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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A tissue checkpoint regulates type 2 immunity
Steven J. Van Dyken,Jesse C. Nussbaum,Jinwoo Lee,Ari B. Molofsky,Hong-Erh Liang,Joshua L. Pollack,Rachel E. Gate,Genevieve E. Haliburton,Chun Jimmie Ye,Alexander Marson,David J. Erle,Richard M. Locksley +11 more
TL;DR: The findings suggest a mechanism by which diverse perturbations can activate type 2 immunity and reveal a shared local-tissue-elicited checkpoint that can be exploited to control both innate and adaptive allergic inflammation.
Journal ArticleDOI
Depletion of RUNX1/ETO in t(8;21) AML cells leads to genome-wide changes in chromatin structure and transcription factor binding
Anetta Ptasinska,Salam A. Assi,D Mannari,Sally R. James,Daniel Williamson,J Dunne,Maarten Hoogenkamp,Mengchu Wu,Matthew A. Care,Hesta McNeill,Pierre Cauchy,M Cullen,Reuben Tooze,Daniel G. Tenen,Daniel G. Tenen,Bryan D. Young,Peter N. Cockerill,Peter N. Cockerill,David R. Westhead,Olaf Heidenreich,Constanze Bonifer,Constanze Bonifer +21 more
TL;DR: It is shown that selective removal of RUNX1/ETO leads to a widespread reversal of epigenetic reprogramming and a genome-wide redistribution of RunX1 binding, resulting in the inhibition of leukemic proliferation and self-renewal, and the induction of differentiation.
Journal ArticleDOI
Epigenomics of human CD8 T cell differentiation and aging.
David Moskowitz,David W. Zhang,David W. Zhang,Bin Hu,Bin Hu,Sabine Le Saux,Sabine Le Saux,Rolando E. Yanes,Rolando E. Yanes,Zhongde Ye,Zhongde Ye,Jason D. Buenrostro,Cornelia M. Weyand,Cornelia M. Weyand,William J. Greenleaf,Jörg J. Goronzy,Jörg J. Goronzy +16 more
TL;DR: The transcriptional circuits uncovered here set the stage for the designing rationales to modulate T cell function in the elderly, and identify BATF- and NRF1-driven gene regulation as potential targets for delaying CD8 T cell aging and restoring function.
Journal ArticleDOI
Control of Embryonic Stem Cell Lineage Commitment by Core Promoter Factor, TAF3
TL;DR: These findings support a new role of TAF3 in mediating long-range chromatin regulatory interactions that safeguard the finely-balanced transcriptional programs underlying pluripotency.
Journal ArticleDOI
Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution
TL;DR: It is found that the repressive H3K27me3 histone mark is overrepresented in the promoter regions of genes that are in conformational linkage over long distances, and a major theme of genome folding in A. thaliana is the formation of structural units that correspond to gene bodies.
References
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Genome-wide location and function of dna binding proteins
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