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
Reads0
Chats0
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
Citations
More filters
Journal ArticleDOI
Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming
Ralph Stadhouders,Ralph Stadhouders,Enrique Vidal,François Serra,Bruno Di Stefano,Bruno Di Stefano,François Le Dily,Javier Quilez,Antonio Gomez,Samuel Collombet,Clara Berenguer,Yasmina Cuartero,Jochen Hecht,Guillaume J. Filion,Miguel Beato,Marc A. Marti-Renom,Thomas Graf +16 more
TL;DR: It is concluded that 3D genome reorganization generally precedes gene expression changes and that removal of locus-specific topological barriers explains why pluripotency genes are activated sequentially during reprogramming.
Journal ArticleDOI
5mC Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming during Differentiation
Gary C. Hon,Chun-Xiao Song,Tingting Du,Fulai Jin,Siddarth Selvaraj,Ah Young Lee,Chia-An Yen,Zhen Ye,Shi-Qing Mao,Bang-An Wang,Samantha Kuan,Lee Edsall,Boxuan Simen Zhao,Guoliang Xu,Chuan He,Bing Ren,Bing Ren +16 more
TL;DR: It is found that deletion of Tet2 causes extensive loss of 5hmC at enhancers, accompanied by enhancer hypermethylation, reduction of enhancer activity, and delayed gene induction in the early steps of differentiation.
Journal ArticleDOI
The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells
Makoto Kurachi,R. Anthony Barnitz,Nir Yosef,Pamela M. Odorizzi,Michael A. DiIorio,Madeleine E. Lemieux,Kathleen B. Yates,Jernej Godec,Martin G Klatt,Aviv Regev,E. John Wherry,W. Nicholas Haining +11 more
TL;DR: A fundamental role is identified for BATF in regulating the differentiation of effector of CD8+ T cells and this checkpoint prevents irreversible commitment to an effector fate until a critical threshold of downstream transcriptional activity has been achieved.
Journal ArticleDOI
High-fat diet reprograms the epigenome of rat spermatozoa and transgenerationally affects metabolism of the offspring
Thais de Castro Barbosa,Thais de Castro Barbosa,Lars R. Ingerslev,Petter S. Alm,Soetkin Versteyhe,Julie Massart,Morten Arendt Rasmussen,Ida Donkin,Rasmus J. O. Sjögren,Jonathan M. Mudry,Laurène Vetterli,Shashank Gupta,Anna Krook,Juleen R. Zierath,Juleen R. Zierath,Romain Barrès +15 more
TL;DR: Insight is provided into mechanisms by which HFD transgenerationally reprograms the epigenome of sperm cells, thereby affecting metabolic tissues of offspring throughout two generations, and induces a transcriptomic shift of the let-7c predicted targets.
Journal ArticleDOI
PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells
TL;DR: Using in vivo RNA-protein cross-linking, it is shown that EZH2 directly binds the 5′ region of nascent RNAs transcribed from a subset of these promoters and that these binding events correlate with decreased H3K27me3.
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.