Targeted chromatin conformation analysis identifies novel distal neural enhancers of ZEB2 in pluripotent stem cell differentiation

MEK inhibition remodels the active chromatin landscape and induces SOX10 genomic recruitment in BRAF(V600E) mutant melanoma cells

(2019) Temesgen D. Fufa et al.   Epigenetics & Chromatin

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

(2018) Luis de la Torre-Ubieta et al.   CELL

Phenotype and genotype of 87 patients with Mowat–Wilson syndrome and recommendations for care

(2018) Ivan Ivanovski et al.   GENETICS IN MEDICINE

Enhancer hubs and loop collisions identified from single-allele topologies

(2018) Amin Allahyar et al.   NATURE GENETICS

Investigation of the spatial structure and interactions of the genome at sub-kilobase-pair resolution using T2C

(2018) Petros Kolovos et al.   Nature Protocols

Genome-wide analysis yields new loci associating with aortic valve stenosis

(2018) Anna Helgadottir et al.   Nature Communications

The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages

(2018) Charlotte L. Scott et al.   IMMUNITY

Differentiation of Mouse Enteric Nervous System Progenitor Cells Is Controlled by Endothelin 3 and Requires Regulation of Ednrb by SOX10 and ZEB2

(2017) Yuli Watanabe et al.   GASTROENTEROLOGY

Conserved non-coding elements: developmental gene regulation meets genome organization

(2017) Dimitris Polychronopoulos et al.   NUCLEIC ACIDS RESEARCH

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response

(2016) Petros Kolovos et al.   GENOME RESEARCH

Personalized genome sequencing coupled with iPSC technology identifies GTDC1 as a gene involved in neurodevelopmental disorders

(2016) Irene Aksoy et al.   HUMAN MOLECULAR GENETICS

The transcription factor Zeb2 regulates development of conventional and plasmacytoid DCs by repressing Id2

(2016) Charlotte L. Scott et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

(2016) Lilija Brant et al.   Molecular Systems Biology

Zeb2 recruits HDAC–NuRD to inhibit Notch and controls Schwann cell differentiation and remyelination

(2016) Lai Man Natalie Wu et al.   NATURE NEUROSCIENCE

Zeb2 is essential for Schwann cell differentiation, myelination and nerve repair

(2016) Susanne Quintes et al.   NATURE NEUROSCIENCE

Zeb2 Regulates Cell Fate at the Exit from Epiblast State in Mouse Embryonic Stem Cells

(2016) Agata Stryjewska et al.   STEM CELLS

Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases

(2016) Yasuhiro Murakawa et al.   TRENDS IN GENETICS

The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes

(2016) Tobias A. Knoch et al.   Epigenetics & Chromatin

Quantitative Analysis of Human Pluripotency and Neural Specification by In-Depth (Phospho)Proteomic Profiling

(2016) Ilyas Singec et al.   Stem Cell Reports

Disruption of ArhGAP15 results in hyperactive Rac1, affects the architecture and function of hippocampal inhibitory neurons and causes cognitive deficits

(2016) Valentina Zamboni et al.   Scientific Reports

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Zeb2: A multifunctional regulator of nervous system development

(2015) Shane V. Hegarty et al.   PROGRESS IN NEUROBIOLOGY

ZEB2 drives immature T-cell lymphoblastic leukaemia development via enhanced tumour-initiating potential and IL-7 receptor signalling

(2015) Steven Goossens et al.   Nature Communications

AP-1-mediated chromatin looping regulates ZEB2 transcription: new insights into TNFα-induced epithelial–mesenchymal transition in triple-negative breast cancer

(2015) Yichun Qiao et al.   Oncotarget

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

(2014) S. Anders et al.   BIOINFORMATICS

Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements

(2014) Petros Kolovos et al.   Epigenetics & Chromatin

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

The pluripotent genome in three dimensions is shaped around pluripotency factors

(2013) Elzo de Wit et al.   NATURE

Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions

(2013) Ralph Stadhouders et al.   Nature Protocols

Dlx1&2-Dependent Expression of Zfhx1b (Sip1, Zeb2) Regulates the Fate Switch between Cortical and Striatal Interneurons

(2013) Gabriel L. McKinsey et al.   NEURON

Directed Migration of Cortical Interneurons Depends on the Cell-Autonomous Action of Sip1

(2013) Veronique van den Berghe et al.   NEURON

A far-upstream (−70 kb) enhancer mediates Sox9 auto-regulation in somatic tissues during development and adult regeneration

(2013) Timothy J. Mead et al.   NUCLEIC ACIDS RESEARCH

Four Amino Acids within a Tandem QxVx Repeat in a Predicted Extended α-Helix of the Smad-Binding Domain of Sip1 Are Necessary for Binding to Activated Smad Proteins

(2013) Andrea Conidi et al.   PLoS One

A novel long-range enhancer regulates postnatal expression of Zeb2: implications for Mowat-Wilson syndrome phenotypes

(2012) M. M. El-Kasti et al.   HUMAN MOLECULAR GENETICS

Opposing Roles for Hoxa2 and Hoxb2 in Hindbrain Oligodendrocyte Patterning

(2012) A. Miguez et al.   JOURNAL OF NEUROSCIENCE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

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

(2012) Elphège P. Nora et al.   NATURE

Sensitive detection of chromatin coassociations using enhanced chromosome conformation capture on chip

(2012) Tom Sexton et al.   Nature Protocols

Dual-Mode Modulation of Smad Signaling by Smad-Interacting Protein Sip1 Is Required for Myelination in the Central Nervous System

(2012) Qinjie Weng et al.   NEURON

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

Few Smad proteins and many Smad-interacting proteins yield multiple functions and action modes in TGFβ/BMP signaling in vivo

(2011) Andrea Conidi et al.   CYTOKINE & GROWTH FACTOR REVIEWS

New insights into the mechanisms of activin action and inhibition

(2011) Kelly L. Walton et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Copy Number Variants in Candidate Genes Are Genetic Modifiers of Hirschsprung Disease

(2011) Qian Jiang et al.   PLoS One

SIP1 Mediates Cell-Fate Decisions between Neuroectoderm and Mesendoderm in Human Pluripotent Stem Cells

(2010) Zhenzhi Chng et al.   Cell Stem Cell

Genetic interaction between Sox10 and Zfhx1b during enteric nervous system development

(2010) Laure Stanchina et al.   DEVELOPMENTAL BIOLOGY

Mowat-Wilson syndrome: Facial phenotype changing with age: Study of 19 Italian patients and review of the literature

(2009) L. Garavelli et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Integrative genomic analyses of ZEB2: Transcriptional regulation of ZEB2 based on SMADs, ETS1, HIF1α, POU/OCT, and NF-κB

(2009) Katoh   INTERNATIONAL JOURNAL OF ONCOLOGY

Long-range regulation at the SOX9 locus in development and disease

(2009) C T Gordon et al.   JOURNAL OF MEDICAL GENETICS

Genomic views of distant-acting enhancers

(2009) Axel Visel et al.   NATURE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Atypical Mowat-Wilson patient confirms the importance of the novel association between ZFHX1B/SIP1 and NuRD corepressor complex

(2008) G. Verstappen et al.   HUMAN MOLECULAR GENETICS

High-resolution circular chromosome conformation capture assay

(2008) Anita Göndör et al.   Nature Protocols