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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Identification of the tumour transition states occurring during EMT
Ievgenia Pastushenko,Audrey Brisebarre,Alejandro Sifrim,Alejandro Sifrim,Marco Fioramonti,Tatiana Revenco,Soufiane Boumahdi,Alexandra Van Keymeulen,Daniel Brown,Virginie Moers,Sophie Lemaire,Sarah De Clercq,Esmeralda Minguijón,Cédric Balsat,Youri Sokolow,Christine Dubois,Florian De Cock,Samuel Scozzaro,Federico Sopena,Angel Lanas,Nicky D'Haene,Isabelle Salmon,Jean-Christophe Marine,Thierry Voet,Thierry Voet,Panagiota A. Sotiropoulou,Cédric Blanpain +26 more
TL;DR: A large panel of cell surface markers in skin and mammary primary tumours is screened, and the existence of multiple tumour subpopulations associated with different EMT stages are identified: from epithelial to completely mesenchymal states, passing through intermediate hybrid states.
Journal ArticleDOI
N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells
TL;DR: Two proteins are identified, the putative m6A MTase, methyltransferase-like 3 (Mettl3; ref. ), and a related but uncharacterized protein Mettl14, that function synergistically to control m 6A formation in mammalian cells.
Journal ArticleDOI
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
TL;DR: Based on the biological observation that histone modifications tend to cluster to form domains, a method that identifies spatial clusters of signals unlikely to appear by chance is presented that outperforms existing methods in the identification of ChIP-enriched signals for histone modification profiles.
Journal ArticleDOI
Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome
Miao Yu,Gary C. Hon,Keith E. Szulwach,Chun-Xiao Song,Liang Zhang,Audrey Kim,Xuekun Li,Qing Dai,Yin Shen,Beomseok Park,Jung Hyun Min,Peng Jin,Bing Ren,Chuan He +13 more
TL;DR: Application of Tet-assisted bisulfite sequencing to embryonic stem cells not only confirms widespread distribution of 5hmC in the mammalian genome but also reveals sequence bias and strand asymmetry at5hmC sites.
Journal ArticleDOI
c-Myc Is a Universal Amplifier of Expressed Genes in Lymphocytes and Embryonic Stem Cells
Zuqin Nie,Gangqing Hu,Gang Wei,Kairong Cui,Arito Yamane,Wolfgang Resch,Ruoning Wang,Douglas R. Green,Lino Tessarollo,Rafael Casellas,Keji Zhao,David Levens +11 more
TL;DR: To observe Myc target expression and function in a system where Myc is temporally and physiologically regulated, the transcriptomes and the genome-wide distributions of Myc, RNA polymerase II, and chromatin modifications were compared during lymphocyte activation and in ES cells as well.
References
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Genome-wide location and function of dna binding proteins
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