Deciphering cis-regulatory control in inflammatory cells

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Noncoding Transcription at Enhancers: General Principles and Functional Models

(2012) Gioacchino Natoli et al.   Annual Review of 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

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function

(2012) Colin R. Lickwar 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

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Requirement for the histone deacetylase Hdac3 for the inflammatory gene expression program in macrophages

(2012) X. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Master Transcription Factors Determine Cell-Type-Specific Responses to TGF-β Signaling

(2011) Alan C. Mullen et al.   CELL

Two Forms of Loops Generate the Chromatin Conformation of the Immunoglobulin Heavy-Chain Gene Locus

(2011) Changying Guo et al.   CELL

Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells

(2011) Oren Ram et al.   CELL

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

Functional and Mechanistic Diversity of Distal Transcription Enhancers

(2011) Michael Bulger et al.   CELL

Genome-wide Analysis of Simultaneous GATA1/2, RUNX1, FLI1, and SCL Binding in Megakaryocytes Identifies Hematopoietic Regulators

(2011) Marloes R. Tijssen et al.   DEVELOPMENTAL CELL

AP-2γ regulates oestrogen receptor-mediated long-range chromatin interaction and gene transcription

(2011) Si Kee Tan et al.   EMBO JOURNAL

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

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

(2011) G. Hu 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

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

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

Multilineage Priming of Enhancer Repertoires Precedes Commitment to the B and Myeloid Cell Lineages in Hematopoietic Progenitors

(2011) Elinore M. Mercer et al.   IMMUNITY

Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding

(2011) Simon C. Biddie et al.   MOLECULAR CELL

GATA4 Regulates Estrogen Receptor-α-Mediated Osteoblast Transcription

(2011) Gustavo A. Miranda-Carboni et al.   MOLECULAR ENDOCRINOLOGY

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

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

Large-scale discovery of enhancers from human heart tissue

(2011) Dalit May et al.   NATURE GENETICS

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

Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes

(2011) Laure Escoubet-Lozach et al.   PLoS Genetics

Epigenetic Priming of a Pre-B Cell-Specific Enhancer through Binding of Sox2 and Foxd3 at the ESC Stage

(2010) Daniel Liber et al.   Cell Stem Cell

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

(2010) Gong-Hong Wei et al.   EMBO JOURNAL

Bcl-6 and NF- B cistromes mediate opposing regulation of the innate immune response

(2010) G. D. Barish et al.   GENES & DEVELOPMENT

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

(2010) Serena Ghisletti et al.   IMMUNITY

Maintaining Cell Identity through Global Control of Genomic Organization

(2010) Gioacchino Natoli   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

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

FOXA1 is a key determinant of estrogen receptor function and endocrine response

(2010) Antoni Hurtado et al.   NATURE GENETICS

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

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

Control of Inducible Gene Expression by Signal-Dependent Transcriptional Elongation

(2009) Diana C. Hargreaves et al.   CELL

A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling

(2009) Vladimir R. Ramirez-Carrozzi 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

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

(2009) Nathaniel D. Heintzman 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

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS