XB-ART-59375
Dev Growth Differ
2022 Dec 01;649:508-516. doi: 10.1111/dgd.12813.
Show Gene links
Show Anatomy links
Epigenomic dynamics of early Xenopus Embryos.
Zhou JJ
,
Cho KWY
.
???displayArticle.abstract???
How the embryonic genome regulates accessibility to transcription factors is one of the major questions in understanding the spatial and temporal dynamics of gene expression during embryogenesis. Epigenomic analyses of embryonic chromatin provide molecular insights into cell-specific gene activities and genomic architectures. In recent years, significant advances have been made to elucidate the dynamic changes behind the activation of the zygotic genome in various model organisms. Here we provide an overview of the recent epigenomic studies pertaining to early Xenopus development.
???displayArticle.pubmedLink??? 36168140
???displayArticle.pmcLink??? PMC10550391
???displayArticle.link??? Dev Growth Differ
???displayArticle.grants??? [+]
R01GM126395 NIH HHS , R35GM139617 NIH HHS , P30 CA062203 NCI NIH HHS , R35 GM139617 NIGMS NIH HHS , R01 GM126395 NIGMS NIH HHS
Species referenced: Xenopus laevis
???attribute.lit??? ???displayArticles.show???
|
|
Figure 1. Characteristics of the epigenome during early Xenopus development. The patterns of different epigenetic signatures that emerge around ZGA are shown in a time window from the zygote to the gastrula stage. Blue dashed lines denote the minor/major ZGA. |
References [+] :
Ahmad,
The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly.
2002, Pubmed
Ahmad, The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. 2002, Pubmed
Akkers, A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. 2009, Pubmed , Xenbase
Allshire, Ten principles of heterochromatin formation and function. 2018, Pubmed
Anderson, Effects of histone acetylation on the equilibrium accessibility of nucleosomal DNA target sites. 2001, Pubmed
Beacon, The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes. 2021, Pubmed
Bernstein, A bivalent chromatin structure marks key developmental genes in embryonic stem cells. 2006, Pubmed
Bird, DNA methylation patterns and epigenetic memory. 2002, Pubmed
Blythe, beta-Catenin primes organizer gene expression by recruiting a histone H3 arginine 8 methyltransferase, Prmt2. 2010, Pubmed , Xenbase
Bogdanovic, Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. 2012, Pubmed , Xenbase
Bogdanovic, Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis. 2011, Pubmed , Xenbase
Bright, Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates. 2021, Pubmed , Xenbase
Cai, H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions. 2021, Pubmed
Chan, Brd4 and P300 Confer Transcriptional Competency during Zygotic Genome Activation. 2019, Pubmed
Chen, A global change in RNA polymerase II pausing during the Drosophila midblastula transition. 2013, Pubmed
Chen, Spatiotemporal Patterning of Zygotic Genome Activation in a Model Vertebrate Embryo. 2019, Pubmed , Xenbase
Chen, Nascent transcriptome reveals orchestration of zygotic genome activation in early embryogenesis. 2022, Pubmed , Xenbase
Chen, Key role for CTCF in establishing chromatin structure in human embryos. 2019, Pubmed
Cho, DNase-seq to Study Chromatin Accessibility in Early Xenopus tropicalis Embryos. 2019, Pubmed , Xenbase
Creyghton, Histone H3K27ac separates active from poised enhancers and predicts developmental state. 2010, Pubmed
Dahl, Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition. 2016, Pubmed
Dimitrov, Chromatin transitions during early Xenopus embryogenesis: changes in histone H4 acetylation and in linker histone type. 1993, Pubmed , Xenbase
Dorighi, Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation. 2017, Pubmed
Du, Allelic reprogramming of 3D chromatin architecture during early mammalian development. 2017, Pubmed
Dunican, xDnmt1 regulates transcriptional silencing in pre-MBT Xenopus embryos independently of its catalytic function. 2008, Pubmed , Xenbase
Eckersley-Maslin, Dynamics of the epigenetic landscape during the maternal-to-zygotic transition. 2018, Pubmed
Esmaeili, Chromatin accessibility and histone acetylation in the regulation of competence in early development. 2020, Pubmed , Xenbase
Espinola, Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development. 2021, Pubmed
Feng, Conservation and divergence of methylation patterning in plants and animals. 2010, Pubmed
Franke, CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression. 2021, Pubmed
Fyodorov, Emerging roles of linker histones in regulating chromatin structure and function. 2018, Pubmed
Gaydos, Gene repression. H3K27me and PRC2 transmit a memory of repression across generations and during development. 2014, Pubmed
Gentsch, Maternal pluripotency factors initiate extensive chromatin remodelling to predefine first response to inductive signals. 2019, Pubmed , Xenbase
Gross, Nuclease hypersensitive sites in chromatin. 1988, Pubmed
Gupta, Developmental enhancers are marked independently of zygotic Nodal signals in Xenopus. 2014, Pubmed , Xenbase
Hake, Histone H3 variants and their potential role in indexing mammalian genomes: the "H3 barcode hypothesis". 2006, Pubmed
Heidari, Genome-wide map of regulatory interactions in the human genome. 2014, Pubmed
Heintzman, Histone modifications at human enhancers reflect global cell-type-specific gene expression. 2009, Pubmed
Henikoff, Nucleosome destabilization in the epigenetic regulation of gene expression. 2008, Pubmed
Herz, Enhancer-associated H3K4 monomethylation by Trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4. 2012, Pubmed
Hontelez, Embryonic transcription is controlled by maternally defined chromatin state. 2015, Pubmed , Xenbase
Hug, Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription. 2017, Pubmed
Hyun, Writing, erasing and reading histone lysine methylations. 2017, Pubmed
Ing-Simmons, Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning. 2021, Pubmed
Inoue, Enzymatic deacetylation of histone. 1969, Pubmed
Kaaij, Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development. 2018, Pubmed
Kadauke, Chromatin loops in gene regulation. 2009, Pubmed
Karimi, DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. 2011, Pubmed
Ke, 3D Chromatin Structures of Mature Gametes and Structural Reprogramming during Mammalian Embryogenesis. 2017, Pubmed
Khoury, Constitutively bound CTCF sites maintain 3D chromatin architecture and long-range epigenetically regulated domains. 2020, Pubmed
Koenecke, Drosophila poised enhancers are generated during tissue patterning with the help of repression. 2017, Pubmed
Kubo, Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. 2021, Pubmed
Kundu, Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation. 2017, Pubmed
Lee, Histone acetyltransferase complexes: one size doesn't fit all. 2007, Pubmed
Li, Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. 1992, Pubmed
Li, Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition. 2014, Pubmed
Lieberman-Aiden, Comprehensive mapping of long-range interactions reveals folding principles of the human genome. 2009, Pubmed
Lindeman, Prepatterning of developmental gene expression by modified histones before zygotic genome activation. 2011, Pubmed
Liu, Inherited DNA methylation primes the establishment of accessible chromatin during genome activation. 2018, Pubmed
Local, Identification of H3K4me1-associated proteins at mammalian enhancers. 2018, Pubmed
Lombard-Banek, Single-cell proteomics in complex tissues using microprobe capillary electrophoresis mass spectrometry. 2019, Pubmed , Xenbase
Lovén, Selective inhibition of tumor oncogenes by disruption of super-enhancers. 2013, Pubmed
Lu, Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development. 2016, Pubmed
McCord, Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function. 2020, Pubmed
Moore, DNA methylation and its basic function. 2013, Pubmed
Moshe, Genome-wide search for Zelda-like chromatin signatures identifies GAF as a pioneer factor in early fly development. 2017, Pubmed
Ng, Epigenetic memory of an active gene state depends on histone H3.3 incorporation into chromatin in the absence of transcription. 2008, Pubmed , Xenbase
Niu, Three-dimensional folding dynamics of the Xenopus tropicalis genome. 2021, Pubmed , Xenbase
Ogiyama, Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development. 2018, Pubmed
Okano, DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. 1999, Pubmed
Ong, CTCF: an architectural protein bridging genome topology and function. 2014, Pubmed
Pan, Orchestration of H3K27 methylation: mechanisms and therapeutic implication. 2018, Pubmed
Paraiso, Endodermal Maternal Transcription Factors Establish Super-Enhancers during Zygotic Genome Activation. 2019, Pubmed , Xenbase
Pombo, Three-dimensional genome architecture: players and mechanisms. 2015, Pubmed
Rada-Iglesias, A unique chromatin signature uncovers early developmental enhancers in humans. 2011, Pubmed , Xenbase
Ramsahoye, Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. 2000, Pubmed
Rao, Histone deacetylase activity has an essential role in establishing and maintaining the vertebrate neural crest. 2018, Pubmed , Xenbase
Rickels, Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is dispensable for development and viability. 2017, Pubmed
Rosa, The miR-430/427/302 family controls mesendodermal fate specification via species-specific target selection. 2009, Pubmed , Xenbase
Rugg-Gunn, Distinct histone modifications in stem cell lines and tissue lineages from the early mouse embryo. 2010, Pubmed
Saha-Shah, Single Cell Proteomics by Data-Independent Acquisition To Study Embryonic Asymmetry in Xenopus laevis. 2019, Pubmed , Xenbase
Schneider, Stage-specific histone modification profiles reveal global transitions in the Xenopus embryonic epigenome. 2011, Pubmed , Xenbase
Schulz, Mechanisms regulating zygotic genome activation. 2019, Pubmed
Schübeler, Function and information content of DNA methylation. 2015, Pubmed
Seto, Erasers of histone acetylation: the histone deacetylase enzymes. 2014, Pubmed
Sexton, Three-dimensional folding and functional organization principles of the Drosophila genome. 2012, Pubmed
Sitbon, Histone variant H3.3 residue S31 is essential for Xenopus gastrulation regardless of the deposition pathway. 2020, Pubmed , Xenbase
Skirkanich, An essential role for transcription before the MBT in Xenopus laevis. 2011, Pubmed , Xenbase
Skvortsova, Functions and mechanisms of epigenetic inheritance in animals. 2018, Pubmed
Smith, Expression of a histone H1-like protein is restricted to early Xenopus development. 1988, Pubmed , Xenbase
Stancheva, Transient depletion of xDnmt1 leads to premature gene activation in Xenopus embryos. 2000, Pubmed , Xenbase
Strahl, The language of covalent histone modifications. 2000, Pubmed
Szenker, The double face of the histone variant H3.3. 2011, Pubmed
Tsompana, Chromatin accessibility: a window into the genome. 2014, Pubmed
Ura, Differential association of HMG1 and linker histones B4 and H1 with dinucleosomal DNA: structural transitions and transcriptional repression. 1996, Pubmed , Xenbase
Vardimon, Expression of a cloned adenovirus gene is inhibited by in vitro methylation. 1982, Pubmed , Xenbase
Vastenhouw, Chromatin signature of embryonic pluripotency is established during genome activation. 2010, Pubmed
Veenstra, Constitutive genomic methylation during embryonic development of Xenopus. 2001, Pubmed , Xenbase
Venkatesh, Histone exchange, chromatin structure and the regulation of transcription. 2015, Pubmed
Wang, Acetylation increases the alpha-helical content of the histone tails of the nucleosome. 2000, Pubmed
Wassie, Expansion microscopy: principles and uses in biological research. 2019, Pubmed
Whyte, Master transcription factors and mediator establish super-enhancers at key cell identity genes. 2013, Pubmed
Wissink, Nascent RNA analyses: tracking transcription and its regulation. 2019, Pubmed
Wolffe, Chromatin disruption and modification. 1999, Pubmed
Xia, Resetting histone modifications during human parental-to-zygotic transition. 2019, Pubmed
Yang, Beta-catenin/Tcf-regulated transcription prior to the midblastula transition. 2002, Pubmed , Xenbase
Yin, Impact of cytosine methylation on DNA binding specificities of human transcription factors. 2017, Pubmed
Zenk, Germ line-inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition. 2017, Pubmed
Zhang, Allelic reprogramming of the histone modification H3K4me3 in early mammalian development. 2016, Pubmed
Zhang, Canonical nucleosome organization at promoters forms during genome activation. 2014, Pubmed
Zheng, Resetting Epigenetic Memory by Reprogramming of Histone Modifications in Mammals. 2016, Pubmed
Zhou, Histone deacetylase 1 maintains lineage integrity through histone acetylome refinement during early embryogenesis. 2023, Pubmed , Xenbase
van Heeringen, Principles of nucleation of H3K27 methylation during embryonic development. 2014, Pubmed , Xenbase
van Kruijsbergen, Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos. 2017, Pubmed , Xenbase