A CRISPR-Cas9 screen identifies essential CTCF anchor sites for estrogen receptor-driven breast cancer cell proliferation

Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element

(2018) Seung Woo Cho et al.   CELL

FOXA1 levels are decreased in pleural breast cancer metastases after adjuvant endocrine therapy, and this is associated with poor outcome

(2018) Willemijne Schrijver et al.   Molecular Oncology

peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data

(2018) Geert Geeven et al.   NUCLEIC ACIDS RESEARCH

CUEDC1 is a primary target of ERα essential for the growth of breast cancer cells

(2018) Rui Lopes et al.   CANCER LETTERS

CTCF-Mediated Enhancer-Promoter Interaction Is a Critical Regulator of Cell-to-Cell Variation of Gene Expression

(2017) Gang Ren et al.   MOLECULAR CELL

PtdIns(3,4,5)P3-dependent Rac Exchanger 1 (PREX1) Rac-Guanine Nucleotide Exchange Factor (GEF) Activity Promotes Breast Cancer Cell Proliferation and Tumor Growth via Activation of Extracellular Signal-regulated Kinase 1/2 (ERK1/2) Signaling

(2016) Heng-Jia Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

(2016) Gozde Korkmaz et al.   NATURE BIOTECHNOLOGY

CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions

(2016) Elisa Fiorito et al.   NUCLEIC ACIDS RESEARCH

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting

(2016) A. J. Aguirre et al.   Cancer Discovery

Unravelling site-specific breast cancer metastasis: a microRNA expression profiling study

(2016) Willemijne A.M.E. Schrijver et al.   Oncotarget

PREX1 integrates G protein-coupled receptor and phosphoinositide 3-kinase signaling to promote glioblastoma invasion

(2016) Alexander Gont et al.   Oncotarget

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

CTCF Binding Polarity Determines Chromatin Looping

(2015) Elzo de Wit et al.   MOLECULAR CELL

Identification of active transcriptional regulatory elements from GRO-seq data

(2015) Charles G Danko et al.   NATURE METHODS

canSAR: an updated cancer research and drug discovery knowledgebase

(2015) Joseph E. Tym et al.   NUCLEIC ACIDS RESEARCH

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

(2014) Jill M. Dowen et al.   CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

P-REX1 creates a positive feedback loop to activate growth factor receptor, PI3K/AKT and MEK/ERK signaling in breast cancer

(2014) L M Dillon et al.   ONCOGENE

Estrogen Induces Global Reorganization of Chromatin Structure in Human Breast Cancer Cells

(2014) Raphaël Mourad et al.   PLoS One

CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer

(2014) Christopher J. Kemp et al.   Cell Reports

A carrier-assisted ChIP-seq method for estrogen receptor-chromatin interactions from breast cancer core needle biopsy samples

(2013) Wilbert Zwart et al.   BMC GENOMICS

Hallmarks of Aromatase Inhibitor Drug Resistance Revealed by Epigenetic Profiling in Breast Cancer

(2013) M. P. H. M. Jansen et al.   CANCER RESEARCH

CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets

(2013) Matthias Merkenschlager et al.   CELL

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Enhancer transcripts mark active estrogen receptor binding sites

(2013) N. Hah et al.   GENOME RESEARCH

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

Uniform, optimal signal processing of mapped deep-sequencing data

(2013) Vibhor Kumar et al.   NATURE BIOTECHNOLOGY

ESR1 ligand-binding domain mutations in hormone-resistant breast cancer

(2013) Weiyi Toy et al.   NATURE GENETICS

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Characterization of Enhancer Function from Genome-Wide Analyses

(2012) Glenn A. Maston et al.   Annual Review of Genomics and Human Genetics

miR-376b controls starvation and mTOR inhibition-related autophagy by targeting ATG4C and BECN1

(2012) Gozde Korkmaz et al.   Autophagy

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

(2012) Christina Curtis et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

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

(2012) Elphège P. Nora et al.   NATURE

Robust 4C-seq data analysis to screen for regulatory DNA interactions

(2012) Harmen J G van de Werken et al.   NATURE METHODS

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

A co-ordinated interaction between CTCF and ER in breast cancer cells

(2011) Caryn S Ross-Innes et al.   BMC GENOMICS

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

(2011) Nasun Hah et al.   CELL

Long- and Short-Range Transcriptional Repressors Induce Distinct Chromatin States on Repressed Genes

(2011) Li M. Li et al.   CURRENT BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

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

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

Identification of the Rac-GEF P-Rex1 as an Essential Mediator of ErbB Signaling in Breast Cancer

(2010) Maria Soledad Sosa et al.   MOLECULAR CELL

Insulators and promoters: closer than we think

(2010) Jesse R. Raab et al.   NATURE REVIEWS GENETICS

P-Rex1 participates in Neuregulin-ErbB signal transduction and its expression correlates with patient outcome in breast cancer

(2010) J C Montero et al.   ONCOGENE

Subtyping of Breast Cancer by Immunohistochemistry to Investigate a Relationship between Subtype and Short and Long Term Survival: A Collaborative Analysis of Data for 10,159 Cases from 12 Studies

(2010) Fiona M. Blows et al.   PLOS MEDICINE

Enhancers: The abundance and function of regulatory sequences beyond promoters

(2009) Michael Bulger et al.   DEVELOPMENTAL BIOLOGY

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

(2009) Dominic Schmidt et al.   METHODS

Resistance to Antiestrogen Arzoxifene Is Mediated by Overexpression of Cyclin D1

(2009) Wilbert Zwart et al.   MOLECULAR ENDOCRINOLOGY

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

CCCTC-Binding Factor Confines the Distal Action of Estrogen Receptor

(2008) Chang S. Chan et al.   CANCER RESEARCH

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY