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

[1]  Chris Berdik.  Bladder cancer: 4 big questions , 2017, Nature.

[2]  Erez Lieberman Aiden,et al.  Cohesin Loss Eliminates All Loop Domains , 2017, Cell.

[3]  Nuno A. Fonseca,et al.  Two independent modes of chromatin organization revealed by cohesin removal , 2017, Nature.

[4]  Manuel E. Lladser,et al.  An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq , 2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[5]  K. Brennand,et al.  Kmt1e regulates a large neuron-specific topological chromatin domain , 2017, Nature Genetics.

[6]  L. Mirny,et al.  Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization , 2017, Cell.

[7]  Anushya Muruganujan,et al.  PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements , 2016, Nucleic Acids Res..

[8]  J. Peterson,et al.  The cohesin subunit Rad21 is a negative regulator of hematopoietic self-renewal through epigenetic repression of HoxA7 and HoxA9 , 2016, Leukemia.

[9]  M. Kimmel,et al.  Chronic Infection Depletes Hematopoietic Stem Cells through Stress-Induced Terminal Differentiation. , 2016, Cell reports.

[10]  Daniel S. Day,et al.  Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control , 2016, Cell.

[11]  E. Nora,et al.  CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation. , 2016, Annual review of genomics and human genetics.

[12]  Juan M. Vaquerizas,et al.  TADtool: visual parameter identification for TAD-calling algorithms , 2016, Bioinform..

[13]  L. Mirny,et al.  Formation of Chromosomal Domains in Interphase by Loop Extrusion , 2015, bioRxiv.

[14]  Elizabeth Ing-Simmons,et al.  Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments , 2016, F1000Research.

[15]  E. Pietras,et al.  Chronic interleukin-1 drives haematopoietic stem cells towards precocious myeloid differentiation at the expense of self-renewal , 2016, Nature Cell Biology.

[16]  B. Nilsson,et al.  Genome-wide RNAi Screen Identifies Cohesin Genes as Modifiers of Renewal and Differentiation in Human HSCs. , 2016, Cell reports.

[17]  L. Mirny,et al.  The 3D Genome as Moderator of Chromosomal Communication , 2016, Cell.

[18]  G. Smyth,et al.  ROBUST HYPERPARAMETER ESTIMATION PROTECTS AGAINST HYPERVARIABLE GENES AND IMPROVES POWER TO DETECT DIFFERENTIAL EXPRESSION. , 2016, The annals of applied statistics.

[19]  Daniel S. Day,et al.  Activation of proto-oncogenes by disruption of chromosome neighborhoods , 2015, Science.

[20]  Panos M. Pardalos,et al.  A New Network Robustness Topology Measure based on Information Theory , 2014, ArXiv.

[21]  Florian Hahne,et al.  Visualizing Genomic Data Using Gviz and Bioconductor , 2016, Statistical Genomics.

[22]  A. Lun,et al.  Infrastructure for genomic interactions: Bioconductor classes for Hi-C, ChIA-PET and related experiments , 2016, F1000Research.

[23]  J. Mesirov,et al.  The Molecular Signatures Database Hallmark Gene Set Collection , 2015 .

[24]  Howard Y. Chang,et al.  Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation. , 2015, Cell stem cell.

[25]  B. Lenhard,et al.  GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data , 2015, BMC Genomics.

[26]  Pedro P. Rocha,et al.  Cohesin loss alters adult hematopoietic stem cell homeostasis, leading to myeloproliferative neoplasms , 2015, The Journal of experimental medicine.

[27]  Christopher J. Ott,et al.  Dose-dependent role of the cohesin complex in normal and malignant hematopoiesis , 2015, The Journal of experimental medicine.

[28]  J. Dekker,et al.  Structural and functional diversity of Topologically Associating Domains , 2015, FEBS letters.

[29]  M. Boyle,et al.  Cornelia de Lange syndrome , 2015, Clinical genetics.

[30]  A. Visel,et al.  Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions , 2015, Cell.

[31]  Pedro P. Rocha,et al.  CTCF establishes discrete functional chromatin domains at the Hox clusters during differentiation , 2015, Science.

[32]  Boris Lenhard,et al.  Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin , 2015 .

[33]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[34]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[35]  C. Glass,et al.  Molecular control of activation and priming in macrophages , 2015, Nature Immunology.

[36]  A. Fisher,et al.  Initiation and maintenance of pluripotency gene expression in the absence of cohesin , 2015, Genes & development.

[37]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[38]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[39]  R. Young,et al.  An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element , 2014, Science.

[40]  Jill M Dowen,et al.  Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes , 2014, Cell.

[41]  R. Levine,et al.  Genetic alterations of the cohesin complex genes in myeloid malignancies. , 2014, Blood.

[42]  A. Stewart,et al.  The Scc2/Scc4 complex acts in sister chromatid cohesion and transcriptional regulation by maintaining nucleosome-free regions , 2014, Nature Genetics.

[43]  Rona S. Gertner,et al.  Single cell RNA Seq reveals dynamic paracrine control of cellular variation , 2014, Nature.

[44]  Rory Stark,et al.  Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data , 2014, Front. Genet..

[45]  Ryan M. O’Connell,et al.  Conversion of danger signals into cytokine signals by hematopoietic stem and progenitor cells for regulation of stress-induced hematopoiesis. , 2014, Cell stem cell.

[46]  Charity W. Law,et al.  voom: precision weights unlock linear model analysis tools for RNA-seq read counts , 2014, Genome Biology.

[47]  Howard Y. Chang,et al.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.

[48]  Masao Nagasaki,et al.  Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms , 2012, Nature Genetics.

[49]  Thomas Whitington,et al.  Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites , 2013, Cell.

[50]  J. Stender,et al.  Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. , 2013, Molecular cell.

[51]  Benjamin J. Raphael,et al.  Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. , 2013, The New England journal of medicine.

[52]  S. Nutt,et al.  M-CSF instructs myeloid lineage fate in single haematopoietic stem cells , 2013, Nature.

[53]  David A. Orlando,et al.  Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes , 2013, Cell.

[54]  Bas van Steensel,et al.  Genome Architecture: Domain Organization of Interphase Chromosomes , 2013, Cell.

[55]  G. Natoli,et al.  Latent Enhancers Activated by Stimulation in Differentiated Cells , 2013, Cell.

[56]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[57]  Elzo de Wit,et al.  Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation. , 2012, Methods.

[58]  Emmanuel Barillot,et al.  HiTC - Exploration of High Throughput ’C’ experiments , 2013 .

[59]  Amos Tanay,et al.  Robust 4C-seq data analysis to screen for regulatory DNA interactions , 2012, Nature Methods.

[60]  Nir Friedman,et al.  A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. , 2012, Molecular cell.

[61]  D. Black,et al.  Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions , 2012, Cell.

[62]  G. Natoli,et al.  Requirement for the histone deacetylase Hdac3 for the inflammatory gene expression program in macrophages , 2012, Proceedings of the National Academy of Sciences.

[63]  Michael D. Wilson,et al.  Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules , 2012, Genome research.

[64]  Benjamin E. Gross,et al.  The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. , 2012, Cancer discovery.

[65]  Davis J. McCarthy,et al.  Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation , 2012, Nucleic acids research.

[66]  Nida Noor,et al.  Cornelia de Lange syndrome. , 2012, Journal of the College of Physicians and Surgeons--Pakistan : JCPSP.

[67]  D. Schatz,et al.  A role for cohesin in T cell receptor rearrangement and thymocyte differentiation , 2011, Nature.

[68]  Christophe Benoist,et al.  Transcriptomes of the B and T Lineages Compared by Multiplatform Microarray Profiling , 2011, The Journal of Immunology.

[69]  K. Nasmyth,et al.  Rec8-containing cohesin maintains bivalents without turnover during the growing phase of mouse oocytes. , 2010, Genes & development.

[70]  David A. Orlando,et al.  Mediator and Cohesin Connect Gene Expression and Chromatin Architecture , 2010, Nature.

[71]  Nathan C Boles,et al.  Quiescent hematopoietic stem cells are activated by IFNγ in response to chronic infection , 2010, Nature.

[72]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[73]  V. Guacci,et al.  Systematic Reduction of Cohesin Differentially Affects Chromosome Segregation, Condensation, and DNA Repair , 2010, Current Biology.

[74]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[75]  M. Robinson,et al.  A scaling normalization method for differential expression analysis of RNA-seq data , 2010, Genome Biology.

[76]  Matthew D. Young,et al.  Gene ontology analysis for RNA-seq: accounting for selection bias , 2010, Genome Biology.

[77]  Kim Nasmyth,et al.  Cohesin: its roles and mechanisms. , 2009, Annual review of genetics.

[78]  Zachary D. Smith,et al.  Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses , 2009 .

[79]  Andreas Trumpp,et al.  IFNα activates dormant haematopoietic stem cells in vivo , 2009, Nature.

[80]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[81]  A. Zlotnik,et al.  The chemokine and chemokine receptor superfamilies and their molecular evolution , 2006, Genome Biology.

[82]  Anne E Carpenter,et al.  CellProfiler: image analysis software for identifying and quantifying cell phenotypes , 2006, Genome Biology.

[83]  S. Akira,et al.  Toll-like receptors on hematopoietic progenitor cells stimulate innate immune system replenishment. , 2006, Immunity.

[84]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[85]  Rudolf Jaenisch,et al.  Rapid generation of inducible mouse mutants. , 2003, Nucleic acids research.

[86]  R. Shiekhattar,et al.  A chromatin remodelling complex that loads cohesin onto human chromosomes , 2002, Nature.

[87]  I. Dybedal,et al.  Tumor necrosis factor (TNF)-mediated activation of the p55 TNF receptor negatively regulates maintenance of cycling reconstituting human hematopoietic stem cells. , 2001, Blood.

[88]  A. Fisher,et al.  Targeting of Ikaros to pericentromeric heterochromatin by direct DNA binding. , 2000, Genes & development.

[89]  R. Zinkernagel,et al.  Aplastic Anemia Rescued by Exhaustion of Cytokine-secreting CD8+ T Cells in Persistent Infection with Lymphocytic Choriomeningitis Virus , 1998, The Journal of experimental medicine.

[90]  H. Gralnick,et al.  Proposals for the Classification of the Acute Leukaemias French‐American‐British (FAB) Co‐operative Group , 1976, British journal of haematology.