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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Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production.
TL;DR: The hypothesis that cytosine methylation (5mC) and histone methylation H3K36me may synergistically repress production of natural antisense transcripts (NATs) in the context of actively expressed genes is proposed.
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An NF-κB Transcription-Factor-Dependent Lineage-Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function
Hyunju Oh,Yenkel Grinberg-Bleyer,Will Liao,Dillon Maloney,Pingzhang Wang,Zikai Wu,Jiguang Wang,Dev M. Bhatt,Nicole Heise,Roland M. Schmid,Matthew S. Hayden,Ulf Klein,Raul Rabadan,Sankar Ghosh +13 more
TL;DR: This work conditionally deleted canonical NF-κB members p65 and c-Rel in developing and mature Treg cells and found they have unique but partially redundant roles and underscores the need for more selective strategies to therapeutically target NF-σκB.
Journal ArticleDOI
The R-loop is a common chromatin feature of the Arabidopsis genome.
TL;DR: In this article, a single-strand DNA ligation-based library preparation technique for genome-wide identification of R-loops is proposed, which exhibits high efficiency, low bias and strand specificity.
Journal ArticleDOI
Microcephaly Gene Links Trithorax and REST/NRSF to Control Neural Stem Cell Proliferation and Differentiation
Yawei J. Yang,Andrew E. Baltus,Andrew E. Baltus,Rebecca S. Mathew,Rebecca S. Mathew,Elisabeth A. Murphy,Elisabeth A. Murphy,Elisabeth A. Murphy,Gilad D. Evrony,Dilenny M. Gonzalez,Dilenny M. Gonzalez,Estee P. Wang,Christine A. Marshall-Walker,Christine A. Marshall-Walker,Brenda J. Barry,Brenda J. Barry,Jernej Murn,Jernej Murn,Antonis Tatarakis,Antonis Tatarakis,Muktar A. Mahajan,Herbert H. Samuels,Yang Shi,Yang Shi,Jeffrey A. Golden,Muhammad Mahajnah,Ruthie Shenhav,Christopher A. Walsh +27 more
TL;DR: This work identifies and characterize a nuclear zinc finger protein, ZNF335/NIF-1, as a causative gene for severe microcephaly, small somatic size, and neonatal death and provides the first direct genetic evidence that this pathway regulates human neurogenesis and neuronal differentiation.
Journal ArticleDOI
Expression2Kinases: mRNA Profiling Linked to Multiple Upstream Regulatory Layers
TL;DR: The X2K approach can advance the understanding of cell signaling and unravel drugs mechanisms of action by integrating chromatin immuno-precipitation data, protein-protein interactions and kinase-substrate phosphorylation reactions, and can better identify regulatory mechanisms upstream of genome-wide differences in gene expression.
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.
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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.