XB-ART-50323
Biochim Biophys Acta
2015 Jun 01;18496:626-36. doi: 10.1016/j.bbagrm.2015.03.006.
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Establishing pluripotency in early development.
Paranjpe SS
,
Veenstra GJ
.
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The earliest steps of embryonic development involve important changes in chromatin and transcription factor networks, which are orchestrated to establish pluripotent cells that will form the embryo. DNA methylation, histone modifications, the pluripotency regulatory network of transcription factors, maternal factors and newly translated proteins all contribute to these transitions in dynamic ways. Moreover, these dynamics are linked to the onset of zygotic transcription. We will review recent progress in our understanding of chromatin state and regulation of gene expression in the context of embryonic development in vertebrates, in particular mouse, Xenopus and zebrafish. We include work on mouse embryonic stem cells and highlight work that illustrates how early embryonic dynamics establish gene regulatory networks and the state of pluripotency.
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References [+] :
Aanes,
Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition.
2011, Pubmed
Aanes, Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition. 2011, Pubmed
Akkers, A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. 2009, Pubmed , Xenbase
Arney, Histone methylation defines epigenetic asymmetry in the mouse zygote. 2002, Pubmed
Banaszynski, Histone variants in metazoan development. 2010, Pubmed
Bannister, Regulation of chromatin by histone modifications. 2011, Pubmed
Bernstein, A bivalent chromatin structure marks key developmental genes in embryonic stem cells. 2006, Pubmed
Bernstein, The mammalian epigenome. 2007, Pubmed
Bird, DNA methylation patterns and epigenetic memory. 2002, Pubmed
Bocker, Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster. 2012, Pubmed
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
Bogdanović, DNA methylation and methyl-CpG binding proteins: developmental requirements and function. 2009, Pubmed , Xenbase
Bogdanović, The epigenome in early vertebrate development. 2012, Pubmed , Xenbase
Borchers, Programming pluripotent precursor cells derived from Xenopus embryos to generate specific tissues and organs. 2010, Pubmed , Xenbase
Boyer, Core transcriptional regulatory circuitry in human embryonic stem cells. 2005, Pubmed
Buecker, Reorganization of enhancer patterns in transition from naive to primed pluripotency. 2014, Pubmed
Bultman, A Brg1 null mutation in the mouse reveals functional differences among mammalian SWI/SNF complexes. 2000, Pubmed
Calo, Modification of enhancer chromatin: what, how, and why? 2013, Pubmed
Cao, POU-V factors antagonize maternal VegT activity and beta-Catenin signaling in Xenopus embryos. 2007, Pubmed , Xenbase
Cao, Oct25 represses transcription of nodal/activin target genes by interaction with signal transducers during Xenopus gastrulation. 2008, Pubmed , Xenbase
Chiu, Genome-wide view of TGFβ/Foxh1 regulation of the early mesendoderm program. 2014, Pubmed , Xenbase
Cifuentes-Rojas, Regulatory interactions between RNA and polycomb repressive complex 2. 2014, Pubmed
Collart, High-resolution analysis of gene activity during the Xenopus mid-blastula transition. 2014, Pubmed , Xenbase
Creyghton, Histone H3K27ac separates active from poised enhancers and predicts developmental state. 2010, Pubmed
Dahl, Histone H3 lysine 27 methylation asymmetry on developmentally-regulated promoters distinguish the first two lineages in mouse preimplantation embryos. 2010, Pubmed
Davidovich, Promiscuous RNA binding by Polycomb repressive complex 2. 2013, Pubmed
Dawlaty, Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development. 2011, Pubmed
Deaton, CpG islands and the regulation of transcription. 2011, Pubmed
Denissov, Mll2 is required for H3K4 trimethylation on bivalent promoters in embryonic stem cells, whereas Mll1 is redundant. 2014, Pubmed
Di Ruscio, DNMT1-interacting RNAs block gene-specific DNA methylation. 2013, Pubmed
Dunican, xDnmt1 regulates transcriptional silencing in pre-MBT Xenopus embryos independently of its catalytic function. 2008, Pubmed , Xenbase
Dunn, Defining an essential transcription factor program for naïve pluripotency. 2014, Pubmed
Ficz, Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. 2011, Pubmed
Fouse, Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. 2008, Pubmed
Frankenberg, The POU-er of gene nomenclature. 2014, Pubmed
Gaspar-Maia, Chd1 regulates open chromatin and pluripotency of embryonic stem cells. 2009, Pubmed
Gu, The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. 2011, Pubmed
Guo, The DNA methylation landscape of human early embryos. 2014, Pubmed
Gupta, Developmental enhancers are marked independently of zygotic Nodal signals in Xenopus. 2014, Pubmed , Xenbase
Guttman, Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. 2009, Pubmed
Guttman, lincRNAs act in the circuitry controlling pluripotency and differentiation. 2011, Pubmed
Guzman-Ayala, Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast. 2015, Pubmed
Habibi, Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells. 2013, Pubmed
Hammoud, Chromatin and transcription transitions of mammalian adult germline stem cells and spermatogenesis. 2014, Pubmed
Han, Epiblast stem cell subpopulations represent mouse embryos of distinct pregastrulation stages. 2010, Pubmed
Hargreaves, ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. 2011, Pubmed
He, Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. 2011, Pubmed
Heintzman, Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. 2007, Pubmed
Heintzman, Histone modifications at human enhancers reflect global cell-type-specific gene expression. 2009, Pubmed
Herz, Enhancer-associated H3K4 monomethylation by Trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4. 2012, Pubmed
Hinkley, Sequential expression of multiple POU proteins during amphibian early development. 1992, Pubmed , Xenbase
Ho, esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function. 2011, Pubmed
Ho, An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. 2009, Pubmed , Xenbase
Hong, Cell fate potential of human pluripotent stem cells is encoded by histone modifications. 2011, Pubmed
Hu, The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells. 2013, Pubmed
Hu, The MLL3/MLL4 branches of the COMPASS family function as major histone H3K4 monomethylases at enhancers. 2013, Pubmed
Hu, H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. 2013, Pubmed
Inoue, Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos. 2011, Pubmed
Iqbal, Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. 2011, Pubmed
Ito, Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. 2011, Pubmed
Ito, Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. 2010, Pubmed
Jiang, A core Klf circuitry regulates self-renewal of embryonic stem cells. 2008, Pubmed
Jiang, Sperm, but not oocyte, DNA methylome is inherited by zebrafish early embryos. 2013, Pubmed
Jullien, HIRA dependent H3.3 deposition is required for transcriptional reprogramming following nuclear transfer to Xenopus oocytes. 2012, Pubmed , Xenbase
Kaji, Mbd3, a component of the NuRD co-repressor complex, is required for development of pluripotent cells. 2007, Pubmed
Kaji, The NuRD component Mbd3 is required for pluripotency of embryonic stem cells. 2006, Pubmed
Kamakaka, Histone variants: deviants? 2005, Pubmed
Kidder, SWI/SNF-Brg1 regulates self-renewal and occupies core pluripotency-related genes in embryonic stem cells. 2009, Pubmed
Koh, Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. 2011, Pubmed
Kohli, TET enzymes, TDG and the dynamics of DNA demethylation. 2013, Pubmed
Kojima, The transcriptional and functional properties of mouse epiblast stem cells resemble the anterior primitive streak. 2014, Pubmed
Lee, Zygotic genome activation during the maternal-to-zygotic transition. 2014, Pubmed , Xenbase
Lee, Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition. 2013, Pubmed
Lee, An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator. 2014, Pubmed
Lee, H3K4 mono- and di-methyltransferase MLL4 is required for enhancer activation during cell differentiation. 2013, Pubmed
Leichsenring, Pou5f1 transcription factor controls zygotic gene activation in vertebrates. 2013, Pubmed , Xenbase
Leitch, Naive pluripotency is associated with global DNA hypomethylation. 2013, Pubmed
Lessard, Chromatin regulatory mechanisms in pluripotency. 2010, Pubmed
Li, Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. 1992, Pubmed
Lienert, Identification of genetic elements that autonomously determine DNA methylation states. 2011, Pubmed
Lim, Zic3 is required for maintenance of pluripotency in embryonic stem cells. 2007, Pubmed
Lim, Optimal histone H3 to linker histone H1 chromatin ratio is vital for mesodermal competence in Xenopus. 2013, Pubmed , Xenbase
Lim, Geminin cooperates with Polycomb to restrain multi-lineage commitment in the early embryo. 2011, Pubmed , Xenbase
Lim, The pluripotency regulator Zic3 is a direct activator of the Nanog promoter in ESCs. 2010, Pubmed
Lin, An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment. 2014, Pubmed
Lindeman, Prepatterning of developmental gene expression by modified histones before zygotic genome activation. 2011, Pubmed
Loh, The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. 2006, Pubmed
Long, Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. 2013, Pubmed , Xenbase
Luna-Zurita, Chromatin modulators as facilitating factors in cellular reprogramming. 2013, Pubmed
Luo, NuRD blocks reprogramming of mouse somatic cells into pluripotent stem cells. 2013, Pubmed
Macleod, Absence of genome-wide changes in DNA methylation during development of the zebrafish. 1999, Pubmed
Margueron, Chromatin structure and the inheritance of epigenetic information. 2010, Pubmed
Marks, Transcription regulation and chromatin structure in the pluripotent ground state. 2014, Pubmed
Marks, The transcriptional and epigenomic foundations of ground state pluripotency. 2012, Pubmed
Mayer, Demethylation of the zygotic paternal genome. 2000, Pubmed
Messerschmidt, DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos. 2014, Pubmed
Mikkelsen, Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. 2007, Pubmed
Nakata, Xenopus Zic3, a primary regulator both in neural and neural crest development. 1997, Pubmed , Xenbase
Newport, A major developmental transition in early Xenopus embryos: I. characterization and timing of cellular changes at the midblastula stage. 1982, Pubmed , Xenbase
Nicetto, Suv4-20h histone methyltransferases promote neuroectodermal differentiation by silencing the pluripotency-associated Oct-25 gene. 2013, Pubmed , Xenbase
Okano, DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. 1999, Pubmed
Oswald, Active demethylation of the paternal genome in the mouse zygote. 2000, Pubmed
Paranjpe, A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development. 2013, Pubmed , Xenbase
Pauli, Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. 2012, Pubmed
Piccolo, Getting rid of DNA methylation. 2014, Pubmed
Pijnappel, A central role for TFIID in the pluripotent transcription circuitry. 2013, Pubmed
Potok, Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern. 2013, Pubmed
Puschendorf, PRC1 and Suv39h specify parental asymmetry at constitutive heterochromatin in early mouse embryos. 2008, Pubmed
Rada-Iglesias, A unique chromatin signature uncovers early developmental enhancers in humans. 2011, Pubmed , Xenbase
Reynolds, NuRD suppresses pluripotency gene expression to promote transcriptional heterogeneity and lineage commitment. 2012, Pubmed
Rishi, CpG methylation of half-CRE sequences creates C/EBPalpha binding sites that activate some tissue-specific genes. 2010, Pubmed
Rugg-Gunn, Distinct histone modifications in stem cell lines and tissue lineages from the early mouse embryo. 2010, Pubmed
Saladi, ATP dependent chromatin remodeling enzymes in embryonic stem cells. 2010, Pubmed
Santos, Dynamic reprogramming of DNA methylation in the early mouse embryo. 2002, Pubmed
Santos, Dynamic chromatin modifications characterise the first cell cycle in mouse embryos. 2005, Pubmed
Scerbo, Ventx factors function as Nanog-like guardians of developmental potential in Xenopus. 2012, Pubmed , Xenbase
Schmitges, Histone methylation by PRC2 is inhibited by active chromatin marks. 2011, Pubmed
Schneider, Stage-specific histone modification profiles reveal global transitions in the Xenopus embryonic epigenome. 2011, Pubmed , Xenbase
Schuettengruber, Genome regulation by polycomb and trithorax proteins. 2007, Pubmed
Shilatifard, The COMPASS family of histone H3K4 methylases: mechanisms of regulation in development and disease pathogenesis. 2012, Pubmed
Simon, Mechanisms of polycomb gene silencing: knowns and unknowns. 2009, Pubmed
Skene, Histone variants in pluripotency and disease. 2013, Pubmed
Smallwood, Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. 2011, Pubmed
Smith, A unique regulatory phase of DNA methylation in the early mammalian embryo. 2012, Pubmed
Smith, DNA methylation dynamics of the human preimplantation embryo. 2014, Pubmed
Smits, Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs. 2014, Pubmed , Xenbase
Solter, From teratocarcinomas to embryonic stem cells and beyond: a history of embryonic stem cell research. 2006, Pubmed
Spruijt, DNA methylation: old dog, new tricks? 2014, Pubmed
Spruijt, Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. 2013, Pubmed
Stancheva, Transient depletion of xDnmt1 leads to premature gene activation in Xenopus embryos. 2000, Pubmed , Xenbase
Steinbach, Somatic linker histones cause loss of mesodermal competence in Xenopus. 1997, Pubmed , Xenbase
Tadros, The maternal-to-zygotic transition: a play in two acts. 2009, Pubmed
Takashima, Resetting transcription factor control circuitry toward ground-state pluripotency in human. 2014, Pubmed
Tan, RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. 2013, Pubmed , Xenbase
Tsumura, Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. 2006, Pubmed
Tutter, Role for Med12 in regulation of Nanog and Nanog target genes. 2009, Pubmed
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
Vesterlund, The zebrafish transcriptome during early development. 2011, Pubmed
Visel, ChIP-seq accurately predicts tissue-specific activity of enhancers. 2009, Pubmed
Voigt, Asymmetrically modified nucleosomes. 2012, Pubmed
Voigt, A double take on bivalent promoters. 2013, Pubmed
Wade, A multiple subunit Mi-2 histone deacetylase from Xenopus laevis cofractionates with an associated Snf2 superfamily ATPase. 1998, Pubmed , Xenbase
Wang, Global analysis of H3K4 methylation defines MLL family member targets and points to a role for MLL1-mediated H3K4 methylation in the regulation of transcriptional initiation by RNA polymerase II. 2009, Pubmed
Wang, INO80 facilitates pluripotency gene activation in embryonic stem cell self-renewal, reprogramming, and blastocyst development. 2014, Pubmed
Welling, Uncovering the true identity of naïve pluripotent stem cells. 2013, Pubmed
Wen, Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. 2009, Pubmed
Williams, TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. 2011, Pubmed
Winata, Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish. 2013, Pubmed
Wu, Role of Oct4 in the early embryo development. 2014, Pubmed
Wu, Establishment of totipotency does not depend on Oct4A. 2013, Pubmed
Xu, Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development. 2012, Pubmed , Xenbase
Yang, Otx2 and Oct4 drive early enhancer activation during embryonic stem cell transition from naive pluripotency. 2014, Pubmed
Yang, Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency. 2014, Pubmed
Yildirim, Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. 2011, Pubmed
Zhang, Histone h1 depletion impairs embryonic stem cell differentiation. 2012, Pubmed
dos Santos, MBD3/NuRD facilitates induction of pluripotency in a context-dependent manner. 2014, Pubmed
van Heeringen, Nucleotide composition-linked divergence of vertebrate core promoter architecture. 2011, Pubmed , Xenbase
van Heeringen, Principles of nucleation of H3K27 methylation during embryonic development. 2014, Pubmed , Xenbase