A unique chromatin signature uncovers early developmental enhancers in humans

Cell-fate transitions involve the integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment. However, identification of genomic sequences that control human embryonic development represents a formidable challenge. Here we show that in human embryonic stem cells (hESCs), unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, monomethylation of histone H3 at lysine 4 (H3K4me1), and low nucleosomal density. In addition, elements of the first class are distinguished by the acetylation of histone H3 at lysine 27 (H3K27ac), overlap with previously characterized hESC enhancers, and are located proximally to genes expressed in hESCs and the epiblast. In contrast, elements of the second class, which we term ‘poised enhancers’, are distinguished by the absence of H3K27ac, enrichment of histone H3 lysine 27 trimethylation (H3K27me3), and are linked to genes inactive in hESCs and instead are involved in orchestrating early steps in embryogenesis, such as gastrulation, mesoderm formation and neurulation. Consistent with the poised identity, during differentiation of hESCs to neuroepithelium, a neuroectoderm-specific subset of poised enhancers acquires a chromatin signature associated with active enhancers. When assayed in zebrafish embryos, poised enhancers are able to direct cell-type and stage-specific expression characteristic of their proximal developmental gene, even in the absence of sequence conservation in the fish genome. Our data demonstrate that early developmental enhancers are epigenetically pre-marked in hESCs and indicate an unappreciated role of H3K27me3 at distal regulatory elements. Moreover, the wealth of new regulatory sequences identified here provides an invaluable resource for studies and isolation of transient, rare cell populations representing early stages of human embryogenesis.

[1]  M. F. Shannon,et al.  Human Granulocyte-Macrophage Colony-Stimulating Factor Enhancer Function Is Associated with Cooperative Interactions between AP-1 and NFATp/c , 1994 .

[2]  J. Gurdon,et al.  Eomesodermin, a Key Early Gene in Xenopus Mesoderm Differentiation , 1996, Cell.

[3]  H. Schöler,et al.  Germline regulatory element of Oct-4 specific for the totipotent cycle of embryonal cells. , 1996, Development.

[4]  Andrew P. McMahon,et al.  Engrailed-1 as a target of the Wnt-1 signalling pathway in vertebrate midbrain development , 1996, Nature.

[5]  L. Silver,et al.  Mapping and expression analysis of the mouse ortholog of Xenopus Eomesodermin , 1999, Mechanisms of Development.

[6]  N. Copeland,et al.  Cloning, expression analysis, and chromosomal localization of murine and human homologues of a Xenopus Mix gene , 2000, Developmental dynamics : an official publication of the American Association of Anatomists.

[7]  J. Y. Kuwada,et al.  The heat-inducible zebrafish hsp70 gene is expressed during normal lens development under non-stress conditions , 2002, Mechanisms of Development.

[8]  O. Marín,et al.  Patterning of the basal telencephalon and hypothalamus is essential for guidance of cortical projections. , 2002, Development.

[9]  N. Wong,et al.  Functional mapping of tissue-specific elements of the human alpha-fetoprotein gene enhancer. , 2004, Biochemical and biophysical research communications.

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

[11]  S. Fisher,et al.  Evaluating the biological relevance of putative enhancers using Tol2 transposon-mediated transgenesis in zebrafish , 2006, Nature Protocols.

[12]  E. Ukkonen,et al.  Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity , 2006, Cell.

[13]  Monte Westerfield,et al.  The Zebrafish Information Network: the zebrafish model organism database , 2005, Nucleic Acids Res..

[14]  Inna Dubchak,et al.  VISTA Enhancer Browser—a database of tissue-specific human enhancers , 2006, Nucleic Acids Res..

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

[16]  C. Sigmund,et al.  Functional characterization of polymorphisms in the kidney enhancer of the human renin gene. , 2007, Endocrinology.

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

[18]  S. Henikoff,et al.  Histone Replacement Marks the Boundaries of cis-Regulatory Domains , 2007, Science.

[19]  S. Batzoglou,et al.  Genome-Wide Analysis of Transcription Factor Binding Sites Based on ChIP-Seq Data , 2008, Nature Methods.

[20]  P. Giresi,et al.  Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). , 2009, Methods.

[21]  M. Furlan-Magaril,et al.  Sequential chromatin immunoprecipitation protocol: ChIP-reChIP. , 2009, Methods in molecular biology.

[22]  Boris Lenhard,et al.  Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. , 2009, Developmental biology.

[23]  Keji Zhao,et al.  An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network , 2009, Proceedings of the National Academy of Sciences.

[24]  A. Visel,et al.  ChIP-seq accurately predicts tissue-specific activity of enhancers , 2009, Nature.

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

[26]  D. Geschwind,et al.  Molecular stages of rapid and uniform neuralization of human embryonic stem cells , 2009, Cell Death and Differentiation.

[27]  A. Visel,et al.  Genomic Views of Distant-Acting Enhancers , 2009, Nature.

[28]  R. Medzhitov,et al.  Control of Inducible Gene Expression by Signal-Dependent Transcriptional Elongation , 2009, Cell.

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

[30]  T. Kerppola.  Polycomb group complexes--many combinations, many functions. , 2009, Trends in cell biology.

[31]  M. Matsuda,et al.  Identification of a novel distal enhancer in human adiponectin gene. , 2009, The Journal of endocrinology.

[32]  H. Ng,et al.  KLF4 and PBX1 Directly Regulate NANOG Expression in Human Embryonic Stem Cells , 2009, Stem cells.

[33]  Michael Q. Zhang,et al.  Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications , 2010, Nature Biotechnology.

[34]  Cory Y. McLean,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[35]  Mark Groudine,et al.  Enhancers: The abundance and function of regulatory sequences beyond promoters , 2010 .

[36]  Christopher B. Burge,et al.  c-Myc Regulates Transcriptional Pause Release , 2010, Cell.

[37]  G. Kreiman,et al.  Widespread transcription at neuronal activity-regulated enhancers , 2010, Nature.

[38]  Masaki Ieda,et al.  Direct reprogramming of fibroblasts into functional cardiomyocytes by defined factors. , 2010, Cell.

[39]  Clifford A. Meyer,et al.  Nucleosome Dynamics Define Transcriptional Enhancers , 2010, Nature Genetics.