Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites

Gene-Specific Actions of Transcriptional Coregulators Facilitate Physiological Plasticity: Evidence for a Physiological Coregulator Code

(2020) Michael R. Stallcup et al.   TRENDS IN BIOCHEMICAL SCIENCES

Transcriptional cofactors display specificity for distinct types of core promoters

(2019) Vanja Haberle et al.   NATURE

Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes

(2019) Judith F. Kribelbauer et al.   Annual Review of Cell and Developmental Biology

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

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

Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer–promoter contacts

(2018) Verena Thormann et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Maria A Sacta et al.   eLife

Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding

(2018) Ning Shen et al.   Cell Systems

Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise

(2018) Stefanie Schöne et al.   PLoS Genetics

SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site

(2017) Liyang Zhang et al.   GENOME RESEARCH

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Agonist-specific Protein Interactomes of Glucocorticoid and Androgen Receptor as Revealed by Proximity Mapping

(2017) Joanna K. Lempiäinen et al.   MOLECULAR & CELLULAR PROTEOMICS

Resolving systematic errors in widely used enhancer activity assays in human cells

(2017) Felix Muerdter et al.   NATURE METHODS

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

(2017) Jaime Abraham Castro-Mondragon et al.   NUCLEIC ACIDS RESEARCH

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

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

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

Endogenous androgen receptor proteomic profiling reveals genomic subcomplex involved in prostate tumorigenesis

(2017) S Stelloo et al.   ONCOGENE

Dynamic regulation of Nanog and stem cell-signaling pathways by Hoxa1 during early neuro-ectodermal differentiation of ES cells

(2017) Bony De Kumar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Binding of Posterior HOXA/D Transcription Factors Reveals Subgrouping and Association with CTCF

(2017) Ivana Jerković et al.   PLoS Genetics

The Interactome of the Glucocorticoid Receptor and Its Influence on the Actions of Glucocorticoids in Combatting Inflammatory and Infectious Diseases

(2016) Ioanna Petta et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes

(2016) Hisham Mohammed et al.   Nature Protocols

SEQMINER: An R-Package to Facilitate the Functional Interpretation of Sequence-Based Associations

(2015) Xiaowei Zhan et al.   GENETIC EPIDEMIOLOGY

Unraveling determinants of transcription factor binding outside the core binding site

(2015) Michal Levo et al.   GENOME RESEARCH

A widespread role of the motif environment in transcription factor binding across diverse protein families

(2015) Iris Dror et al.   GENOME RESEARCH

ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors

(2015) Stephan R. Starick et al.   GENOME RESEARCH

Agonist and antagonist switch DNA motifs recognized by human androgen receptor in prostate cancer

(2014) Z. Chen et al.   EMBO JOURNAL

Pioneer transcription factors in cell reprogramming

(2014) Makiko Iwafuchi-Doi et al.   GENES & DEVELOPMENT

Androgen receptor uses relaxed response element stringency for selective chromatin binding and transcriptional regulation in vivo

(2014) Biswajyoti Sahu et al.   NUCLEIC ACIDS RESEARCH

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Glucocorticoid Receptor Confers Resistance to Antiandrogens by Bypassing Androgen Receptor Blockade

(2013) Vivek K. Arora et al.   CELL

Hierarchical Mechanisms for Direct Reprogramming of Fibroblasts to Neurons

(2013) Orly L. Wapinski et al.   CELL

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Endogenous Purification Reveals GREB1 as a Key Estrogen Receptor Regulatory Factor

(2013) Hisham Mohammed et al.   Cell Reports

Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape

(2013) Raluca Gordân et al.   Cell Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

FoxA1 Specifies Unique Androgen and Glucocorticoid Receptor Binding Events in Prostate Cancer Cells

(2012) B. Sahu et al.   CANCER RESEARCH

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

(2012) R. Fenouil et al.   GENOME RESEARCH

The Hypersensitive Glucocorticoid Response Specifically Regulates Period 1 and Expression of Circadian Genes

(2012) T. E. Reddy et al.   MOLECULAR AND CELLULAR BIOLOGY

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity

(2012) Alok K Tewari et al.   GENOME BIOLOGY

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

(2011) Matthew Slattery et al.   CELL

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

(2011) L. Song et al.   GENOME RESEARCH

Regulation of Androgen Receptor-dependent Transcription by Coactivator MED1 Is Mediated through a Newly Discovered Noncanonical Binding Motif

(2011) Feng Jin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

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

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay 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

Dissecting the functional specificities of two Hox proteins

(2010) R. Joshi et al.   GENES & DEVELOPMENT

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias 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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity

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

Glucocorticoid-induced osteoporosis: treatment update and review

(2009) Lisa-Ann Fraser et al.   Therapeutic Advances in Musculoskeletal Disease

Interaction of the Glucocorticoid Receptor with the Chromatin Landscape

(2008) Sam John et al.   MOLECULAR CELL

Functional Diversification of Paralogous Transcription Factors via Divergence in DNA Binding Site Motif and in Expression

(2008) Larry N. Singh et al.   PLoS One

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY