Bivalent histone modifications in early embryogenesis.

[1]  Michael F. Lin,et al.  Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. , 2012, Genome research.

[2]  A. Tanay,et al.  Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome , 2012, Cell.

[3]  D. Patel,et al.  A Poised Chromatin Platform for TGF-β Access to Master Regulators , 2011, Cell.

[4]  D. Bartel,et al.  Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution , 2011, Cell.

[5]  Sinnakaruppan Mathavan,et al.  Prepatterning of developmental gene expression by modified histones before zygotic genome activation. , 2011, Developmental cell.

[6]  Avi Ma’ayan,et al.  Oct4 links multiple epigenetic pathways to the pluripotency network , 2011, Cell Research.

[7]  Ahsan Huda,et al.  Faculty Opinions recommendation of Mapping and analysis of chromatin state dynamics in nine human cell types. , 2011 .

[8]  David A. Orlando,et al.  Master Transcription Factors Determine Cell-Type-Specific Responses to TGF-β Signaling , 2011, Cell.

[9]  Pengzhi Yu,et al.  Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency , 2011, Cell Research.

[10]  M. Evans,et al.  Discovering pluripotency: 30 years of mouse embryonic stem cells , 2011, Nature Reviews Molecular Cell Biology.

[11]  Eugene Bolotin,et al.  The noncoding RNA Mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin. , 2011, Molecular cell.

[12]  D. Moazed.  Mechanisms for the Inheritance of Chromatin States , 2011, Cell.

[13]  J. M. Arteaga-Salas,et al.  Stage-Specific Histone Modification Profiles Reveal Global Transitions in the Xenopus Embryonic Epigenome , 2011, PloS one.

[14]  Jung Bok Lee,et al.  Cell fate potential of human pluripotent stem cells is encoded by histone modifications. , 2011, Cell stem cell.

[15]  Leighton J. Core,et al.  The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo. , 2011, Molecular cell.

[16]  A. Akhtar,et al.  Multiple facets of nuclear periphery in gene expression control. , 2011, Current opinion in cell biology.

[17]  I. Wilmut,et al.  Histone H4K20me3 and HP1α are late heterochromatin markers in development, but present in undifferentiated embryonic stem cells , 2011, Journal of Cell Science.

[18]  O. Rando,et al.  Patterns and Mechanisms of Ancestral Histone Protein Inheritance in Budding Yeast , 2011, PLoS biology.

[19]  Thomas A. Milne,et al.  Recognition of a Mononucleosomal Histone Modification Pattern by BPTF via Multivalent Interactions , 2011, Cell.

[20]  Jonathan M. Monk,et al.  Wdr5 Mediates Self-Renewal and Reprogramming via the Embryonic Stem Cell Core Transcriptional Network , 2011, Cell.

[21]  Howard Y. Chang,et al.  A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression , 2011, Nature.

[22]  Leighton J. Core,et al.  Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells. , 2011, Genes & development.

[23]  S. Mango,et al.  Locking the genome: nuclear organization and cell fate. , 2011, Current opinion in genetics & development.

[24]  Danny Reinberg,et al.  Chromatin higher-order structures and gene regulation. , 2011, Current opinion in genetics & development.

[25]  B. Cairns,et al.  Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm. , 2011, Genome research.

[26]  Richard A Young,et al.  Control of the Embryonic Stem Cell State , 2011, Cell.

[27]  B. Bernstein,et al.  Role for Dpy-30 in ES Cell-Fate Specification by Regulation of H3K4 Methylation within Bivalent Domains , 2011, Cell.

[28]  Andrew J. Bannister,et al.  Regulation of chromatin by histone modifications , 2011, Cell Research.

[29]  Ryan A. Flynn,et al.  A unique chromatin signature uncovers early developmental enhancers in humans , 2011, Nature.

[30]  Benjamin Leblanc,et al.  Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila , 2011, Cell.

[31]  M. Torres-Padilla,et al.  Epigenetic reprogramming and development: a unique heterochromatin organization in the preimplantation mouse embryo. , 2010, Briefings in functional genomics.

[32]  Bradley E. Bernstein,et al.  GC-Rich Sequence Elements Recruit PRC2 in Mammalian ES Cells , 2010, PLoS genetics.

[33]  R. Young,et al.  Histone H3K27ac separates active from poised enhancers and predicts developmental state , 2010, Proceedings of the National Academy of Sciences.

[34]  K. Helin,et al.  Polycomb group protein displacement and gene activation through MSK-dependent H3K27me3S28 phosphorylation. , 2010, Molecular cell.

[35]  Edwin Smith,et al.  The Language of Histone Crosstalk , 2010, Cell.

[36]  A. Rechtsteiner,et al.  The Histone H3K36 Methyltransferase MES-4 Acts Epigenetically to Transmit the Memory of Germline Gene Expression to Progeny , 2010, PLoS genetics.

[37]  N. Akizu,et al.  H3K27me3 regulates BMP activity in developing spinal cord , 2010, Development.

[38]  Shelby A. Blythe,et al.  beta-Catenin primes organizer gene expression by recruiting a histone H3 arginine 8 methyltransferase, Prmt2. , 2010, Developmental cell.

[39]  Howard Y. Chang,et al.  Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes , 2010, Science.

[40]  Martin M. Matzuk,et al.  MLL2 Is Required in Oocytes for Bulk Histone 3 Lysine 4 Trimethylation and Transcriptional Silencing , 2010, PLoS biology.

[41]  M. Kuehn,et al.  Nodal Signaling Recruits the Histone Demethylase Jmjd3 to Counteract Polycomb-Mediated Repression at Target Genes , 2010, Science Signaling.

[42]  J. Rossant,et al.  Inaugural Article: Distinct histone modifications in stem cell lines and tissue lineages from the early mouse embryo , 2010 .

[43]  Antoine H. F. M. Peters,et al.  Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa , 2010, Nature Structural &Molecular Biology.

[44]  Wendy A Bickmore,et al.  Ring1B compacts chromatin structure and represses gene expression independent of histone ubiquitination. , 2010, Molecular cell.

[45]  J. Rossant,et al.  Global Chromatin Architecture Reflects Pluripotency and Lineage Commitment in the Early Mouse Embryo , 2010, PloS one.

[46]  Lee E. Edsall,et al.  Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. , 2010, Cell stem cell.

[47]  J. Epstein,et al.  Ash2l interacts with Tbx1 and is required during early embryogenesis , 2010, Experimental biology and medicine.

[48]  Robert S. Illingworth,et al.  CpG islands influence chromatin structure via the CpG-binding protein Cfp1 , 2010, Nature.

[49]  Steven Henikoff,et al.  Histone variants — ancient wrap artists of the epigenome , 2010, Nature Reviews Molecular Cell Biology.

[50]  Juri Rappsilber,et al.  JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells , 2010, Nature.

[51]  Aviv Regev,et al.  Chromatin signature of embryonic pluripotency is established during genome activation , 2010, Nature.

[52]  Nevan J Krogan,et al.  Polycomb-like 2 associates with PRC2 and regulates transcriptional networks during mouse embryonic stem cell self-renewal and differentiation. , 2010, Cell stem cell.

[53]  M. Jaritz,et al.  Polycomb complexes act redundantly to repress genomic repeats and genes. , 2010, Genes & development.

[54]  Gang Li,et al.  Jarid2 and PRC2, partners in regulating gene expression. , 2010, Genes & development.

[55]  P. Park,et al.  A Region of the Human HOXD Cluster that Confers Polycomb-Group Responsiveness , 2010, Cell.

[56]  G. Crabtree,et al.  Chromatin remodelling during development , 2010, Nature.

[57]  S. Orkin,et al.  Jumonji Modulates Polycomb Activity and Self-Renewal versus Differentiation of Stem Cells , 2009, Cell.

[58]  Arend Sidow,et al.  Jarid2/Jumonji Coordinates Control of PRC2 Enzymatic Activity and Target Gene Occupancy in Pluripotent Cells , 2009, Cell.

[59]  R. Young,et al.  SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. , 2009, Genes & development.

[60]  D. Reinberg,et al.  Role of the polycomb protein EED in the propagation of repressive histone marks , 2009, Nature.

[61]  Robert E. Kingston,et al.  Mechanisms of Polycomb gene silencing: knowns and unknowns , 2009, Nature Reviews Molecular Cell Biology.

[62]  H. Stunnenberg,et al.  A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. , 2009, Developmental cell.

[63]  P. Scacheri,et al.  CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing , 2009, Development.

[64]  H. Lipshitz,et al.  A Vertebrate Polycomb Response Element Governs Segmentation of the Posterior Hindbrain , 2009, Cell.

[65]  Madelaine Gogol,et al.  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, Molecular and Cellular Biology.

[66]  M. Levine,et al.  Synchronous and Stochastic Patterns of Gene Activation in the Drosophila Embryo , 2009, Science.

[67]  S. Kozubek,et al.  Genome‐wide reduction in H3K9 acetylation during human embryonic stem cell differentiation , 2009, Journal of cellular physiology.

[68]  H. Cedar,et al.  Linking DNA methylation and histone modification: patterns and paradigms , 2009, Nature Reviews Genetics.

[69]  A. F. Stewart,et al.  The histone 3 lysine 4 methyltransferase, Mll2, is only required briefly in development and spermatogenesis , 2009, Epigenetics & Chromatin.

[70]  Nathaniel D. Heintzman,et al.  Histone modifications at human enhancers reflect global cell-type-specific gene expression , 2009, Nature.

[71]  Dustin E. Schones,et al.  Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. , 2009, Cell stem cell.

[72]  Amos Tanay,et al.  Functional Anatomy of Polycomb and Trithorax Chromatin Landscapes in Drosophila Embryos , 2009, PLoS biology.

[73]  Guo-Cheng Yuan,et al.  EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. , 2008, Molecular cell.

[74]  Jennifer A. Erwin,et al.  Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome , 2008, Science.

[75]  Juri Rappsilber,et al.  A model for transmission of the H3K27me3 epigenetic mark , 2008, Nature Cell Biology.

[76]  A. Miele,et al.  Long-range chromosomal interactions and gene regulation. , 2008, Molecular bioSystems.

[77]  Simon Kasif,et al.  Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains , 2008, PLoS genetics.

[78]  D. Gifford,et al.  Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET , 2008, Genome Biology.

[79]  Michael Q. Zhang,et al.  Combinatorial patterns of histone acetylations and methylations in the human genome , 2008, Nature Genetics.

[80]  Michael B. Stadler,et al.  Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. , 2008, Molecular cell.

[81]  Terry Magnuson,et al.  Polycomb Repressive Complex 2 Is Dispensable for Maintenance of Embryonic Stem Cell Pluripotency , 2008, Stem cells.

[82]  L. Wessels,et al.  Ubiquitin E3 Ligase Ring1b/Rnf2 of Polycomb Repressive Complex 1 Contributes to Stable Maintenance of Mouse Embryonic Stem Cells , 2008, PloS one.

[83]  O. Ohara,et al.  Polycomb group proteins Ring1A/B are functionally linked to the core transcriptional regulatory circuitry to maintain ES cell identity , 2008, Development.

[84]  S. Orkin,et al.  An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells , 2008, Cell.

[85]  Richard A Young,et al.  Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells. , 2008, Genes & development.

[86]  Matteo Pellegrini,et al.  Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. , 2008, Cell stem cell.

[87]  Ping Zhu,et al.  Histone H2A monoubiquitination represses transcription by inhibiting RNA polymerase II transcriptional elongation. , 2008, Molecular cell.

[88]  Haruhiko Koseki,et al.  Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells , 2007, Nature Cell Biology.

[89]  D. Skalnik,et al.  Wdr82 Is a C-Terminal Domain-Binding Protein That Recruits the Setd1A Histone H3-Lys4 Methyltransferase Complex to Transcription Start Sites of Transcribed Human Genes , 2007, Molecular and Cellular Biology.

[90]  Min Gyu Lee,et al.  Demethylation of H3K27 Regulates Polycomb Recruitment and H2A Ubiquitination , 2007, Science.

[91]  Matthias Mann,et al.  Selective Anchoring of TFIID to Nucleosomes by Trimethylation of Histone H3 Lysine 4 , 2007, Cell.

[92]  Atif Shahab,et al.  Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. , 2007, Cell stem cell.

[93]  G. Pan,et al.  Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. , 2007, Cell stem cell.

[94]  T. Mikkelsen,et al.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.

[95]  M. Leeb,et al.  Ring1B is crucial for the regulation of developmental control genes and PRC1 proteins but not X inactivation in embryonic cells , 2007, The Journal of cell biology.

[96]  R. Jaenisch,et al.  A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells , 2007, Cell.

[97]  Howard Y. Chang,et al.  Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs , 2007, Cell.

[98]  A. F. Stewart,et al.  Increased apoptosis and skewed differentiation in mouse embryonic stem cells lacking the histone methyltransferase Mll2. , 2007, Molecular biology of the cell.

[99]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

[100]  Kristian Helin,et al.  The Polycomb Group Protein Suz12 Is Required for Embryonic Stem Cell Differentiation , 2007, Molecular and Cellular Biology.

[101]  Shusheng Wang,et al.  Polycomblike‐2‐deficient mice exhibit normal left–right asymmetry , 2007, Developmental dynamics : an official publication of the American Association of Anatomists.

[102]  Nathaniel D. Heintzman,et al.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.

[103]  Daniel Chourrout,et al.  Genome Regulation by Polycomb and Trithorax Proteins , 2007, Cell.

[104]  R. Paro,et al.  Polycomb/Trithorax response elements and epigenetic memory of cell identity , 2007, Development.

[105]  C. Allis,et al.  Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. , 2007, Molecular cell.

[106]  Suresh Cuddapah,et al.  The genomic landscape of histone modifications in human T cells , 2006, Proceedings of the National Academy of Sciences.

[107]  D. Reinberg,et al.  Histone H2B Monoubiquitination Functions Cooperatively with FACT to Regulate Elongation by RNA Polymerase II , 2006, Cell.

[108]  J. Zeitlinger,et al.  Polycomb complexes repress developmental regulators in murine embryonic stem cells , 2006, Nature.

[109]  Megan F. Cole,et al.  Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells , 2006, Cell.

[110]  James A. Cuff,et al.  A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells , 2006, Cell.

[111]  A. F. Stewart,et al.  Multiple epigenetic maintenance factors implicated by the loss of Mll2 in mouse development , 2006, Development.

[112]  Stephan Sauer,et al.  Chromatin signatures of pluripotent cell lines , 2006, Nature Cell Biology.

[113]  X. Chen,et al.  The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells , 2006, Nature Genetics.

[114]  Megan F. Cole,et al.  Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells , 2005, Cell.

[115]  Thomas A. Milne,et al.  WDR5 Associates with Histone H3 Methylated at K4 and Is Essential for H3 K4 Methylation and Vertebrate Development , 2005, Cell.

[116]  Stormy J. Chamberlain,et al.  The Murine Polycomb Group Protein Eed Is Required for Global Histone H3 Lysine-27 Methylation , 2005, Current Biology.

[117]  Tsutomu Ohta,et al.  Histone methyltransferases G9a and GLP form heteromeric complexes and are both crucial for methylation of euchromatin at H3-K9. , 2005, Genes & development.

[118]  L. Zon,et al.  An Mll-Dependent Hox Program Drives Hematopoietic Progenitor Expansion , 2004, Current Biology.

[119]  Haruhiko Koseki,et al.  Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation. , 2004, Developmental cell.

[120]  Kristian Helin,et al.  Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity , 2004, The EMBO journal.

[121]  Charles Kooperberg,et al.  The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. , 2004, Genes & development.

[122]  G. Kay,et al.  Conditional Inactivation of the Men1 Gene Leads to Pancreatic and Pituitary Tumorigenesis but Does Not Affect Normal Development of These Tissues , 2004, Molecular and Cellular Biology.

[123]  Hong Lei,et al.  Histone H3-K9 Methyltransferase ESET Is Essential for Early Development , 2004, Molecular and Cellular Biology.

[124]  Andrew J. Bannister,et al.  Consequences of the depletion of zygotic and embryonic enhancer of zeste 2 during preimplantation mouse development , 2003, Development.

[125]  Zhao-Qi Wang,et al.  Heterozygous Men1 mutant mice develop a range of endocrine tumors mimicking multiple endocrine neoplasia type 1. , 2003, Molecular endocrinology.

[126]  Kevin Struhl,et al.  Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. , 2003, Molecular cell.

[127]  J. Voncken,et al.  Rnf2 (Ring1b) deficiency causes gastrulation arrest and cell cycle inhibition , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[128]  H. Kato,et al.  G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis. , 2002, Genes & development.

[129]  Karl Mechtler,et al.  Loss of the Suv39h Histone Methyltransferases Impairs Mammalian Heterochromatin and Genome Stability , 2001, Cell.

[130]  M. Surani,et al.  The Polycomb-Group GeneEzh2 Is Required for Early Mouse Development , 2001, Molecular and Cellular Biology.

[131]  M. Vidal,et al.  Mice doubly deficient for the Polycomb Group genes Mel18 and Bmi1 reveal synergy and requirement for maintenance but not initiation of Hox gene expression. , 2001, Development.

[132]  E Pennisi,et al.  The Human Genome , 2001, Science.

[133]  F. Collins,et al.  A mouse model of multiple endocrine neoplasia, type 1, develops multiple endocrine tumors. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[134]  M. Vidal,et al.  Loss- and gain-of-function mutations show a polycomb group function for Ring1A in mice. , 2000, Development.

[135]  C. Allis,et al.  The language of covalent histone modifications , 2000, Nature.

[136]  Yang Shi,et al.  Targeted Disruption of Mouse Yin Yang 1 Transcription Factor Results in Peri-Implantation Lethality , 1999, Molecular and Cellular Biology.

[137]  T. Komori,et al.  Growth disturbance in fetal liver hematopoiesis of Mll-mutant mice. , 1998, Blood.

[138]  M. A. Motaleb,et al.  Targeted disruption of the mouse homologue of the Drosophila polyhomeotic gene leads to altered anteroposterior patterning and neural crest defects. , 1997, Development.

[139]  T. Richmond,et al.  Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.

[140]  T. Takeuchi,et al.  Organogenesis of the liver, thymus and spleen is affected in jumonji mutant mice , 1997, Mechanisms of Development.

[141]  M. Aurrand-Lions,et al.  Altered cellular proliferation and mesoderm patterning in Polycomb-M33-deficient mice. , 1997, Development.

[142]  T. Magnuson,et al.  Positional cloning of a global regulator of anterior–posterior patterning in mice , 1996, Nature.

[143]  Mark J Alkema,et al.  The Polycomb-group homolog Bmi-1 is a regulator of murine Hox gene expression , 1996, Mechanisms of Development.

[144]  R. Balling,et al.  A role for mel-18, a Polycomb group-related vertebrate gene, during theanteroposterior specification of the axial skeleton. , 1996, Development.

[145]  P. Gruss,et al.  Pax and vertebrate development. , 1996, The International journal of developmental biology.

[146]  S. Korsmeyer,et al.  Altered Hox expression and segmental identity in Mll-mutant mice , 1995, Nature.

[147]  T. Takeuchi,et al.  Gene trap capture of a novel mouse gene, jumonji, required for neural tube formation. , 1995, Genes & development.

[148]  T. Magnuson,et al.  The eed mutation disrupts anterior mesoderm production in mice. , 1995, Development.

[149]  M. Sofroniew,et al.  Posterior transformation, neurological abnormalities, and severe hematopoietic defects in mice with a targeted deletion of the bmi-1 proto-oncogene. , 1994, Genes & development.

[150]  Jahnvi Pflueger,et al.  Distinctive chromatin in human sperm packages genes for embryo development , 2009 .

[151]  T. Misteli,et al.  Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. , 2006, Developmental cell.

[152]  T. Magnuson,et al.  Positional cloning of a global regulator of anterior–posterior patterning in mice , 1996, Nature.

[153]  I. Amit,et al.  Supporting Online Material Materials and Methods Som Text Comprehensive Mapping of Long-range Interactions Reveals Folding Principles of the Human Genome , 2022 .