Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang,Tao Liu,Clifford A. Meyer,Jérôme Eeckhoute,David S. Johnson,Bradley E. Bernstein,Bradley E. Bernstein,Chad Nusbaum,Richard M. Myers,Myles Brown,Wei Li,X. Shirley Liu +11 more
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TLDR
This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.Abstract:
We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available.read more
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Comparative analysis of regulatory information and circuits across distant species
Alan P. Boyle,Carlos L. Araya,Cathleen M. Brdlik,Philip Cayting,Chao Cheng,Yong Cheng,Kathryn E. Gardner,LaDeana W. Hillier,J. Janette,Lixia Jiang,Dionna M. Kasper,Trupti Kawli,Pouya Kheradpour,Anshul Kundaje,Anshul Kundaje,Jingyi Jessica Li,Jingyi Jessica Li,Lijia Ma,Wei Niu,E. Jay Rehm,Joel Rozowsky,Matthew Slattery,Rebecca Spokony,Robert Terrell,D. Vafeados,Daifeng Wang,Peter Weisdepp,Yi-Chieh Wu,Dan Xie,Koon-Kiu Yan,Elise A. Feingold,Peter J. Good,Michael J. Pazin,Haiyan Huang,Peter J. Bickel,Steven E. Brenner,Valerie Reinke,Robert H. Waterston,Mark Gerstein,Kevin P. White,Manolis Kellis,Michael Snyder +41 more
TL;DR: The results suggest that gene-regulatory properties previously observed for individual factors are general principles of metazoan regulation that are remarkably well-preserved despite extensive functional divergence of individual network connections.
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Genome-wide tissue-specific farnesoid X receptor binding in mouse liver and intestine.
TL;DR: This study reports genome‐wide FXR binding in vivo and the results clearly demonstrate tissue‐specific FXR/gene interaction, indicating that FXR may be involved in regulating broader biological pathways in maintaining hepatic and intestinal homeostasis.
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Tissue-resident macrophages provide a pro-tumorigenic niche to early NSCLC cells.
Maria Casanova-Acebes,Erica Dalla,Andrew Leader,Jessica LeBerichel,Jovan Nikolic,Blanca M. Morales,Markus Brown,Christie Chang,Leanna Troncoso,Steven T. Chen,Ana Sastre-Perona,Matthew D. Park,Alexandra Tabachnikova,Maxime Dhainaut,Pauline Hamon,Barbara Maier,Catherine M. Sawai,Esperanza Agulló-Pascual,Markus Schober,Brian D. Brown,Boris Reizis,Thomas U. Marron,Ephraim Kenigsberg,Christine Moussion,Philippe Benaroch,Julio A. Aguirre-Ghiso,Miriam Merad +26 more
TL;DR: In this article, single-cell RNA sequencing and imaging of macrophages in human non-small cell lung cancer and in a mouse model of lung adenocarcinoma was performed.
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Combinatorial Assembly of Developmental Stage-Specific Enhancers Controls Gene Expression Programs during Human Erythropoiesis
Jian Xu,Zhen Shao,Kimberly Glass,Daniel E. Bauer,Luca Pinello,Ben Van Handel,Serena Hou,John A. Stamatoyannopoulos,Hanna K. A. Mikkola,Guo-Cheng Yuan,Stuart H. Orkin,Stuart H. Orkin +11 more
TL;DR: It is found that erythroid master regulators GATA1 and TAL1 act cooperatively within active enhancers but confer little predictive value for stage specificity, and a set of stage-specific coregulators collaborates with master regulators and contributes to differential gene expression.
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Disturbed mitochondrial dynamics in CD8 + TILs reinforce T cell exhaustion
Yi-Ru Yu,Yi-Ru Yu,Hana Imrichova,Haiping Wang,Haiping Wang,Tung Chao,Tung Chao,Zhengtao Xiao,Min Gao,Marcela Rincon-Restrepo,Marcela Rincon-Restrepo,Fabien Franco,Fabien Franco,Raphael Genolet,Raphael Genolet,Wan-Chen Cheng,Wan-Chen Cheng,Camilla Jandus,Camilla Jandus,George Coukos,George Coukos,Yi-Fan Jiang,Jason W. Locasale,Alfred Zippelius,Alfred Zippelius,Pu-Ste Liu,Li Tang,Christoph Bock,Christoph Bock,Nicola Vannini,Nicola Vannini,Ping-Chih Ho,Ping-Chih Ho +32 more
TL;DR: It is reported that mitochondrial dysfunction and impaired mitophagy triggered by the tumor microenvironment lead to subsequent epigenetic changes and cause permanent T cell exhaustion and dysfunction.
References
More filters
Journal ArticleDOI
High-resolution profiling of histone methylations in the human genome.
Artem Barski,Suresh Cuddapah,Kairong Cui,Tae-Young Roh,Dustin E. Schones,Zhibin Wang,Gang Wei,Iouri Chepelev,Keji Zhao +8 more
TL;DR: High-resolution maps for the genome-wide distribution of 20 histone lysine and arginine methylations as well as histone variant H2A.Z, RNA polymerase II, and the insulator binding protein CTCF across the human genome using the Solexa 1G sequencing technology are generated.
Journal ArticleDOI
Global variation in copy number in the human genome
Richard Redon,Shumpei Ishikawa,Karen R. Fitch,Lars Feuk,George H. Perry,T. Daniel Andrews,Heike Fiegler,Michael H. Shapero,Andrew R. Carson,Wenwei Chen,Eun Kyung Cho,Stephanie Dallaire,Jennifer L. Freeman,Juan R. González,Mònica Gratacòs,Jing Huang,Dimitrios Kalaitzopoulos,Daisuke Komura,Jeffrey R. MacDonald,Christian R. Marshall,Rui Mei,Lyndal Montgomery,Keunihiro Nishimura,Kohji Okamura,Fan Shen,Martin J. Somerville,Joelle Tchinda,Armand Valsesia,Cara Woodwark,Fengtang Yang,Junjun Zhang,Tatiana Zerjal,Jane Zhang,Lluís Armengol,Donald F. Conrad,Xavier Estivill,Chris Tyler-Smith,Nigel P. Carter,Hiroyuki Aburatani,Charles Lee,Keith W. Jones,Stephen W. Scherer,Matthew E. Hurles +42 more
TL;DR: A first-generation CNV map of the human genome is constructed through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia, underscoring the importance of CNV in genetic diversity and evolution and the utility of this resource for genetic disease studies.
Journal ArticleDOI
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Tarjei S. Mikkelsen,Manching Ku,Manching Ku,David B. Jaffe,Biju Issac,Biju Issac,Erez Lieberman Aiden,Erez Lieberman Aiden,Georgia Giannoukos,Pablo Alvarez,William Brockman,Tae Kyung Kim,Richard Koche,Richard Koche,Richard Koche,William Lee,Eric M. Mendenhall,Eric M. Mendenhall,Aisling O'Donovan,Aviva Presser,Carsten Russ,Xiaohui Xie,Alexander Meissner,Marius Wernig,Rudolf Jaenisch,Chad Nusbaum,Eric S. Lander,Eric S. Lander,Bradley E. Bernstein,Bradley E. Bernstein +29 more
TL;DR: The application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells is reported and it is shown that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms.
Journal ArticleDOI
Genome-Wide Mapping of in Vivo Protein-DNA Interactions
David S. Johnson,Ali Mortazavi,Ali Mortazavi,Richard M. Myers,Richard M. Myers,Barbara J. Wold,Barbara J. Wold +6 more
TL;DR: A large-scale chromatin immunoprecipitation assay based on direct ultrahigh-throughput DNA sequencing was developed, which was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF; also known as REST) to 1946 locations in the human genome.
PatentDOI
Genome-wide location and function of dna binding proteins
TL;DR: In this paper, a method for identifying a set of genes where cell cycle regulator binding correlates with gene expression and identifying genomic targets of cell cycle transcription activators in living cells is also encompassed.