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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Integrative functional genomic analysis of human brain development and neuropsychiatric risks
Mingfeng Li,Gabriel Santpere,Yuka Imamura Kawasawa,Yuka Imamura Kawasawa,Oleg V. Evgrafov,Forrest O. Gulden,Sirisha Pochareddy,Susan M. Sunkin,Zhen Li,Yurae Shin,Yurae Shin,Ying Zhu,André M. M. Sousa,Donna M. Werling,Robert R. Kitchen,Hyo Jung Kang,Hyo Jung Kang,Mihovil Pletikos,Mihovil Pletikos,Jinmyung Choi,Sydney Muchnik,Xuming Xu,Daifeng Wang,Belen Lorente-Galdos,Shuang Liu,Paola Giusti-Rodríguez,Hyejung Won,Christiaan de Leeuw,Antonio F. Pardiñas,PsychENCODE Developmental Subgroup,Ming Hu,Fulai Jin,Yun Li,Michael John Owen,Michael Conlon O'Donovan,James T.R. Walters,Danielle Posthuma,Mark Reimers,Pat Levitt,Pat Levitt,Daniel R. Weinberger,Thomas M. Hyde,Joel E. Kleinman,Daniel H. Geschwind,Michael Hawrylycz,Matthew W. State,Stephen Sanders,Patrick F. Sullivan,Mark Gerstein,Ed S. Lein,James A. Knowles,Nenad Sestan +51 more
TL;DR: The generation and analysis of a variety of genomic data modalities at the tissue and single-cell levels, including transcriptome, DNA methylation, and histone modifications across multiple brain regions ranging in age from embryonic development through adulthood, reveal insights into neurodevelopment and the genomic basis of neuropsychiatric risks.
Journal ArticleDOI
RYBP-PRC1 Complexes Mediate H2A Ubiquitylation at Polycomb Target Sites Independently of PRC2 and H3K27me3
Lígia Tavares,Emilia Dimitrova,David Oxley,Judith Webster,Raymond A. Poot,Jeroen Demmers,Karel Bezstarosti,Stephen Taylor,Hiroki Ura,Hiroshi Koide,Anton Wutz,Miguel Vidal,Sarah Elderkin,Neil Brockdorff +13 more
TL;DR: It is shown that RING1B, the catalytic subunit of PRC1, and associated monoubiquitylation of histone H2A are targeted to closely overlapping sites in wild-type and PRC2-deficient mouse embryonic stem cells (mESCs), demonstrating an H3K27me3-independent pathway for recruitment ofPRC1 activity.
Journal ArticleDOI
MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures
Tanmoy Mondal,Santhilal Subhash,Roshan Vaid,Stefan Enroth,Sireesha Uday,Björn Reinius,Sanhita Mitra,Arif Mohammed,Alva Rani James,Emily Hoberg,Aristidis Moustakas,Ulf Gyllensten,Steven J.M. Jones,Claes M. Gustafsson,Andrew H. Sims,Fredrik Westerlund,Eduardo Gorab,Chandrasekhar Kanduri +17 more
TL;DR: It is shown that MEG3 and EZH2 share common target genes, including the TGF-β pathway genes, and RNA–DNA triplex formation could be a general characteristic of target gene recognition by the chromatin-interacting lncRNAs.
Journal ArticleDOI
Intragenic DNA methylation prevents spurious transcription initiation
Francesco Neri,Stefania Rapelli,Anna Krepelova,Danny Incarnato,Caterina Parlato,Giulia Basile,Mara Maldotti,Francesca Anselmi,Salvatore Oliviero +8 more
TL;DR: It is shown that, in mouse embryonic stem cells, Dnmt3b-dependent intragenic DNA methylation protects the gene body from spurious RNA polymerase II entry and cryptic transcription initiation, with implications for intragenics hypomethylation in cancer.
Journal ArticleDOI
Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons.
Orly L. Wapinski,Thomas Vierbuchen,Kun Qu,Qian Yi Lee,Soham Chanda,Daniel R. Fuentes,Paul G. Giresi,Yi Han Ng,Samuele Marro,Norma F. Neff,Daniela Drechsel,Ben Martynoga,Diogo S. Castro,Ashley E. Webb,Thomas C. Südhof,Anne Brunet,François Guillemot,Howard Y. Chang,Howard Y. Chang,Marius Wernig +19 more
TL;DR: A precise match between pioneer factors and the chromatin context at key target genes is determinative for transdifferentiation to neurons and likely other cell types.
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