HNF4A modulates glucocorticoid action in the liver

A test of the pioneer factor hypothesis using ectopic liver gene activation

(2022) Jeffrey L Hansen et al.   eLife

Genome-wide binding potential and regulatory activity of the glucocorticoid receptor’s monomeric and dimeric forms

(2021) Thomas A. Johnson et al.   Nature Communications

Liver-fibrosis-activated transcriptional networks govern hepatocyte reprogramming and intra-hepatic communication

(2021) Anne Loft et al.   Cell Metabolism

HNF4A defines tissue-specific circadian rhythms by beaconing BMAL1::CLOCK chromatin binding and shaping the rhythmic chromatin landscape

(2021) Meng Qu et al.   Nature Communications

Bookmarking by Non-pioneer Transcription Factors during Liver Development Establishes Competence for Future Gene Activation

(2020) Panagiota Karagianni et al.   Cell Reports

Glucocorticoids rapidly inhibit cell migration through a novel, non-transcriptional HDAC6 pathway

(2020) Stephen Kershaw et al.   JOURNAL OF CELL SCIENCE

ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation

(2020) Jake J. Reske et al.   Epigenetics & Chromatin

Anti-inflammatory functions of the glucocorticoid receptor require DNA binding

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

A negative reciprocal regulatory axis between cyclin D1 and HNF4α modulates cell cycle progression and metabolism in the liver

(2020) Heng Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nuclear receptor REVERBα is a state-dependent regulator of liver energy metabolism

(2020) A. Louise Hunter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multifaceted Control of GR Signaling and Its Impact on Hepatic Transcriptional Networks and Metabolism

(2020) Stine M. Præstholm et al.   Frontiers in Endocrinology

Estrogen Receptor on the move: Cistromic plasticity and its implications in breast cancer

(2020) Isabel Mayayo-Peralta et al.   MOLECULAR ASPECTS OF MEDICINE

Molecular Co-occupancy Identifies Transcription Factor Binding Cooperativity In Vivo

(2020) Can Sönmezer et al.   MOLECULAR CELL

E47 modulates hepatic glucocorticoid action

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

Tissue-specific BMAL1 cistromes reveal that rhythmic transcription is associated with rhythmic enhancer–enhancer interactions

(2019) Joshua R. Beytebiere et al.   GENES & DEVELOPMENT

An improved method for quantitative ChIP studies of nuclear receptor function

(2019) Ann Louise Hunter et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

ZIC3 Controls the Transition from Naive to Primed Pluripotency

(2019) Shen-Hsi Yang et al.   Cell Reports

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

(2019) Fabiana Quagliarini et al.   MOLECULAR CELL

Circadian variation in pulmonary inflammatory responses is independent of rhythmic glucocorticoid signaling in airway epithelial cells

(2018) Louise M. Ince et al.   FASEB JOURNAL

GIGGLE: a search engine for large-scale integrated genome analysis

(2018) Ryan M Layer et al.   NATURE METHODS

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

Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids

(2018) Anthony M. D'Ippolito et al.   Cell Systems

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

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

REVERBa couples the circadian clock to hepatic glucocorticoid action

(2018) Giorgio Caratti et al.   JOURNAL OF CLINICAL INVESTIGATION

Nuclear receptor HNF4A transrepresses CLOCK:BMAL1 and modulates tissue-specific circadian networks

(2018) Meng Qu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Incompatibility of the circadian protein BMAL1 and HNF4α in hepatocellular carcinoma

(2018) Baharan Fekry et al.   Nature Communications

The hepatic circadian clock fine-tunes the lipogenic response to feeding through RORα/γ

(2017) Yuxiang Zhang et al.   GENES & DEVELOPMENT

Anti-Inflammatory Chromatinscape Suggests Alternative Mechanisms of Glucocorticoid Receptor Action

(2017) Kyu-Seon Oh et al.   IMMUNITY

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Conventional and pioneer modes of glucocorticoid receptor interaction with enhancer chromatin in vivo

(2017) Thomas A Johnson et al.   NUCLEIC ACIDS RESEARCH

An HDAC3-PROX1 corepressor module acts on HNF4α to control hepatic triglycerides

(2017) Sean M. Armour et al.   Nature Communications

Single-molecule analysis of steroid receptor and cofactor action in living cells

(2017) Ville Paakinaho et al.   Nature Communications

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

(2017) Jonathan Aryeh Sobel et al.   PLOS BIOLOGY

Transcription factor assisted loading and enhancer dynamics dictate the hepatic fasting response

(2016) Ido Goldstein et al.   GENOME RESEARCH

ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization

(2016) Guangchuang Yu et al.   Molecular BioSystems

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

Hierarchy within the mammary STAT5-driven Wap super-enhancer

(2016) Ha Youn Shin et al.   NATURE GENETICS

Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation

(2016) Michael I. Love et al.   NUCLEIC ACIDS RESEARCH

An Alternative Approach to ChIP-Seq Normalization Enables Detection of Genome-Wide Changes in Histone H3 Lysine 27 Trimethylation upon EZH2 Inhibition

(2016) Brian Egan et al.   PLoS One

Genetic Variation Determines PPARγ Function and Anti-diabetic Drug Response In Vivo

(2015) Raymond E. Soccio et al.   CELL

Genomic redistribution of GR monomers and dimers mediates transcriptional response to exogenous glucocorticoid in vivo

(2015) Hee-Woong Lim et al.   GENOME RESEARCH

Enhancer Turnover Is Associated with a Divergent Transcriptional Response to Glucocorticoid in Mouse and Human Macrophages

(2015) Alasdair W. Jubb et al.   JOURNAL OF IMMUNOLOGY

csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

(2015) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Reprogramming the Chromatin Landscape: Interplay of the Estrogen and Glucocorticoid Receptors at the Genomic Level

(2013) T. B. Miranda et al.   CANCER RESEARCH

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

(2013) Lars Grøntved et al.   EMBO JOURNAL

Distinct Properties of Cell-Type-Specific and Shared Transcription Factor Binding Sites

(2013) Jason Gertz et al.   MOLECULAR CELL

Genome-wide mapping of FOXM1 binding reveals co-binding with estrogen receptor alpha in breast cancer cells

(2013) Deborah A Sanders et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

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

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Widespread Negative Response Elements Mediate Direct Repression by Agonist- Liganded Glucocorticoid Receptor

(2011) Milan Surjit et al.   CELL

Molecular dynamics of ultradian glucocorticoid receptor action

(2011) Becky L. Conway-Campbell et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

Multiple, temporal-specific roles for HNF6 in pancreatic endocrine and ductal differentiation

(2009) Hongjie Zhang et al.   MECHANISMS OF DEVELOPMENT

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY