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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FOXA1, GATA3 and PPARɣ Cooperate to Drive Luminal Subtype in Bladder Cancer: A Molecular Analysis of Established Human Cell Lines
Joshua I. Warrick,Joshua I. Warrick,Vonn Walter,Hironobu Yamashita,Eunah Chung,Lauren Shuman,Vasty Osei Amponsa,Zongyu Zheng,Wilson Chan,Tiffany L. Whitcomb,Feng Yue,Tejaswi Iyyanki,Yuka Imamura Kawasawa,Matthew Kaag,Wansong Guo,Jay D. Raman,Joo-Seop Park,David J. DeGraff,David J. DeGraff +18 more
TL;DR: This analysis identified a set of human cell lines suitable for the study of molecular subtypes in bladder cancer, and indicates a cooperative regulatory network consisting of GATA3, FOXA1, and PPARɣ drive luminal cell fate.
Journal ArticleDOI
CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities
M. Sanchez-Castillo,David Ruau,Adam C. Wilkinson,Felicia S L Ng,Rebecca Hannah,Evangelia Diamanti,Patrick Lombard,Nicola K. Wilson,Berthold Göttgens +8 more
TL;DR: CODEX provides one of the most complete resources of publicly available NGS data for the direct interrogation of transcriptional programmes that regulate cellular identity and fate in the context of mammalian development, homeostasis and disease.
Journal ArticleDOI
Tissue-specific RNA expression marks distant-acting developmental enhancers.
Han Wu,Alexander Nord,Jennifer A. Akiyama,Malak Shoukry,Veena Afzal,Edward M. Rubin,Len A. Pennacchio,Axel Visel +7 more
TL;DR: The results demonstrate that tissue-specific e RNA expression is a common feature of in vivo enhancers, as well as a major source of extragenic transcription, and that eRNA expression signatures can be used to predict tissue- specific enhancers independent of known epigenomic enhancer marks.
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Region-specific RNA m6A methylation represents a new layer of control in the gene regulatory network in the mouse brain
Mengqi Chang,Hongyi Lv,Hongyi Lv,Weilong Zhang,Chunhui Ma,Xue He,Shunli Zhao,Zhi Wei Zhang,Yi-Xin Zeng,Shuhui Song,Yamei Niu,Wei-Min Tong +11 more
TL;DR: The results imply that RNA m6A methylation is a newly identified element in the region-specific gene regulatory network in the mouse brain, and is likely to be used for selective recognition of target mRNAs by FMRP in the synapse.
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Metabolic control of regulatory T cell (Treg) survival and function by Lkb1.
Nanhai He,Weiwei Fan,Brian Henriquez,Ruth T. Yu,Annette R. Atkins,Christopher Liddle,Ye Zheng,Michael Downes,Ronald M. Evans +8 more
TL;DR: This work defines a metabolic checkpoint in Tregs that couples metabolic regulation to immune homeostasis and tolerance and highlights LKB1 as metabolic regulator that links cellular metabolism to immune cell functions.
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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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
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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.