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      Sperm is epigenetically programmed to regulate gene transcription in embryos

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          Abstract

          For a long time, it has been assumed that the only role of sperm at fertilization is to introduce the male genome into the egg. Recently, ideas have emerged that the epigenetic state of the sperm nucleus could influence transcription in the embryo. However, conflicting reports have challenged the existence of epigenetic marks on sperm genes, and there are no functional tests supporting the role of sperm epigenetic marking on embryonic gene expression. Here, we show that sperm is epigenetically programmed to regulate embryonic gene expression. By comparing the development of sperm- and spermatid-derived frog embryos, we show that the programming of sperm for successful development relates to its ability to regulate transcription of a set of developmentally important genes. During spermatid maturation into sperm, these genes lose H3K4me2/3 and retain H3K27me3 marks. Experimental removal of these epigenetic marks at fertilization de-regulates gene expression in the resulting embryos in a paternal chromatin-dependent manner. This demonstrates that epigenetic instructions delivered by the sperm at fertilization are required for correct regulation of gene expression in the future embryos. The epigenetic mechanisms of developmental programming revealed here are likely to relate to the mechanisms involved in transgenerational transmission of acquired traits. Understanding how parental experience can influence development of the progeny has broad potential for improving human health.

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          Disruption of histone methylation in developing sperm impairs offspring health transgenerationally.

          A father's lifetime experiences can be transmitted to his offspring to affect health and development. However, the mechanisms underlying paternal epigenetic transmission are unclear. Unlike in somatic cells, there are few nucleosomes in sperm, and their function in epigenetic inheritance is unknown. We generated transgenic mice in which overexpression of the histone H3 lysine 4 (H3K4) demethylase KDM1A (also known as LSD1) during spermatogenesis reduced H3K4 dimethylation in sperm. KDM1A overexpression in one generation severely impaired development and survivability of offspring. These defects persisted transgenerationally in the absence of KDM1A germline expression and were associated with altered RNA profiles in sperm and offspring. We show that epigenetic inheritance of aberrant development can be initiated by histone demethylase activity in developing sperm, without changes to DNA methylation at CpG-rich regions.
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            Distinctive Chromatin in Human Sperm Packages Genes for Embryo Development

            Summary As nucleosomes are widely replaced by protamine in mature human sperm, epigenetic contributions of sperm chromatin to embryo development have been considered highly limited. However, we find the retained nucleosomes significantly enriched at loci of developmental importance including imprinted gene clusters, miRNA clusters, HOX gene clusters, and the promoters of stand-alone developmental transcription and signaling factors. Importantly, histone modifications localize to particular developmental loci. H3K4me2 is enriched at certain developmental promoters, whereas large blocks of H3K4me3 localize to a subset of developmental promoters, regions in HOX clusters, certain non-coding RNAs, and generally to paternally-expressed imprinted loci, but not paternally-repressed loci. Notably, H3K27me3 is significantly enriched at developmental promoters that are repressed in early embryos, including many bivalent (H3K4me3/H3K27me3) promoters in embryonic stem cells. Finally, developmental promoters are generally DNA hypomethylated in sperm, but acquire methylation during differentiation. Taken together, epigenetic marking in sperm is extensive, and correlated with developmental regulators.
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              Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa.

              In mammalian spermatozoa, most but not all of the genome is densely packaged by protamines. Here we reveal the molecular logic underlying the retention of nucleosomes in mouse spermatozoa, which contain only 1% residual histones. We observe high enrichment throughout the genome of nucleosomes at CpG-rich sequences that lack DNA methylation. Residual nucleosomes are largely composed of the histone H3.3 variant and are trimethylated at Lys4 of histone H3 (H3K4me3). Canonical H3.1 and H3.2 histones are also enriched at CpG-rich promoters marked by Polycomb-mediated H3K27me3, a modification predictive of gene repression in preimplantation embryos. Histone variant-specific nucleosome retention in sperm is strongly associated with nucleosome turnover in round spermatids. Our data show evolutionary conservation of the basic principles of nucleosome retention in mouse and human sperm, supporting a model of epigenetic inheritance by nucleosomes between generations.
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                Author and article information

                Journal
                Genome Res
                Genome Res
                genome
                genome
                GENOME
                Genome Research
                Cold Spring Harbor Laboratory Press
                1088-9051
                1549-5469
                August 2016
                August 2016
                : 26
                : 8
                : 1034-1046
                Affiliations
                [1 ]Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, United Kingdom;
                [2 ]Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, United Kingdom;
                [3 ]Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland;
                [4 ]Faculty of Sciences, University of Basel, 4001 Basel, Switzerland;
                [5 ]Department of Molecular Bioscience, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
                Author notes
                [6]

                These authors contributed equally to this work.

                [7]

                Present address: EMBL Heidelberg, 69117 Heidelberg, Germany

                Article
                9509184
                10.1101/gr.201541.115
                4971762
                27034506
                1dd18fec-80a9-4ac1-a52f-6298a7e7b23b
                © 2016 Teperek et al.; Published by Cold Spring Harbor Laboratory Press

                This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.

                History
                : 16 November 2015
                : 29 March 2016
                Page count
                Pages: 13
                Funding
                Funded by: Medical Research Council http://dx.doi.org/10.13039/501100000265
                Award ID: WT089613
                Award ID: MR/K011022/1
                Award ID: AICR 10-0908
                Award ID: MR/K011022/1
                Funded by: Herchel Smith Postdoctoral
                Funded by: National Institutes of Health http://dx.doi.org/10.13039/100000002
                Funded by: National Science Foundation http://dx.doi.org/10.13039/100000001
                Funded by: Cancer Prevention Research Institute of Texas http://dx.doi.org/10.13039/100004917
                Funded by: Welch Foundation http://dx.doi.org/10.13039/100000928
                Award ID: F1515
                Funded by: Wellcome Trust http://dx.doi.org/10.13039/100004440
                Award ID: WT101050/Z/13/Z
                Funded by: Swiss National Science Foundation http://dx.doi.org/10.13039/501100001711
                Award ID: 31003A_125386
                Funded by: Novartis Research Foundation
                Award ID: CRUK C6946/A14492
                Award ID: WT092096
                Categories
                Research

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