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      Insights into epigenetic patterns in mammalian early embryos

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          Abstract

          Mammalian fertilization begins with the fusion of two specialized gametes, followed by major epigenetic remodeling leading to the formation of a totipotent embryo. During the development of the pre-implantation embryo, precise reprogramming progress is a prerequisite for avoiding developmental defects or embryonic lethality, but the underlying molecular mechanisms remain elusive. For the past few years, unprecedented breakthroughs have been made in mapping the regulatory network of dynamic epigenomes during mammalian early embryo development, taking advantage of multiple advances and innovations in low-input genome-wide chromatin analysis technologies. The aim of this review is to highlight the most recent progress in understanding the mechanisms of epigenetic remodeling during early embryogenesis in mammals, including DNA methylation, histone modifications, chromatin accessibility and 3D chromatin organization.

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          Regulation of chromatin by histone modifications.

          Andrew Bannister, Tony Kouzarides (2011)
          Chromatin is not an inert structure, but rather an instructive DNA scaffold that can respond to external cues to regulate the many uses of DNA. A principle component of chromatin that plays a key role in this regulation is the modification of histones. There is an ever-growing list of these modifications and the complexity of their action is only just beginning to be understood. However, it is clear that histone modifications play fundamental roles in most biological processes that are involved in the manipulation and expression of DNA. Here, we describe the known histone modifications, define where they are found genomically and discuss some of their functional consequences, concentrating mostly on transcription where the majority of characterisation has taken place.
          Article 0 comments Cited 975 times – based on 0 reviews     Review now
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            Naive and primed pluripotent states.

            Jennifer Nichols, Austin Smith (2009)
            After maternal predetermination gives way to zygotic regulation, a ground state is established within the mammalian embryo. This tabula rasa for embryogenesis is present only transiently in the preimplantation epiblast. Here, we consider how unrestricted cells are first generated and then prepared for lineage commitment. We propose that two phases of pluripotency can be defined: naive and primed. This distinction extends to pluripotent stem cells derived from embryos or by molecular reprogramming ex vivo.
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              A map of the cis-regulatory sequences in the mouse genome.

              Yin Shen, Feng Yue, David F. McCleary … (2012)
              The laboratory mouse is the most widely used mammalian model organism in biomedical research. The 2.6 × 10(9) bases of the mouse genome possess a high degree of conservation with the human genome, so a thorough annotation of the mouse genome will be of significant value to understanding the function of the human genome. So far, most of the functional sequences in the mouse genome have yet to be found, and the cis-regulatory sequences in particular are still poorly annotated. Comparative genomics has been a powerful tool for the discovery of these sequences, but on its own it cannot resolve their temporal and spatial functions. Recently, ChIP-Seq has been developed to identify cis-regulatory elements in the genomes of several organisms including humans, Drosophila melanogaster and Caenorhabditis elegans. Here we apply the same experimental approach to a diverse set of 19 tissues and cell types in the mouse to produce a map of nearly 300,000 murine cis-regulatory sequences. The annotated sequences add up to 11% of the mouse genome, and include more than 70% of conserved non-coding sequences. We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we show that much of the mouse genome is organized into domains of coordinately regulated enhancers and promoters. Our results provide a resource for the annotation of functional elements in the mammalian genome and for the study of mechanisms regulating tissue-specific gene expression.
              Article 0 comments Cited 659 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Xiaoyu Liu:
                ORCID: https://orcid.org/0000-0001-6622-9316
                liuxiaoyu@tongji.edu.cn
                Shaorong Gao:
                ORCID: https://orcid.org/0000-0003-1041-3928
                gaoshaorong@tongji.edu.cn
                Journal
                Journal ID (nlm-ta): Protein Cell
                Journal ID (iso-abbrev): Protein Cell
                Title: Protein & Cell
                Publisher: Higher Education Press (Beijing )
                ISSN (Print): 1674-800X
                ISSN (Electronic): 1674-8018
                Publication date (Electronic): 15 July 2020
                Publication date PMC-release: 15 July 2020
                Publication date (Print): January 2021
                Volume: 12
                Issue: 1
                Pages: 7-28
                Affiliations
                [1 ]GRID grid.24516.34, ISNI 0000000123704535, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, , Tongji University, ; Shanghai, 200092 China
                [2 ]GRID grid.24516.34, ISNI 0000000123704535, Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, , Tongji University, ; Shanghai, 200092 China
                [3 ]GRID grid.24516.34, ISNI 0000000123704535, Tsingtao Advanced Research Institute, , Tongji University, ; Qingdao, 266071 China
                Author information
                https://orcid.org/0000-0002-8746-6350
                https://orcid.org/0000-0002-2862-1357
                https://orcid.org/0000-0001-6622-9316
                https://orcid.org/0000-0003-1041-3928
                Article
                Publisher ID: 757
                DOI: 10.1007/s13238-020-00757-z
                PMC ID: 7815849
                PubMed ID: 32671792
                SO-VID: 7211f81f-b1ec-4d08-b092-c45d20a0852a
                Copyright © © The Author(s) 2020
                License:

                Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                Date received : 12 April 2020
                Date accepted : 9 June 2020
                Categories
                Subject: Review
                Custom metadata
                issue-copyright-statement © The Author(s) 2021

                Keywords: epigenetic reprogramming,dna methylation,histone modifications,early embryo development
                Data availability:
                Keywords: epigenetic reprogramming, dna methylation, histone modifications, early embryo development

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