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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Epigenetic Signatures of Autism: Trimethylated H3K4 Landscapes in Prefrontal Neurons
Hennady P. Shulha,Iris Cheung,Catheryne Whittle,Jie Wang,Daniel Virgil,Cong L. Lin,Yin Guo,Andree Lessard,Schahram Akbarian,Zhiping Weng +9 more
TL;DR: Prefrontal cortex neurons from subjects with autism show changes in chromatin structures at hundreds of loci genome-wide, revealing considerable overlap between genetic and epigenetic risk maps of developmental brain disorders.
Journal ArticleDOI
DNA methylation heterogeneity defines a disease spectrum in Ewing sarcoma
Nathan C. Sheffield,Gaëlle Pierron,Johanna Klughammer,Paul Datlinger,Andreas Schönegger,Michael Schuster,Johanna Hadler,Didier Surdez,Delphine Guillemot,Eve Lapouble,Paul Fréneaux,Jacqueline Champigneulle,Raymonde Bouvier,Diana Walder,I.M. Ambros,Caroline Hutter,Caroline Hutter,Eva Sorz,Ana Teresa Amaral,Enrique de Álava,Katharina Schallmoser,Dirk Strunk,Beate Rinner,Bernadette Liegl-Atzwanger,Berthold Huppertz,Andreas Leithner,Gonzague de Pinieux,Philippe Terrier,V. Laurence,Jean Michon,Ruth Ladenstein,Ruth Ladenstein,Wolfgang Holter,Wolfgang Holter,Reinhard Windhager,Uta Dirksen,Peter F. Ambros,Olivier Delattre,Heinrich Kovar,Christoph Bock,Eleni M. Tomazou +40 more
TL;DR: This study performed genome-scale DNA methylation sequencing for a large cohort of Ewing sarcoma tumors and observed consistent DNA hypomethylation at enhancers regulated by the disease-defining EWS-FLI1 fusion protein, thus establishing epigenomic enhancer reprogramming as a ubiquitous and characteristic feature of Ewings Sarcoma.
Journal ArticleDOI
The prevalence, evolution and chromatin signatures of plant regulatory elements
Zefu Lu,Alexandre P. Marand,William A. Ricci,Christina L. Ethridge,Xiaoyu Zhang,Robert J. Schmitz +5 more
TL;DR: Plant distal CREs are prevalent in plants, highly dynamic during evolution and function through distinct chromatin pathways to regulate gene expression, as well as sequence conservation in 13 plant species.
Journal ArticleDOI
The interaction of PRC2 with RNA or chromatin is mutually antagonistic.
Manuel Beltran,Christopher M. Yates,Lenka Skalska,Marcus Dawson,Filipa P. Reis,Keijo Viiri,Cynthia L. Fisher,Christopher R. Sibley,Benjamin M. Foster,Till Bartke,Jernej Ule,Richard G. Jenner +11 more
TL;DR: It is shown here that PRC2 binds nascent RNA at essentially all active genes, and that mutual antagonism between RNA and chromatin underlies the pattern ofPRC2 chromatin association across the genome.
Journal ArticleDOI
Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders.
Liis Uusküla-Reimand,Huayun Hou,Payman Samavarchi-Tehrani,Matteo Vietri Rudan,Minggao Liang,Alejandra Medina-Rivera,Hisham Mohammed,Hisham Mohammed,Dominic Schmidt,Petra C. Schwalie,Edwin J. Young,Jüri Reimand,Jüri Reimand,Suzana Hadjur,Anne-Claude Gingras,Anne-Claude Gingras,Michael D. Wilson +16 more
TL;DR: TOP2B is positioned to solve topological problems at diverse cis-regulatory elements and its occupancy is a highly ordered and prevalent feature of CTCF/cohesin binding sites that flank TADs.
References
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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.