1):269–96. https://doi.org/10.1146/annurev-arplant-043014-115627.
Article
CAS
PubMed
Google Scholar
Schuettengruber B, Bourbon H-M, Di Croce L, Cavalli G. Genome regulation by Polycomb and Trithorax: 70 years and counting. Cell. 2017;171(1):34–57. https://doi.org/10.1016/j.cell.2017.08.002.
Article
CAS
PubMed
Google Scholar
Francis NJ, Kingston RE, Woodcock CL. Chromatin compaction by a Polycomb group protein complex. Science. American Association for the Advancement of Science. 2004;306(5701):1574–7. https://doi.org/10.1126/science.1100576.
Article
CAS
PubMed
Google Scholar
Bratzel F, López-Torrejón G, Koch M, Del Pozo JC, Calonje M. Keeping cell identity in Arabidopsis requires PRC1 RING-finger homologs that catalyze H2A monoubiquitination. Curr Biol. 2010;20(20):1853–9. https://doi.org/10.1016/j.cub.2010.09.046.
Article
CAS
PubMed
Google Scholar
Eskeland R, Leeb M, Grimes GR, Kress C, Boyle S, Sproul D, et al. Ring1B compacts chromatin structure and represses gene expression independent of histone ubiquitination. Mol Cell. 2010;38(3):452–64. https://doi.org/10.1016/j.molcel.2010.02.032.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xiao J, Wagner D. Polycomb repression in the regulation of growth and development in Arabidopsis. Curr Opin Plant Biol. 2015;23:15–24. https://doi.org/10.1016/j.pbi.2014.10.003.
Article
CAS
PubMed
Google Scholar
Cao R, Wang L, Wang H, Xia L, Erdjument-Bromage H, Tempst P, et al. Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science. American Association for the Advancement of Science. 2002;298(5595):1039–43. https://doi.org/10.1126/science.1076997.
Article
CAS
PubMed
Google Scholar
Czermin B, Melfi R, McCabe D, Seitz V, Imhof A, Pirrotta V. Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal polycomb sites. Cell. 2002;111(2):185–96. https://doi.org/10.1016/S0092-8674(02)00975-3.
Article
CAS
PubMed
Google Scholar
Kuzmichev A, Nishioka K, Erdjument-Bromage H, Tempst P, Reinberg D. Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev. 2002;16(22):2893–905. https://doi.org/10.1101/gad.1035902.
Article
CAS
PubMed
PubMed Central
Google Scholar
Müller J, Hart CM, Francis NJ, Vargas ML, Sengupta A, Wild B, et al. Histone methyltransferase activity of a Drosophila polycomb group repressor complex. Cell. 2002;111(2):197–208. https://doi.org/10.1016/S0092-8674(02)00976-5.
Article
PubMed
Google Scholar
Gao Z, Zhang J, Bonasio R, Strino F, Sawai A, Parisi F, et al. PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Mol Cell. 2012;45(3):344–56. https://doi.org/10.1016/j.molcel.2012.01.002.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hauri S, Comoglio F, Seimiya M, Gerstung M, Glatter T, Hansen K, et al. A high-density map for navigating the human polycomb complexome. Cell Rep. 2016;17(2):583–95. https://doi.org/10.1016/j.celrep.2016.08.096.
Article
CAS
PubMed
Google Scholar
Wang H, Wang L, Erdjument-Bromage H, Vidal M, Tempst P, Jones RS, et al. Role of histone H2A ubiquitination in Polycomb silencing. Nature. Nature Publishing Group. 2004;431:873–8.
Article
CAS
PubMed
Google Scholar
Shao Z, Raible F, Mollaaghababa R, Guyon JR, Wu C, Bender W, et al. Stabilization of chromatin structure by PRC1, a polycomb complex. Cell. 1999;98(1):37–46. https://doi.org/10.1016/S0092-8674(00)80604-2.
Article
CAS
PubMed
Google Scholar
Francis NJ, Saurin AJ, Shao Z, Kingston RE. Reconstitution of a functional core polycomb repressive complex. Mol Cell. 2001;8(3):545–56. https://doi.org/10.1016/S1097-2765(01)00316-1.
Article
CAS
PubMed
Google Scholar
Lo SM, Ahuja NK, Francis NJ. Polycomb group protein suppressor 2 of Zeste is a functional homolog of posterior sex combs. Mol Cell Biol. American Society for Microbiology Journals. 2009;29:515–25.
Article
CAS
PubMed
Google Scholar
Xu L, Shen W-H. Polycomb silencing of KNOX genes confines shoot stem cell niches in Arabidopsis. Curr Biol. 2008;18(24):1966–71. https://doi.org/10.1016/j.cub.2008.11.019.
Article
CAS
PubMed
Google Scholar
Bratzel F, Yang C, Angelova A, López-Torrejón G, Koch M, del Pozo JC, et al. Regulation of the New Arabidopsis Imprinted Gene AtBMI1C Requires the Interplay of Different Epigenetic Mechanisms. Mol Plant. Elsevier. 2012;5(1):260–9. https://doi.org/10.1093/mp/ssr078.
Article
CAS
PubMed
Google Scholar
Yang C, Bratzel F, Hohmann N, Koch M, Turck F, Calonje M. VAL- and AtBMI1-mediated H2Aub initiate the switch from embryonic to postgerminative growth in Arabidopsis. Curr Biol. 2013;23(14):1324–9. https://doi.org/10.1016/j.cub.2013.05.050.
Article
CAS
PubMed
Google Scholar
Morey L, Aloia L, Cozzuto L, Benitah SA, Di Croce L. RYBP and Cbx7 define specific biological functions of polycomb complexes in mouse embryonic stem cells. Cell Rep. 2013;3(1):60–9. https://doi.org/10.1016/j.celrep.2012.11.026.
Article
CAS
PubMed
Google Scholar
Tavares L, Dimitrova E, Oxley D, Webster J, Poot R, Demmers J, et al. RYBP-PRC1 complexes mediate H2A ubiquitylation at polycomb target sites independently of PRC2 and H3K27me3. Cell. 2012;148(4):664–78. https://doi.org/10.1016/j.cell.2011.12.029.
Article
CAS
PubMed
PubMed Central
Google Scholar
Blackledge NP, Farcas AM, Kondo T, King HW, McGouran JF, Hanssen LLP, et al. Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation. Cell. 2014;157(6):1445–59. https://doi.org/10.1016/j.cell.2014.05.004.
Article
CAS
PubMed
PubMed Central
Google Scholar
Endoh M, Endo TA, Endoh T, Isono K, Sharif J, Ohara O, et al. Histone H2A mono-ubiquitination is a crucial step to mediate PRC1-dependent repression of developmental genes to maintain ES cell identity. PLoS Genet. Public Library of Science. 2012;8:e1002774.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cooper S, Dienstbier M, Hassan R, Schermelleh L, Sharif J, Blackledge NP, et al. Targeting polycomb to pericentric heterochromatin in embryonic stem cells reveals a role for H2AK119u1 in PRC2 recruitment. Cell Rep. 2014;7(5):1456–70. https://doi.org/10.1016/j.celrep.2014.04.012.
Article
CAS
PubMed
PubMed Central
Google Scholar
Illingworth RS, Moffat M, Mann AR, Read D, Hunter CJ, Pradeepa MM, et al. The E3 ubiquitin ligase activity of RING1B is not essential for early mouse development. Genes Dev. 2015;29(18):1897–902. https://doi.org/10.1101/gad.268151.115.
Article
CAS
PubMed
PubMed Central
Google Scholar
Blackledge NP, Fursova NA, Kelley JR, Huseyin MK, Feldmann A, Klose RJ. PRC1 catalytic activity is central to polycomb system function. Mol Cell. 2020;77:857–874.e9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tamburri S, Lavarone E, Fernández-Pérez D, Conway E, Zanotti M, Manganaro D, et al. Histone H2AK119 mono-ubiquitination is essential for polycomb-mediated transcriptional repression. Mol Cell. 2020;77:840–856.e5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pengelly AR, Kalb R, Finkl K, Müller J. Transcriptional repression by PRC1 in the absence of H2A monoubiquitylation. Genes Dev. Cold Spring Harbor Laboratory Press. 2015;29:1487.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kahn TG, Dorafshan E, Schultheis D, Zare A, Stenberg P, Reim I, et al. Interdependence of PRC1 and PRC2 for recruitment to polycomb response elements. Nucleic Acids Res. Oxford Academic. 2016;44:10132–49.
CAS
PubMed
PubMed Central
Google Scholar
Tsuboi M, Kishi Y, Yokozeki W, Koseki H, Hirabayashi Y, Gotoh Y. Ubiquitination-independent repression of PRC1 targets during neuronal fate restriction in the developing mouse neocortex. Dev Cell. 2018;47:758–772.e5.
Article
CAS
PubMed
Google Scholar
Zhou Y, Romero-Campero FJ, Gómez-Zambrano Á, Turck F, Calonje M. H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activity. Genome Biol. 2017;18(1):69. https://doi.org/10.1186/s13059-017-1197-z.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kralemann LEM, Liu S, Trejo-Arellano MS, Muñoz-Viana R, Köhler C, Hennig L. Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis. Genome Biol. 2020;21(1):144. https://doi.org/10.1186/s13059-020-02062-8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yin X, Romero-Campero FJ, de Los Reyes P, Yan P, Yang J, Tian G, et al. H2AK121ub in Arabidopsis associates with a less accessible chromatin state at transcriptional regulation hotspots. Nat Commun. Nature Publishing Group. 2021;12:315.
Article
CAS
PubMed
PubMed Central
Google Scholar
Derkacheva M, Liu S, Figueiredo DD, Gentry M, Mozgova I, Nanni P, et al. H2A deubiquitinases UBP12/13 are part of the Arabidopsis polycomb group protein system. Nat Plants. Nature Publishing Group. 2016;2:1–10.
Article
Google Scholar
Bowman JL, Kohchi T, Yamato KT, Jenkins J, Shu S, Ishizaki K, et al. Insights into land plant evolution garnered from the Marchantia polymorpha genome. Cell. 2017;171:287–304.e15.
Article
CAS
PubMed
Google Scholar
Kawashima T, Lorković ZJ, Nishihama R, Ishizaki K, Axelsson E, Yelagandula R, et al. Diversification of histone H2A variants during plant evolution. Trends Plant Sci. 2015;20(7):419–25. https://doi.org/10.1016/j.tplants.2015.04.005.
Article
CAS
PubMed
Google Scholar
Montgomery SA, Tanizawa Y, Galik B, Wang N, Ito T, Mochizuki T, et al. Chromatin organization in early land plants reveals an ancestral association between H3K27me3, transposons, and constitutive heterochromatin. Curr Biol. 2020;30:573–588.e7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sanchez-Pulido L, Devos D, Sung ZR, Calonje M. RAWUL: A new ubiquitin-like domain in PRC1 Ring finger proteins that unveils putative plant and worm PRC1 orthologs. BMC Genomics. 2008;9(1):308. https://doi.org/10.1186/1471-2164-9-308.
Article
CAS
PubMed
PubMed Central
Google Scholar
Junco SE, Wang R, Gaipa JC, Taylor AB, Schirf V, Gearhart MD, et al. Structure of the polycomb group protein PCGF1 in complex with BCOR reveals basis for binding selectivity of PCGF homologs. Structure. 2013;21(4):665–71. https://doi.org/10.1016/j.str.2013.02.013.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gray F, Cho HJ, Shukla S, He S, Harris A, Boytsov B, et al. BMI1 regulates PRC1 architecture and activity through homo- and hetero-oligomerization. Nat Commun. Nature Publishing Group. 2016;7:13343.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wong SJ, Gearhart MD, Taylor AB, Nanyes DR, Ha DJ, Robinson AK, et al. KDM2B recruitment of the polycomb group ccomplex, PRC1.1, requires cooperation between PCGF1 and BCORL1. Structure. 2016;24(10):1795–801. https://doi.org/10.1016/j.str.2016.07.011.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chittock EC, Latwiel S, Miller TCR, Müller CW. Molecular architecture of polycomb repressive complexes. Biochem Soc Trans. Portland Press. 2017;45(1):193–205. https://doi.org/10.1042/BST20160173.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu S, de Jonge J, Trejo-Arellano MS, Santos-González J, Köhler C, Hennig L. Role of H1 and DNA methylation in selective regulation of transposable elements during heat stress. New Phytol. 2020; Available from: https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.17018;229(4):2238–50.
Article
PubMed
PubMed Central
Google Scholar
Gómez-Zambrano Á, Merini W, Calonje M. The repressive role of Arabidopsis H2A.Z in transcriptional regulation depends on AtBMI1 activity. Nat Commun. Nature Publishing Group. 2019;10:2828.
Article
PubMed
PubMed Central
Google Scholar
Gao Z, Lee P, Stafford JM, von Schimmelmann M, Schaefer A, Reinberg D. An AUTS2–Polycomb complex activates gene expression in the CNS. Nature. Nature Publishing Group. 2014;516:349–54.
Article
CAS
PubMed
PubMed Central
Google Scholar
Linde A-M, Eklund DM, Kubota A, Pederson ERA, Holm K, Gyllenstrand N, et al. Early evolution of the land plant circadian clock. New Phytol. 2017;216(2):576–90. https://doi.org/10.1111/nph.14487.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ishizaki K, Nishihama R, Ueda M, Inoue K, Ishida S, Nishimura Y, et al. Development of gateway binary vector series with four different selection markers for the liverwort Marchantia polymorpha. PLoS One. Public Library of Science. 2015;10:e0138876.
Article
PubMed
PubMed Central
Google Scholar
Sugano SS, Nishihama R, Shirakawa M, Takagi J, Matsuda Y, Ishida S, et al. Efficient CRISPR/Cas9-based genome editing and its application to conditional genetic analysis in Marchantia polymorpha. PLoS One. Public Library of Science. 2018;13:e0205117.
Article
PubMed
PubMed Central
Google Scholar
Eklund DM, Kanei M, Flores-Sandoval E, Ishizaki K, Nishihama R, Kohchi T, et al. An evolutionarily conserved abscisic acid signaling pathway regulates dormancy in the liverwort Marchantia polymorpha. Curr Biol. 2018;28:3691–3699.e3.
Article
CAS
PubMed
Google Scholar
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. Oxford Academic. 2013;29(1):15–21. https://doi.org/10.1093/bioinformatics/bts635.
Article
CAS
PubMed
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. https://doi.org/10.1186/s13059-014-0550-8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Villar CBR, Köhler C. Plant chromatin immunoprecipitation. In: Hennig L, Köhler C, editors. Plant Dev Biol Methods Protoc [Internet]. Totowa: Humana Press; 2010. p. 401–11. https://doi.org/10.1007/978-1-60761-765-5_27.
Chapter
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. Oxford Academic. 2014;30(15):2114–20. https://doi.org/10.1093/bioinformatics/btu170.
Article
CAS
PubMed
PubMed Central
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. Nature Publishing Group. 2012;9(4):357–9. https://doi.org/10.1038/nmeth.1923.
Article
CAS
PubMed
PubMed Central
Google Scholar
Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38(4):576–89. https://doi.org/10.1016/j.molcel.2010.05.004.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. Oxford Academic. 2013;14(2):178–92. https://doi.org/10.1093/bib/bbs017.
Article
CAS
PubMed
Google Scholar
Ramírez F, Dündar F, Diehl S, Grüning BA, Manke T. deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Res. Oxford Academic. 2014;42:W187–91.
Article
PubMed
PubMed Central
Google Scholar
Van Bel M, Diels T, Vancaester E, Kreft L, Botzki A, Van de Peer Y, et al. PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics. Nucleic Acids Res. Oxford Academic. 2018;46:D1190–6.
Article
PubMed
Google Scholar
Liu S, Trejo-Arellano MS, Qiu Y, Eklund DM, Köhler C, Hennig L. H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha. ChIP-seq and RNA seq data. Gene Expression Omnibus. 2021. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE164394. Accessed 13 Aug 2021.