Enhancer RNA Expression in Response to Glucocorticoid Treatment in Murine Macrophages

The corepressors GPS2 and SMRT control enhancer and silencer remodeling via eRNA transcription during inflammatory activation of macrophages

(2021) Zhiqiang Huang et al.   MOLECULAR CELL

BET inhibition disrupts transcription but retains enhancer-promoter contact

(2021) Nicholas T. Crump et al.   Nature Communications

The glucocorticoid receptor recruits the COMPASS complex to regulate inflammatory transcription at macrophage enhancers

(2021) Franziska Greulich et al.   Cell Reports

Negative elongation factor complex enables macrophage inflammatory responses by controlling anti-inflammatory gene expression

(2020) Li Yu et al.   Nature Communications

Dexamethasone in Hospitalized Patients with Covid-19 — Preliminary Report

(2020)   NEW ENGLAND JOURNAL OF MEDICINE

Anti-inflammatory functions of the glucocorticoid receptor require DNA binding

(2020) Laura Escoter-Torres et al.   NUCLEIC ACIDS RESEARCH

Enhancer RNAs Mediate Estrogen-Induced Decommissioning of Selective Enhancers by Recruiting ERα and Its Cofactor

(2020) Mei Yang et al.   Cell Reports

E47 modulates hepatic glucocorticoid action

(2019) M. Charlotte Hemmer et al.   Nature Communications

Immune regulation by glucocorticoids can be linked to cell type–dependent transcriptional responses

(2019) Luis M. Franco et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Transcriptional cofactors display specificity for distinct types of core promoters

(2019) Vanja Haberle et al.   NATURE

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression

(2019) Sarah K. Sasse et al.   GENOME RESEARCH

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

(2019) Nezha S. Benabdallah et al.   MOLECULAR CELL

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Fighting the Fire: Mechanisms of Inflammatory Gene Regulation by the Glucocorticoid Receptor

(2019) Laura Escoter-Torres et al.   Frontiers in Immunology

Cistromic Reprogramming of the Diurnal Glucocorticoid Hormone Response by High-Fat Diet

(2019) Fabiana Quagliarini et al.   MOLECULAR CELL

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Cryptic glucocorticoid receptor-binding sites pervade genomic NF-κB response elements

(2018) William H. Hudson et al.   Nature Communications

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

(2018) Maria A Sacta et al.   eLife

Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding

(2018) Ian C. McDowell et al.   GENOME RESEARCH

RNAs interact with BRD4 to promote enhanced chromatin engagement and transcription activation

(2018) Homa Rahnamoun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2019

(2018) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Brd4 binds to active enhancers to control cell identity gene induction in adipogenesis and myogenesis

(2017) Ji-Eun Lee et al.   Nature Communications

Rapid Genome-wide Recruitment of RNA Polymerase II Drives Transcription, Splicing, and Translation Events during T Cell Responses

(2017) Kathrin Davari et al.   Cell Reports

Glucocorticoid Receptor Binding Induces Rapid and Prolonged Large-Scale Chromatin Decompaction at Multiple Target Loci

(2017) Alasdair W. Jubb et al.   Cell Reports

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

(2017) Jonathan Aryeh Sobel et al.   PLOS BIOLOGY

Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome

(2016) Christopher M. Vockley et al.   CELL

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

(2016) Makiko Iwafuchi-Doi et al.   MOLECULAR CELL

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

There goes the neighborhood: Assembly of transcriptional complexes during the regulation of metabolism and inflammation by the glucocorticoid receptor

(2016) Franziska Greulich et al.   STEROIDS

Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity

(2016) Stefanie Schöne et al.   Nature Communications

The interplay of histone modifications - writers that read

(2015) T. Zhang et al.   EMBO REPORTS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

GR SUMOylation and formation of an SUMO-SMRT/NCoR1-HDAC3 repressing complex is mandatory for GC-induced IR nGRE-mediated transrepression

(2015) Guoqiang Hua et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Glucocorticoid-induced tethered transrepression requires SUMOylation of GR and formation of a SUMO-SMRT/NCoR1-HDAC3 repressing complex

(2015) Guoqiang Hua et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Circadian Enhancers Coordinate Multiple Phases of Rhythmic Gene Transcription In Vivo

(2014) Bin Fang et al.   CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Brd4 activates P-TEFb for RNA polymerase II CTD phosphorylation

(2014) Friederike Itzen et al.   NUCLEIC ACIDS RESEARCH

Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes

(2014) Nicholas E. Ilott et al.   Nature Communications

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

(2014) Sankari Nagarajan et al.   Cell Reports

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

SET1 and p300 Act Synergistically, through Coupled Histone Modifications, in Transcriptional Activation by p53

(2013) Zhanyun Tang et al.   CELL

C/EBP maintains chromatin accessibility in liver and facilitates glucocorticoid receptor recruitment to steroid response elements

(2013) Lars Grøntved et al.   EMBO JOURNAL

Ligand-Induced Repression of the Glucocorticoid Receptor Gene Is Mediated by an NCoR1 Repression Complex Formed by Long-Range Chromatin Interactions with Intragenic Glucocorticoid Response Elements

(2013) Sivapriya Ramamoorthy et al.   MOLECULAR AND CELLULAR BIOLOGY

Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

(2013) Minna U. Kaikkonen et al.   MOLECULAR CELL

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Glucocorticoid receptor signaling in health and disease

(2013) Mahita Kadmiel et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture

(2013) Bernd Rädle et al.   Jove-Journal of Visualized Experiments

Involvement of GR and p300 in the Induction of H6PD by Cortisol in Human Amnion Fibroblasts

(2012) Weihua Wang et al.   ENDOCRINOLOGY

Bromodomain-containing Protein 4 (BRD4) Regulates RNA Polymerase II Serine 2 Phosphorylation in Human CD4+ T Cells

(2012) Weishi Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates

(2012) Mikhail Pachkov et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Readers of histone modifications

(2011) Miyong Yun et al.   CELL RESEARCH

Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding

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

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

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

(2010) Qihuang Jin et al.   EMBO JOURNAL

Cellular Processing of the Glucocorticoid Receptor Gene and Protein: New Mechanisms for Generating Tissue-specific Actions of Glucocorticoids

(2010) Robert H. Oakley et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Chromatin Signaling Pathway: Diverse Mechanisms of Recruitment of Histone-Modifying Enzymes and Varied Biological Outcomes

(2010) Edwin Smith et al.   MOLECULAR CELL

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Control of Inducible Gene Expression by Signal-Dependent Transcriptional Elongation

(2009) Diana C. Hargreaves et al.   CELL

Regulation of gene expression via the core promoter and the basal transcriptional machinery

(2009) Tamar Juven-Gershon et al.   DEVELOPMENTAL BIOLOGY

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity

(2009) S. H. Meijsing et al.   SCIENCE

The significance of glucocorticoid pulsatility

(2008) Stafford L. Lightman et al.   EUROPEAN JOURNAL OF PHARMACOLOGY

Interaction of the Glucocorticoid Receptor with the Chromatin Landscape

(2008) Sam John et al.   MOLECULAR CELL

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY