Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation

Bladder Cancer: 4 Big questions

(2017) Chris Berdik   NATURE

The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain

(2017) Yan Jiang et al.   NATURE GENETICS

Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression

(2016) Belinda Phipson et al.   Annals of Applied Statistics

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

(2016) Matthias Merkenschlager et al.   Annual Review of Genomics and Human Genetics

TADtool: visual parameter identification for TAD-calling algorithms

(2016) Kai Kruse et al.   BIOINFORMATICS

Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control

(2016) Denes Hnisz et al.   CELL

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

The cohesin subunit Rad21 is a negative regulator of hematopoietic self-renewal through epigenetic repression of Hoxa7 and Hoxa9

(2016) J B Fisher et al.   LEUKEMIA

Chronic interleukin-1 exposure drives haematopoietic stem cells towards precocious myeloid differentiation at the expense of self-renewal

(2016) Eric M. Pietras et al.   NATURE CELL BIOLOGY

Molecular control of activation and priming in macrophages

(2016) Christopher K Glass et al.   NATURE IMMUNOLOGY

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

(2016) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Information theory perspective on network robustness

(2016) Tiago A. Schieber et al.   PHYSICS LETTERS A

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Genome-wide RNAi Screen Identifies Cohesin Genes as Modifiers of Renewal and Differentiation in Human HSCs

(2016) Roman Galeev et al.   Cell Reports

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Chronic Infection Depletes Hematopoietic Stem Cells through Stress-Induced Terminal Differentiation

(2016) Katie A. Matatall et al.   Cell Reports

GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data

(2015) Nathan Harmston et al.   BMC GENOMICS

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

(2015) Darío G. Lupiáñez et al.   CELL

Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation

(2015) Claire Mazumdar et al.   Cell Stem Cell

Structural and functional diversity of Topologically Associating Domains

(2015) Job Dekker et al.   FEBS LETTERS

Initiation and maintenance of pluripotency gene expression in the absence of cohesin

(2015) Thais Lavagnolli et al.   GENES & DEVELOPMENT

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin

(2015) Elizabeth Ing-Simmons et al.   GENOME RESEARCH

Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis

(2015) Aaron D. Viny et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Cohesin loss alters adult hematopoietic stem cell homeostasis, leading to myeloproliferative neoplasms

(2015) Jasper Mullenders et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

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

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

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

(2014) S. Anders et al.   BIOINFORMATICS

Genetic alterations of the cohesin complex genes in myeloid malignancies

(2014) S. Thota et al.   BLOOD

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

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

(2014) Jill M. Dowen et al.   CELL

Conversion of Danger Signals into Cytokine Signals by Hematopoietic Stem and Progenitor Cells for Regulation of Stress-Induced Hematopoiesis

(2014) Jimmy L. Zhao et al.   Cell Stem Cell

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

(2014) Alex K. Shalek et al.   NATURE

The Scc2–Scc4 complex acts in sister chromatid cohesion and transcriptional regulation by maintaining nucleosome-free regions

(2014) Lidia Lopez-Serra et al.   NATURE GENETICS

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

(2014) Thomas S. Carroll et al.   Frontiers in Genetics

Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites

(2013) Jian Yan et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Latent Enhancers Activated by Stimulation in Differentiated Cells

(2013) Renato Ostuni et al.   CELL

Genome Architecture: Domain Organization of Interphase Chromosomes

(2013) Wendy A. Bickmore et al.   CELL

Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

(2013) Minna U. Kaikkonen et al.   MOLECULAR CELL

M-CSF instructs myeloid lineage fate in single haematopoietic stem cells

(2013) Noushine Mossadegh-Keller et al.   NATURE

Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms

(2013) Ayana Kon et al.   NATURE GENETICS

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

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

HiTC: exploration of high-throughput ‘C’ experiments

(2012) Nicolas Servant et al.   BIOINFORMATICS

Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions

(2012) Dev M. Bhatt et al.   CELL

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

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

Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation

(2012) Erik Splinter et al.   METHODS

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

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

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

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Requirement for the histone deacetylase Hdac3 for the inflammatory gene expression program in macrophages

(2012) X. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Transcriptomes of the B and T Lineages Compared by Multiplatform Microarray Profiling

(2011) M. W. Painter et al.   JOURNAL OF IMMUNOLOGY

A role for cohesin in T-cell-receptor rearrangement and thymocyte differentiation

(2011) Vlad C. Seitan et al.   NATURE

Whole-exome sequencing for finding de novo mutations in sporadic mental retardation

(2011) Peter N Robinson   GENOME BIOLOGY

Systematic Reduction of Cohesin Differentially Affects Chromosome Segregation, Condensation, and DNA Repair

(2010) Jill M. Heidinger-Pauli et al.   CURRENT BIOLOGY

Rec8-containing cohesin maintains bivalents without turnover during the growing phase of mouse oocytes

(2010) K. Tachibana-Konwalski et al.   GENES & DEVELOPMENT

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Quiescent haematopoietic stem cells are activated by IFN-γ in response to chronic infection

(2010) Megan T. Baldridge et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Cohesin: Its Roles and Mechanisms

(2009) Kim Nasmyth et al.   Annual Review of Genetics

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

IFNα activates dormant haematopoietic stem cells in vivo

(2009) Marieke A. G. Essers et al.   NATURE

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

(2009) I. Amit et al.   SCIENCE