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1.
Nat Struct Mol Biol ; 28(6): 501-511, 2021 06.
Article in English | MEDLINE | ID: mdl-34117481

ABSTRACT

The mammalian SWI/SNF complex, or BAF complex, has a conserved and direct role in antagonizing Polycomb-mediated repression. Yet, BAF also promotes repression by Polycomb in stem cells and cancer. How BAF both antagonizes and promotes Polycomb-mediated repression remains unknown. Here, we utilize targeted protein degradation to dissect the BAF-Polycomb axis in mouse embryonic stem cells on short timescales. We report that rapid BAF depletion redistributes Polycomb repressive complexes PRC1 and PRC2 from highly occupied domains, like Hox clusters, to weakly occupied sites normally opposed by BAF. Polycomb redistribution from highly repressed domains results in their decompaction, gain of active epigenomic features and transcriptional derepression. Surprisingly, through dose-dependent degradation of PRC1 and PRC2, we identify a conventional role for BAF in Polycomb-mediated repression, in addition to global Polycomb redistribution. These findings provide new mechanistic insight into the highly dynamic state of the Polycomb-Trithorax axis.


Subject(s)
Chromatin Assembly and Disassembly/physiology , Epigenetic Repression/physiology , Gene Expression Regulation/physiology , Multiprotein Complexes/physiology , Polycomb-Group Proteins/physiology , Animals , CRISPR-Cas Systems , Cells, Cultured , Chromatin Assembly and Disassembly/genetics , DNA Helicases/genetics , DNA Helicases/metabolism , DNA-Binding Proteins/physiology , Embryonic Stem Cells/metabolism , Epigenesis, Genetic , Epigenetic Repression/genetics , Gene Editing , Gene Expression Regulation/genetics , Genes, Homeobox , Genome , HEK293 Cells , Homeodomain Proteins/genetics , Homeodomain Proteins/metabolism , Humans , Loss of Function Mutation , Mice , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Proteolysis , Recombinant Fusion Proteins/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Transcription Factors/physiology
2.
Mol Cell ; 81(12): 2625-2639.e5, 2021 06 17.
Article in English | MEDLINE | ID: mdl-33887196

ABSTRACT

The Polycomb repressive complex 2 (PRC2) is an essential epigenetic regulator that deposits repressive H3K27me3. PRC2 subunits form two holocomplexes-PRC2.1 and PRC2.2-but the roles of these two PRC2 assemblies during differentiation are unclear. We employed auxin-inducible degradation to deplete PRC2.1 subunit MTF2 or PRC2.2 subunit JARID2 during differentiation of embryonic stem cells (ESCs) to neural progenitors (NPCs). Depletion of either MTF2 or JARID2 resulted in incomplete differentiation due to defects in gene regulation. Distinct sets of Polycomb target genes were derepressed in the absence of MTF2 or JARID2. MTF2-sensitive genes were marked by H3K27me3 in ESCs and remained silent during differentiation, whereas JARID2-sensitive genes were preferentially active in ESCs and became newly repressed in NPCs. Thus, MTF2 and JARID2 contribute non-redundantly to Polycomb silencing, suggesting that PRC2.1 and PRC2.2 have distinct functions in maintaining and establishing, respectively, Polycomb repression during differentiation.


Subject(s)
Polycomb Repressive Complex 2/metabolism , Animals , Cell Differentiation/physiology , Embryonic Stem Cells/metabolism , Gene Expression Regulation, Developmental/genetics , Histones/metabolism , Mice , Mice, Inbred C57BL , Neural Stem Cells/metabolism , Polycomb Repressive Complex 2/physiology , Polycomb-Group Proteins/metabolism , Polycomb-Group Proteins/physiology , Protein Binding/genetics
3.
Biochem Soc Trans ; 49(1): 71-77, 2021 02 26.
Article in English | MEDLINE | ID: mdl-33616630

ABSTRACT

The Polycomb system is essential for stable gene silencing in many organisms. This regulation is achieved in part through addition of the histone modifications H3K27me2/me3 by Polycomb Repressive Complex 2 (PRC2). These modifications are believed to be the causative epigenetic memory elements of PRC2-mediated silencing. As these marks are stored locally in the chromatin, PRC2-based memory is a cis-acting system. A key feature of stable epigenetic memory in cis is PRC2-mediated, self-reinforcing feedback from K27-methylated histones onto nearby histones in a read-write paradigm. However, it was not clear under what conditions such feedback can lead to stable memory, able, for example, to survive the perturbation of histone dilution at DNA replication. In this context, computational modelling has allowed a rigorous exploration of possible underlying memory mechanisms and has also greatly accelerated our understanding of switching between active and silenced states. Specifically, modelling has predicted that switching and memory at Polycomb loci is digital, with a locus being either active or inactive, rather than possessing intermediate, smoothly varying levels of activation. Here, we review recent advances in models of Polycomb control, focusing on models of epigenetic switching through nucleation and spreading of H3K27me2/me3. We also examine models that incorporate transcriptional feedback antagonism and those including bivalent chromatin states. With more quantitative experimental data on histone modification kinetics, as well as single-cell resolution data on transcription and protein levels for PRC2 targets, we anticipate an expanded need for modelling to help dissect increasingly interconnected and complex memory mechanisms.


Subject(s)
Computer Simulation , Epigenesis, Genetic/physiology , Polycomb-Group Proteins/physiology , Animals , Gene Silencing , Histones/metabolism , Humans , Models, Theoretical , Polycomb Repressive Complex 2/physiology , Protein Processing, Post-Translational
4.
Oncol Rep ; 45(1): 239-253, 2021 01.
Article in English | MEDLINE | ID: mdl-33200221

ABSTRACT

Dysregulated circular RNAs (circRNAs) often contribute to the occurrence and development of various tumors; however, the function and mechanism of circRNAs are largely unknown in human bladder cancer (BC). In the present study, dysregulated circRNAs between BC and adjacent non­neoplastic bladder tissues were analyzed by circRNA microarray. We randomly selected 10 upregulated and five downregulated circRNAs for validation by quantitative real­time PCR. Bioinformatics analysis was further conducted to investigate the potential function of these differentially expressed circRNAs, with the differential expression of hsa_circRNA_100876, mir­136­5p, and mRNA­chromobox 4 (CBX4) subsequently verified. A total of 512 differentially expressed circRNAs were identified after scanning and normalization (340 upregulated and 172 downregulated circRNAs), with pathway and Gene Ontology analyses revealing their association with multiple significant cancer pathways. Construction of a circRNA­microRNA­mRNA network suggested additional potential roles of these circRNAs. The expression of hsa_circRNA_100876 and CBX4 was significantly negatively correlated with the expression of miR­136­5p. Additionally, hsa_circRNA_100876 was highly positively correlated with CBX4 expression. The results revealed that hsa_circRNA_100876 inhibition suppressed BC cell proliferation and it was associated with advanced T stage and lymphatic metastasis, and poor overall survival of BC patients. In conclusion, these differentially expressed circRNAs offer novel insights into potential biological markers or new therapeutic targets for the treatment of BC. Furthermore, hsa_circRNA_100876 may increase the expression of CBX4 by competing with miR­136­5p, ultimately promoting the malignant biological behavior of BC. Aberrantly expressed hsa_circRNA_100876 could be used as a potential non­invasive biomarker for the early detection and screening of BC.


Subject(s)
RNA, Circular/physiology , Urinary Bladder Neoplasms/etiology , Aged , Cell Line, Tumor , Cell Proliferation , Computational Biology , Female , Humans , Ligases/analysis , Ligases/physiology , Male , Microarray Analysis , Middle Aged , Polycomb-Group Proteins/analysis , Polycomb-Group Proteins/physiology , RNA, Circular/analysis , Urinary Bladder/chemistry , Urinary Bladder Neoplasms/genetics , Urinary Bladder Neoplasms/pathology
5.
Nat Plants ; 6(10): 1211-1218, 2020 10.
Article in English | MEDLINE | ID: mdl-32958896

ABSTRACT

Some plants can 'remember' past environmental experience to become adapted to a given environment. For instance, after experiencing prolonged low-temperature exposure in winter (winter cold), vernalization-responsive plants remember past cold experience when temperature rises in spring, to acquire competence to flower at a later season favourable for seed production1,2. In Arabidopsis thaliana, prolonged cold induces silencing of the potent floral repressor FLOWERING LOCUS C (FLC) by Polycomb group (PcG) chromatin modifiers. This Polycomb-repressed chromatin state is epigenetically maintained and thus 'memorized' in subsequent growth and development upon return to warmth1,3. 'Memory of winter cold' has been viewed as being mitotically stable but meiotically unstable3-5, and thus not to be transmitted intergenerationally. In general, whether and how chromatin-mediated environmental memories are transmitted across generations are unknown in plants. Here, we show that the cold-induced Polycomb-repressed chromatin state at FLC or memory of winter cold is maintained in the egg cell, that is meiotically stable in the process of female gamete formation, and provide evidence that this Polycomb-mediated memory is not maintained in the sperm cell. Moreover, we show that this cold memory is inherited maternally but not paternally to the zygote and early embryos. Our study demonstrates and further provides mechanistic insights into intergenerational transmission of chromatin state-mediated environmental memories in plants.


Subject(s)
Acclimatization/genetics , Arabidopsis/genetics , Cold Temperature , Epigenesis, Genetic , Arabidopsis/physiology , Arabidopsis Proteins/genetics , Arabidopsis Proteins/physiology , Inheritance Patterns , MADS Domain Proteins/genetics , MADS Domain Proteins/physiology , Ovum/physiology , Polycomb-Group Proteins/physiology , Reproduction/genetics
6.
Biochem Soc Trans ; 48(4): 1697-1706, 2020 08 28.
Article in English | MEDLINE | ID: mdl-32725200

ABSTRACT

Polycomb group (PcG) proteins are highly conserved chromatin-modifying complexes that implement gene silencing in higher eukaryotes. Thousands of genes and multiple developmental processes are regulated by PcG proteins. As the first chromatin modifier been identified in model plant Arabidopsis thaliana, the methyltransferase CURLY LEAF (CLF) and its catalyzed histone H3 Lysine 27 trimethylation (H3K27me3) have already become well-established paradigm in plant epigenetic study. Like in animals, PcG proteins mediate plant development and repress homeotic gene expression by antagonizing with trithorax group proteins. Recent researches have advanced our understanding on plant PcG proteins, including the plant-specific components of these well-conserved protein complexes, the close association with transcription factors and noncoding RNA for the spatial and temporal specificity, the dynamic regulation of the repressive mark H3K27me3 and the PcG-mediated chromatin conformation alterations in gene expression. In this review, we will summarize the molecular mechanisms of PcG-implemented gene repression and the relationship between H3K27me3 and another repressive mark histone H2A Lysine 121 mono-ubiquitination (H2A121ub) will also be discussed.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/metabolism , Histones/metabolism , Lysine/metabolism , Polycomb-Group Proteins/metabolism , Animals , Arabidopsis/genetics , Arabidopsis Proteins/physiology , Epigenesis, Genetic , Gene Silencing/physiology , Histones/chemistry , Methylation , Polycomb-Group Proteins/physiology , RNA, Untranslated/metabolism , Transcription Factors/metabolism
7.
Mol Cell ; 77(4): 825-839.e7, 2020 02 20.
Article in English | MEDLINE | ID: mdl-31837995

ABSTRACT

In mammals, chromatin organization undergoes drastic reorganization during oocyte development. However, the dynamics of three-dimensional chromatin structure in this process is poorly characterized. Using low-input Hi-C (genome-wide chromatin conformation capture), we found that a unique chromatin organization gradually appears during mouse oocyte growth. Oocytes at late stages show self-interacting, cohesin-independent compartmental domains marked by H3K27me3, therefore termed Polycomb-associating domains (PADs). PADs and inter-PAD (iPAD) regions form compartment-like structures with strong inter-domain interactions among nearby PADs. PADs disassemble upon meiotic resumption from diplotene arrest but briefly reappear on the maternal genome after fertilization. Upon maternal depletion of Eed, PADs are largely intact in oocytes, but their reestablishment after fertilization is compromised. By contrast, depletion of Polycomb repressive complex 1 (PRC1) proteins attenuates PADs in oocytes, which is associated with substantial gene de-repression in PADs. These data reveal a critical role of Polycomb in regulating chromatin architecture during mammalian oocyte growth and early development.


Subject(s)
Chromatin/chemistry , Oocytes/growth & development , Oogenesis/genetics , Polycomb-Group Proteins/physiology , Animals , Blastocyst/chemistry , Cell Cycle Proteins/physiology , Chromosomal Proteins, Non-Histone/physiology , Embryo, Mammalian/chemistry , Gene Silencing , Histone Code , Mice , Oocytes/chemistry , Transcription, Genetic , Cohesins
8.
Brief Funct Genomics ; 18(6): 358-366, 2019 11 19.
Article in English | MEDLINE | ID: mdl-31673701

ABSTRACT

Polycomb group proteins (PcGs) control the epigenetic and transcriptional state of developmental genes and regulatory elements during mammalian embryogenesis. Moreover, PcGs can also contribute to 3D genome organization, adding an additional layer of complexity to their regulatory functions. Understanding the mechanistic basis and the dynamics of PcG-dependent chromatin structures will help us untangle the full complexity of PcG function during development. Since most studies concerning the 3D organization of PcG-bound chromatin in mammals have been performed in embryonic stem cells (ESCs), here we will focus on this cell type characterized by its unique self-renewal and pluripotency properties. More specifically, we will highlight recent findings and discuss open questions regarding how PcG-dependent changes in 3D chromatin architecture control gene expression, cellular identity and differentiation potential in ESCs. We believe that this can serve to illustrate the diverse regulatory mechanisms by which PcG proteins control the proper execution of gene expression programs during mammalian embryogenesis.


Subject(s)
Chromatin/metabolism , DNA Packaging/physiology , Embryonic Stem Cells/metabolism , Genome/physiology , Polycomb-Group Proteins/physiology , Animals , Chromatin/chemistry , Humans , Nucleic Acid Conformation , Polycomb-Group Proteins/metabolism , Protein Domains/physiology , Protein Folding
9.
Cell Rep ; 26(13): 3643-3656.e7, 2019 03 26.
Article in English | MEDLINE | ID: mdl-30917318

ABSTRACT

CBX4, a component of polycomb repressive complex 1 (PRC1), plays important roles in the maintenance of cell identity and organ development through gene silencing. However, whether CBX4 regulates human stem cell homeostasis remains unclear. Here, we demonstrate that CBX4 counteracts human mesenchymal stem cell (hMSC) aging via the maintenance of nucleolar homeostasis. CBX4 protein is downregulated in aged hMSCs, whereas CBX4 knockout in hMSCs results in destabilized nucleolar heterochromatin, enhanced ribosome biogenesis, increased protein translation, and accelerated cellular senescence. CBX4 maintains nucleolar homeostasis by recruiting nucleolar protein fibrillarin (FBL) and heterochromatin protein KRAB-associated protein 1 (KAP1) at nucleolar rDNA, limiting the excessive expression of rRNAs. Overexpression of CBX4 alleviates physiological hMSC aging and attenuates the development of osteoarthritis in mice. Altogether, our findings reveal a critical role of CBX4 in counteracting cellular senescence by maintaining nucleolar homeostasis, providing a potential therapeutic target for aging-associated disorders.


Subject(s)
Cell Nucleolus/physiology , Cellular Senescence/physiology , Homeostasis , Ligases/physiology , Mesenchymal Stem Cells/physiology , Osteoarthritis/therapy , Polycomb-Group Proteins/physiology , Animals , Chromosomal Proteins, Non-Histone/metabolism , Gene Knockout Techniques , Genetic Therapy , HEK293 Cells , Humans , Ligases/genetics , Male , Mice, Inbred C57BL , Mice, Inbred NOD , Polycomb-Group Proteins/genetics
10.
Int J Hematol ; 110(2): 170-178, 2019 Aug.
Article in English | MEDLINE | ID: mdl-30706327

ABSTRACT

Polycomb proteins function in the maintenance of gene silencing via post-translational modifications of histones and chromatin compaction. Genetic and biochemical studies have revealed that the repressive function of Polycomb repressive complexes (PRCs) in transcription is counteracted by the activating function of Trithorax-group complexes; this balance fine-tunes the expression of genes critical for development and tissue homeostasis. The function of PRCs is frequently dysregulated in various cancer cells due to altered expression or recurrent somatic mutations in PRC genes. The tumor suppressive functions of EZH2-containing PRC2 and a PRC2-related protein ASXL1 have been investigated extensively in the pathogenesis of hematological malignancies, including myeloproliferative neoplasms (MPN). BCOR, a component of non-canonical PRC1, suppresses various hematological malignancies including MPN. In this review, we focus on recent findings on the role of PRCs in the pathogenesis of MPN and the therapeutic impact of targeting the pathological functions of PRCs in MPN.


Subject(s)
Cell Transformation, Neoplastic/genetics , Myeloproliferative Disorders/genetics , Neoplasm Proteins/physiology , Polycomb-Group Proteins/physiology , Cell Cycle Proteins/physiology , Enhancer of Zeste Homolog 2 Protein/antagonists & inhibitors , Enhancer of Zeste Homolog 2 Protein/deficiency , Enhancer of Zeste Homolog 2 Protein/physiology , Gain of Function Mutation , Gene Expression Regulation, Neoplastic , Hematopoiesis , Histone Code , Histone-Lysine N-Methyltransferase/physiology , Humans , Molecular Targeted Therapy , Myeloid-Lymphoid Leukemia Protein/physiology , Myeloproliferative Disorders/metabolism , Neoplasm Proteins/deficiency , Neoplasm Proteins/genetics , Polycomb Repressive Complex 2/antagonists & inhibitors , Polycomb-Group Proteins/deficiency , Polycomb-Group Proteins/genetics , Proto-Oncogene Proteins/physiology , Repressor Proteins/physiology , Transcription Factors/physiology
11.
Sci Rep ; 9(1): 197, 2019 01 17.
Article in English | MEDLINE | ID: mdl-30655550

ABSTRACT

Chromobox 6 (CBX6) is a subunit of Polycomb Repressive Complex 1 (PRC1) that mediates epigenetic gene repression and acts as an oncogene or tumor suppressor in a cancer type-dependent manner. The specific function of CBX6 in breast cancer is currently undefined. In this study, a comprehensive analysis of The Cancer Genome Atlas (TCGA) dataset led to the identification of CBX6 as a consistently downregulated gene in breast cancer. We provided evidence showing enhancer of zeste homolog 2 (EZH2) negatively regulated CBX6 expression in a Polycomb Repressive Complex 2 (PRC2)-dependent manner. Exogenous overexpression of CBX6 inhibited cell proliferation and colony formation, and induced cell cycle arrest along with suppression of migration and invasion of breast cancer cells in vitro. Microarray analyses revealed that CBX6 governs a complex gene expression program. Moreover, CBX6 induced significant downregulation of bone marrow stromal cell antigen-2 (BST2), a potential therapeutic target, via interactions with its promoter region. Our collective findings support a tumor suppressor role of CBX6 in breast cancer.


Subject(s)
Breast Neoplasms/pathology , Enhancer of Zeste Homolog 2 Protein/physiology , Genes, Tumor Suppressor , Polycomb-Group Proteins/physiology , Antigens, CD/metabolism , Breast Neoplasms/metabolism , Cell Line, Tumor , Cell Movement , Cell Proliferation , Down-Regulation , GPI-Linked Proteins/metabolism , Gene Expression Regulation, Neoplastic , Humans , Polycomb-Group Proteins/genetics
12.
Exp Hematol ; 68: 10-14, 2018 12.
Article in English | MEDLINE | ID: mdl-30554637

ABSTRACT

Polycomb group (PcG) proteins are the key epigenetic regulators of normal hematopoiesis and the dysregulation of their functions is closely involved in the pathogenesis of hematological malignancies. These proteins function in the multimeric complexes called polycomb repressive complex (PRC) 1 and 2. In addition to canonical PRC1, four noncanonical PRC1 complexes have been identified. In contrast to canonical PRC1, which is recruited to its target sites in a manner dependent on H3K27me3, noncanonical PRC1 complexes are recruited to their target sites independently of H3K27me3. Among them, PRC1.1, consisting of PCGF1, RING1A/B, KDM2B, and BCL6 corepressor (BCOR) or BCLRL1, regulates diverse biological processes, including pluripotency, reprogramming, and hematopoiesis. PRC1.1 has been implicated in myelopoiesis and lymphopoiesis and is targeted by somatic gene mutations in various hematological malignancies. These findings revealed the more complex regulation of epigenetic cellular memory by PcG proteins than we expected and propose PRC1.1 as a novel therapeutic target in hematological malignancies.


Subject(s)
Hematologic Neoplasms/physiopathology , Hematopoiesis/physiology , Polycomb-Group Proteins/physiology , Animals , Embryonic Stem Cells/metabolism , Forecasting , Gene Expression Regulation, Developmental , Gene Knockdown Techniques , Hematologic Neoplasms/genetics , Hematologic Neoplasms/therapy , Histone Code/genetics , Histone Code/physiology , Humans , Mice , Mice, Knockout , Molecular Targeted Therapy , Mutation , Myeloid Cells/cytology , Myeloid Cells/metabolism , Neoplasm Proteins/physiology , Polycomb-Group Proteins/genetics , Zinc Fingers/physiology
13.
Nucleic Acids Res ; 46(13): 6608-6626, 2018 07 27.
Article in English | MEDLINE | ID: mdl-29846670

ABSTRACT

Histone post-translational modifications regulate chromatin structure and function largely through interactions with effector proteins that often contain multiple histone-binding domains. PHF1 [plant homeodomain (PHD) finger protein 1], which contains two kinds of histone reader modules, a Tudor domain and two PHD fingers, is an essential factor for epigenetic regulation and genome maintenance. While significant progress has been made in characterizing the function of the Tudor domain, the roles of the two PHD fingers are poorly defined. Here, we demonstrated that the N-terminal PHD finger of PHF1 recognizes symmetric dimethylation of H4R3 (H4R3me2s) catalyzed by PRMT5-WDR77. However, the C-terminal PHD finger of PHF1, instead of binding to modified histones, directly interacts with DDB1, the main component of the CUL4B-Ring E3 ligase complex (CRL4B), which is responsible for H2AK119 mono-ubiquitination (H2AK119ub1). We showed that PHF1, PRMT5-WDR77, and CRL4B reciprocally interact with one another and collaborate as a functional unit. Genome-wide analysis of PHF1/PRMT5/CUL4B targets identified a cohort of genes including E-cadherin and FBXW7, which are critically involved in cell growth and migration. We demonstrated that PHF1 promotes cell proliferation, invasion, and tumorigenesis in vivo and in vitro and found that its expression is markedly upregulated in a variety of human cancers. Our data identified a new reader for H4R3me2s and provided a molecular basis for the functional interplay between histone arginine methylation and ubiquitination. The results also indicated that PHF1 is a key factor in cancer progression, supporting the pursuit of PHF1 as a target for cancer therapy.


Subject(s)
Carcinogenesis , DNA-Binding Proteins/metabolism , Histones/metabolism , Polycomb-Group Proteins/metabolism , Animals , Biomarkers, Tumor/metabolism , Breast Neoplasms/metabolism , Breast Neoplasms/pathology , Cadherins/genetics , Cadherins/metabolism , Carcinoma/metabolism , Cell Line , Cell Proliferation , Cullin Proteins/metabolism , DNA-Binding Proteins/physiology , F-Box-WD Repeat-Containing Protein 7/genetics , F-Box-WD Repeat-Containing Protein 7/metabolism , Female , HEK293 Cells , Humans , Methylation , Mice , Neoplasm Metastasis , Polycomb-Group Proteins/physiology , Protein-Arginine N-Methyltransferases/chemistry , Protein-Arginine N-Methyltransferases/metabolism , Transcription Factors/metabolism , Transcription, Genetic
14.
Plant J ; 95(1): 17-29, 2018 07.
Article in English | MEDLINE | ID: mdl-29667247

ABSTRACT

Many plants sense the seasonal cues, day length or photoperiod changes, to align the timing of the developmental transition to flowering with changing seasons for reproductive success. Inductive day lengths through the photoperiod pathway induce the expression of FLOWERING LOCUS T (FT) or FT relatives that encode a major mobile florigen to promote flowering. In Arabidopsis thaliana, under inductive long days the photoperiod pathway output CONSTANS (CO) accumulates toward the end of the day, and associates with the B and C subunits of Nuclear Factor Y (NF-Y) to form the NF-CO complex that acts to promote FT expression near dusk, whereas Polycomb group (PcG) proteins function to silence FT expression. How NF-CO acts to antagonize the function of PcG proteins to regulate FT expression remains unclear. Here, we show that the NF-CO complex bound to the proximal FT promoter, through chromatin looping, acts in concert with an NF-Y complex bound to a distal enhancer to reduce the levels of PcG proteins, including both Polycomb repressive complex 1 (PRC1) and PRC2 at the FT promoter, leading to a relieving of Polycomb silencing and thus FT de-repression near dusk. Thus, our study provides molecular insights on how the 'active' photoperiod pathway and the 'repressive' Polycomb silencing system interact to control temporal FT expression, conferring the long-day induction of flowering in Arabidopsis.


Subject(s)
Arabidopsis Proteins/genetics , Arabidopsis/genetics , DNA-Binding Proteins/genetics , Gene Expression Regulation, Plant/genetics , Transcription Factors/genetics , Arabidopsis/metabolism , Arabidopsis/physiology , Arabidopsis Proteins/metabolism , Arabidopsis Proteins/physiology , DNA-Binding Proteins/physiology , Flowers/growth & development , Glucosyltransferases/metabolism , Photoperiod , Polycomb Repressive Complex 2 , Polycomb-Group Proteins/genetics , Polycomb-Group Proteins/metabolism , Polycomb-Group Proteins/physiology , Repressor Proteins/metabolism , Transcription Factors/physiology
15.
PLoS Genet ; 14(2): e1007233, 2018 02.
Article in English | MEDLINE | ID: mdl-29462142

ABSTRACT

The sex chromosomes are enriched with germline genes that are activated during the late stages of spermatogenesis. Due to meiotic sex chromosome inactivation (MSCI), these sex chromosome-linked genes must escape silencing for activation in spermatids, thereby ensuring their functions for male reproduction. RNF8, a DNA damage response protein, and SCML2, a germline-specific Polycomb protein, are two major, known regulators of this process. Here, we show that RNF8 and SCML2 cooperate to regulate ubiquitination during meiosis, an early step to establish active histone modifications for subsequent gene activation. Double mutants of Rnf8 and Scml2 revealed that RNF8-dependent monoubiquitination of histone H2A at Lysine 119 (H2AK119ub) is deubiquitinated by SCML2, demonstrating interplay between RNF8 and SCML2 in ubiquitin regulation. Additionally, we identify distinct functions of RNF8 and SCML2 in the regulation of ubiquitination: SCML2 deubiquitinates RNF8-independent H2AK119ub but does not deubiquitinate RNF8-dependent polyubiquitination. RNF8-dependent polyubiquitination is required for the establishment of H3K27 acetylation, a marker of active enhancers, while persistent H2AK119ub inhibits establishment of H3K27 acetylation. Following the deposition of H3K27 acetylation, H3K4 dimethylation is established as an active mark on poised promoters. Together, we propose a model whereby regulation of ubiquitin leads to the organization of poised enhancers and promoters during meiosis, which induce subsequent gene activation from the otherwise silent sex chromosomes in postmeiotic spermatids.


Subject(s)
Histones/metabolism , Polycomb-Group Proteins/physiology , Sex Chromosomes/genetics , Transcriptional Activation/genetics , Ubiquitin-Protein Ligases/physiology , Ubiquitination/genetics , Acetylation , Animals , Female , Male , Meiosis/genetics , Mice , Mice, Inbred C57BL , Mice, Knockout , Sex Chromosomes/metabolism , Spermatids/physiology , Spermatogenesis/genetics
16.
Genome Biol ; 19(1): 18, 2018 02 08.
Article in English | MEDLINE | ID: mdl-29422066

ABSTRACT

BACKGROUND: Previous studies showed that the majority of developmental genes are devoid of DNA methylation at promoters even when they are repressed. Such hypomethylated regions at developmental genes are unusually large and extend well beyond proximal promoters, forming DNA methylation valleys (DMVs) or DNA methylation canyons. However, it remains elusive how most developmental genes can evade DNA methylation regardless of their transcriptional states. RESULTS: We show that DMVs are hypomethylated in development and are highly conserved across vertebrates. Importantly, DMVs are hotspots of regulatory regions for key developmental genes and show low levels of deamination mutation rates. By analyzing a panel of DNA methylomes from mouse tissues, we identify a subset of DMVs that are dynamically methylated. These DMVs are strongly enriched for Polycomb-deposited H3K27me3 when the associated genes are silenced, and surprisingly show elevated DNA methylation upon gene activation. 4C-seq analyses indicates that Polycomb-bound DMVs form insulated and self-interacting chromatin domains. Further investigations show that DNA hypomethylation is better correlated with the binding of Polycomb than with H3K27me3. In support of a role of Polycomb in DMV hypomethylation, we observe aberrant methylation in DMVs in mouse embryonic stem cells deficient in the EED protein. Finally, we show that Polycomb regulates hypomethylation of DMVs likely through ten-eleven translocation (TET) proteins. CONCLUSIONS: We show that Polycomb promotes the hypomethylation of DMVs near key developmental genes. These data reveal a delicate interplay between histone modifiers and DNA methylation, which contributes to their division at distinct gene targets, allowing lineage-specifying genes to largely maintain DNA methylation-free at regulatory elements.


Subject(s)
DNA Methylation , Polycomb-Group Proteins/physiology , Animals , Base Sequence , Binding Sites , Conserved Sequence , DNA-Binding Proteins/metabolism , Gene Expression , Genome , Growth and Development/genetics , Transcription Factors/metabolism , Vertebrates/genetics
17.
PLoS Genet ; 14(1): e1007187, 2018 01.
Article in English | MEDLINE | ID: mdl-29357360

ABSTRACT

In response to stress and injury a coordinated activation of conserved signalling modules, such as JNK and JAK/STAT, is critical to trigger regenerative tissue restoration. While these pathways rebuild homeostasis and promote faithful organ recovery, it is intriguing that they also become activated in various tumour conditions. Therefore, it is crucial to understand how similar pathways can achieve context-dependent functional outputs, likely depending on cellular states. Compromised chromatin regulation, upon removal of the Polycomb group member polyhomeotic, leads to tumour formation with ectopic activation of JNK signalling, mediated by egr/grnd, in addition to JAK/STAT and Notch. Employing quantitative analyses, we show that blocking ectopic signalling impairs ph tumour growth. Furthermore, JAK/STAT functions in parallel to JNK, while Notch relies on JNK. Here, we reveal a signalling hierarchy in ph tumours that is distinct from the regenerative processes regulated by these pathways. Absence of ph renders a permissive state for expression of target genes, but our results suggest that both loss of repression and the presence of activators may collectively regulate gene expression during tumorigenesis. Further dissecting the effect of signalling, developmental or stress-induced factors will thus elucidate the regulation of physiological responses and the contribution of context-specific cellular states.


Subject(s)
Carcinogenesis/genetics , Gene Silencing/physiology , Neoplasms/genetics , Polycomb-Group Proteins/physiology , Animals , Animals, Genetically Modified , Drosophila melanogaster/embryology , Drosophila melanogaster/genetics , Embryo, Nonmammalian , Gene Expression Regulation, Developmental , Gene Expression Regulation, Neoplastic , Humans , Janus Kinases/genetics , Janus Kinases/metabolism , MAP Kinase Signaling System/genetics , Neoplasms/pathology , Receptor Cross-Talk/physiology , Receptors, Notch/genetics , Receptors, Notch/metabolism , STAT Transcription Factors/genetics , STAT Transcription Factors/metabolism , Signal Transduction/physiology
18.
J Biol Chem ; 292(52): 21527-21537, 2017 12 29.
Article in English | MEDLINE | ID: mdl-29054931

ABSTRACT

Polycomb group (PcG) proteins are epigenetic transcriptional repressors that orchestrate numerous developmental processes and have been implicated in the maintenance of embryonic stem (ES) cell state. More recent evidence suggests that a subset of PcG proteins engages in transcriptional activation in some cellular contexts, but how this property is exerted remains largely unknown. Here, we generated ES cells with single or combined disruption of polycomb group RING finger protein 3 (Pcgf3) and Pcgf5 with the CRISPR-Cas9 technique. We report that although these mutant cells maintained their self-renewal and colony-forming capacity, they displayed severe defects in mesoderm differentiation in vitro and in vivo Using RNA-seq to analyze transcriptional profiles of ES cells with single or combined Pcgf3/5 deficiencies, we found that in contrast to the canonical role of the related polycomb repressive complex 1 (PRC1) in gene repression, Pcgf3/5 mainly function as transcriptional activators driving expression of many genes involved in mesoderm differentiation. Proteomic approaches and promoter occupancy analyses helped to establish an extended Pcgf3/5 interactome and identified several novel Pcgf3/5 interactors. These included testis-expressed 10 (Tex10), which may directly contribute to transcriptional activation via the transcriptional co-activator p300. Furthermore, Pcgf3/5 deletion in ES cells substantially reduced the occupancy of Tex10 and p300 at target genes. Finally, we demonstrated that Pcgf3/5 are essential for regulating global levels of the histone modifier H2AK119ub1 in ES cells. Our findings establish Pcgf3/5 as transcriptional activators that interact with Tex10 and p300 in ES cells and point to redundant activity of Pcgf3/5 in pluripotency maintenance.


Subject(s)
Polycomb-Group Proteins/metabolism , Animals , Cell Differentiation/genetics , Cell Line , Histones/metabolism , Mice , Mouse Embryonic Stem Cells/cytology , Nuclear Proteins/metabolism , Polycomb Repressive Complex 1/metabolism , Polycomb-Group Proteins/genetics , Polycomb-Group Proteins/physiology , Promoter Regions, Genetic/genetics , Transcriptional Activation/physiology
19.
Nat Genet ; 49(10): 1546-1552, 2017 Oct.
Article in English | MEDLINE | ID: mdl-28825728

ABSTRACT

Disruption of gene silencing by Polycomb protein complexes leads to homeotic transformations and altered developmental-phase identity in plants. Here we define short genomic fragments, known as Polycomb response elements (PREs), that direct Polycomb repressive complex 2 (PRC2) placement at developmental genes regulated by silencing in Arabidopsis thaliana. We identify transcription factor families that bind to these PREs, colocalize with PRC2 on chromatin, physically interact with and recruit PRC2, and are required for PRC2-mediated gene silencing in vivo. Two of the cis sequence motifs enriched in the PREs are cognate binding sites for the identified transcription factors and are necessary and sufficient for PRE activity. Thus PRC2 recruitment in Arabidopsis relies in large part on binding of trans-acting factors to cis-localized DNA sequence motifs.


Subject(s)
Arabidopsis Proteins/physiology , Arabidopsis/genetics , Epigenetic Repression/genetics , Gene Expression Regulation, Plant , Gene Silencing , Polycomb Repressive Complex 2/physiology , Polycomb-Group Proteins/physiology , Response Elements/genetics , Amino Acid Motifs , Arabidopsis/metabolism , Arabidopsis Proteins/biosynthesis , Arabidopsis Proteins/genetics , Binding Sites , DNA, Plant/genetics , DNA, Plant/metabolism , Flowers/growth & development , Gene Ontology , High-Throughput Screening Assays , Multigene Family , Plant Leaves/ultrastructure , Plants, Genetically Modified , Protein Binding , Protein Interaction Mapping , Transcription Factors/metabolism
20.
Med Sci (Paris) ; 33(5): 499-505, 2017 May.
Article in French | MEDLINE | ID: mdl-28612725

ABSTRACT

Polycomb Group proteins (PcG) are repressive epigenetic factors essential for development and involved in numerous cancer processes, yet their modes of action and recruitment to specific genomic loci are not fully understood. Recently, it has been shown that the PcG protein recruitment is a dynamic process, contrary to what was foreseen in the initial hierarchical model. In addition, EZH2, a key PcG protein, can be associated to transcribed genes, challenging the former function of PcG proteins as transcriptional repressors. Furthermore, the dual role of EZH2, which can act as an oncogene or a tumor suppressor depending on the cellular type, illustrates the functional complexity of PcG proteins.


Subject(s)
Enhancer of Zeste Homolog 2 Protein/physiology , Polycomb-Group Proteins/physiology , Animals , Cell Differentiation/genetics , Cell Proliferation/genetics , Gene Expression Regulation , Gene Regulatory Networks/genetics , Genes, Tumor Suppressor , Humans , Oncogenes/physiology , Signal Transduction/genetics
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