Polycomb repressive complex 1 defines the nucleosome landscape but not accessibility at target genes

Chromatin Domains ◽

Genetic Ablation ◽

ABSTRACTPolycomb group (PcG) proteins are transcriptional repressors that play important roles regulating gene expression during animal development. In vitro experiments have shown that PcG protein complexes can compact chromatin limiting the activity of chromatin remodelling enzymes and access of the transcriptional machinery to DNA. In fitting with these ideas, gene promoters associated with PcG proteins have been reported to be less accessible than other gene promotors. However, it remains largely untested in vivo whether PcG proteins define chromatin accessibility or other chromatin features. To address this important question, we measured chromatin accessibility and examined the nucleosome landscape at PcG protein-bound promoters in mouse embryonic stem cells using the assay for transposase accessible chromatin (ATAC)-seq. Combined with genetic ablation strategies, we unexpectedly discover that although PcG protein-occupied gene promoters exhibit reduced accessibility, this does not rely on PcG proteins. Instead, the Polycomb repressive complex 1 (PRC1) appears to play a unique role in driving elevated nucleosome occupancy and decreased nucleosomal spacing in Polycomb chromatin domains. Our new genome-scale observations argue, in contrast to the prevailing view, that PcG proteins and Polycomb chromatin domains do not significantly affect chromatin accessibility and highlight an underappreciated complexity in the relationship between chromatin accessibility, the nucleosome landscape and PcG-mediated transcriptional repression.

The polycomb group protein PCGF6 mediates germline gene silencing by recruiting histone-modifying proteins to target gene promoters

Journal of Biological Chemistry ◽

10.1074/jbc.ra119.012121 ◽

2020 ◽

Vol 295 (28) ◽

pp. 9712-9724 ◽

Cited By ~ 2

Author(s):

Mengjie Liu ◽

Yaru Zhu ◽

Fei Xing ◽

Shuang Liu ◽

Yin Xia ◽

...

Keyword(s):

Germ Cell ◽

Target Genes ◽

Critical Role ◽

Embryonic Stem ◽

Polycomb Group ◽

Gene Promoters ◽

Polycomb Group Protein ◽

Aberrant Expression ◽

Histone Deacetylase 1 ◽

Deficient Mice

Polycomb group (PcG) proteins are essential for maintenance of lineage fidelity by coordinating developmental gene expression programs. Polycomb group ring finger 6 (PCGF6) has been previously reported to repress expression of lineage-specific genes, especially germ cell–related genes in mouse embryonic stem cells (ESCs) via the noncanonical polycomb repressive complex PRC1.6. However, the molecular mechanism of this repression remains largely unknown. Here, using RNA-Seq, real-time RT-PCR, immunohistochemistry, immunoprecipitation, and ChIP analyses, we demonstrate that PCGF6 plays an essential role in embryonic development, indicated by the partially penetrant embryonic lethality in homozygous PCGF6 (Pcgf6−/−)-deficient mice. We also found that surviving Pcgf6-deficient mice exhibit reduced fertility. Using the Pcgf6-deficient mice, we observed that ablation of Pcgf6 in somatic tissues robustly derepresses germ cell–related genes. We further provide evidence that these genes are direct targets of PCGF6 in ESCs and that endogenous PCGF6 co-localizes with the histone-modifying proteins G9A histone methyltransferase (G9A)/G9a-like protein (GLP) and histone deacetylase 1/2 (HDAC1/2) on the promoters of the germ cell–related genes. Moreover, the binding of these proteins to their target genes correlated with methylation of Lys-9 of histone 3 and with the status of histone acetylation at these genes. Moreover, the recruitment of G9A/GLP and HDAC1/2 to target promoters depended on the binding of PCGF6. Our findings indicate that PCGF6 has a critical role in safeguarding lineage decisions and in preventing aberrant expression of germ cell–related genes.

RYBP stimulates PRC1 to shape chromatin-based communication between Polycomb repressive complexes

eLife ◽

10.7554/elife.18591 ◽

2016 ◽

Vol 5 ◽

Cited By ~ 46

Author(s):

Nathan R Rose ◽

Hamish W King ◽

Neil P Blackledge ◽

Nadezda A Fursova ◽

Katherine JI Ember ◽

...

Keyword(s):

Gene Regulation ◽

Histone Modification ◽

Target Genes ◽

Embryonic Stem ◽

Polycomb Group ◽

Chromatin Domain ◽

Polycomb Repressive Complex 2 ◽

Ubiquitin Ligase Activity ◽

Inappropriate Gene Expression

Polycomb group (PcG) proteins function as chromatin-based transcriptional repressors that are essential for normal gene regulation during development. However, how these systems function to achieve transcriptional regulation remains very poorly understood. Here, we discover that the histone H2AK119 E3 ubiquitin ligase activity of Polycomb repressive complex 1 (PRC1) is defined by the composition of its catalytic subunits and is highly regulated by RYBP/YAF2-dependent stimulation. In mouse embryonic stem cells, RYBP plays a central role in shaping H2AK119 mono-ubiquitylation at PcG targets and underpins an activity-based communication between PRC1 and Polycomb repressive complex 2 (PRC2) which is required for normal histone H3 lysine 27 trimethylation (H3K27me3). Without normal histone modification-dependent communication between PRC1 and PRC2, repressive Polycomb chromatin domains can erode, rendering target genes susceptible to inappropriate gene expression signals. This suggests that activity-based communication and histone modification-dependent thresholds create a localized form of epigenetic memory required for normal PcG chromatin domain function in gene regulation.

Identification of polycomb repressive complex 1 and 2 core components in hexaploid bread wheat

BMC Plant Biology ◽

10.1186/s12870-020-02384-6 ◽

2020 ◽

Vol 20 (S1) ◽

Author(s):

Beáta Strejčková ◽

Radim Čegan ◽

Ales Pecinka ◽

Zbyněk Milec ◽

Jan Šafář

Keyword(s):

Bread Wheat ◽

Developmental Stages ◽

Gene Families ◽

Polycomb Group ◽

Transcriptional Analysis ◽

Histone H2a ◽

Core Components ◽

High Level ◽

Abstract Background Polycomb repressive complexes 1 and 2 play important roles in epigenetic gene regulation by posttranslationally modifying specific histone residues. Polycomb repressive complex 2 is responsible for the trimethylation of lysine 27 on histone H3; Polycomb repressive complex 1 catalyzes the monoubiquitination of histone H2A at lysine 119. Both complexes have been thoroughly studied in Arabidopsis, but the evolution of polycomb group gene families in monocots, particularly those with complex allopolyploid origins, is unknown. Results Here, we present the in silico identification of the Polycomb repressive complex 1 and 2 (PRC2, PRC1) subunits in allohexaploid bread wheat, the reconstruction of their evolutionary history and a transcriptional analysis over a series of 33 developmental stages. We identified four main subunits of PRC2 [E(z), Su(z), FIE and MSI] and three main subunits of PRC1 (Pc, Psc and Sce) and determined their chromosomal locations. We found that most of the genes coding for subunit proteins are present as paralogs in bread wheat. Using bread wheat RNA-seq data from different tissues and developmental stages throughout plant ontogenesis revealed variable transcriptional activity for individual paralogs. Phylogenetic analysis showed a high level of protein conservation among temperate cereals. Conclusions The identification and chromosomal location of the Polycomb repressive complex 1 and 2 core components in bread wheat may enable a deeper understanding of developmental processes, including vernalization, in commonly grown winter wheat.

RING1B O-GlcNAcylation regulates gene targeting of polycomb repressive complex 1 in human embryonic stem cells

Stem Cell Research ◽

10.1016/j.scr.2015.06.007 ◽

2015 ◽

Vol 15 (1) ◽

pp. 182-189 ◽

Cited By ~ 13

Author(s):

Julien Jean Pierre Maury ◽

Chadi A. EL Farran ◽

Daniel Ng ◽

Yuin-Han Loh ◽

Xuezhi Bi ◽

...

Keyword(s):

Stem Cells ◽

Embryonic Stem Cells ◽

Gene Targeting ◽

Human Embryonic Stem Cells ◽

Embryonic Stem ◽

Functional characterization of human Polycomb-like 3 isoforms identifies them as components of distinct EZH2 protein complexes

Biochemical Journal ◽

10.1042/bj20100944 ◽

2011 ◽

Vol 434 (2) ◽

pp. 333-342 ◽

Cited By ~ 26

Author(s):

Gaylor Boulay ◽

Claire Rosnoblet ◽

Cateline Guérardel ◽

Pierre-Olivier Angrand ◽

Dominique Leprince

Keyword(s):

Cell Fate ◽

Target Genes ◽

Protein Complexes ◽

Functional Characterization ◽

Polycomb Group ◽

Phd Finger ◽

Reverse Transcription Pcr ◽

Tudor Domain ◽

Self Association ◽

PcG (Polycomb group) proteins are conserved transcriptional repressors essential to regulate cell fate and to maintain epigenetic cellular memory. They work in concert through two main families of chromatin-modifying complexes, PRC1 (Polycomb repressive complex 1) and PRC2–4. In Drosophila, PRC2 contains the H3K27 histone methyltransferase E(Z) whose trimethylation activity towards PcG target genes is stimulated by PCL (Polycomb-like). In the present study, we have examined hPCL3, one of its three human paralogues. Through alternative splicing, hPCL3 encodes a long isoform, hPCL3L, containing an N-terminal TUDOR domain and two PHDs (plant homeodomains) and a smaller isoform, hPCL3S, lacking the second PHD finger (PHD2). By quantitative reverse transcription–PCR analyses, we showed that both isoforms are widely co-expressed at high levels in medulloblastoma. By co-immunoprecipitation analyses, we demonstrated that both isoforms interact with EZH2 through their common TUDOR domain. However, the hPCL3L-specific PHD2 domain, which is better conserved than PHD1 in the PCL family, is also involved in this interaction and implicated in the self-association of hPCL3L. Finally, we have demonstrated that both hPCL3 isoforms are physically associated with EZH2, but in different complexes. Our results provide the first evidence that the two hPCL3 isoforms belong to different complexes and raise important questions about their relative functions, particularly in tumorigenesis.

Role of Polycomb Repressive Complex 1 (PRC1) In Runx1 Mediated Gene Regulation

Blood ◽

10.1182/blood.v116.21.3863.3863 ◽

2010 ◽

Vol 116 (21) ◽

pp. 3863-3863

Author(s):

Ming Yu ◽

Tali Mazor ◽

Hui Huang ◽

Emily Huang ◽

Katie Kathrein ◽

...

Keyword(s):

Gene Regulation ◽

Board Of Directors ◽

Target Genes ◽

Advisory Committees ◽

Hematopoietic Stem ◽

Human T Cell ◽

Equity Ownership ◽

Abstract Abstract 3863 The transcription factor Runx1 is required for the generation of all definitive hematopoietic stem cells (HSCs), and for normal megakaryocyte, lymphocyte and granulocyte terminal maturation. Runx1 and its cofactor CBF-β are also the most common targets of chromosomal translocations in human leukemias. Somatic and germline point mutations in Runx1 occur in myelodysplastic syndrome and undifferentiated leukemias, and are associated with a poor prognosis. Despite the key roles that Runx1 plays in normal and malignant hematopoiesis, its transcriptional mechanisms remain incompletely understood. In this study, we purified Runx1 containing multiprotein complexes from megakaryocytic cells and identified several associated chromatin-remodeling complexes, including Polycomb Repressive Complex 1 (PRC1), NuRD, SWI/SNF and MLL/TrxG. Interactions were validated by independent biochemical assays and demonstrate a direct interaction between Runx1 and the PRC1 component Bmi1. ChIP-seq studies identified a large overlap between Runx1/CBF-β and Ring1b (another PRC1 core component) occupied sites, with 45% of the peaks at these genes < 200 bp from each other. ShRNA mediated gene knockdown of CBF-β shows differential gene expression of many of the co-occupied genes. Among the direct CBF-β/Ring1b co-occupied targets are other key hematopoietic transcription factors including FOG-1, SCL and Lyl1, and a number of cell adhesion related genes. ShRNA knockdown of Ring1b impairs megakaryocyte endomitosis, partially phenocopying Runx1 deficient megakaryocytes. Morpholino mediated knockdown of Ring1b or Bmi1 in zebrafish embryos reduces the number of phenotypic definitive HSCs, also partially phenocopying Runx1 morphants. We also show that Runx1/CBF-β interact with Ring1b in the human T cell line Jurkat, and that Ring1b occupies Runx1/CBF-β bound sites of key direct target genes in primary murine thymocytes, including CD4, TCRβ, and Th-POK. Surprisingly, we did not find enrichment for histone 2A monoubiquitination at most of the megakaryocytic and T-lymphocyte co-occupied sites examined, suggesting that PRC1 acts through alternate mechanisms at these genes. Collectively, these data provide evidence for a broad role of PRC1 in Runx1 mediated gene regulation. Disclosures: Zon: FATE, Inc.: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties; Stemgent: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees. Cantor:Amgen, Inc: Consultancy.

USP7 Cooperates with SCML2 To Regulate the Activity of PRC1

Molecular and Cellular Biology ◽

10.1128/mcb.01197-14 ◽

2015 ◽

Vol 35 (7) ◽

pp. 1157-1168 ◽

Cited By ~ 37

Author(s):

Emilio Lecona ◽

Varun Narendra ◽

Danny Reinberg

Keyword(s):

Chromatin Immunoprecipitation ◽

Essential Role ◽

Target Genes ◽

Polycomb Group ◽

Histone H2a ◽

Polycomb Group Protein ◽

Specific Component ◽

Group Protein ◽

The Common ◽

USP7 is a protein deubiquitinase with an essential role in development. Here, we provide evidence that USP7 regulates the activity of Polycomb repressive complex 1 (PRC1) in coordination with SCML2. There are six versions of PRC1 defined by the association of one of the PCGF homologues (PCGF1 to PCGF6) with the common catalytic subunit RING1B. First, we show that SCML2, a Polycomb group protein that associates with PRC1.2 (containing PCGF2/MEL18) and PRC1.4 (containing PCGF4/BMI1), modulates the localization of USP7 and bridges USP7 with PRC1.4, allowing for the stabilization of BMI1. Chromatin immunoprecipitation (ChIP) experiments demonstrate that USP7 is found at SCML2 and BMI1 target genes. Second, inhibition of USP7 leads to a reduction in the level of ubiquitinated histone H2A (H2Aub), the catalytic product of PRC1 and key for its repressive activity. USP7 regulates the posttranslational status of RING1B and BMI1, a specific component of PRC1.4. Thus, not only does USP7 stabilize PRC1 components, its catalytic activity is also necessary to maintain a functional PRC1, thereby ensuring appropriate levels of repressive H2Aub.

Loss of polycomb repressive complex 1 activity and chromosomal instability drive uveal melanoma progression

Nature Communications ◽

10.1038/s41467-021-25529-z ◽

2021 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

Mathieu F. Bakhoum ◽

Jasmine H. Francis ◽

Albert Agustinus ◽

Ethan M. Earlie ◽

Melody Di Bona ◽

...

Keyword(s):

Tumor Progression ◽

Uveal Melanoma ◽

Chromosomal Instability ◽

Target Genes ◽

Transcriptional Response ◽

Double Stranded Dna ◽

Sting Pathway ◽

Functional Analyses ◽

AbstractChromosomal instability (CIN) and epigenetic alterations have been implicated in tumor progression and metastasis; yet how these two hallmarks of cancer are related remains poorly understood. By integrating genetic, epigenetic, and functional analyses at the single cell level, we show that progression of uveal melanoma (UM), the most common intraocular primary cancer in adults, is driven by loss of Polycomb Repressive Complex 1 (PRC1) in a subpopulation of tumor cells. This leads to transcriptional de-repression of PRC1-target genes and mitotic chromosome segregation errors. Ensuing CIN leads to the formation of rupture-prone micronuclei, exposing genomic double-stranded DNA (dsDNA) to the cytosol. This provokes tumor cell-intrinsic inflammatory signaling, mediated by aberrant activation of the cGAS-STING pathway. PRC1 inhibition promotes nuclear enlargement, induces a transcriptional response that is associated with significantly worse patient survival and clinical outcomes, and enhances migration that is rescued upon pharmacologic inhibition of CIN or STING. Thus, deregulation of PRC1 can promote tumor progression by inducing CIN and represents an opportunity for early therapeutic intervention.

BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome

10.1101/2020.11.13.381251 ◽

2020 ◽

Author(s):

Nadezda A. Fursova ◽

Anne H. Turberfield ◽

Neil P. Blackledge ◽

Emma L. Findlater ◽

Anna Lastuvkova ◽

...

Keyword(s):

Gene Expression ◽

Histone Modifications ◽

Transcription Initiation ◽

Target Genes ◽

Regulatory Elements ◽

Polycomb Group ◽

Gene Promoters ◽

Histone H2a ◽

Gene Regulatory Elements ◽

Gene Regulatory

AbstractHistone-modifying systems play fundamental roles in gene regulation and the development of multicellular organisms. Histone modifications that are enriched at gene regulatory elements have been heavily studied, but the function of modifications that are found more broadly throughout the genome remains poorly understood. This is exemplified by histone H2A mono-ubiquitylation (H2AK119ub1) which is enriched at Polycomb-repressed gene promoters, but also covers the genome at lower levels. Here, using inducible genetic perturbations and quantitative genomics, we discover that the BAP1 deubiquitylase plays an essential role in constraining H2AK119ub1 throughout the genome. Removal of BAP1 leads to pervasive accumulation of H2AK119ub1, which causes widespread reductions in gene expression. We show that elevated H2AK119ub1 represses gene expression by counteracting transcription initiation from gene regulatory elements, causing reductions in transcription-associated histone modifications. Furthermore, failure to constrain pervasive H2AK119ub1 compromises Polycomb complex occupancy at a subset of Polycomb target genes leading to their derepression, therefore explaining the original genetic characterisation of BAP1 as a Polycomb group gene. Together, these observations reveal that the transcriptional potential of the genome can be modulated by regulating the levels of a pervasive histone modification, without the need for elaborate gene-specific targeting mechanisms.

Knowing When to Silence: Roles of Polycomb-Group Proteins in SAM Maintenance, Root Development, and Developmental Phase Transition

International Journal of Molecular Sciences ◽

10.3390/ijms21165871 ◽

2020 ◽

Vol 21 (16) ◽

pp. 5871

Author(s):

Bowen Yan ◽

Yanpeng Lv ◽

Chunyu Zhao ◽

Xiaoxue Wang

Keyword(s):

Phase Transition ◽

Root Development ◽

Target Genes ◽

Polycomb Group ◽

Developmental Phase ◽

Heterochromatin Protein 1 ◽

Heterochromatin Protein ◽

Developmental Defects ◽

Histone 3 ◽

Polycomb repressive complex 1 (PRC1) and PRC2 are the major complexes composed of polycomb-group (PcG) proteins in plants. PRC2 catalyzes trimethylation of lysine 27 on histone 3 to silence target genes. Like Heterochromatin Protein 1/Terminal Flower 2 (LHP1/TFL2) recognizes and binds to H3K27me3 generated by PRC2 activities and enrolls PRC1 complex to further silence the chromatin through depositing monoubiquitylation of lysine 119 on H2A. Mutations in PcG genes display diverse developmental defects during shoot apical meristem (SAM) maintenance and differentiation, seed development and germination, floral transition, and so on so forth. PcG proteins play essential roles in regulating plant development through repressing gene expression. In this review, we are focusing on recent discovery about the regulatory roles of PcG proteins in SAM maintenance, root development, embryo development to seedling phase transition, and vegetative to reproductive phase transition.