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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Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.
Stefan Bonn,Robert P. Zinzen,Charles Girardot,E. Hilary Gustafson,Alexis Perez-Gonzalez,Nicolas Delhomme,Yad Ghavi-Helm,Bartek Wilczyński,Andrew Riddell,Eileen E. M. Furlong +9 more
TL;DR: This new approach to obtain cell type–specific information on chromatin state and RNA polymerase II (Pol II) occupancy within the multicellular Drosophila melanogaster embryo identifies dynamic enhancer usage, an essential step in deciphering developmental networks.
Journal ArticleDOI
Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants
Lorenzo Pasquali,Kyle J. Gaulton,Kyle J. Gaulton,Kyle J. Gaulton,Santiago A. Rodríguez-Seguí,Loris Mularoni,Irene Miguel-Escalada,Ildem Akerman,Juan J. Tena,Ignasi Moran,Carlos Gómez-Marín,Martijn van de Bunt,Martijn van de Bunt,Martijn van de Bunt,Joan Ponsa-Cobas,Natalia Castro,Takao Nammo,Inês Cebola,Javier García-Hurtado,Miguel Angel Maestro,François Pattou,Lorenzo Piemonti,Thierry Berney,Anna L. Gloyn,Anna L. Gloyn,Philippe Ravassard,José Luis Gómez Skarmeta,Ferenc Müller,Mark I. McCarthy,Mark I. McCarthy,Mark I. McCarthy,Jorge Ferrer +31 more
TL;DR: This work mapped and examined the function of human islet cis-regulatory networks and identifies genomic sequences that are targeted by islet transcription factors to drive islet-specific gene activity and shows that most such sequences reside in clusters of enhancers that form physical three-dimensional chromatin domains.
Journal ArticleDOI
CEAS: cis-regulatory element annotation system.
TL;DR: This stand-alone extension of the web application CEAS provides summary statistics on ChIP enrichment in important genomic regions such as individual chromosomes, promoters, gene bodies or exons, and infers the genes most likely to be regulated by the binding factor under study.
Journal ArticleDOI
Regeneration of the lung alveolus by an evolutionarily conserved epithelial progenitor
William J. Zacharias,David B. Frank,Jarod A. Zepp,Michael Morley,Farrah A. Alkhaleel,Jun Kong,Su Zhou,Edward Cantu,Edward E. Morrisey +8 more
TL;DR: The results identify the AEP lineage as an evolutionarily conserved alveolar progenitor that represents a new target for human lung regeneration strategies.
Journal ArticleDOI
Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer
Shaokun Shu,Charles Y. Lin,Housheng Hansen He,Robert M. Witwicki,Doris P. Tabassum,Justin M. Roberts,Michalina Janiszewska,Sung Jin Huh,Yi Liang,Jeremy Ryan,Ernest Doherty,Hisham Mohammed,Hao Guo,Daniel G. Stover,Muhammad B. Ekram,Guillermo Peluffo,Jonathan D. Brown,Clive D'Santos,Ian E. Krop,Deborah A. Dillon,Michael R. McKeown,Christopher J. Ott,Jun Qi,Min Ni,Prakash Rao,Melissa Duarte,Shwu Yuan Wu,Cheng Ming Chiang,Lars Anders,Richard A. Young,Eric P. Winer,Antony Letai,William T. Barry,Jason S. Carroll,Henry W. Long,Myles Brown,X. Shirley Liu,X. Shirley Liu,Clifford A. Meyer,James E. Bradner,James E. Bradner,Kornelia Polyak,Kornelia Polyak +42 more
TL;DR: In this article, the preferential sensitivity of triple negative breast cancer (TNBC) cells to BET bromodomain inhibition in vitro and in vivo has been investigated and a rationale for clinical investigation and further motivation to understand mechanisms of resistance.
References
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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.