Transcription factor-mediated intestinal metaplasia and the role of a shadow enhancer

Human gastrointestinal epithelia of the esophagus, stomach, and duodenum resolved at single-cell resolution

(2021) Georg A. Busslinger et al.   Cell Reports

Hybrid Stomach-Intestinal Chromatin States Underlie Human Barrett’s Metaplasia

(2021) Harshabad Singh et al.   GASTROENTEROLOGY

Molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition

(2021) Karol Nowicki-Osuch et al.   SCIENCE

Molecular characterization of Barrett’s esophagus at single-cell resolution

(2021) Georg A. Busslinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HDAC6/HNF4α loop mediated by miR-1 promotes bile acids-induced gastric intestinal metaplasia

(2020) Na Wang et al.   Gastric Cancer

Boundary sequences flanking the mouse tyrosinase locus ensure faithful pattern of gene expression

(2020) Davide Seruggia et al.   Scientific Reports

Identification of a primitive intestinal transcription factor network shared between esophageal adenocarcinoma and its precancerous precursor state

(2019) Connor Rogerson et al.   GENOME RESEARCH

A reinforcing HNF4–SMAD4 feed-forward module stabilizes enterocyte identity

(2019) Lei Chen et al.   NATURE GENETICS

Rational targeting of a NuRD subcomplex guided by comprehensive in situ mutagenesis

(2019) Falak Sher et al.   NATURE GENETICS

Genomic and Epigenomic Profiling of High-Risk Intestinal Metaplasia Reveals Molecular Determinants of Progression to Gastric Cancer

(2018) Kie Kyon Huang et al.   CANCER CELL

Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch

(2018) Nan Liu et al.   CELL

Enhancer, transcriptional, and cell fate plasticity precedes intestinal determination during endoderm development

(2018) Kushal K. Banerjee et al.   GENES & DEVELOPMENT

Single cell RNA-seq reveals profound transcriptional similarity between Barrett’s oesophagus and oesophageal submucosal glands

(2018) Richard Peter Owen et al.   Nature Communications

Transcription factor-dependent ‘anti-repressive’ mammalian enhancers exclude H3K27me3 from extended genomic domains

(2017) Madhurima Saxena et al.   GENES & DEVELOPMENT

Integrated genomic characterization of oesophageal carcinoma

(2017)   NATURE

Transitional basal cells at the squamous–columnar junction generate Barrett’s oesophagus

(2017) Ming Jiang et al.   NATURE

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

(2017) M Ryan Corces et al.   NATURE METHODS

Complementary information derived from CRISPR Cas9 mediated gene deletion and suppression

(2017) Joseph Rosenbluh et al.   Nature Communications

Bivariate Genomic Footprinting Detects Changes in Transcription Factor Activity

(2017) Songjoon Baek et al.   Cell Reports

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks

(2016) Enrico Cannavò et al.   CURRENT BIOLOGY

Cell fate control by pioneer transcription factors

(2016) Makiko Iwafuchi-Doi et al.   DEVELOPMENT

Models of human core transcriptional regulatory circuitries

(2016) Violaine Saint-André et al.   GENOME RESEARCH

Active medulloblastoma enhancers reveal subgroup-specific cellular origins

(2016) Charles Y. Lin et al.   NATURE

A Modular Assembly Platform for Rapid Generation of DNA Constructs

(2016) Elliot H. Akama-Garren et al.   Scientific Reports

Sox2 Suppresses Gastric Tumorigenesis in Mice

(2016) Abby Sarkar et al.   Cell Reports

Cdx and T Brachyury Co-activate Growth Signaling in the Embryonic Axial Progenitor Niche

(2016) Shilu Amin et al.   Cell Reports

CDX-2 Expression in Primary Lung Adenocarcinoma

(2016) Morgan L. Cowan et al.   APPLIED IMMUNOHISTOCHEMISTRY & MOLECULAR MORPHOLOGY

Paired exome analysis of Barrett's esophagus and adenocarcinoma

(2015) Matthew D Stachler et al.   NATURE GENETICS

Functional validation of mouse tyrosinase non-coding regulatory DNA elements by CRISPR–Cas9-mediated mutagenesis

(2015) Davide Seruggia et al.   NUCLEIC ACIDS RESEARCH

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

The stem cell organisation, and the proliferative and gene expression profile of Barrett's epithelium, replicates pyloric-type gastric glands

(2014) Danielle L Lavery et al.   GUT

Transcription Factors GATA4 and HNF4A Control Distinct Aspects of Intestinal Homeostasis in Conjunction with Transcription Factor CDX2

(2014) Adrianna K. San Roman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Transformation of intestinal stem cells into gastric stem cells on loss of transcription factor Cdx2

(2014) Salvatore Simmini et al.   Nature Communications

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

(2014) Shaun Mahony et al.   PLoS Computational Biology

Transcriptional Regulation and Its Misregulation in Disease

(2013) Tong Ihn Lee et al.   CELL

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

Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals

(2013) Esteban O Mazzoni et al.   NATURE NEUROSCIENCE

In vitro expansion and genetic modification of gastrointestinal stem cells in spheroid culture

(2013) Hiroyuki Miyoshi et al.   Nature Protocols

The Role of CDX2 in Intestinal Metaplasia Evaluated Using Immunohistochemistry

(2012) Byoung Hwan Lee et al.   Gut and Liver

Intestinal Master Transcription Factor CDX2 Controls Chromatin Access for Partner Transcription Factor Binding

(2012) M. P. Verzi et al.   MOLECULAR AND CELLULAR BIOLOGY

Regulation of the tumor suppressor homeogene Cdx2 by HNF4α in intestinal cancer

(2012) T Saandi et al.   ONCOGENE

Evidence for a functional role of epigenetically regulated midcluster HOXB genes in the development of Barrett esophagus

(2012) M. di Pietro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SOX2 redirects the developmental fate of the intestinal epithelium toward a premature gastric phenotype

(2012) Lalini Raghoebir et al.   Journal of Molecular Cell Biology

Sox2+ Adult Stem and Progenitor Cells Are Important for Tissue Regeneration and Survival of Mice

(2011) Katrin Arnold et al.   Cell Stem Cell

GATA Factors Regulate Proliferation, Differentiation, and Gene Expression in Small Intestine of Mature Mice

(2011) Eva Beuling et al.   GASTROENTEROLOGY

Ectopic Cdx2 Expression in Murine Esophagus Models an Intermediate Stage in the Emergence of Barrett's Esophagus

(2011) Jianping Kong et al.   PLoS One

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

Pathology of Gastric Intestinal Metaplasia: Clinical Implications

(2010) Pelayo Correa et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Lgr5+ve Stem Cells Drive Self-Renewal in the Stomach and Build Long-Lived Gastric Units In Vitro

(2010) Nick Barker et al.   Cell Stem Cell

Differentiation-Specific Histone Modifications Reveal Dynamic Chromatin Interactions and Partners for the Intestinal Transcription Factor CDX2

(2010) Michael P. Verzi et al.   DEVELOPMENTAL CELL

Cdx2 regulates endo-lysosomal function and epithelial cell polarity

(2010) N. Gao et al.   GENES & DEVELOPMENT

CDX2 autoregulation in human intestinal metaplasia of the stomach: impact on the stability of the phenotype

(2010) R. Barros et al.   GUT

Establishment of Intestinal Identity and Epithelial-Mesenchymal Signaling by Cdx2

(2009) Nan Gao et al.   DEVELOPMENTAL CELL

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Cdx2initiates histodifferentiation of the midgut endoderm

(2008) Emma J. Stringer et al.   FEBS LETTERS

Multiple Regulatory Regions Control the Complex Expression Pattern of the Mouse Cdx2 Homeobox Gene

(2008) Fairouz Benahmed et al.   GASTROENTEROLOGY

Cdx1 and c-Myc Foster the Initiation of Transdifferentiation of the Normal Esophageal Squamous Epithelium toward Barrett's Esophagus

(2008) Douglas B. Stairs et al.   PLoS One