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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Chromatin states define tumour-specific T cell dysfunction and reprogramming
Mary Philip,Lauren Fairchild,Lauren Fairchild,Liping Sun,Ellen L. Horste,Steven Camara,Mojdeh Shakiba,Mojdeh Shakiba,Andrew Scott,Andrew Scott,Agnes Viale,Peter Lauer,Taha Merghoub,Taha Merghoub,Matthew D. Hellmann,Matthew D. Hellmann,Jedd D. Wolchok,Jedd D. Wolchok,Christina S. Leslie,Andrea Schietinger,Andrea Schietinger +20 more
TL;DR: It is shown that T cells in mouse tumours differentiate through two discrete chromatin states: a plastic dysfunctional state from which T cells can be rescued, and a fixed dysfunctional state in which the cells are resistant to reprogramming.
Journal ArticleDOI
Integrative annotation of chromatin elements from ENCODE data
Michael M. Hoffman,Jason Ernst,Jason Ernst,Jason Ernst,Steven P. Wilder,Anshul Kundaje,Anshul Kundaje,Robert S. Harris,Max Libbrecht,Belinda Giardine,Paul Ellenbogen,Jeff A. Bilmes,Ewan Birney,Ross C. Hardison,Ian Dunham,Manolis Kellis,Manolis Kellis,William Stafford Noble +17 more
TL;DR: These methods rediscover and summarize diverse aspects of chromatin architecture, elucidate the interplay between chromatin activity and RNA transcription, and reveal that a large proportion of the genome lies in a quiescent state, even across multiple cell types.
Journal ArticleDOI
Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies.
Andrew E. Jaffe,Peter Murakami,Hwajin Lee,Jeffrey T. Leek,M. Daniele Fallin,Andrew P. Feinberg,Rafael A. Irizarry +6 more
TL;DR: A data analysis pipeline is presented that effectively models measurement error, removes batch effects, detects regions of interest and attaches statistical uncertainty to identified regions, and shows that addressing unexplained heterogeneity like batch effects reduces the number of false-positive regions.
Journal ArticleDOI
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility
Darren A. Cusanovich,Andrew J. Hill,Delasa Aghamirzaie,Riza M. Daza,Hannah A. Pliner,Joel B. Berletch,Galina N. Filippova,Xingfan Huang,Lena Christiansen,William S DeWitt,Choli Lee,Samuel G. Regalado,David F. Read,Frank J. Steemers,Christine M. Disteche,Cole Trapnell,Jay Shendure,Jay Shendure +17 more
TL;DR: By intersecting mouse chromatin accessibility with human genome-wide association summary statistics, this work identifies cell-type-specific enrichments of the heritability signal for hundreds of complex traits.
Journal ArticleDOI
Distinct emt programs control normal mammary stem cells and tumour-initiating cells
Xin Ye,Wai Leong Tam,Wai Leong Tam,Tsukasa Shibue,Yasemin Kaygusuz,Ferenc Reinhardt,Elinor Ng Eaton,Robert A. Weinberg +7 more
TL;DR: It is shown that normal gland-reconstituting mammary stem cells residing in the basal layer of the mammary epithelium and breast TICs originating in the luminal layer exploit the paralogous EMT-TFs Slug and Snail, respectively, which induce distinct EMT programs.
References
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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.