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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Super-Enhancer-Mediated RNA Processing Revealed by Integrative MicroRNA Network Analysis
TL;DR: It is reported that super-enhancers drive the biogenesis of master miRNAs crucial for cell identity by enhancing both transcription and Drosha/DGCR8-mediated primary miRNA (pri-miRNA) processing.
Journal ArticleDOI
An oncogenic Ezh2 mutation induces tumors through global redistribution of histone 3 lysine 27 trimethylation.
George P. Souroullas,William R. Jeck,Joel S. Parker,Jeremy M. Simon,Jie Yu Liu,Joshiawa Paulk,Jessie Xiong,Kelly S. Clark,Yuri Fedoriw,Jun Qi,Christin E. Burd,James E. Bradner,Norman E. Sharpless +12 more
TL;DR: It is suggested that Ezh2Y641F induces lymphoma and melanoma through a vast reorganization of chromatin structure, inducing both repression and activation of polycomb-regulated loci.
Journal ArticleDOI
PRC1 Catalytic Activity Is Central to Polycomb System Function
Neil P. Blackledge,Nadezda A. Fursova,Jessica R. Kelley,Miles K. Huseyin,Angelika Feldmann,Robert J. Klose +5 more
TL;DR: It is found that Polycomb-mediated gene repression requires PRC1 catalytic activity, and this discovery provides compelling evidence thatPRC1 catalysis is central to Polycomb system function and gene regulation.
Journal ArticleDOI
Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis
Chenlong Li,Chenlong Li,Lianfeng Gu,Lianfeng Gu,Lianfeng Gu,Lei Gao,Chen Chen,Chen Chen,Chuang-Qi Wei,Chuang-Qi Wei,Qi Qiu,Chih Wei Chien,Suikang Wang,Suikang Wang,Lihua Jiang,Lian-Feng Ai,Chia-Yang Chen,Songguang Yang,Vi Nguyen,Yanhua Qi,Michael Snyder,Alma L. Burlingame,Susanne E. Kohalmi,Shangzhi Huang,Xiaofeng Cao,Zhi-Yong Wang,Keqiang Wu,Xuemei Chen,Yuhai Cui,Yuhai Cui +29 more
TL;DR: This work identifies a new genomic targeting mechanism for an H3K27 demethylase and demonstrates its key role in recruiting the BRM chromatin remodeler.
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PeakRanger: A cloud-enabled peak caller for ChIP-seq data
TL;DR: PeakRanger is introduced, a peak caller software package that works equally well on punctate and broad sites, can resolve closely-spaced peaks, has excellent performance, and is easily customized.
References
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Artem Barski,Suresh Cuddapah,Kairong Cui,Tae-Young Roh,Dustin E. Schones,Zhibin Wang,Gang Wei,Iouri Chepelev,Keji Zhao +8 more
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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
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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.