Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
Sven Heinz,Christopher Benner,Nathanael J. Spann,Eric Bertolino,Yin C. Lin,Peter Laslo,Jason X. Cheng,Cornelis Murre,Harinder Singh,Harinder Singh,Christopher K. Glass +10 more
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TLDR
It is demonstrated in macrophages and B cells that collaborative interactions of the common factor PU.1 with small sets of macrophage- or B cell lineage-determining transcription factors establish cell-specific binding sites that are associated with the majority of promoter-distal H3K4me1-marked genomic regions.About:
This article is published in Molecular Cell.The article was published on 2010-05-28 and is currently open access. It has received 9620 citations till now. The article focuses on the topics: Pioneer factor & General transcription factor.read more
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A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution
Takeshi Kawakami,Linnéa Smeds,Niclas Backström,Arild Husby,Anna Qvarnström,Carina F. Mugal,Pall I Olason,Hans Ellegren +7 more
TL;DR: It is found that flycatcher and zebra finch chromosomes are entirely syntenic but that inversions at mean rates of 1.5–2.0 event per chromosome have changed the organization within chromosomes, rates high enough for inversions to potentially have been involved with many speciation events during avian evolution.
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An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder.
Donna M. Werling,Harrison Brand,Harrison Brand,Joon Yong An,Matthew R. Stone,Lingxue Zhu,Joseph T. Glessner,Joseph T. Glessner,Ryan L. Collins,Shan Dong,Ryan M. Layer,Eirene Markenscoff-Papadimitriou,Andrew Farrell,Grace Schwartz,Harold Z. Wang,Benjamin Currall,Benjamin Currall,Xuefang Zhao,Xuefang Zhao,Jeanselle Dea,Clif Duhn,Carolyn A. Erdman,Michael C. Gilson,Rachita Yadav,Rachita Yadav,Robert E. Handsaker,Robert E. Handsaker,Seva Kashin,Seva Kashin,Lambertus Klei,Jeffrey D. Mandell,Tomasz J. Nowakowski,Yuwen Liu,Sirisha Pochareddy,Louw Smith,Michael F. Walker,Matthew J. Waterman,Xin He,Arnold R. Kriegstein,John L.R. Rubenstein,Nenad Sestan,Steven A. McCarroll,Steven A. McCarroll,Benjamin M. Neale,Benjamin M. Neale,Hilary Coon,A. Jeremy Willsey,Joseph D. Buxbaum,Mark J. Daly,Mark J. Daly,Matthew W. State,Aaron R. Quinlan,Gabor T. Marth,Kathryn Roeder,Bernie Devlin,Michael E. Talkowski,Stephen Sanders +56 more
TL;DR: Analyses of 519 autism spectrum disorder families did not identify association with any categories after correction for 4,123 effective tests, and the work suggests that robust results from WGS studies will require large cohorts and strategies that consider the substantial multiple-testing burden.
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HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models
Ivan V. Kulakovskiy,Ivan V. Kulakovskiy,Ilya E. Vorontsov,Ivan S. Yevshin,Anastasiia V. Soboleva,Artem S. Kasianov,Haitham Ashoor,Wail Ba-alawi,Vladimir B. Bajic,Yulia A. Medvedeva,Fedor A. Kolpakov,Vsevolod J. Makeev,Vsevolod J. Makeev,Vsevolod J. Makeev +13 more
TL;DR: The expanded and enhanced version of HOCOMOCO now provides position weight matrix (PWM) models for binding sites of 601 human TFs and, in addition, PWMs for 396 mouse TFs, and introduces the largest up to date collection of dinucleotide PWM models for 86 (52) human (mouse) TFs.
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SREBP1 Contributes to Resolution of Pro-inflammatory TLR4 Signaling by Reprogramming Fatty Acid Metabolism
Yumiko Oishi,Yumiko Oishi,Nathanael J. Spann,Verena M. Link,Evan D. Muse,Tobias Strid,Chantle Edillor,Matthew J. Kolar,Takashi Matsuzaka,Sumio Hayakawa,Jenhan Tao,Minna U. Kaikkonen,Aaron F. Carlin,Michael T. Lam,Ichiro Manabe,Hitoshi Shimano,Alan Saghatelian,Christopher K. Glass +17 more
TL;DR: It is shown that SREBP1 contributes to the resolution phase of TLR4-induced gene activation by reprogramming macrophage lipid metabolism and results in the uncoupling of NFκB binding from gene activation.
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Widespread long-range cis-regulatory elements in the maize genome.
William A. Ricci,Zefu Lu,Lexiang Ji,Alexandre P. Marand,Christina L. Ethridge,Nathalie G. Murphy,Jaclyn M. Noshay,Mary Galli,María Katherine Mejía-Guerra,Maria Colomé-Tatché,Frank Johannes,M. Jordan Rowley,Victor G. Corces,Jixian Zhai,Michael J. Scanlon,Edward S. Buckler,Andrea Gallavotti,Nathan M. Springer,Robert J. Schmitz,Robert J. Schmitz,Xiaoyu Zhang +20 more
TL;DR: Functional support is provided for the widespread existence of CREs that act over large genomic distances to control gene expression in the maize genome.
References
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TL;DR: The introduction of a mutation in RAG-1 into the germline of mice via gene targeting in embryonic stem cells is described and it is shown that this mutation either activates or catalyzes the V(D)J recombination reaction of immunoglobulin and T cell receptor genes.
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Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells
Xi Chen,Han Xu,Ping Yuan,Fang Fang,Fang Fang,Mikael Huss,Vinsensius B. Vega,Eleanor Wong,Yuriy L. Orlov,Weiwei Zhang,Weiwei Zhang,Jianming Jiang,Jianming Jiang,Yuin-Han Loh,Yuin-Han Loh,Hock Chuan Yeo,Zhen Xuan Yeo,Vipin Narang,Kunde R Govindarajan,Bernard Leong,Atif Shahab,Yijun Ruan,Guillaume Bourque,Wing-Kin Sung,Neil D. Clarke,Chia-Lin Wei,Huck-Hui Ng,Huck-Hui Ng +27 more
TL;DR: This study uses chromatin immunoprecipitation coupled with ultra-high-throughput DNA sequencing to map the locations of TF-binding sites and identifies important features of the transcriptional regulatory networks that define ES-cell identity.
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Genome-scale DNA methylation maps of pluripotent and differentiated cells
Alexander Meissner,Tarjei S. Mikkelsen,Tarjei S. Mikkelsen,Hongcang Gu,Marius Wernig,Jacob H. Hanna,Andrey Sivachenko,Xiaolan Zhang,Bradley E. Bernstein,Bradley E. Bernstein,Chad Nusbaum,David B. Jaffe,Andreas Gnirke,Rudolf Jaenisch,Eric S. Lander +14 more
TL;DR: Low-throughput reduced representation bisulphite sequencing is established as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.