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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Dissecting neural differentiation regulatory networks through epigenetic footprinting
Michael J. Ziller,Michael J. Ziller,Reuven Edri,Yakey Yaffe,Julie Donaghey,Julie Donaghey,Ramona Pop,Ramona Pop,William Mallard,William Mallard,Robbyn Issner,Casey A. Gifford,Casey A. Gifford,Alon Goren,Alon Goren,Jeffrey C. Xing,Hongcang Gu,Davide Cacchiarelli,Alexander M. Tsankov,Alexander M. Tsankov,Charles B. Epstein,John L. Rinn,John L. Rinn,Tarjei S. Mikkelsen,Oliver Kohlbacher,Andreas Gnirke,Bradley E. Bernstein,Bradley E. Bernstein,Yechiel Elkabetz,Alexander Meissner,Alexander Meissner +30 more
TL;DR: A computational framework to infer key regulators of each cell-state transition based on the progressive remodelling of the epigenetic landscape is developed and a general framework, not limited to the context of the neural lineage, to dissect regulatory circuits of differentiation is outlined.
Journal ArticleDOI
Accurate Recycling of Parental Histones Reproduces the Histone Modification Landscape during DNA Replication.
Nazaret Reverón-Gómez,Cristina González-Aguilera,Kathleen R. Stewart-Morgan,Nataliya Petryk,Valentin Flury,Simona Graziano,Jens Vilstrup Johansen,Janus S. Jakobsen,Constance Alabert,Anja Groth +9 more
TL;DR: ChOR-seq demonstrates that accurate parental histone recycling preserves positional information and allows PTM transmission to daughter cells while modification of new histones gives rise to complex epigenome fluctuations across the cell cycle that could underlie cell-to-cell heterogeneity.
Journal ArticleDOI
Epigenetic landscapes reveal transcription factors that regulate CD8 + T cell differentiation
Bingfei Yu,Kai Zhang,J. Justin Milner,Clara Toma,Runqiang Chen,James P. Scott-Browne,Renata M. Pereira,Shane Crotty,Shane Crotty,John T. Chang,Matthew E. Pipkin,Wei Wang,Ananda W. Goldrath +12 more
TL;DR: A new bioinformatics method using the PageRank algorithm is developed to reveal key TFs that influence the generation of effector and memory populations in naive, terminal-effector, memory-precursor and memory CD8+ T cell populations induced during the in vivo response to bacterial infection.
Journal ArticleDOI
DAF-16 employs the chromatin remodeller SWI/SNF to promote stress resistance and longevity
Christian G. Riedel,Robert H. Dowen,Guinevere F. Lourenco,Natalia V. Kirienko,Thomas Heimbucher,Jason A. West,Sarah K. Bowman,Robert E. Kingston,Andrew Dillin,John M. Asara,John M. Asara,Gary Ruvkun +11 more
TL;DR: Insight is given into the mechanisms of DAF-16/FOXO-mediated transcriptional regulation and a critical link between ATP-dependent chromatin remodelling and lifespan regulation is established.
Journal ArticleDOI
Acetate Promotes T Cell Effector Function during Glucose Restriction
Jing Qiu,Matteo Villa,David E. Sanin,Michael D. Buck,David O’Sullivan,Reagan W. Ching,Mai Matsushita,Katarzyna M. Grzes,Frances Winkler,Chih-Hao Chang,Jonathan D. Curtis,Ryan Kyle,Nikki van Teijlingen Bakker,Mauro Corrado,Fabian Haessler,Francesca Alfei,Joy Edwards-Hicks,Leonard B. Maggi,Dietmar Zehn,Takeshi Egawa,Bertram Bengsch,Ramon I. Klein Geltink,Thomas Jenuwein,Edward J. Pearce,Edward J. Pearce,Erika L. Pearce +25 more
TL;DR: Hyporesponsive T cells can be epigenetically remodeled and reactivated by acetate, suggesting that pathways regulating the use of substrates alternative to glucose could be therapeutically targeted to promote T cell function during cancer.
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