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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PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix.
TL;DR: PWMScan, a fast web-based tool to scan server-resident genomes for matches to a user-supplied PWM or transcription factor binding site model from a public database, is presented.
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Deleting an Nr4a1 Super-Enhancer Subdomain Ablates Ly6C low Monocytes while Preserving Macrophage Gene Function.
Graham D. Thomas,Richard N. Hanna,Neelakantan T Vasudevan,Anouk A.J. Hamers,Casey E. Romanoski,Sara McArdle,K. Ross,Amy Blatchley,Deborah Yoakum,Bruce A. Hamilton,Zbigniew Mikulski,Mukesh K. Jain,Christopher K. Glass,Catherine C. Hedrick +13 more
TL;DR: Combining ChIP-seq and molecular approaches, a single, conserved, sub-domain within the Nr4a1 enhancer was identified that was essential for Ly6Clow monocyte development and decoupling these processes allows Ly6clow monocytes to be studied independently.
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Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts.
Jason C. Bell,David Jukam,Nicole A. Teran,Viviana I. Risca,Owen K. Smith,Whitney L Johnson,Jan M. Skotheim,William J. Greenleaf,Aaron F. Straight +8 more
TL;DR: It is shown that ChAR-seq provides unbiased, de novo identification of targets of chromatin-bound RNAs including nascent transcripts, chromosome-specific dosage compensation ncRNAs, and genome-wide trans-associated RNAs involved in co-transcriptional RNA processing.
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The regulatory network of B-cell differentiation: a focused view of early B-cell factor 1 function.
Sören Boller,Rudolf Grosschedl +1 more
TL;DR: A model in which extrinsic signals and intrinsic cues establish a permissive chromatin context upon which a regulatory network of transcription factors and epigenetic modifiers act to guide the differentiation of hematopoietic lineages is proposed.
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Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates
Zachary Baker,Molly Schumer,Molly Schumer,Yuki Haba,Lisa Bashkirova,Chris Holland,Gil G. Rosenthal,Molly Przeworski +7 more
TL;DR: It is shown that swordtail fish carrying only a partial but conserved ortholog share recombination properties with PRDM9 knock-outs, suggesting that all domains are necessary for directing recombination.
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
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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.