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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Deregulation of DUX4 and ERG in acute lymphoblastic leukemia
Jinghui Zhang,Kelly McCastlain,Hiroki Yoshihara,Beisi Xu,Yunchao Chang,Michelle L. Churchman,Gang Wu,Yongjin Li,Lei Wei,Ilaria Iacobucci,Yu Liu,Chunxu Qu,Ji Wen,Michael N. Edmonson,Debbie Payne-Turner,Kerstin B. Kaufmann,Shin-ichiro Takayanagi,Shin-ichiro Takayanagi,Erno Wienholds,Esmé Waanders,Esmé Waanders,Panagiotis Ntziachristos,Sofia Bakogianni,Jingjing Wang,Iannis Aifantis,Iannis Aifantis,Kathryn G. Roberts,Jing Ma,Guangchun Song,John Easton,Heather L. Mulder,Xiang Chen,Scott Newman,Xiaotu Ma,Michael Rusch,Pankaj Gupta,Kristy Boggs,Bhavin Vadodaria,James Dalton,Yanling Liu,Marcus L Valentine,Li Ding,Charles Lu,Robert S. Fulton,Lucinda Fulton,Yashodhan Tabib,Kerri Ochoa,Meenakshi Devidas,Deqing Pei,Cheng Cheng,Jun J. Yang,William E. Evans,Mary V. Relling,Ching-Hon Pui,Sima Jeha,Richard C. Harvey,I-Ming L. Chen,Cheryl L. Willman,Guido Marcucci,Clara D. Bloomfield,Jessica Kohlschmidt,Krzysztof Mrózek,Elisabeth Paietta,Martin S. Tallman,Wendy Stock,Matthew C. Foster,Janis Racevskis,Jacob M. Rowe,Selina M. Luger,Steven M. Kornblau,Sheila A. Shurtleff,Susana C. Raimondi,Elaine R. Mardis,Richard K. Wilson,John E. Dick,Stephen P. Hunger,Mignon L. Loh,James R. Downing,Charles G. Mullighan +78 more
TL;DR: A unique paradigm of transcription factor deregulation in leukemia is illustrated in which DUX4 deregulation results in loss of function of ERG, either by deletion or induced expression of an isoform that is a dominant-negative inhibitor of wild-type ERG function.
Journal ArticleDOI
Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)
Paul G. Giresi,Jason D. Lieb +1 more
TL;DR: FAIRE has utility in establishing chromatin profiles of diverse cell types in health and disease, isolating DNA regulatory elements en masse for further characterization, and as a screening assay for the effects of small molecules on chromatin organization.
Journal ArticleDOI
YAP Drives Growth by Controlling Transcriptional Pause Release from Dynamic Enhancers
Giorgio G. Galli,Giorgio G. Galli,Matteo Carrara,Wei-Chien Yuan,Wei-Chien Yuan,Christian Valdes-Quezada,Basanta Gurung,Basanta Gurung,Brian J. Pepe-Mooney,Brian J. Pepe-Mooney,Tinghu Zhang,Geert Geeven,Nathanael S. Gray,Wouter de Laat,Raffaele A. Calogero,Fernando D. Camargo,Fernando D. Camargo +16 more
TL;DR: Global chromatin occupancy analyses are utilized to demonstrate that robust YAP binding is restricted to a relatively small number of distal regulatory elements in the genome, and uncover the molecular mechanisms employed by YAP to exert its growth and oncogenic functions, and suggest strategies for intervention.
Journal ArticleDOI
Dynamic binding of RBPJ is determined by Notch signaling status
David Castel,Philippos Mourikis,Stefanie J. J. Bartels,Arie B. Brinkman,Shahragim Tajbakhsh,Hendrik G. Stunnenberg +5 more
TL;DR: This work demonstrates dynamic binding of RBPJ in response to Notch activation at essentially all sites co-occupied by NICD and identifies a distinct set of sites whereRBPJ recruits neither NICD nor p300 and binds DNA statically, irrespective of Notch activity.
Journal ArticleDOI
ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments.
Jeanne Chèneby,Marius Gheorghe,Marie Artufel,Marie Artufel,Anthony Mathelier,Anthony Mathelier,Benoit Ballester,Benoit Ballester +7 more
TL;DR: ReMap 2018 provides a significant update of the ReMap database, providing an in depth view of the complexity of the regulatory landscape in human.
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