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
RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity
Anja Nitzsche,Maciej Paszkowski-Rogacz,Filomena Matarese,Eva M. Janssen-Megens,Nina C. Hubner,Herbert Schulz,Ingrid de Vries,Li Ding,Norbert Huebner,Matthias Mann,Hendrik G. Stunnenberg,Frank Buchholz +11 more
TL;DR: It is proposed that a dynamic placement of cohesin by pluripotency transcription factors contributes to a chromosome organization supporting the ESC expression program.
Journal ArticleDOI
Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements
Priscilla Turelli,Nathaly Castro-Diaz,Flavia Marzetta,Adamandia Kapopoulou,Charlène Raclot,Julien Duc,Vannary Tieng,Simon Quenneville,Didier Trono +8 more
TL;DR: It is demonstrated that KRAB/TRIM28-mediated regulation is responsible for controlling a very broad range of human-specific endogenous retroelements in human embryonic stem (ES) cells and that it exerts a marked effect on the transcriptional dynamics of these cells.
Journal ArticleDOI
METTL3 regulates heterochromatin in mouse embryonic stem cells
Wenqi Xu,Jiahui Li,Chenxi He,Jing Wen,Honghui Ma,Bowen Rong,Jianbo Diao,Liyong Wang,Jiahua Wang,Feizhen Wu,Li Tan,Yujiang Geno Shi,Yang Shi,Hongjie Shen +13 more
TL;DR: It is demonstrated that METTL3-catalysed m6A modification of RNA is important for the integrity of IAP heterochromatin in mouse embryonic stem cells, revealing a mechanism of heterochromeatin regulation in mammals.
Journal ArticleDOI
m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome.
Yujiao Tang,Yujiao Tang,Kunqi Chen,Kunqi Chen,Bowen Song,Bowen Song,Jiongming Ma,Xiangyu Wu,Xiangyu Wu,Qingru Xu,Zhen Wei,Jionglong Su,Gang Liu,Rong Rong,Rong Rong,Zhi-Liang Lu,Zhi-Liang Lu,João Pedro de Magalhães,Daniel J. Rigden,Jia Meng,Jia Meng +20 more
TL;DR: A user-friendly graphical user interface was constructed to support the query, visualization and sharing of the m6A epitranscriptomes annotated with sites specifying their interaction with post-transcriptional machinery and interactively display the landscape of multiple RNA modifications.
Journal ArticleDOI
Recurrent mutations, including NPM1c, activate a BRD4-dependent core transcriptional program in acute myeloid leukemia.
Mark A. Dawson,Emma Gudgin,Sarah J. Horton,George Giotopoulos,Eshwar Meduri,Samuel Robson,Ester Cannizzaro,Hikari Osaki,Meike Wiese,S Putwain,C Y Fong,Carolyn Grove,Jenny I.O. Craig,Antje Dittmann,Dave Lugo,Philip D. Jeffrey,Gerard Drewes,Kevin Lee,Lars Bullinger,Rab K. Prinjha,Tony Kouzarides,George S. Vassiliou,Brian J. P. Huntly +22 more
TL;DR: It is demonstrated that a common ‘core’ transcriptional program, which is HOX gene independent, is downregulated in AML and underlies sensitivity to I-BET treatment, and this program can independently classify AML patients into distinct cytogenetic and molecular subgroups, suggesting that it contains biomarkers of sensitivity and response.
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.