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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PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants.
Chi Nga Chow,Tzong-Yi Lee,Yu Cheng Hung,Guan Zhen Li,Kuan Chieh Tseng,Ya Hsin Liu,Po Li Kuo,Han Qin Zheng,Wen Chi Chang +8 more
TL;DR: The PlantPAN 3.0 can not only be efficiently used to investigate critical cis- and trans-regulatory elements in plant promoters, but also to reconstruct high-confidence relationships among TF–targets under specific conditions.
Journal ArticleDOI
KLRG1+ Effector CD8+ T Cells Lose KLRG1, Differentiate into All Memory T Cell Lineages, and Convey Enhanced Protective Immunity.
Dietmar Herndler-Brandstetter,Harumichi Ishigame,Ryo Shinnakasu,Valerie Plajer,Carmen Stecher,Jun Zhao,Melanie Lietzenmayer,Lina Kroehling,Akiko Takumi,Kohei Kometani,Takeshi Inoue,Yuval Kluger,Susan M. Kaech,Tomohiro Kurosaki,Takaharu Okada,Richard A. Flavell +15 more
TL;DR: It is demonstrated that developmental plasticity of KLRG1+ effector CD8+ T cells is important in promoting functionally versatile memory cells and long‐term protective immunity and drives functional diversity within memory T cell lineages and promotes enhanced anti‐influenza and anti‐tumor immunity.
Journal ArticleDOI
Multi-level engineering facilitates the production of phenylpropanoid compounds in tomato.
Yang Zhang,Eugenio Butelli,Saleh Alseekh,Takayuki Tohge,Ghanasyam Rallapalli,Jie Luo,Prashant G. Kawar,Lionel Hill,Angelo Santino,Alisdair R. Fernie,Cathie Martin +10 more
TL;DR: It is shown that AtMYB12 not only increases the demand of flavonoid biosynthesis but also increases the supply of carbon from primary metabolism, energy and reducing power, which may fuel the shikimate and phenylalanine biosynthetic pathways to supply more aromatic amino acids for secondary metabolism.
Journal ArticleDOI
Recombination initiation maps of individual human genomes
Florencia Pratto,Kevin Brick,Pavel P. Khil,Fatima Smagulova,Galina V. Petukhova,R. Daniel Camerini-Otero +5 more
TL;DR: High-resolution, individual-specific maps of meiotic DSBs in the human genome are built and analysis and comparison of the resultant PRDM9-specific, personal genome-wide maps offers insights into the mechanisms that initiate meiosis, genome evolution, crossover formation, human population structure, and predisposition to genomic disorders.
Journal ArticleDOI
Suv39h-Dependent H3K9me3 Marks Intact Retrotransposons and Silences LINE Elements in Mouse Embryonic Stem Cells
Aydan Bulut-Karslioglu,Inti A. De La Rosa-Velázquez,Fidel Ramírez,Maxim Barenboim,Megumi Onishi-Seebacher,Julia Arand,Carmen Galán,Georg E. Winter,Bettina Engist,Borbala Gerle,Roderick J. O'Sullivan,Joost H.A. Martens,Jörn Walter,Thomas Manke,Monika Lachner,Thomas Jenuwein +15 more
TL;DR: A function for Suv39h-dependent H3K9me3 chromatin to specifically repress intact LINE elements in the ESC epigenome is provided.
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.