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 single-cell genomics data by coupled nonnegative matrix factorizations
Zhana Duren,Xi Chen,Mahdi Zamanighomi,Wanwen Zeng,Wanwen Zeng,Ansuman T. Satpathy,Howard Y. Chang,Yong Wang,Wing Hung Wong +8 more
TL;DR: This paper develops an approach for its solution based on the coupling of two nonnegative matrix factorizations (coupled NMF) and suggests the method should be useful for integrative single-cell genomics analysis tasks such as the joint analysis of single- Cell RNA-sequencing and single- cell ATAC- Sequencing data.
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Erk1/2 Activity Promotes Chromatin Features and RNAPII Phosphorylation at Developmental Promoters in Mouse ESCs
TL;DR: Findings underscore a key role for Erk1/2 activation in promoting the primed status of developmental genes in mouse ES cells and suggest that the transcription complex at developmental genes is different than the complexes formed at other genes, offering alternative pathways of regulation.
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Acetylation-dependent regulation of PD-L1 nuclear translocation dictates the efficacy of anti-PD-1 immunotherapy
Yang Gao,Yang Gao,Naoe Taira Nihira,Naoe Taira Nihira,Naoe Taira Nihira,Xia Bu,Chen Chu,Jinfang Zhang,Aleksandra Kolodziejczyk,Yizeng Fan,Yizeng Fan,Ngai Ting Chan,Leina Ma,Jing Liu,Dong Wang,Xiaoming Dai,Huadong Liu,Masaya Ono,Akira Nakanishi,Hiroyuki Inuzuka,Brian J. North,Yu Han Huang,Samanta Sharma,Yan Geng,Wei Xu,X. Shirley Liu,Lei Li,Yoshio Miki,Piotr Sicinski,Gordon J. Freeman,Wenyi Wei +30 more
TL;DR: It is reported that PD-L1 translocates from the plasma membrane into the nucleus through interactions with components of the endocytosis and nucleocytoplasmic transport pathways, regulated by p300-mediated acetylation and HDAC2-dependent deacetylation of PD- L1.
Journal ArticleDOI
Identification and analysis of adenine N6-methylation sites in the rice genome.
Chao Zhou,Changshi Wang,Hongbo Liu,Qiangwei Zhou,Qian Liu,Yan Guo,Ting Peng,Jiaming Song,Jianwei Zhang,Ling-Ling Chen,Yu Zhao,Zhixiong Zeng,Dao-Xiu Zhou,Dao-Xiu Zhou +13 more
TL;DR: A map of N6-methyladenine in the rice genome is provided, its association with gene expression and 5-methylcytosine is examined and a potential demethylase for this epigenomic mark is reported.
Journal ArticleDOI
Epigenomic landscapes of retinal rods and cones
Alisa Mo,Chongyuan Luo,Fred P. Davis,Eran A. Mukamel,Gilbert L. Henry,Joseph R. Nery,Mark A. Urich,Serge Picard,Ryan Lister,Ryan Lister,Sean R. Eddy,Michael A. Beer,Michael A. Beer,Joseph R. Ecker,Jeremy Nathans +14 more
TL;DR: The epigenomic landscapes of rods and cones are defined, revealing features relevant to photoreceptor development and function and Surprisingly, a substantial fraction of DNA hypo-methylated regions in adult rods that are not in active chromatin are found.
References
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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.