Gene-specific mechanisms direct glucocorticoid-receptor-driven repression of inflammatory response genes in macrophages

Anti-Inflammatory Chromatinscape Suggests Alternative Mechanisms of Glucocorticoid Receptor Action

(2017) Kyu-Seon Oh et al.   IMMUNITY

Glucocorticoid receptor control of transcription: precision and plasticity via allostery

(2017) Emily R. Weikum et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Tethering not required: the glucocorticoid receptor binds directly to activator protein-1 recognition motifs to repress inflammatory genes

(2017) Emily R. Weikum et al.   NUCLEIC ACIDS RESEARCH

Glucocorticoid Signaling: An Update from a Genomic Perspective

(2016) Maria A. Sacta et al.   Annual Review of Physiology

A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation

(2016) Ann-Jay Tong et al.   CELL

The transcriptional repressor Hes1 attenuates inflammation by regulating transcription elongation

(2016) Yingli Shang et al.   NATURE IMMUNOLOGY

Molecular control of activation and priming in macrophages

(2016) Christopher K Glass et al.   NATURE IMMUNOLOGY

Multiple P-TEFbs cooperatively regulate the release of promoter-proximally paused RNA polymerase II

(2016) Xiaodong Lu et al.   NUCLEIC ACIDS RESEARCH

Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation

(2016) B. A. Gibson et al.   SCIENCE

The transcriptional coregulator GRIP1 controls macrophage polarization and metabolic homeostasis

(2016) Maddalena Coppo et al.   Nature Communications

Homeostasis, Inflammation, and Disease Susceptibility

(2015) Maya E. Kotas et al.   CELL

BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia

(2015) Jae-Seok Roe et al.   MOLECULAR CELL

Chromatin Contributions to the Regulation of Innate Immunity

(2014) Stephen T. Smale et al.   Annual Review of Immunology

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(2014) A. Akalin et al.   BIOINFORMATICS

Glucocorticoid receptor coordinates transcription factor-dominated regulatory network in macrophages

(2014) Yurii Chinenov et al.   BMC GENOMICS

NF-κB Directs Dynamic Super Enhancer Formation in Inflammation and Atherogenesis

(2014) Jonathan D. Brown et al.   MOLECULAR CELL

The Mechanisms behind the Therapeutic Activity of BET Bromodomain Inhibition

(2014) Junwei Shi et al.   MOLECULAR CELL

Enhancer RNA Facilitates NELF Release from Immediate Early Genes

(2014) Katie Schaukowitch et al.   MOLECULAR CELL

Preparing the First Responders: Building the Inflammatory Transcriptome from the Ground Up

(2014) Inez Rogatsky et al.   MOLECULAR CELL

Motif-based analysis of large nucleotide data sets using MEME-ChIP

(2014) Wenxiu Ma et al.   Nature Protocols

BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones

(2014) Tomohiko Kanno et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Brd4 activates P-TEFb for RNA polymerase II CTD phosphorylation

(2014) Friederike Itzen et al.   NUCLEIC ACIDS RESEARCH

Transcriptional Control of Inflammatory Responses

(2014) S. T. Smale et al.   Cold Spring Harbor Perspectives in Biology

Bromodomain Protein BRD4 Is Required for Estrogen Receptor-Dependent Enhancer Activation and Gene Transcription

(2014) Sankari Nagarajan et al.   Cell Reports

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

(2014) Thomas S. Carroll et al.   Frontiers in Genetics

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Nuclear receptors in inflammation control: Repression by GR and beyond

(2013) Yurii Chinenov et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Glucocorticoid receptor represses proinflammatory genes at distinct steps of the transcription cycle

(2013) Rebecca Gupte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-Scale Quality Analysis of Published ChIP-seq Data

(2013) Georgi K. Marinov et al.   G3-Genes Genomes Genetics

Regulating the regulators: the pervasive effects of Pol II pausing on stimulus-responsive gene networks

(2012) D. A. Gilchrist et al.   GENES & DEVELOPMENT

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

The Stat3/GR Interaction Code: Predictive Value of Direct/Indirect DNA Recruitment for Transcription Outcome

(2012) David Langlais et al.   MOLECULAR CELL

Insights into Negative Regulation by the Glucocorticoid Receptor from Genome-wide Profiling of Inflammatory Cistromes

(2012) N. Henriette Uhlenhaut et al.   MOLECULAR CELL

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Role of transcriptional coregulator GRIP1 in the anti-inflammatory actions of glucocorticoids

(2012) Y. Chinenov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Defining the Status of RNA Polymerase at Promoters

(2012) Leighton J. Core et al.   Cell Reports

Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes

(2011) N. A. S. Rao et al.   GENOME RESEARCH

Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding

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

Mechanisms Establishing TLR4-Responsive Activation States of Inflammatory Response Genes

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

Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation

(2010) Sergei Nechaev et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Promoter-proximal pausing and its release: Molecular mechanisms and physiological functions

(2010) Kunitoshi Chiba et al.   EXPERIMENTAL CELL RESEARCH

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

Suppression of inflammation by a synthetic histone mimic

(2010) Edwige Nicodeme et al.   NATURE

The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation

(2010) Sohail Malik et al.   NATURE REVIEWS GENETICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation

(2009) T. E. Reddy et al.   GENOME RESEARCH

Mouse Cofactor of BRCA1 (Cobra1) Is Required for Early Embryogenesis

(2009) Asma Amleh et al.   PLoS One

Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling

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

Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila

(2009) S. Nechaev et al.   SCIENCE

NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly

(2008) D. A. Gilchrist et al.   GENES & DEVELOPMENT

Postrecruitment Regulation of RNA Polymerase II Directs Rapid Signaling Responses at the Promoters of Estrogen Target Genes

(2008) M. Kininis et al.   MOLECULAR AND CELLULAR BIOLOGY

Brd4 Coactivates Transcriptional Activation of NF- B via Specific Binding to Acetylated RelA

(2008) B. Huang et al.   MOLECULAR AND CELLULAR BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY