The Chromatin Fingerprint of Gene Enhancer Elements

Functional and Mechanistic Diversity of Distal Transcription Enhancers

(2011) Michael Bulger 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

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

DNA methylation status predicts cell type-specific enhancer activity

(2011) Malgorzata Wiench et al.   EMBO JOURNAL

DNA Methylation of Intronic Enhancers Directs Tissue-Specific Expression of Steroidogenic Factor 1/Adrenal 4 Binding Protein (SF-1/Ad4BP)

(2011) Erling A. Hoivik et al.   ENDOCRINOLOGY

Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1

(2011) G. Hu et al.   GENOME RESEARCH

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

(2011) W. Wu et al.   GENOME RESEARCH

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

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

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

Genome-wide identification of conserved regulatory function in diverged sequences

(2011) L. Taher et al.   GENOME RESEARCH

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

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

Genetic and expressional alterations of CHD genes in gastric and colorectal cancers

(2011) Min Sung Kim et al.   HISTOPATHOLOGY

Dynamic BRG1 Recruitment during T Helper Differentiation and Activation Reveals Distal Regulatory Elements

(2011) S. De et al.   MOLECULAR AND CELLULAR BIOLOGY

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response

(2011) Olivier Harismendy et al.   NATURE

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

The nucleosome map of the mammalian liver

(2011) Zhaoyu Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PU.1 and C/EBP  synergistically program distinct response to NF- B activation through establishing monocyte specific enhancers

(2011) F. Jin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart

(2011) A. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone modification: cause or cog?

(2011) Steven Henikoff et al.   TRENDS IN GENETICS

Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease

(2011) Alvaro Rada-Iglesias et al.   Genome Medicine

Germline Nonsense Mutation and Somatic Inactivation of SMARCA4/BRG1 in a Family with Rhabdoid Tumor Predisposition Syndrome

(2010) Reinhard Schneppenheim et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Molecular and phenotypic aspects ofCHD7mutation in CHARGE syndrome

(2010) Gabriel E. Zentner et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Genomics of Long-Range Regulatory Elements

(2010) James P. Noonan et al.   Annual Review of Genomics and Human Genetics

BRG1 expression is increased in human cutaneous melanoma

(2010) H. Lin et al.   BRITISH JOURNAL OF DERMATOLOGY

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation

(2010) Qihuang Jin et al.   EMBO JOURNAL

Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver

(2010) B. G. Hoffman et al.   GENOME RESEARCH

Massive parallel DNA pyrosequencing analysis of the tumor suppressor BRG1/SMARCA4 in lung primary tumors

(2010) Salvador Rodriguez-Nieto et al.   HUMAN MUTATION

Identification and Characterization of Enhancers Controlling the Inflammatory Gene Expression Program in Macrophages

(2010) Serena Ghisletti et al.   IMMUNITY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

CHD7 cooperates with PBAF to control multipotent neural crest formation

(2010) Ruchi Bajpai 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

Nucleosome dynamics define transcriptional enhancers

(2010) Housheng Hansen He et al.   NATURE GENETICS

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

A map of open chromatin in human pancreatic islets

(2010) Kyle J Gaulton et al.   NATURE GENETICS

Histone variants — ancient wrap artists of the epigenome

(2010) Paul B. Talbert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Characterization of an antagonistic switch between histone H3 lysine 27 methylation and acetylation in the transcriptional regulation of Polycomb group target genes

(2010) Diego Pasini et al.   NUCLEIC ACIDS RESEARCH

ENCODE whole-genome data in the UCSC genome browser (2011 update)

(2010) Brian J. Raney et al.   NUCLEIC ACIDS RESEARCH

Genome-wide assessment of differential roles for p300 and CBP in transcription regulation

(2010) Y. F. M. Ramos 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

Genome-Wide Kinetics of Nucleosome Turnover Determined by Metabolic Labeling of Histones

(2010) R. B. Deal et al.   SCIENCE

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

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

(2010) Francesca De Santa et al.   PLOS BIOLOGY

CHD7 Targets Active Gene Enhancer Elements to Modulate ES Cell-Specific Gene Expression

(2010) Michael P. Schnetz et al.   PLoS Genetics

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

(2010) Guoliang Li et al.   GENOME BIOLOGY

Genome-wide Mapping of HATs and HDACs Reveals Distinct Functions in Active and Inactive Genes

(2009) Zhibin Wang et al.   CELL

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing

(2009) F. Tie et al.   DEVELOPMENT

SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state

(2009) S. Bilodeau et al.   GENES & DEVELOPMENT

Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers

(2009) J. Eeckhoute et al.   GENOME RESEARCH

Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns

(2009) M. P. Schnetz et al.   GENOME RESEARCH

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

(2009) C. Schmidl et al.   GENOME RESEARCH

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

(2009) Nathaniel D. Heintzman et al.   NATURE

A small-cell lung cancer genome with complex signatures of tobacco exposure

(2009) Erin D. Pleasance et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

H3.3/H2A.Z double variant–containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions

(2009) Chunyuan Jin et al.   NATURE GENETICS

Processing the H3K36me3 signature

(2009) Robert J Sims III et al.   NATURE GENETICS

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

HHMD: the human histone modification database

(2009) Yan Zhang et al.   NUCLEIC ACIDS RESEARCH

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

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

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

(2008) Mathieu Lupien et al.   CELL

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

(2008) A. G. Robertson et al.   GENOME RESEARCH

A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations

(2008) V. K. Tiwari et al.   GENOME RESEARCH

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

(2008) Axel Visel et al.   NATURE GENETICS

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

The chromatin-remodeling enzyme BRG1 coordinates CIITA induction through many interdependent distal enhancers

(2008) Zuyao Ni et al.   NATURE IMMUNOLOGY

H2A.Z: View from the Top

(2008) Jordanka Zlatanova et al.   STRUCTURE

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

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