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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ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity
Matthew D. Young,Tracy A. Willson,Matthew Wakefield,Evelyn Trounson,Douglas J. Hilton,Marnie E. Blewitt,Alicia Oshlack,Ian J. Majewski +7 more
TL;DR: This work has used ChIP-seq to generate genome-wide maps of H3K27me3 enrichment, and has identified three enrichment profiles with distinct regulatory consequences, including an enrichment profile with a peak in the promoter of genes that is associated with active transcription.
Journal ArticleDOI
Epigenetic regulation of brain region-specific microglia clearance activity
Pinar Ayata,Ana Badimon,Hayley J. Strasburger,Mary Kaye Duff,Sarah E. Montgomery,Yong-Hwee E. Loh,Anja Ebert,Anna A. Pimenova,Brianna R. Ramirez,Andrew T. Chan,Josefa M. Sullivan,Immanuel Purushothaman,Joseph R. Scarpa,Alison Goate,Meinrad Busslinger,Li Shen,Bojan Losic,Anne Schaefer +17 more
TL;DR: It is shown that microglia clearance activity in the adult brain is regionally regulated and depends on the rate of neuronal attrition, which highlights a key role of epigenetic mechanisms in preventing microglian-induced neuronal alterations that are frequently associated with neurodegenerative and psychiatric diseases.
Journal ArticleDOI
A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code
Hirotaka Nakahashi,Kyong Rim Kieffer Kwon,Wolfgang Resch,Laura Vian,Marei Dose,Diana A. Stavreva,Ofir Hakim,Nathanael Pruett,Steevenson Nelson,Arito Yamane,Jason Qian,Wendy Dubois,Scott Welsh,Robert D. Phair,B. Franklin Pugh,Victor V. Lobanenkov,Gordon L. Hager,Rafael Casellas +17 more
TL;DR: It is found that CTCF reads sequence diversity through ZF clustering and associates with a wide array of DNA modules via combinatorial clustering of its 11 ZFs.
Journal ArticleDOI
T Cell–Inflamed versus Non-T Cell–Inflamed Tumors: A Conceptual Framework for Cancer Immunotherapy Drug Development and Combination Therapy Selection
TL;DR: To maximize the impact of immunotherapy drug development, pretreatment stratification of targets associated with either the T cell–inflated or noninflamed tumor microenvironment should be employed and biomarkers predictive of responsiveness to specific immunomodulatory therapies should guide therapy selection.
Journal ArticleDOI
ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression
Hong Wen,Yuanyuan Li,Yuanxin Xi,Shiming Jiang,Sabrina A. Stratton,Danni Peng,Kaori Tanaka,Yongfeng Ren,Zheng Xia,Jun Wu,Bing Li,Michelle Craig Barton,Wei Li,Haitao Li,Xiaobing Shi +14 more
TL;DR: This study identifies ZMYND11 as an H3.3-specific reader of H3K36me3 that links the histone-variant-mediated transcription elongation control to tumour suppression.
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.