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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Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis
Arun C. Habermann,Austin J. Gutierrez,Linh T. Bui,Stephanie L. Yahn,Nichelle I. Winters,Carla L. Calvi,Lance M. Peter,Mei-I Chung,Chase J. Taylor,Christopher S. Jetter,Latha Raju,Jamie Roberson,Guixiao Ding,Lori Wood,Jennifer M.S. Sucre,Bradley W. Richmond,Bradley W. Richmond,Ana P. Serezani,Wyatt J. McDonnell,Simon B. Mallal,Simon B. Mallal,Matthew J. Bacchetta,James E. Loyd,Ciara M. Shaver,Lorraine B. Ware,Ross M. Bremner,Rajat Walia,Timothy S. Blackwell,Timothy S. Blackwell,Timothy S. Blackwell,Nicholas E. Banovich,Jonathan A. Kropski,Jonathan A. Kropski,Jonathan A. Kropski +33 more
TL;DR: It is reported that a remarkable shift in epithelial cell phenotypes occurs in the peripheral lung in PF and several previously unrecognized epithelialcell phenotypes are identified, including a KRT5−/KRT17+ pathologic, ECM-producing epithel cell population that was highly enriched in PF lungs.
Journal ArticleDOI
Enhancer RNAs and regulated transcriptional programs
TL;DR: Emerging evidence suggesting that at least some eRNAs contribute to enhancer function is reviewed, and potential mechanisms of action of e RNAs and other ncRNAs in regulated gene expression are discussed.
Journal ArticleDOI
Regulation of macrophage development and function in peripheral tissues.
TL;DR: It is suggested that most macrophages seed the tissues during embryonic development and functionally specialize in response to cytokines and metabolites that are released by the stroma and drive the expression of unique transcription factors.
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m6A RNA Methylation Is Regulated by MicroRNAs and Promotes Reprogramming to Pluripotency
Tong Chen,Ya-Juan Hao,Ya-Juan Hao,Ying Zhang,Miao-Miao Li,Miao-Miao Li,Meng Wang,Weifang Han,Yong-Sheng Wu,Ying Lv,Ying Lv,Jie Hao,Libin Wang,Ang Li,Ang Li,Ying Yang,Ying Yang,Kang-Xuan Jin,Kang-Xuan Jin,Xu Zhao,Xu Zhao,Yuhuan Li,Xiao-Li Ping,Xiao-Li Ping,Weiyi Lai,Li-Gang Wu,Guibin Jiang,Hailin Wang,Lisi Sang,Xiu-Jie Wang,Yun-Gui Yang,Qi Zhou +31 more
TL;DR: A role for miRNAs is uncovered in regulating m( 6)A formation of mRNAs and provide a foundation for future functional studies of m(6)A modification in cell reprogramming.
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Identification of Genetic Variants That Affect Histone Modifications in Human Cells
Graham McVicker,Graham McVicker,Bryce van de Geijn,Jacob F. Degner,Carolyn E. Cain,Nicholas E. Banovich,Anil Raj,Anil Raj,Noah Lewellen,Marsha Myrthil,Yoav Gilad,Jonathan K. Pritchard +11 more
TL;DR: Hundreds of quantitative trait loci, genome-wide, that affect histone modification or RNA polymerase II (Pol II) occupancy in Yoruba lymphoblastoid cell lines (LCLs) are identified.
References
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Artem Barski,Suresh Cuddapah,Kairong Cui,Tae-Young Roh,Dustin E. Schones,Zhibin Wang,Gang Wei,Iouri Chepelev,Keji Zhao +8 more
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RAG-1-deficient mice have no mature B and T lymphocytes
Peter Mombaerts,John Iacomini,Randall S. Johnson,Karl Herrup,Susumu Tonegawa,Virginia E. Papaioannou +5 more
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.