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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Endogenous purification reveals GREB1 as a key estrogen receptor regulatory factor.
Hisham Mohammed,Clive D'Santos,Aurélien A. Sérandour,H. Raza Ali,Gordon D. Brown,Alan Atkins,Oscar M. Rueda,Kelly A. Holmes,Vasiliki Theodorou,Jessica L. L. Robinson,Wilbert Zwart,Amel Saadi,Caryn S. Ross-Innes,Suet-Feung Chin,Suraj Menon,John Stingl,Carlo Palmieri,Carlos Caldas,Jason S. Carroll +18 more
TL;DR: Findings reveal an unexpected role for GREB1 as an estrogen-specific ER cofactor that is expressed in drug-sensitive contexts, and predicts good clinical outcome.
Journal ArticleDOI
Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome
Stefan Schoenfelder,Robert Sugar,Andrew Dimond,Biola-Maria Javierre,Harry J. Armstrong,Borbala Mifsud,Borbala Mifsud,Emilia Dimitrova,Emilia Dimitrova,Louise S. Matheson,Filipe Tavares-Cadete,Mayra Furlan-Magaril,Anne Segonds-Pichon,Wiktor Jurkowski,Steven W. Wingett,Kristina Tabbada,Simon Andrews,Bram Herman,Emily M LeProust,Cameron S. Osborne,Haruhiko Koseki,Peter Fraser,Nicholas M. Luscombe,Sarah Elderkin +23 more
TL;DR: PRC1 physically constrains developmental transcription factor genes and their enhancers in a silenced but poised spatial network and it is proposed that the selective release of genes from this spatial network underlies cell fate specification during early embryonic development.
Journal ArticleDOI
Recognition of a Mononucleosomal Histone Modification Pattern by BPTF via Multivalent Interactions
Alexander J. Ruthenburg,Haitao Li,Thomas A. Milne,Scott Dewell,Robert K. McGinty,Melanie Yuen,Beatrix Ueberheide,Yali Dou,Tom W. Muir,Dinshaw J. Patel,C. David Allis +10 more
TL;DR: This work examines how additional heterotypic modifications influence BPTF binding and calls attention to nucleosomal patterning of covalent marks in dictating critical chromatin associations.
Journal ArticleDOI
Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin
Syuzo Kaneko,Roberto Bonasio,Ricardo Saldaña-Meyer,Takahaki Yoshida,Jinsook Son,Koichiro Nishino,Akihiro Umezawa,Danny Reinberg +7 more
TL;DR: Findings show that lncRNAs facilitate JARID2-PRC2 interactions on chromatin and suggest a mechanism by which lnc RNAs contribute to PRC2 recruitment.
Journal ArticleDOI
The MLL3/MLL4 Branches of the COMPASS Family Function as Major Histone H3K4 Monomethylases at Enhancers
TL;DR: In this paper, the authors used chromatin immunoprecipitation-sequencing (ChIP-seq) to find that the Trithorax-related (Trr) branch of the COMPASS family regulates enhancer activity and is responsible for the implementation of H3K4me1 at these regions.
References
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