The selection and function of cell type-specific enhancers

[1]  J. Stender,et al.  Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities , 2015, Cell.

[2]  I. Amit,et al.  Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment , 2014, Cell.

[3]  André L. Martins,et al.  Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers , 2014, Nature Genetics.

[4]  Tae-Kyung Kim,et al.  Enhancer RNA facilitates NELF release from immediate early genes. , 2014, Molecular cell.

[5]  Jill M Dowen,et al.  Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes , 2014, Cell.

[6]  Peter J. Park,et al.  Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming , 2014, Nature Communications.

[7]  A. Dean,et al.  Enhancer function: mechanistic and genome-wide insights come together. , 2014, Molecular cell.

[8]  Wolfgang Huber,et al.  Enhancer loops appear stable during development and are associated with paused polymerase , 2014, Nature.

[9]  Adelina Rogowska-Wrzesinska,et al.  Transcription factor cooperativity in early adipogenic hotspots and super-enhancers. , 2014, Cell reports.

[10]  E. Lander,et al.  Development and Applications of CRISPR-Cas9 for Genome Engineering , 2014, Cell.

[11]  Daphne Koller,et al.  Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes , 2014, Science.

[12]  Łukasz M. Boryń,et al.  Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin. , 2014, Molecular cell.

[13]  T. Meehan,et al.  An atlas of active enhancers across human cell types and tissues , 2014, Nature.

[14]  A. Shilatifard,et al.  Enhancer malfunction in cancer. , 2014, Molecular cell.

[15]  Mark I. McCarthy,et al.  Pancreatic islet enhancer clusters enriched in type 2 diabetes risk–associated variants , 2013, Nature Genetics.

[16]  A. Visel,et al.  Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development , 2013, Cell.

[17]  Chia-Lin Wei,et al.  Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation , 2013, Cell.

[18]  M. Rosenfeld,et al.  Brd4 and JMJD6-Associated Anti-Pause Enhancers in Regulation of Transcriptional Pause Release , 2013, Cell.

[19]  Peggy Hall,et al.  The NHGRI GWAS Catalog, a curated resource of SNP-trait associations , 2013, Nucleic Acids Res..

[20]  M. Sung,et al.  Overlapping Chromatin Remodeling Systems Collaborate Genome-wide at Dynamic Chromatin Transitions , 2013, Nature Structural &Molecular Biology.

[21]  Weiqun Peng,et al.  H3K4 mono- and di-methyltransferase MLL4 is required for enhancer activation during cell differentiation , 2013, eLife.

[22]  Leighton J. Core,et al.  Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription , 2013, Science.

[23]  Jonathan K. Pritchard,et al.  Identification of Genetic Variants That Affect Histone Modifications in Human Cells , 2013, Science.

[24]  R. Young,et al.  Super-Enhancers in the Control of Cell Identity and Disease , 2013, Cell.

[25]  Yan Li,et al.  A high-resolution map of three-dimensional chromatin interactome in human cells , 2013, Nature.

[26]  Stephen C. J. Parker,et al.  Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants , 2013, Proceedings of the National Academy of Sciences.

[27]  C. Glass,et al.  Impact of natural genetic variation on enhancer selection and function , 2013, Nature.

[28]  Matthew C. Canver,et al.  An Erythroid Enhancer of BCL11A Subject to Genetic Variation Determines Fetal Hemoglobin Level , 2013, Science.

[29]  Dan Xie,et al.  Extensive Variation in Chromatin States Across Humans , 2013, Science.

[30]  A. Tanay,et al.  Single cell Hi-C reveals cell-to-cell variability in chromosome structure , 2013, Nature.

[31]  Thomas Whitington,et al.  Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites , 2013, Cell.

[32]  J. Stender,et al.  Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. , 2013, Molecular cell.

[33]  Michael D. Wilson,et al.  Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals , 2013, Cell.

[34]  C. Glass,et al.  Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription , 2013, Nature.

[35]  C. Glass,et al.  Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation , 2013, Nature.

[36]  Christopher B. Burge,et al.  Promoter directionality is controlled by U1 snRNP and polyadenylation signals , 2013, Nature.

[37]  C. Benner,et al.  Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1 , 2013, Nucleic acids research.

[38]  David A. Orlando,et al.  Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes , 2013, Cell.

[39]  K. Neugebauer,et al.  How cells get the message: dynamic assembly and function of mRNA–protein complexes , 2013, Nature Reviews Genetics.

[40]  J. Wysocka,et al.  Modification of enhancer chromatin: what, how, and why? , 2013, Molecular cell.

[41]  G. Natoli,et al.  Latent Enhancers Activated by Stimulation in Differentiated Cells , 2013, Cell.

[42]  B. Stranger,et al.  Chromatin marks identify critical cell types for fine mapping complex trait variants , 2012, Nature Genetics.

[43]  P. Ferrier Faculty Opinions recommendation of Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate. , 2012 .

[44]  L. Aaltonen,et al.  Mice Lacking a Myc Enhancer That Includes Human SNP rs6983267 Are Resistant to Intestinal Tumors , 2012, Science.

[45]  Alexander S. Garruss,et al.  Enhancer-associated H3K4 monomethylation by Trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4. , 2012, Genes & development.

[46]  Greg Donahue,et al.  Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome , 2012, Cell.

[47]  Yuka Kanno,et al.  STATs Shape the Active Enhancer Landscape of T Cell Populations , 2012, Cell.

[48]  Steven J. M. Jones,et al.  Bromodomain-containing Protein 4 (BRD4) Regulates RNA Polymerase II Serine 2 Phosphorylation in Human CD4+ T Cells* , 2012, The Journal of Biological Chemistry.

[49]  A. Stark,et al.  Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding , 2012, Genome research.

[50]  Luca Pinello,et al.  Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. , 2012, Developmental cell.

[51]  Shane J. Neph,et al.  Foxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification , 2012, Cell.

[52]  Nathan C. Sheffield,et al.  The accessible chromatin landscape of the human genome , 2012, Nature.

[53]  J. Dekker,et al.  The long-range interaction landscape of gene promoters , 2012, Nature.

[54]  S. Batzoglou,et al.  Linking disease associations with regulatory information in the human genome , 2012, Genome research.

[55]  David G. Knowles,et al.  The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression , 2012, Genome research.

[56]  Swneke D. Bailey,et al.  Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression , 2012, Nature Genetics.

[57]  Nicole I Bieberstein,et al.  First exon length controls active chromatin signatures and transcription. , 2012, Cell reports.

[58]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[59]  M. Groudine,et al.  The hypersensitive sites of the murine β-globin locus control region act independently to affect nuclear localization and transcriptional elongation. , 2012, Blood.

[60]  Jesse R. Dixon,et al.  Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.

[61]  Monika S. Kowalczyk,et al.  Intragenic enhancers act as alternative promoters. , 2012, Molecular cell.

[62]  Scott Barolo,et al.  Shadow enhancers: Frequently asked questions about distributed cis‐regulatory information and enhancer redundancy , 2012, BioEssays : news and reviews in molecular, cellular and developmental biology.

[63]  Raymond K. Auerbach,et al.  Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation , 2012, Cell.

[64]  E. Furlong,et al.  Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development , 2012, Nature Genetics.

[65]  Matthew Stephens,et al.  Dissecting the regulatory architecture of gene expression QTLs , 2012, Genome Biology.

[66]  Joseph K. Pickrell,et al.  DNaseI sensitivity QTLs are a major determinant of human expression variation , 2011, Nature.

[67]  Reza Kalhor,et al.  Genome architectures revealed by tethered chromosome conformation capture and population-based modeling , 2011, Nature Biotechnology.

[68]  Vijay K. Tiwari,et al.  DNA-binding factors shape the mouse methylome at distal regulatory regions , 2011, Nature.

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

[70]  L. Zon,et al.  Lineage Regulators Direct BMP and Wnt Pathways to Cell-Specific Programs during Differentiation and Regeneration , 2011, Cell.

[71]  Elinore M Mercer,et al.  Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors. , 2011, Immunity.

[72]  Ty C. Voss,et al.  Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism , 2011, Cell.

[73]  M. Gut,et al.  Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters , 2011, Nature Structural &Molecular Biology.

[74]  P. Scacheri,et al.  Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. , 2011, Genome research.

[75]  C. Glass,et al.  Reprogramming Transcription via Distinct Classes of Enhancers Functionally Defined by eRNA , 2011, Nature.

[76]  Raymond K. Auerbach,et al.  Diverse Roles and Interactions of the SWI/SNF Chromatin Remodeling Complex Revealed Using Global Approaches , 2011, PLoS genetics.

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

[78]  J. Stamatoyannopoulos,et al.  Chromatin accessibility pre-determines glucocorticoid receptor binding patterns , 2011, Nature Genetics.

[79]  J. Dixon,et al.  Bcl-6 and NF-kappaB cistromes mediate opposing regulation of the innate immune response. , 2010, Genes & development.

[80]  C. Glass,et al.  Serum Response Factor Utilizes Distinct Promoter- and Enhancer-Based Mechanisms To Regulate Cytoskeletal Gene Expression in Macrophages , 2010, Molecular and Cellular Biology.

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

[82]  Sohail Malik,et al.  The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation , 2010, Nature Reviews Genetics.

[83]  Inanc Birol,et al.  Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver. , 2010, Genome research.

[84]  David A. Orlando,et al.  Mediator and Cohesin Connect Gene Expression and Chromatin Architecture , 2010, Nature.

[85]  Manolis Kellis,et al.  Discovery and characterization of chromatin states for systematic annotation of the human genome , 2010, Nature Biotechnology.

[86]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[87]  J. Ragoussis,et al.  A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers , 2010, PLoS biology.

[88]  M. Gerstein,et al.  Variation in Transcription Factor Binding Among Humans , 2010, Science.

[89]  J. Ragoussis,et al.  Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. , 2010, Immunity.

[90]  Petra C. Schwalie,et al.  A CTCF-independent role for cohesin in tissue-specific transcription. , 2010, Genome research.

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

[92]  G. Tuteja,et al.  Cell-Specific Determinants of Peroxisome Proliferator-Activated Receptor γ Function in Adipocytes and Macrophages , 2010, Molecular and Cellular Biology.

[93]  Kyle J. Gaulton,et al.  A map of open chromatin in human pancreatic islets , 2010, Nature Genetics.

[94]  Dustin E. Schones,et al.  Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes , 2009, Cell.

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

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

[97]  Leighton J. Core,et al.  Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters , 2008, Science.

[98]  H. Stunnenberg,et al.  Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis. , 2008, Genes & development.

[99]  M. Levine,et al.  Shadow Enhancers as a Source of Evolutionary Novelty , 2008, Science.

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

[101]  Kari Stefansson,et al.  A common variant on chromosome 9p21 affects the risk of myocardial infarction. , 2007, Science.

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

[103]  Alan M. Moses,et al.  In vivo enhancer analysis of human conserved non-coding sequences , 2006, Nature.

[104]  D. Reinberg,et al.  Histone H3 Lys 4 methylation: caught in a bind? , 2006, Genes & development.

[105]  Clifford A. Meyer,et al.  Genome-wide analysis of estrogen receptor binding sites , 2006, Nature Genetics.

[106]  David Tollervey,et al.  RNA-quality control by the exosome , 2006, Nature Reviews Molecular Cell Biology.

[107]  Thomas Cremer,et al.  Chromosome territories--a functional nuclear landscape. , 2006, Current opinion in cell biology.

[108]  V. Lunyak,et al.  Sensors and signals: a coactivator/corepressor/epigenetic code for integrating signal-dependent programs of transcriptional response. , 2006, Genes & development.

[109]  Clifford A. Meyer,et al.  Chromosome-Wide Mapping of Estrogen Receptor Binding Reveals Long-Range Regulation Requiring the Forkhead Protein FoxA1 , 2005, Cell.

[110]  B. Göttgens,et al.  Transcriptional Regulation of the SCL Locus: Identification of an Enhancer That Targets the Primitive Erythroid Lineage In Vivo , 2005, Molecular and Cellular Biology.

[111]  M. Meisterernst,et al.  The Mediator of RNA polymerase II , 2005, Chromosoma.

[112]  J. Kutok,et al.  Acute myeloid leukemia induced by graded reduction of a lineage-specific transcription factor, PU.1 , 2004, Nature Genetics.

[113]  B. Göttgens,et al.  The scl +18/19 Stem Cell Enhancer Is Not Required for Hematopoiesis: Identification of a 5′ Bifunctional Hematopoietic-Endothelial Enhancer Bound by Fli-1 and Elf-1 , 2004, Molecular and Cellular Biology.

[114]  Frank Grosveld,et al.  Spatial organization of gene expression: the active chromatin hub , 2003, Chromosome Research.

[115]  B. Oostra,et al.  A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. , 2003, Human molecular genetics.

[116]  Tom Misteli,et al.  The double bromodomain protein Brd4 binds to acetylated chromatin during interphase and mitosis , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[117]  Qiang Zhou,et al.  Stimulatory effect of splicing factors on transcriptional elongation , 2001, Nature.

[118]  N. L. La Thangue,et al.  p300/CBP proteins: HATs for transcriptional bridges and scaffolds. , 2001, Journal of cell science.

[119]  M. Méchali,et al.  Rearrangement of chromatin domains during development in Xenopus. , 2000, Genes & development.

[120]  B. Göttgens,et al.  An SCL 3' enhancer targets developing endothelium together with embryonic and adult haematopoietic progenitors. , 1999, Development.

[121]  G. Felsenfeld,et al.  Tissue‐specific factors additively increase the probability of the all‐or‐none formation of a hypersensitive site. , 1996, The EMBO journal.

[122]  C C Adams,et al.  Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative , 1995, Molecular and cellular biology.

[123]  E. Scott,et al.  Requirement of transcription factor PU.1 in the development of multiple hematopoietic lineages. , 1994, Science.

[124]  F. Grosveld,et al.  Definition of the minimal requirements within the human beta‐globin gene and the dominant control region for high level expression. , 1990, The EMBO journal.

[125]  J. Banerji,et al.  Expression of a β-globin gene is enhanced by remote SV40 DNA sequences , 1981, Cell.

[126]  Jian Xu,et al.  Pioneer factors, genetic competence, and inductive signaling: programming liver and pancreas progenitors from the endoderm. , 2008, Cold Spring Harbor symposia on quantitative biology.

[127]  C. Glass,et al.  Sensors and Signals: a Coactivator/ Corepressor/epigenetic Code for Integrating Signal-dependent Programs of Transcriptional Response , 2006 .

[128]  N. L. Thangue,et al.  Summary p 300 / CBP proteins : HATs for transcriptional bridges and scaffolds , 2001 .

[129]  M. Brodsky,et al.  Escholarship@umms Program in Gene Function and Expression Publications and Presentations Program in Gene Function and Expression Widespread Evidence of Cooperative Dna Binding by Transcription Factors in Drosophila Development Repository Citation Widespread Evidence of Cooperative Dna Binding by Tra , 2022 .

[130]  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 .

[131]  Klaudia Walter,et al.  Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development , 2004, PLoS biology.