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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Use of human embryonic stem cells to model pediatric gliomas with H3.3K27M histone mutation
TL;DR: A stem cell model of a lethal brain tumor in children shows how a recurrent histone mutation leads to cancer, and indicates a resetting of the transformed precursors to a developmentally more primitive stem cell state, with evidence of major modifications of histone marks at several master regulator genes.
Journal ArticleDOI
AF9 YEATS Domain Links Histone Acetylation to DOT1L-Mediated H3K79 Methylation.
Yuanyuan Li,Hong Wen,Yuanxin Xi,Kaori Tanaka,Haibo Wang,Danni Peng,Yongfeng Ren,Qihuang Jin,Sharon Y.R. Dent,Wei Li,Haitao Li,Xiaobing Shi,Xiaobing Shi +12 more
TL;DR: The studies identified the evolutionarily conserved YEATS domain as a novel acetyllysine-binding module and established a direct link between histone acetylation and DOT1L-mediated H3K79 methylation in transcription control.
Journal ArticleDOI
Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity.
Chrysothemis C. Brown,Chrysothemis C. Brown,Herman Gudjonson,Yuri Pritykin,Deeksha Deep,Vincent-Philippe Lavallée,Alejandra Mendoza,Rachel M. Fromme,Linas Mazutis,Charlotte E. Ariyan,Christina S. Leslie,Dana Pe'er,Alexander Y. Rudensky +12 more
TL;DR: Two principal cDC2 lineages are identified defined by distinct developmental pathways and transcriptional regulators, including T-bet and RORγt, two key transcription factors known to define innate and adaptive lymphocyte subsets in human cancer.
Journal ArticleDOI
RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12.
Alberto Santos-Zavaleta,Heladia Salgado,Socorro Gama-Castro,Mishael Sánchez-Pérez,Laura Gómez-Romero,Daniela Ledezma-Tejeida,Jair S. García-Sotelo,Kevin Alquicira-Hernández,Luis Muñiz-Rascado,Pablo Peña-Loredo,Cecilia Ishida-Gutiérrez,David A. Velázquez-Ramírez,Víctor Del Moral-Chávez,César Bonavides-Martínez,Carlos-Francisco Méndez-Cruz,James E. Galagan,Julio Collado-Vides,Julio Collado-Vides +17 more
TL;DR: The literature is curated to keep RegulonDB up to date, and curation of ChIP and gSELEX experiments are initiated, and the Microbial Conditions Ontology with a controlled vocabulary for the minimal properties to reproduce an experiment contributes to integrate data from high throughput and classic literature.
Journal ArticleDOI
Sequential regulatory activity prediction across chromosomes with convolutional neural networks
David R. Kelley,Yakir A. Reshef,Maxwell L. Bileschi,David Belanger,Cory Y. McLean,Jasper Snoek +5 more
TL;DR: It is shown that model predictions for the influence of genomic variants on gene expression align well to causal variants underlying eQTLs in human populations and can be useful for generating mechanistic hypotheses to enable fine mapping of disease loci.
References
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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.