Rewiring of 3D Chromatin Topology Orchestrates Transcriptional Reprogramming and the Development of Human Dilated Cardiomyopathy
暂无分享,去创建一个
Min Wang | R. Pedersen | A. Jegga | S. Pauklin | Xiaohong Wang | Wei Huang | Yigang Wang | G. Fan | Shuang-Yin Wang | S. Sadayappan | Haiyang Chen | Ji-Dong Fu | Chen Gao | Lei Jiang | Mohit Kumar | Zhao V. Wang | F. Liu | Shuang-Yin Wang | Jianyong Ma | Yuliang Feng | M. Watson | F. Huang | Qingshan Geng | Liuyang Cai | Wan-zi Hong | Chun-xiang Zhang | Ning Tan | Cheng Wang | Yuanxi Mo | Changjun Luo | Yan Lin | Feng Liu
[1] M. Nóbrega,et al. Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression. , 2021, Circulation.
[2] P. Pinton,et al. Mitochondrial Function and Dysfunction in Dilated Cardiomyopathy , 2021, Frontiers in Cell and Developmental Biology.
[3] Bjoern Peters,et al. Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants , 2020, Nature Genetics.
[4] M. Nóbrega,et al. Altered Enhancer and Promoter Usage Leads to Differential Gene Expression in the Normal and Failed Human Heart , 2020, Circulation. Heart failure.
[5] T. Misteli. The Self-Organizing Genome: Principles of Genome Architecture and Function , 2020, Cell.
[6] J. Wong,et al. The Gridlock transcriptional repressor impedes vertebrate heart regeneration by restricting expression of lysine methyltransferase , 2020, Development.
[7] R. Qu,et al. An Overview of the Cytoskeleton-Associated Role of PDLIM5 , 2020, Frontiers in Physiology.
[8] E. Kranias,et al. Phosphorylation of cardiac myosin–binding protein-C contributes to calcium homeostasis , 2020, The Journal of Biological Chemistry.
[9] May Yin Lee,et al. Epigenomes of Human Hearts Reveal New Genetic Variants Relevant for Cardiac Disease and Phenotype , 2020, Circulation research.
[10] Rolf Backofen,et al. Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization , 2020, Nucleic Acids Res..
[11] Howard Y. Chang,et al. Circular ecDNA promotes accessible chromatin and high oncogene expression , 2019, Nature.
[12] William A. Flavahan,et al. Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs , 2019, Nature.
[13] N. Pereira,et al. Genetics of dilated cardiomyopathy: practical implications for heart failure management , 2019, Nature Reviews Cardiology.
[14] P. Ellinor,et al. Antisense regulation of atrial natriuretic peptide expression. , 2019, JCI insight.
[15] Wei Xie,et al. The role of 3D genome organization in development and cell differentiation , 2019, Nature Reviews Molecular Cell Biology.
[16] Xiao-gang Guo,et al. Novel polymorphisms in PDLIM3 and PDLIM5 gene encoding Z‐line proteins increase risk of idiopathic dilated cardiomyopathy , 2019, Journal of cellular and molecular medicine.
[17] Ze-Min Fang,et al. Histone methyltransferase SMYD2: ubiquitous regulator of disease , 2019, Clinical Epigenetics.
[18] Stefan Schoenfelder,et al. Long-range enhancer–promoter contacts in gene expression control , 2019, Nature Reviews Genetics.
[19] Guoliang Li,et al. Chromatin interaction analysis with updated ChIA-PET Tool (V3) , 2019 .
[20] Yibin Wang,et al. Epigenetics in dilated cardiomyopathy , 2019, Current opinion in cardiology.
[21] P. Bovolenta,et al. Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance , 2019, Cell stem cell.
[22] Nezar Abdennur,et al. Cooler: scalable storage for Hi-C data and other genomically-labeled arrays , 2019, bioRxiv.
[23] Sandy L. Klemm,et al. Chromatin accessibility and the regulatory epigenome , 2019, Nature Reviews Genetics.
[24] Jasmin I. Maier,et al. AIF1L regulates actomyosin contractility and filopodial extensions in human podocytes , 2018, PloS one.
[25] Howard Y. Chang,et al. Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element , 2018, Cell.
[26] Min Wang,et al. Loss of microRNA-128 promotes cardiomyocyte proliferation and heart regeneration , 2018, Nature Communications.
[27] Aristotelis Tsirigos,et al. Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries , 2018, Nature Communications.
[28] P. Elliott,et al. Evolving concepts in dilated cardiomyopathy , 2018, European journal of heart failure.
[29] J. Epstein,et al. Genome-Nuclear Lamina Interactions Regulate Cardiac Stem Cell Lineage Restriction , 2017, Cell.
[30] Howard Y. Chang,et al. Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements , 2017, Nature Genetics.
[31] E. Petretto,et al. Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy , 2017, Genome Biology.
[32] Nadav Ahituv,et al. Gene Regulatory Elements, Major Drivers of Human Disease. , 2017, Annual review of genomics and human genetics.
[33] Michael Q. Zhang,et al. In Situ Capture of Chromatin Interactions by Biotinylated dCas9 , 2017, Cell.
[34] William Stafford Noble,et al. HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient , 2017, bioRxiv.
[35] Lan T M Dao,et al. Genome-wide characterization of mammalian promoters with distal enhancer functions , 2017, Nature Genetics.
[36] B. Li,et al. A tiling1deletion based genetic screen for cis-regulatory element identification in mammalian cells , 2017, Nature Methods.
[37] K. Hong,et al. Progesterone Protects Against Bisphenol A–Induced Arrhythmias in Female Rat Cardiac Myocytes via Rapid Signaling , 2017, Endocrinology.
[38] I. Moskowitz,et al. TBX5: A Key Regulator of Heart Development. , 2017, Current topics in developmental biology.
[39] Miao Yu,et al. Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq , 2016, Cell Research.
[40] Clint L. Miller,et al. PDE1C deficiency antagonizes pathological cardiac remodeling and dysfunction , 2016, Proceedings of the National Academy of Sciences.
[41] Howard Y. Chang,et al. HiChIP: efficient and sensitive analysis of protein-directed genome architecture , 2016, Nature Methods.
[42] Ri-tai Huang,et al. HAND1 loss-of-function mutation associated with familial dilated cardiomyopathy , 2016, Clinical chemistry and laboratory medicine.
[43] Neva C. Durand,et al. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. , 2016, Cell systems.
[44] Måns Magnusson,et al. MultiQC: summarize analysis results for multiple tools and samples in a single report , 2016, Bioinform..
[45] Jesse R. Dixon,et al. Chromatin Domains: The Unit of Chromosome Organization. , 2016, Molecular cell.
[46] G. Fonarow,et al. Epidemiology and aetiology of heart failure , 2016, Nature Reviews Cardiology.
[47] L. Zentilin,et al. A mouse model for adult cardiac-specific gene deletion with CRISPR/Cas9 , 2015, Proceedings of the National Academy of Sciences.
[48] Jean-Philippe Vert,et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing , 2015, Genome Biology.
[49] Michael P. Snyder,et al. Mango: a bias-correcting ChIA-PET analysis pipeline , 2015, Bioinform..
[50] A. Visel,et al. Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions , 2015, Cell.
[51] J. Dekker,et al. Condensin-Driven Remodeling of X-Chromosome Topology during Dosage Compensation , 2015, Nature.
[52] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[53] Fidel Ramírez,et al. deepTools: a flexible platform for exploring deep-sequencing data , 2014, Nucleic Acids Res..
[54] Yong-liang Wang,et al. Progressive decay of Ca2+ homeostasis in the development of diabetic cardiomyopathy , 2014, Cardiovascular Diabetology.
[55] Wei Shi,et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..
[56] L. D. de Windt,et al. Regulation of fetal gene expression in heart failure. , 2013, Biochimica et biophysica acta.
[57] 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.
[58] Helga Thorvaldsdóttir,et al. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..
[59] Thomas R. Gingeras,et al. STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..
[60] R. Moss,et al. Ablation of the Cardiac-Specific Gene Leucine-Rich Repeat Containing 10 (Lrrc10) Results in Dilated Cardiomyopathy , 2012, PloS one.
[61] Job Dekker,et al. Analysis of long-range chromatin interactions using Chromosome Conformation Capture. , 2012, Methods.
[62] E. Liu,et al. Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks , 2012, Cell reports.
[63] Yong Zhang,et al. Identifying ChIP-seq enrichment using MACS , 2012, Nature Protocols.
[64] J. Sedat,et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre , 2012, Nature.
[65] Euan A. Ashley,et al. Patient-Specific Induced Pluripotent Stem Cells as a Model for Familial Dilated Cardiomyopathy , 2012, Science Translational Medicine.
[66] Raymond K. Auerbach,et al. Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation , 2012, Cell.
[67] M. Ashraf,et al. Reduced collagen deposition in infarcted myocardium facilitates induced pluripotent stem cell engraftment and angiomyogenesis for improvement of left ventricular function. , 2011, Journal of the American College of Cardiology.
[68] S. Moon,et al. A novel Fbxo25 acts as an E3 ligase for destructing cardiac specific transcription factors. , 2011, Biochemical and biophysical research communications.
[69] Timothy J. Durham,et al. "Systematic" , 1966, Comput. J..
[70] R. Young,et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state , 2010, Proceedings of the National Academy of Sciences.
[71] Aaron R. Quinlan,et al. BIOINFORMATICS APPLICATIONS NOTE , 2022 .
[72] Mark D. Robinson,et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..
[73] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[74] Jing Chen,et al. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization , 2009, Nucleic Acids Res..
[75] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[76] I. Sjaastad,et al. Slowing of cardiomyocyte Ca2+ release and contraction during heart failure progression in postinfarction mice. , 2009, American journal of physiology. Heart and circulatory physiology.
[77] E. Liu,et al. Regulation of Estrogen Receptor-mediated Long Range Transcription via Evolutionarily Conserved Distal Response Elements* , 2008, Journal of Biological Chemistry.
[78] Da-Zhi Wang,et al. The MEF2D transcription factor mediates stress-dependent cardiac remodeling in mice. , 2008, The Journal of clinical investigation.
[79] I. Sjaastad,et al. Increased cardiomyocyte function and Ca2+ transients in mice during early congestive heart failure. , 2007, Journal of molecular and cellular cardiology.
[80] Wouter de Laat,et al. Quantitative analysis of chromosome conformation capture assays (3C-qPCR) , 2007, Nature Protocols.
[81] B. Aronow,et al. Myocyte Enhancer Factors 2A and 2C Induce Dilated Cardiomyopathy in Transgenic Mice* , 2006, Journal of Biological Chemistry.
[82] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[83] M. Bang,et al. Myopalladin, a Novel 145-Kilodalton Sarcomeric Protein with Multiple Roles in Z-Disc and I-Band Protein Assemblies , 2001, The Journal of cell biology.
[84] E. Olson,et al. Regulation of skeletal myogenesis by association of the MEF2 transcription factor with class II histone deacetylases. , 2000, Molecular cell.
[85] J. Cross,et al. The Hand1 bHLH transcription factor is essential for placentation and cardiac morphogenesis , 1998, Nature Genetics.
[86] S. Chien,et al. Regulation of cardiac gene expression during myocardial growth and hypertrophy: molecular studies of an adaptive physiologic response , 1991, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.