Dynamic Estrogen Receptor Interactomes Control Estrogen-Responsive Trefoil Factor (TFF) Locus Cell-Specific Activities

Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?

(2013) Elphège P. Nora et al.   BIOESSAYS

Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation

(2013) Junbai Wang et al.   BMC GENOMICS

Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes

(2013) Yuanyuan Li et al.   BMC GENOMICS

The role of chromatin insulators in nuclear architecture and genome function

(2013) Kevin Van Bortle et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Communication of genome regulatory elements in a folded chromosome

(2013) Sergey V. Razin et al.   FEBS LETTERS

Enhancer transcripts mark active estrogen receptor binding sites

(2013) N. Hah et al.   GENOME RESEARCH

The genomic landscape of cohesin-associated chromatin interactions

(2013) L. E. DeMare et al.   GENOME RESEARCH

Biological Implications and Regulatory Mechanisms of Long-range Chromosomal Interactions

(2013) Zong Wei et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Hierarchy of the 3D Genome

(2013) Johan H. Gibcus et al.   MOLECULAR CELL

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Functional implications of genome topology

(2013) Giacomo Cavalli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub

(2013) Alexey A. Gavrilov et al.   NUCLEIC ACIDS RESEARCH

Development of bis-locked nucleic acid (bisLNA) oligonucleotides for efficient invasion of supercoiled duplex DNA

(2013) Pedro M. D. Moreno et al.   NUCLEIC ACIDS RESEARCH

Chromatin and epigenetic features of long-range gene regulation

(2013) N. Harmston et al.   NUCLEIC ACIDS RESEARCH

Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers

(2013) C. Attanasio et al.   SCIENCE

Genome-Wide Control of RNA Polymerase II Activity by Cohesin

(2013) Cheri A. Schaaf et al.   PLoS Genetics

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

(2012) A. J. Faure et al.   GENOME RESEARCH

GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility

(2012) V. Theodorou et al.   GENOME RESEARCH

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Cyclopamine cooperates with EGFR inhibition to deplete stem-like cancer cells in glioblastoma-derived spheroid cultures

(2012) Sandrine Eimer et al.   NEURO-ONCOLOGY

Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers

(2012) Aurélien A. Sérandour et al.   NUCLEIC ACIDS RESEARCH

A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells

(2011) Nasun Hah et al.   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

Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers

(2011) A. A. Serandour et al.   GENOME RESEARCH

Cellular reprogramming by the conjoint action of ER , FOXA1, and GATA3 to a ligand-inducible growth state

(2011) S. L. Kong et al.   Molecular Systems Biology

Pioneer factors: directing transcriptional regulators within the chromatin environment

(2011) Luca Magnani et al.   TRENDS IN GENETICS

PBX1 Genomic Pioneer Function Drives ERα Signaling Underlying Progression in Breast Cancer

(2011) Luca Magnani et al.   PLoS Genetics

Mechanisms of triplex DNA-mediated inhibition of transcription initiation in cells

(2010) Aklank Jain et al.   BIOCHIMIE

Gene Targeting and Expression Modulation by Peptide Nucleic Acids (PNA)

(2010) Peter E. Nielsen   CURRENT PHARMACEUTICAL DESIGN

Growth factor stimulation induces a distinct ER  cistrome underlying breast cancer endocrine resistance

(2010) M. Lupien et al.   GENES & DEVELOPMENT

A CTCF-independent role for cohesin in tissue-specific transcription

(2010) D. Schmidt et al.   GENOME RESEARCH

Estrogen-mediated epigenetic repression of large chromosomal regions through DNA looping

(2010) P.-Y. Hsu et al.   GENOME RESEARCH

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

(2010) V. Gotea et al.   GENOME RESEARCH

CCCTC-binding Factor Acts Upstream of FOXA1 and Demarcates the Genomic Response to Estrogen

(2010) Yu Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

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

(2010) Antoni Hurtado et al.   NATURE GENETICS

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Cyclical Chromatin Looping and Transcription Factor Association on the Regulatory Regions of the p21 (CDKN1A) Gene in Response to 1α,25-Dihydroxyvitamin D3

(2009) Anna Saramäki et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genomic Responses from the Estrogen-responsive Element-dependent Signaling Pathway Mediated by Estrogen Receptor α Are Required to Elicit Cellular Alterations

(2009) Stephanie L. Nott et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Defining specificity of transcription factor regulatory activities

(2009) J. Eeckhoute et al.   JOURNAL OF CELL SCIENCE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Triplex Formation on DNA Targets: How To Choose the Oligonucleotide

(2008) Pierre Vekhoff et al.   BIOCHEMISTRY

QuantPrime - a flexible tool for reliable high-throughput primer design for quantitative PCR

(2008) Samuel Arvidsson et al.   BMC BIOINFORMATICS

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

(2008) Mathieu Lupien et al.   CELL

Global transcriptional regulation of the locus encoding the skeletal muscle determination genes Mrf4 and Myf5

(2008) J. J. Carvajal et al.   GENES & DEVELOPMENT

High-resolution circular chromosome conformation capture assay

(2008) Anita Göndör et al.   Nature Protocols

NCBI GEO: archive for high-throughput functional genomic data

(2008) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Cluster specific regulation pattern of upstream regulatory elements in human α- and β-globin gene clusters

(2007) Yi Tang et al.   EXPERIMENTAL CELL RESEARCH