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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Macrophage heterogeneity in the context of rheumatoid arthritis
TL;DR: Preliminary results in mouse models of arthritis have contributed to the understanding of the phenotype and ontogeny of synovial macrophages, and to deciphering the properties of monocyte-derived infiltrating and tissue-resident macrophage properties.
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Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor
TL;DR: It is shown thatcircRNAs of EGF-stimulated mammary cells are stably expressed, while mRNAs and microRNAs change within minutes, implying that altered abundance of circRNAs, unlike changes in the levels of other RNAs, might not play critical roles in signaling cascades and downstream transcriptional networks that rapidly commit cells to specific outcomes.
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Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin.
Sai Ma,Bing Zhang,Lindsay M. LaFave,Andrew S. Earl,Zachary Chiang,Yan Hu,Jiarui Ding,Alison Brack,Vinay K. Kartha,Tristan Tay,Travis Law,Caleb A. Lareau,Ya-Chieh Hsu,Aviv Regev,Aviv Regev,Aviv Regev,Jason D. Buenrostro,Jason D. Buenrostro +17 more
TL;DR: This work computationally infer chromatin potential as a quantitative measure of chromatin lineage-priming and use it to predict cell fate outcomes, and develops simultaneous high-throughput ATAC and RNA expression with sequencing (SHARE-seq), a highly scalable approach for measurement of Chromatin accessibility and gene expression in the same single cell.
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Integrative Genome-wide Analysis Reveals Cooperative Regulation of Alternative Splicing by hnRNP Proteins
Stephanie C. Huelga,Anthony Q. Vu,Justin D. Arnold,Tiffany Y. Liang,Patrick Liu,Bernice Y. Yan,John Paul Donohue,Lily Shiue,Shawn Hoon,Sydney Brenner,Manuel Ares,Gene W. Yeo,Gene W. Yeo +12 more
TL;DR: A comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate alternative pre-mRNA splicing (AS) in human cells.
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Foxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification
Robert M. Samstein,Aaron Arvey,Steven Z. Josefowicz,Xiao Peng,Alex Reynolds,Richard Sandstrom,Shane Neph,Peter J. Sabo,Jeong M. Kim,Will Liao,Ming O. Li,Christina S. Leslie,John A. Stamatoyannopoulos,Alexander Y. Rudensky +13 more
TL;DR: In a late cellular differentiation process, Foxp3 defines Treg cell functionality in an "opportunistic" manner by largely exploiting the preformed enhancer network instead of establishing a new enhancer landscape.
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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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.