Chromatin and epigenetic features of long-range gene regulation

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

(2013) Jiang Zhu et al.   CELL

Developmentally Regulated Subnuclear Genome Reorganization Restricts Neural Progenitor Competence in Drosophila

(2013) Minoree Kohwi et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

An Integrated Holo-Enhancer Unit Defines Tissue and Gene Specificity of the Fgf8 Regulatory Landscape

(2013) Mirna Marinić et al.   DEVELOPMENTAL CELL

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions

(2013) Ralph Stadhouders et al.   Nature Protocols

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci

(2013) Emily V. Chambers et al.   PLoS Computational Biology

Genome-Wide Control of RNA Polymerase II Activity by Cohesin

(2013) Cheri A. Schaaf et al.   PLoS Genetics

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

(2012) Guillaume Junion et al.   CELL

Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor

(2012) Wulan Deng et al.   CELL

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization

(2012) Iouri Chepelev et al.   CELL RESEARCH

Chromosome organization in the nucleus – charting new territory across the Hi-Cs

(2012) Josée Dostie et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Combinatorial complexity in chromatin structure and function: revisiting the histone code

(2012) Oliver J Rando   CURRENT OPINION IN GENETICS & DEVELOPMENT

Comparing Enhancer Action in Cis and in Trans

(2012) J. R. Bateman et al.   GENETICS

An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement

(2012) I. Maeso et al.   GENOME RESEARCH

Coding exons function as tissue-specific enhancers of nearby genes

(2012) Ramon Y. Birnbaum et al.   GENOME RESEARCH

Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes

(2012) K. Kritsas et al.   GENOME RESEARCH

Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints

(2012) M. Irimia et al.   GENOME RESEARCH

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

(2012) R. Fenouil et al.   GENOME RESEARCH

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

(2012) Justin Cotney et al.   GENOME RESEARCH

Resolving the variable genome and epigenome in human disease

(2012) J. C. Knight   JOURNAL OF INTERNAL MEDICINE

eMouseAtlas, EMAGE, and the spatial dimension of the transcriptome

(2012) Chris Armit et al.   MAMMALIAN GENOME

Cell-Type-Specific Control of Enhancer Activity by H3K9 Trimethylation

(2012) Yina Zhu et al.   MOLECULAR CELL

eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription

(2012) Carlos A. Melo et al.   MOLECULAR CELL

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

(2012) Boris Lenhard et al.   NATURE REVIEWS GENETICS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Conserved Noncoding Sequences Highlight Shared Components of Regulatory Networks in Dicotyledonous Plants

(2012) Laura Baxter et al.   PLANT CELL

Complexity of chromatin folding is captured by the strings and binders switch model

(2012) M. Barbieri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks

(2012) Kuljeet Singh Sandhu et al.   Cell Reports

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila

(2011) Frédéric Bantignies et al.   CELL

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification

(2011) Minjia Tan et al.   CELL

Rapid Evolutionary Rewiring of a Structurally Constrained Eye Enhancer

(2011) Christina I. Swanson et al.   CURRENT BIOLOGY

Dynamic long-range chromatin interactions controlMybproto-oncogene transcription during erythroid development

(2011) Ralph Stadhouders et al.   EMBO JOURNAL

DNA methylation status predicts cell type-specific enhancer activity

(2011) Malgorzata Wiench et al.   EMBO JOURNAL

Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers

(2011) A. A. Serandour et al.   GENOME RESEARCH

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Large-scale discovery of enhancers from human heart tissue

(2011) Dalit May et al.   NATURE GENETICS

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

DNA Methylation Profiling of Embryonic Stem Cell Differentiation into the Three Germ Layers

(2011) Takayuki Isagawa et al.   PLoS One

CCCTC-binding factor (CTCF) and cohesin influence the genomic architecture of the Igh locus and antisense transcription in pro-B cells

(2011) S. C. Degner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct Interaction of RNA Polymerase II and Mediator Required for Transcription in Vivo

(2011) J. Soutourina et al.   SCIENCE

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

Interactions among Polycomb Domains Are Guided by Chromosome Architecture

(2011) Bas Tolhuis et al.   PLoS Genetics

Discovery of active enhancers through bidirectional expression of short transcripts

(2011) Michael F Melgar et al.   GENOME BIOLOGY

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

(2010) Tarjei S. Mikkelsen et al.   CELL

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Combinatorial Transcriptional Control In Blood Stem/Progenitor Cells: Genome-wide Analysis of Ten Major Transcriptional Regulators

(2010) Nicola K. Wilson et al.   Cell Stem Cell

Structural Rules and Complex Regulatory Circuitry Constrain Expression of a Notch- and EGFR-Regulated Eye Enhancer

(2010) Christina I. Swanson et al.   DEVELOPMENTAL CELL

An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer

(2010) N. F. Wasserman et al.   GENOME RESEARCH

A systems approach to analyze transcription factors in mammalian cells

(2010) Eric Soler et al.   METHODS

Short RNAs Are Transcribed from Repressed Polycomb Target Genes and Interact with Polycomb Repressive Complex-2

(2010) Aditi Kanhere et al.   MOLECULAR CELL

Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide

(2010) Marco Botta et al.   Molecular Systems Biology

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

CpG islands influence chromatin structure via the CpG-binding protein Cfp1

(2010) John P. Thomson et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

Targets and dynamics of promoter DNA methylation during early mouse development

(2010) Julie Borgel et al.   NATURE GENETICS

Insulators and promoters: closer than we think

(2010) Jesse R. Raab et al.   NATURE REVIEWS GENETICS

The role of transcription factories-mediated interchromosomal contacts in the organization of nuclear architecture

(2010) Julien Dorier et al.   NUCLEIC ACIDS RESEARCH

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

Histone Crosstalk between H3S10ph and H4K16ac Generates a Histone Code that Mediates Transcription Elongation

(2009) Alessio Zippo et al.   CELL

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation

(2009) Kairong Cui et al.   Cell Stem Cell

DNA methylation and methyl-CpG binding proteins: developmental requirements and function

(2009) Ozren Bogdanović et al.   CHROMOSOMA

Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster

(2009) Tsuyoshi Mishiro et al.   EMBO JOURNAL

Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity

(2009) C. Schmidl et al.   GENOME RESEARCH

A Model for all Genomes: The Role of Transcription Factories

(2009) Peter R. Cook   JOURNAL OF MOLECULAR BIOLOGY

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Genomic views of distant-acting enhancers

(2009) Axel Visel et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells

(2009) Bo Wen et al.   NATURE GENETICS

Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence

(2009) Sabina Benko et al.   NATURE GENETICS

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons

(2009) Xianjun Dong et al.   NUCLEIC ACIDS RESEARCH

CpG-depleted promoters harbor tissue-specific transcription factor binding signals—implications for motif overrepresentation analyses

(2009) Helge G. Roider et al.   NUCLEIC ACIDS RESEARCH

Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3

(2009) A. Ragvin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition

(2009) K. M. Lower et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Disease-Causing 7.4 kb Cis-Regulatory Deletion Disrupting Conserved Non-Coding Sequences and Their Interaction with the FOXL2 Promotor: Implications for Mutation Screening

(2009) Barbara D'haene et al.   PLoS Genetics

A Common Variant Associated with Dyslexia Reduces Expression of the KIAA0319 Gene

(2009) Megan Y. Dennis et al.   PLoS Genetics

Transcriptional features of genomic regulatory blocks

(2009) Altuna Akalin et al.   GENOME BIOLOGY

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

(2008) Mathieu Lupien et al.   CELL

The enhanceosome

(2008) Daniel Panne   CURRENT OPINION IN STRUCTURAL BIOLOGY

Chromosomal Dynamics at the Shh Locus: Limb Bud-Specific Differential Regulation of Competence and Active Transcription

(2008) Takanori Amano et al.   DEVELOPMENTAL CELL

H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome

(2008) F. M. Pauler et al.   GENOME RESEARCH

Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors

(2008) Fabio Mohn et al.   MOLECULAR CELL

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

An ultraconserved Hox–Pbx responsive element resides in the coding sequence of Hoxa2 and is active in rhombomere 4

(2008) Xavier Lampe et al.   NUCLEIC ACIDS RESEARCH

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping

(2008) Vijay K Tiwari et al.   PLOS BIOLOGY

Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation

(2008) Emily E. Hare et al.   PLoS Genetics

Global Chromatin Domain Organization of the Drosophila Genome

(2008) Elzo de Wit et al.   PLoS Genetics

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome

(2008) Yutao Fu et al.   PLoS Genetics

Recruitment to the Nuclear Periphery Can Alter Expression of Genes in Human Cells

(2008) Lee E. Finlan et al.   PLoS Genetics

Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes

(2008) Pär G Engström et al.   GENOME BIOLOGY

Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b

(2007) D. M. McGaughey et al.   GENOME RESEARCH