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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Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening
Silin Zhong,Zhangjun Fei,Zhangjun Fei,Yun-Ru Chen,Yi Zheng,Mingyun Huang,Julia Vrebalov,Ryan P. McQuinn,Nigel E. Gapper,Bao Liu,Jenny Xiang,Ying Shao,James J. Giovannoni,James J. Giovannoni +13 more
TL;DR: The data show that the epigenome is not static during development and may have been selected to ensure the fidelity of developmental processes such as ripening, and Crop-improvement strategies could benefit by taking into account not only DNA sequence variation among plant lines, but also the information encoded in the epigenomes.
Journal ArticleDOI
Organization of Chromatin by Intrinsic and Regulated Phase Separation
Bryan A. Gibson,Lynda K. Doolittle,Maximillian W.G. Schneider,Liv E. Jensen,Nathan Gamarra,Lisa Henry,Daniel W. Gerlich,Sy Redding,Michael K. Rosen +8 more
TL;DR: It is demonstrated that reconstituted chromatin undergoes histone tail-driven liquid-liquid phase separation (LLPS) in physiologic salt and when microinjected into cell nuclei, producing dense and dynamic droplets.
Journal ArticleDOI
Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases
TL;DR: A linear amplification–mediated modification of a previously published high-throughput, genome-wide, translocation sequencing (HTGTS) method that robustly detects DNA double-stranded breaks (DSBs) generated by engineered nucleases across the human genome based on their translocation to other endogenous or ectopic DSBs is described.
Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes
Jill M. Dowen,Zi Peng Fan,Denes Hnisz,Gang Ren,Brian J. Abraham,Abraham S. Weintraub,Jurian Schuijers,Tong Ihn Lee,Keji Zhao,Lyndon Nuoxi Zhang,Richard A. Young +10 more
TL;DR: In this article, the authors used ESC cohesin ChIA-PET data to identify the local chromosomal structures at both active and repressed genes across the genome and reveal that super-enhancer-driven genes generally occur within chromosome structures that are formed by the looping of two interacting CTCF sites co-occupied by co-hesin.
Journal ArticleDOI
REST and stress resistance in ageing and Alzheimer’s disease
Tao Lu,Liviu Aron,Joseph M. Zullo,Ying Pan,Haeyoung Kim,Yiwen Chen,Tun Hsiang Yang,Hyun-Min Kim,Derek Drake,X. Shirley Liu,David A. Bennett,Monica P. Colaiácovo,Bruce A. Yankner +12 more
TL;DR: It is shown that induction of the repressor element 1-silencing transcription factor (REST) is a universal feature of normal ageing in human cortical and hippocampal neurons, and levels during ageing are closely correlated with cognitive preservation and longevity.
References
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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.