Functional genomics uncovers the transcription factor BNC2 as required for myofibroblastic activation in fibrosis

[1]  Y. Saeys,et al.  Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches , 2021, bioRxiv.

[2]  Judith B. Zaugg,et al.  Transcription factors: Bridge between cell signaling and gene regulation , 2021, Proteomics.

[3]  X. Trepat,et al.  Extracellular Matrix Remodeling in Chronic Liver Disease , 2021, Current Tissue Microenvironment Reports.

[4]  J. Davie,et al.  The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes , 2021, Clinical epigenetics.

[5]  N. Rosenthal,et al.  Fibroblasts: Origins, definitions, and functions in health and disease , 2021, Cell.

[6]  H. Stunnenberg,et al.  Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes , 2021, Genome research.

[7]  J. Eeckhoute,et al.  Loss of hepatocyte identity following aberrant YAP activation: a key mechanism in alcoholic hepatitis. , 2021, Journal of hepatology.

[8]  A. Koehler,et al.  Advances in targeting ‘undruggable’ transcription factors with small molecules , 2021, Nature Reviews Drug Discovery.

[9]  S. Fleury,et al.  Deletion of the nuclear receptor RORα in macrophages does not modify the development of obesity, insulin resistance and NASH , 2020, Scientific Reports.

[10]  Jérôme Eeckhoute,et al.  GIANT: galaxy-based tool for interactive analysis of transcriptomic data , 2020, Scientific Reports.

[11]  Victor G. Puelles,et al.  Decoding myofibroblast origins in human kidney fibrosis , 2020, Nature.

[12]  T. Wynn,et al.  Fibrosis: from mechanisms to medicines , 2020, Nature.

[13]  D. Brenner,et al.  Molecular and cellular mechanisms of liver fibrosis and its regression , 2020, Nature Reviews Gastroenterology & Hepatology.

[14]  Raphael Gottardo,et al.  Integrated analysis of multimodal single-cell data , 2020, Cell.

[15]  David Gomez-Cabrero,et al.  GeneSetCluster: a tool for summarizing and integrating gene-set analysis results , 2020, BMC Bioinformatics.

[16]  B. Hinz,et al.  The myofibroblast at a glance , 2020, Journal of Cell Science.

[17]  T. Shaw,et al.  Dissecting Fibroblast Heterogeneity in Health and Fibrotic Disease , 2020, Current Rheumatology Reports.

[18]  F. Pattou,et al.  Bariatric Surgery Provides Long-term Resolution of Nonalcoholic Steatohepatitis and Regression of Fibrosis. , 2020, Gastroenterology.

[19]  J. Cooke,et al.  Machine learning uncovers cell identity regulator by histone code , 2020, Nature Communications.

[20]  J. Eeckhoute,et al.  Perspectives on the use of super-enhancers as a defining feature of cell/tissue-identity genes. , 2020, Epigenomics.

[21]  J. Eeckhoute,et al.  Hepatic Molecular Signatures Highlight the Sexual Dimorphism of Nonalcoholic Steatohepatitis (NASH) , 2020, Hepatology.

[22]  G. Van den Berghe,et al.  Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver , 2020, Molecular systems biology.

[23]  N. Kaminski,et al.  Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis , 2020, Nature Communications.

[24]  K. Natarajan,et al.  Transcriptional Dynamics of Hepatic Sinusoid‐Associated Cells After Liver Injury , 2020, Hepatology.

[25]  Shasha Bian,et al.  HiCoP, a simple and robust method for detecting interactions of regulatory regions , 2020, Epigenetics & Chromatin.

[26]  V. Fellman,et al.  A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase , 2019, bioRxiv.

[27]  Phillip A. Richmond,et al.  JASPAR 2020: update of the open-access database of transcription factor binding profiles , 2019, Nucleic Acids Res..

[28]  K. Clauser,et al.  MatrisomeDB: the ECM-protein knowledge database , 2019, Nucleic Acids Res..

[29]  M. Whitfield,et al.  Shared and distinct mechanisms of fibrosis , 2019, Nature Reviews Rheumatology.

[30]  Matthew C. Hill,et al.  Hippo pathway deletion in adult resting cardiac fibroblasts initiates a cell state transition with spontaneous and self-sustaining fibrosis , 2019, Genes & development.

[31]  Anshul Kundaje,et al.  The ENCODE Blacklist: Identification of Problematic Regions of the Genome , 2019, Scientific Reports.

[32]  A. Shilatifard,et al.  Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis , 2019, American journal of respiratory and critical care medicine.

[33]  F. Pattou,et al.  Hepatic transcriptomic signatures of statin treatment are associated with impaired glucose homeostasis in severely obese patients , 2019, BMC Medical Genomics.

[34]  S. Fleury,et al.  Transcriptional network analysis implicates altered hepatic immune function in NASH development and resolution , 2019, Nature Metabolism.

[35]  Daniela Pankova,et al.  RASSF1A controls tissue stiffness and cancer stem‐like cells in lung adenocarcinoma , 2019, The EMBO journal.

[36]  Arwen W. Gao,et al.  Identifying gene function and module connections by the integration of multispecies expression compendia , 2019, bioRxiv.

[37]  I. V. van Rooij,et al.  Rare Variants in BNC2 Are Implicated in Autosomal-Dominant Congenital Lower Urinary-Tract Obstruction , 2019, American journal of human genetics.

[38]  W. Lu,et al.  Epithelial-Mesenchymal Plasticity in Cancer Progression and Metastasis. , 2019, Developmental cell.

[39]  Olga Tanaseichuk,et al.  Metascape provides a biologist-oriented resource for the analysis of systems-level datasets , 2019, Nature Communications.

[40]  S. Mandrup,et al.  Transcriptional regulation of Hepatic Stellate Cell activation in NASH , 2019, Scientific Reports.

[41]  Simon G. Coetzee,et al.  Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus. , 2018, Cancer research.

[42]  Damian Szklarczyk,et al.  STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets , 2018, Nucleic Acids Res..

[43]  Xiaoyan Zhang,et al.  Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis , 2018, Nucleic Acids Res..

[44]  Akira Hasegawa,et al.  Update of the FANTOM web resource: expansion to provide additional transcriptome atlases , 2018, Nucleic Acids Res..

[45]  Benjamin L Ebert,et al.  Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN , 2018, Science.

[46]  J. Eeckhoute,et al.  The nuclear bile acid receptor FXR is a PKA- and FOXA2-sensitive activator of fasting hepatic gluconeogenesis. , 2018, Journal of hepatology.

[47]  Mark Gerstein,et al.  GENCODE reference annotation for the human and mouse genomes , 2018, Nucleic Acids Res..

[48]  Hui Hu,et al.  AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors , 2018, Nucleic Acids Res..

[49]  R. Shamir,et al.  FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map , 2018, Genome Biology.

[50]  J. Molkentin,et al.  Specialized fibroblast differentiated states underlie scar formation in the infarcted mouse heart , 2018, The Journal of clinical investigation.

[51]  Alba Santos,et al.  Matrix Stiffness: the Conductor of Organ Fibrosis , 2018, Current Rheumatology Reports.

[52]  C. Henke,et al.  Extracellular matrix as a driver of progressive fibrosis. , 2018, The Journal of clinical investigation.

[53]  K. Ozato,et al.  Brd4 binds to active enhancers to control cell identity gene induction in adipogenesis and myogenesis , 2017, Nature Communications.

[54]  F. A. Kolpakov,et al.  HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis , 2017, Nucleic Acids Res..

[55]  J. Michael Cherry,et al.  The Encyclopedia of DNA elements (ENCODE): data portal update , 2017, Nucleic Acids Res..

[56]  A. Duhamel,et al.  Main drivers of outcome differ between short term and long term in severe alcoholic hepatitis: A prospective study , 2017, Hepatology.

[57]  J. Eeckhoute,et al.  Interspecies NASH disease activity whole-genome profiling identifies a fibrogenic role of PPARα-regulated dermatopontin. , 2017, JCI insight.

[58]  C. Theillet,et al.  Transcription Factor Networks derived from Breast Cancer Stem Cells control the immune response in the Basal subtype , 2017, Scientific Reports.

[59]  J. Eeckhoute,et al.  The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions. , 2017, Genome research.

[60]  G. Wagner,et al.  The origin and evolution of cell types , 2016, Nature Reviews Genetics.

[61]  Peiman Hematti,et al.  Fibroblasts and Mesenchymal Stromal/Stem Cells Are Phenotypically Indistinguishable , 2016, Acta Haematologica.

[62]  John Chilton,et al.  The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update , 2016, Nucleic Acids Res..

[63]  Fidel Ramírez,et al.  deepTools2: a next generation web server for deep-sequencing data analysis , 2016, Nucleic Acids Res..

[64]  R. Chung,et al.  Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins , 2016, Genome Medicine.

[65]  B. Staels,et al.  Pathophysiology and Mechanisms of Nonalcoholic Fatty Liver Disease. , 2016, Annual review of physiology.

[66]  J. Carroll,et al.  Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes , 2016, Nature Protocols.

[67]  R. Evans,et al.  BRD4 is a novel therapeutic target for liver fibrosis , 2015, Proceedings of the National Academy of Sciences.

[68]  R. Bank,et al.  Signaling in Fibrosis: TGF-β, WNT, and YAP/TAZ Converge , 2015, Front. Med..

[69]  G. Halder,et al.  The Hippo pathway effector YAP controls mouse hepatic stellate cell activation. , 2015, Journal of hepatology.

[70]  Xi Chen,et al.  Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes , 2015, Nature Genetics.

[71]  Y. Kamatani,et al.  A Functional SNP in BNC2 Is Associated with Adolescent Idiopathic Scoliosis. , 2015, American journal of human genetics.

[72]  D. J. Kim,et al.  Combining Data From Liver Disease Scoring Systems Better Predicts Outcomes of Patients With Alcoholic Hepatitis. , 2015, Gastroenterology.

[73]  I. Clay,et al.  YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers , 2015, PLoS genetics.

[74]  M. Leslie.  The liver's weighty problem. , 2015, Science.

[75]  S. Carr,et al.  Lenalidomide induces ubiquitination and degradation of CK1α in del(5q) MDS , 2015, Nature.

[76]  M. Kojima,et al.  Gastrointestinal Fibroblasts Have Specialized, Diverse Transcriptional Phenotypes: A Comprehensive Gene Expression Analysis of Human Fibroblasts , 2015, PloS one.

[77]  Don C Rockey,et al.  Fibrosis--a common pathway to organ injury and failure. , 2015, The New England journal of medicine.

[78]  Michael Q. Zhang,et al.  Integrative analysis of 111 reference human epigenomes , 2015, Nature.

[79]  R. Schwabe,et al.  High-yield and high-purity isolation of hepatic stellate cells from normal and fibrotic mouse livers , 2015, Nature Protocols.

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

[81]  F. Pattou,et al.  Roux-en-Y Gastric Bypass Versus Adjustable Gastric Banding to Reduce Nonalcoholic Fatty Liver Disease: A 5-Year Controlled Longitudinal Study , 2014, Annals of surgery.

[82]  Yu Xue,et al.  AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors , 2014, Nucleic Acids Res..

[83]  J. Eeckhoute,et al.  A dynamic CTCF chromatin binding landscape promotes DNA hydroxymethylation and transcriptional induction of adipocyte differentiation , 2014, Nucleic acids research.

[84]  Paul Theodor Pyl,et al.  HTSeq – A Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[85]  K. Iwaisako,et al.  Origin of myofibroblasts in the fibrotic liver in mice , 2014, Proceedings of the National Academy of Sciences.

[86]  R. Schwabe,et al.  Fate-tracing reveals hepatic stellate cells as dominant contributors to liver fibrosis independent of its etiology , 2013, Nature Communications.

[87]  R. Young,et al.  Super-Enhancers in the Control of Cell Identity and Disease , 2013, Cell.

[88]  Soumitra S Ghosh,et al.  Diet-induced mouse model of fatty liver disease and nonalcoholic steatohepatitis reflecting clinical disease progression and methods of assessment. , 2013, American journal of physiology. Gastrointestinal and liver physiology.

[89]  Amber L. Couzens,et al.  The CRAPome: a Contaminant Repository for Affinity Purification Mass Spectrometry Data , 2013, Nature Methods.

[90]  R. Evans,et al.  A Vitamin D Receptor/SMAD Genomic Circuit Gates Hepatic Fibrotic Response , 2013, Cell.

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

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

[93]  Brian T. Lee,et al.  The UCSC Genome Browser database: extensions and updates 2013. , 2012, Nucleic acids research.

[94]  Shane J. Neph,et al.  Circuitry and Dynamics of Human Transcription Factor Regulatory Networks , 2012, Cell.

[95]  J. Helden,et al.  A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs , 2012, Nature Protocols.

[96]  B. Staels,et al.  The human hepatocyte cell lines IHH and HepaRG: models to study glucose, lipid and lipoprotein metabolism , 2012, Archives of physiology and biochemistry.

[97]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[98]  Steven A. Carr,et al.  The Matrisome: In Silico Definition and In Vivo Characterization by Proteomics of Normal and Tumor Extracellular Matrices , 2011, Molecular & Cellular Proteomics.

[99]  S. Friedman,et al.  Scraping fibrosis: Expressway to the core of fibrosis , 2011, Nature Medicine.

[100]  Salvatore Spicuglia,et al.  A unique H3K4me2 profile marks tissue-specific gene regulation. , 2010, Genome research.

[101]  Cory Y. McLean,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[102]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[103]  K. Yamamura,et al.  Basonuclin 2 has a function in the multiplication of embryonic craniofacial mesenchymal cells and is orthologous to disco proteins , 2009, Proceedings of the National Academy of Sciences.

[104]  Ann E. Loraine,et al.  The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets , 2009, Bioinform..

[105]  Jing Chen,et al.  ToppGene Suite for gene list enrichment analysis and candidate gene prioritization , 2009, Nucleic Acids Res..

[106]  Olivia T. Abar,et al.  Functional linkage of cirrhosis‐predictive single nucleotide polymorphisms of toll‐like receptor 4 to hepatic stellate cell responses , 2009, Hepatology.

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

[108]  R. Schwabe,et al.  Gene expression profiles during hepatic stellate cell activation in culture and in vivo. , 2007, Gastroenterology.

[109]  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.

[110]  Hans A. Kestler,et al.  Transcriptome analysis of human hepatic and pancreatic stellate cells: organ-specific variations of a common transcriptional phenotype , 2005, Journal of Molecular Medicine.

[111]  K. Yamamura,et al.  Characterization of an exchangeable gene trap using pU‐17 carrying a stop codon‐βgeo cassette , 2005, Development, growth & differentiation.

[112]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[113]  P Willett,et al.  Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.

[114]  Hiroshi I. Suzuki,et al.  TBX4 is involved in the super-enhancer-driven transcriptional programs underlying features specific to lung fibroblasts. , 2018, American journal of physiology. Lung cellular and molecular physiology.

[115]  G. Mills,et al.  Verteporfin inhibits YAP function through up-regulating 14-3-3σ sequestering YAP in the cytoplasm. , 2016, American journal of cancer research.

[116]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[117]  Alex E. Lash,et al.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..