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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Latent Enhancers Activated by Stimulation in Differentiated Cells
Renato Ostuni,Viviana Piccolo,Iros Barozzi,Sara Polletti,Alberto Termanini,Silvia Bonifacio,Alessia Curina,Elena Prosperini,Serena Ghisletti,Gioacchino Natoli +9 more
TL;DR: In this article, the authors describe latent enhancers, regions of the genome that in terminally differentiated cells are unbound by TFs and lack the histone marks characteristic of enhancers but acquire these features in response to stimulation.
Journal ArticleDOI
The dynamic N 1 -methyladenosine methylome in eukaryotic messenger RNA
Dan Dominissini,Dan Dominissini,Sigrid Nachtergaele,Sigrid Nachtergaele,Sharon Moshitch-Moshkovitz,Eyal Peer,Eyal Peer,Nitzan Kol,Moshe Shay Ben-Haim,Moshe Shay Ben-Haim,Qing Dai,Qing Dai,Ayelet Di Segni,Mali Salmon-Divon,Wesley C. Clark,Guanqun Zheng,Tao Pan,Oz Solomon,Oz Solomon,Eran Eyal,Vera Hershkovitz,Dali Han,Dali Han,Louis C. Dore,Louis C. Dore,Ninette Amariglio,Ninette Amariglio,Gideon Rechavi,Gideon Rechavi,Chuan He,Chuan He +30 more
TL;DR: It is shown that m1A is enriched around the start codon upstream of the first splice site: it preferentially decorates more structured regions around canonical and alternative translation initiation sites, is dynamic in response to physiological conditions, and correlates positively with protein production.
Journal ArticleDOI
EZH2 Oncogenic Activity in Castration-Resistant Prostate Cancer Cells Is Polycomb-Independent
Kexin Xu,Zhenhua Jeremy Wu,Anna C. Groner,Housheng Hansen He,Changmeng Cai,Rosina T. Lis,Rosina T. Lis,Xiaoqiu Wu,Edward C. Stack,Edward C. Stack,Massimo Loda,Tao Liu,Han Xu,Laura Cato,James E. Thornton,James E. Thornton,Richard I. Gregory,Richard I. Gregory,Colm Morrissey,Robert L. Vessella,Rodolfo Montironi,Cristina Magi-Galluzzi,Philip W. Kantoff,Steven P. Balk,X. Shirley Liu,Myles Brown +25 more
TL;DR: It is found that the oncogenic function of EZH2 in cells of castration-resistant prostate cancer is independent of its role as a transcriptional repressor, and involves the ability of EzH2 to act as a coactivator for critical transcription factors including the androgen receptor.
Journal ArticleDOI
R-2HG Exhibits Anti-tumor Activity by Targeting FTO/m6A/MYC/CEBPA Signaling
Rui Su,Lei Dong,Chenying Li,Sigrid Nachtergaele,Mark Wunderlich,Ying Qing,Xiaolan Deng,Yungui Wang,Yungui Wang,Xiaocheng Weng,Chao Hu,Chao Hu,Mengxia Yu,Jennifer R. Skibbe,Qing Dai,Dongling Zou,Tong Wu,Kangkang Yu,Hengyou Weng,Huilin Huang,Kyle Ferchen,Xi Qin,Bin Zhang,Jun Qi,Atsuo T. Sasaki,David R. Plas,James E. Bradner,Minjie Wei,Guido Marcucci,Xi Jiang,James C. Mulloy,Jie Jin,Chuan He,Jianjun Chen,Jianjun Chen +34 more
TL;DR: While R-2HG accumulated in IDH1/2 mutant cancers contributes to cancer initiation, this work demonstrates anti-tumor effects of 2HG in inhibiting proliferation/survival of FTO-high cancer cells via targeting FTO/m6A/MYC/CEBPA signaling.
Journal ArticleDOI
Combinatorial transcriptional control in blood stem/progenitor cells: Genome-wide analysis of ten major transcriptional regulators
Nicola K. Wilson,Samuel D. Foster,Xiaonan Wang,Kathy Knezevic,Judith Schütte,Polynikis Kaimakis,Paulina M. Chilarska,Sarah Kinston,Willem H. Ouwehand,Elaine Dzierzak,John E. Pimanda,Marella F. T. R. de Bruijn,Berthold Göttgens +12 more
TL;DR: The power of genome-wide analysis of complex binding patterns and combinatorial interactions for ten key regulators of blood stem/progenitor cells is reported, providing the most comprehensive TF data set for any adult stem/ Progenitor cell type to date.
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