SNAIL1-mediated downregulation of FOXA proteins facilitates the inactivation of transcriptional enhancer elements at key epithelial genes in colorectal cancer cells

Enhancer decommissioning by Snail1-induced competitive displacement of TCF7L2 and down-regulation of transcriptional activators results in EPHB2 silencing

(2016) Oskar Schnappauf et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Cell fate control by pioneer transcription factors

(2016) Makiko Iwafuchi-Doi et al.   DEVELOPMENT

Dissection of transcriptional andcis‐regulatory control of differentiation in human pancreatic cancer

(2016) Giuseppe R Diaferia et al.   EMBO JOURNAL

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

FOXA1 defines cancer cell specificity

(2016) G. Zhang et al.   Science Advances

Enhancer cooperativity as a novel mechanism underlying the transcriptional regulation of E-cadherin during mesenchymal to epithelial transition

(2015) Hani Alotaibi et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

FOXA2 attenuates the epithelial to mesenchymal transition by regulating the transcription of E-cadherin and ZEB2 in human breast cancer

(2015) Zhen Zhang et al.   CANCER LETTERS

Architectural and Functional Commonalities between Enhancers and Promoters

(2015) Tae-Kyung Kim et al.   CELL

A self-enforcing CD44s/ZEB1 feedback loop maintains EMT and stemness properties in cancer cells

(2015) Bogdan-Tiberius Preca et al.   INTERNATIONAL JOURNAL OF CANCER

Epithelial-to-mesenchymal transition is dispensable for metastasis but induces chemoresistance in pancreatic cancer

(2015) Xiaofeng Zheng et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Epithelial-to-mesenchymal transition is not required for lung metastasis but contributes to chemoresistance

(2015) Kari R. Fischer et al.   NATURE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Loss of CDX2 expression is associated with poor prognosis in colorectal cancer patients

(2015) Jeong Mo Bae   WORLD JOURNAL OF GASTROENTEROLOGY

Distinct Processes and Transcriptional Targets Underlie CDX2 Requirements in Intestinal Stem Cells and Differentiated Villus Cells

(2015) Adrianna K. San Roman et al.   Stem Cell Reports

Cross-regulation between FOXA1 and ErbB2 Signaling in Estrogen Receptor-Negative Breast Cancer

(2015) Ali Naderi et al.   NEOPLASIA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

B-Raf Inhibitors Induce Epithelial Differentiation in BRAF-Mutant Colorectal Cancer Cells

(2014) R. Herr et al.   CANCER RESEARCH

FOXA2 suppresses the metastasis of hepatocellular carcinoma partially through matrix metalloproteinase-9 inhibition

(2014) Jian Wang et al.   CARCINOGENESIS

Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer

(2014) Phillippa C. Taberlay et al.   GENOME RESEARCH

SNAIL1 combines competitive displacement of ASCL2 and epigenetic mechanisms to rapidly silence the EPHB3 tumor suppressor in colorectal cancer

(2014) Kerstin Rönsch et al.   Molecular Oncology

ATM-mediated stabilization of ZEB1 promotes DNA damage response and radioresistance through CHK1

(2014) Peijing Zhang et al.   NATURE CELL BIOLOGY

Molecular mechanisms of epithelial–mesenchymal transition

(2014) Samy Lamouille et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Silencing of the EPHB3 tumor-suppressor gene in human colorectal cancer through decommissioning of a transcriptional enhancer

(2014) Sabine Jägle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer

(2013) Haiyun Wang et al.   BMC GENOMICS

EMT is the dominant program in human colon cancer

(2013) Andre Loboda et al.   BMC Medical Genomics

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Foxa1 and Foxa2 Are Essential for Sexual Dimorphism in Liver Cancer

(2012) Zhaoyu Li et al.   CELL

E-cadherin is required for intestinal morphogenesis in the mouse

(2012) Benjamin J. Bondow et al.   DEVELOPMENTAL BIOLOGY

The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent ‘+4’ cell markers

(2012) Javier Muñoz et al.   EMBO JOURNAL

Cadherin-11, a Marker of the Mesenchymal Phenotype, Regulates Glioblastoma Cell Migration and Survival In Vivo

(2012) H. Kaur et al.   MOLECULAR CANCER RESEARCH

A Novel Network Integrating a miRNA-203/SNAI1 Feedback Loop which Regulates Epithelial to Mesenchymal Transition

(2012) Michèle Moes et al.   PLoS One

Epigenomic Enhancer Profiling Defines a Signature of Colon Cancer

(2012) B. Akhtar-Zaidi et al.   SCIENCE

FoxA1 is a Key Mediator of Hormonal Response in Breast and Prostate Cancer

(2012) Jessica L. L. Robinson et al.   Frontiers in Endocrinology

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

The Intestinal Stem Cell Signature Identifies Colorectal Cancer Stem Cells and Predicts Disease Relapse

(2011) Anna Merlos-Suárez et al.   Cell Stem Cell

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

A p53/miRNA-34 axis regulates Snail1-dependent cancer cell epithelial–mesenchymal transition

(2011) Nam Hee Kim et al.   JOURNAL OF CELL BIOLOGY

Critical and Reciprocal Regulation of KLF4 and SLUG in Transforming Growth Factor  -Initiated Prostate Cancer Epithelial-Mesenchymal Transition

(2011) Y.-N. Liu et al.   MOLECULAR AND CELLULAR BIOLOGY

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development

(2011) Jason A. Watts et al.   PLoS Genetics

Loss of FOXA1/2 Is Essential for the Epithelial-to-Mesenchymal Transition in Pancreatic Cancer

(2010) Y. Song et al.   CANCER RESEARCH

FOXA2 functions as a suppressor of tumor metastasis by inhibition of epithelial-to-mesenchymal transition in human lung cancers

(2010) Yunneng Tang et al.   CELL RESEARCH

Alternative splicing of Tcf7l2 transcripts generates protein variants with differential promoter-binding and transcriptional activation properties at Wnt/β-catenin targets

(2010) Andreas Weise et al.   NUCLEIC ACIDS RESEARCH

A Key Role for E-cadherin in Intestinal Homeostasis and Paneth Cell Maturation

(2010) Marlon R. Schneider et al.   PLoS One

Core epithelial-to-mesenchymal transition interactome gene-expression signature is associated with claudin-low and metaplastic breast cancer subtypes

(2010) J. H. Taube et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

GAGE: generally applicable gene set enrichment for pathway analysis

(2009) Weijun Luo et al.   BMC BIOINFORMATICS

The biological role and regulation of versican levels in cancer

(2009) Carmela Ricciardelli et al.   CANCER AND METASTASIS REVIEWS

Over-expression of EphB3 enhances cell–cell contacts and suppresses tumor growth in HT-29 human colon cancer cells

(2009) Sou-Tyau Chiu et al.   CARCINOGENESIS

Relationship of CDX2 Loss with Molecular Features and Prognosis in Colorectal Cancer

(2009) Y. Baba et al.   CLINICAL CANCER RESEARCH

Establishment of Intestinal Identity and Epithelial-Mesenchymal Signaling by Cdx2

(2009) Nan Gao et al.   DEVELOPMENTAL CELL

Foxa1 and Foxa2 Control the Differentiation of Goblet and Enteroendocrine L- and D-Cells in Mice

(2009) Diana Z. Ye et al.   GASTROENTEROLOGY

The basics of epithelial-mesenchymal transition

(2009) Raghu Kalluri et al.   JOURNAL OF CLINICAL INVESTIGATION

Jagged1 is the pathological link between Wnt and Notch pathways in colorectal cancer

(2009) V. Rodilla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Double-Negative Feedback Loop between ZEB1-SIP1 and the microRNA-200 Family Regulates Epithelial-Mesenchymal Transition

(2008) C. P. Bracken et al.   CANCER RESEARCH

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

(2008) Mathieu Lupien et al.   CELL

A reciprocal repression between ZEB1 and members of the miR-200 family promotes EMT and invasion in cancer cells

(2008) Ulrike Burk et al.   EMBO REPORTS

Genome-Wide Pattern of TCF7L2/TCF4 Chromatin Occupancy in Colorectal Cancer Cells

(2008) P. Hatzis et al.   MOLECULAR AND CELLULAR BIOLOGY

Identification of DNA regions and a set of transcriptional regulatory factors involved in transcriptional regulation of several human liver-enriched transcription factor genes

(2008) Hisashi Miura et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY