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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In vivo transcriptional governance of hair follicle stem cells by canonical Wnt regulators
TL;DR: The studies unveil TCF3/4–TLE histone deacetylases as a repressive rheostat, whose action can be relieved by Wnt–β-catenin signalling, and who is dispensable for HFSC viability and proliferation if TCF 3/4 levels are sufficiently reduced.
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Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene Repression
Nadezda A. Fursova,Neil P. Blackledge,Manabu Nakayama,Shinsuke Ito,Yoko Koseki,Anca M. Farcas,Hamish W King,Haruhiko Koseki,Robert J. Klose +8 more
TL;DR: It is demonstrated that canonical Polycomb repressive complex 1 (PRC1), which mediates higher-order chromatin structures, contributes little to gene repression, and a new variant PRC1-dependent logic for Polycomb-mediated gene repression is revealed.
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TERRA RNA Antagonizes ATRX and Protects Telomeres
Hsueh-Ping Chu,Catherine Cifuentes-Rojas,Catherine Cifuentes-Rojas,Barry Kesner,Barry Kesner,Eric Aeby,Eric Aeby,Hun-Goo Lee,Hun-Goo Lee,Chunyao Wei,Chunyao Wei,Hyun Jung Oh,Hyun Jung Oh,Myriam Boukhali,Wilhelm Haas,Jeannie T. Lee,Jeannie T. Lee +16 more
TL;DR: It is concluded that TERRA functions as an epigenomic modulator in trans and as an essential regulator of telomeres in cis and in trans to genic targets.
Journal ArticleDOI
Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers
Aurélien A. Sérandour,Stéphane Avner,Frédérik Oger,Maud Bizot,Frédéric Percevault,Céline Lucchetti-Miganeh,Gaëlle Palierne,Céline Gheeraert,Frédérique Barloy-Hubler,Christine Le Péron,Thierry Madigou,Emmanuelle Durand,Philippe Froguel,Bart Staels,Philippe Lefebvre,Raphaël Métivier,Jérôme Eeckhoute,Gilles Salbert +17 more
TL;DR: Functional annotation reveals that regions gaining 5hmC are associated with genes expressed either in neural tissues when P19 cells undergo neural differentiation or in adipose tissue when 3T3-L1 cells undergo adipocyte differentiation, and acquisition of5hmC in cell-specific distal regulatory regions may represent a major event of enhancer progression toward an active state.
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Epigenetic control of innate and adaptive immune memory.
Colleen M. Lau,Nicholas M. Adams,Clair D. Geary,Orr-El Weizman,Moritz Rapp,Yuri Pritykin,Christina S. Leslie,Joseph C. Sun,Joseph C. Sun +8 more
TL;DR: It is demonstrated that differentiating and ‘memory’ NK cells possess distinct chromatin accessibility states and that their epigenetic profiles reveal a ‘poised’ regulatory program at the memory stage, and how individual STAT transcription factors differentially control epigenetic and transcriptional states early during infection is elucidated.
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.