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      EZHIP constrains Polycomb Repressive Complex 2 activity in germ cells

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          Abstract

          The Polycomb group of proteins is required for the proper orchestration of gene expression due to its role in maintaining transcriptional silencing. It is composed of several chromatin modifying complexes, including Polycomb Repressive Complex 2 (PRC2), which deposits H3K27me2/3. Here, we report the identification of a cofactor of PRC2, EZHIP (EZH1/2 Inhibitory Protein), expressed predominantly in the gonads. EZHIP limits the enzymatic activity of PRC2 and lessens the interaction between the core complex and its accessory subunits, but does not interfere with PRC2 recruitment to chromatin. Deletion of Ezhip in mice leads to a global increase in H3K27me2/3 deposition both during spermatogenesis and at late stages of oocyte maturation. This does not affect the initial number of follicles but is associated with a reduction of follicles in aging. Our results suggest that mature oocytes Ezhip−/− might not be fully functional and indicate that fertility is strongly impaired in Ezhip−/− females. Altogether, our study uncovers EZHIP as a regulator of chromatin landscape in gametes.

          Abstract

          Polycomb Repressive Complex 2 (PRC2) plays critical roles in transcriptional silencing during development. Here the authors identify EZHIP as a cofactor of PRC2 expressed predominantly in the gonads, finding that EZHIP limits the enzymatic activity of PRC2 in germ cells in mice.

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          Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L.

          Mammalian genomes employ heritable cytosine methylation in the long-term silencing of retrotransposons and genes subject to genomic imprinting and X chromosome inactivation. Little is known of the mechanisms that direct cytosine methylation to specific sequences. Here we show that DNA methyltransferase 3-like (Dnmt3L (ref. 1)) is expressed in testes during a brief perinatal period in the non-dividing precursors of spermatogonial stem cells at a stage where retrotransposons undergo de novo methylation. Deletion of the Dnmt3L gene prevented the de novo methylation of both long-terminal-repeat (LTR) and non-LTR retrotransposons, which were transcribed at high levels in spermatogonia and spermatocytes. Loss of Dnmt3L from early germ cells also caused meiotic failure in spermatocytes, which do not express Dnmt3L. Whereas dispersed repeated sequences were demethylated in mutant germ cells, tandem repeats in pericentric regions were methylated normally. This result indicates that the Dnmt3L protein might have a function in the de novo methylation of dispersed repeated sequences in a premeiotic genome scanning process that occurs in male germ cells at about the time of birth.
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            Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos.

            Histone modifications have critical roles in regulating the expression of developmental genes during embryo development in mammals. However, genome-wide analyses of histone modifications in pre-implantation embryos have been impeded by the scarcity of the required materials. Here, by using a small-scale chromatin immunoprecipitation followed by sequencing (ChIP-seq) method, we map the genome-wide profiles of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 trimethylation (H3K27me3), which are associated with gene activation and repression, respectively, in mouse pre-implantation embryos. We find that the re-establishment of H3K4me3, especially on promoter regions, occurs much more rapidly than that of H3K27me3 following fertilization, which is consistent with the major wave of zygotic genome activation at the two-cell stage. Furthermore, H3K4me3 and H3K27me3 possess distinct features of sequence preference and dynamics in pre-implantation embryos. Although H3K4me3 modifications occur consistently at transcription start sites, the breadth of the H3K4me3 domain is a highly dynamic feature. Notably, the broad H3K4me3 domain (wider than 5 kb) is associated with higher transcription activity and cell identity not only in pre-implantation development but also in the process of deriving embryonic stem cells from the inner cell mass and trophoblast stem cells from the trophectoderm. Compared to embryonic stem cells, we found that the bivalency (that is, co-occurrence of H3K4me3 and H3K27me3) in early embryos is relatively infrequent and unstable. Taken together, our results provide a genome-wide map of H3K4me3 and H3K27me3 modifications in pre-implantation embryos, facilitating further exploration of the mechanism for epigenetic regulation in early embryos.
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              Nucleosome-interacting proteins regulated by DNA and histone methylation.

              Modifications on histones or on DNA recruit proteins that regulate chromatin function. Here, we use nucleosomes methylated on DNA and on histone H3 in an affinity assay, in conjunction with a SILAC-based proteomic analysis, to identify "crosstalk" between these two distinct classes of modification. Our analysis reveals proteins whose binding to nucleosomes is regulated by methylation of CpGs, H3K4, H3K9, and H3K27 or a combination thereof. We identify the origin recognition complex (ORC), including LRWD1 as a subunit, to be a methylation-sensitive nucleosome interactor that is recruited cooperatively by DNA and histone methylation. Other interactors, such as the lysine demethylase Fbxl11/KDM2A, recognize nucleosomes methylated on histones, but their recruitment is disrupted by DNA methylation. These data establish SILAC nucleosome affinity purifications (SNAP) as a tool for studying the dynamics between different chromatin modifications and provide a modification binding "profile" for proteins regulated by DNA and histone methylation. Copyright © 2010 Elsevier Inc. All rights reserved.
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                Author and article information

                Contributors
                raphael.margueron@curie.fr
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                26 August 2019
                26 August 2019
                2019
                : 10
                : 3858
                Affiliations
                [1 ]ISNI 0000 0001 2308 1657, GRID grid.462844.8, Institut Curie, PSL Research University, , Sorbonne University, INSERM U934/ CNRS UMR3215, ; 26, rue d’Ulm, 75005 Paris, France
                [2 ]ISNI 0000000122931605, GRID grid.5590.9, Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, , Radboud University Nijmegen, ; Route 274 M850.03.87 Geert Grooteplein 28, Nijmegen, 6525 GA Netherlands
                [3 ]ISNI 0000 0001 2097 6957, GRID grid.58140.38, INSERM U900, Mines ParisTech, ; 26, rue d’Ulm, Paris, France
                [4 ]Commissariat à l’énergie atomique et aux énergies alternatives, Institut de radiobiologie cellulaire et moléculaire, Laboratoire des Cellules Souches Germinales, INSERM U967, Fontenay-aux-Roses, 92260 France
                [5 ]ISNI 0000 0004 0483 2525, GRID grid.4567.0, Institute of Epigenetics and Stem Cells (IES), , Helmholtz Zentrum München, ; D-81377 München, Germany
                [6 ]ISNI 0000 0004 1936 973X, GRID grid.5252.0, Faculty of Biology, , Ludwig Maximilians Universität, ; D-81377 München, Germany
                [7 ]ISNI 0000 0004 0639 6384, GRID grid.418596.7, ICGex Next-Generation Sequencing Platform, Curie Institute, ; 26, rue d’Ulm, Paris, France
                Author information
                http://orcid.org/0000-0002-2117-9754
                http://orcid.org/0000-0002-2801-8910
                http://orcid.org/0000-0003-1678-7410
                Article
                11800
                10.1038/s41467-019-11800-x
                6710278
                31451685
                6d811177-8c92-4983-9ec3-1791d310cb39
                © The Author(s) 2019

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 5 November 2018
                : 6 August 2019
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                Custom metadata
                © The Author(s) 2019

                Uncategorized
                germline development,development,gene regulation,chromatin,transcription
                Uncategorized
                germline development, development, gene regulation, chromatin, transcription

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