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
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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Comprehensive Integration of Single-Cell Data.
Tim Stuart,Andrew Butler,Paul J. Hoffman,Christoph Hafemeister,Efthymia Papalexi,William M. Mauck,Yuhan Hao,Marlon Stoeckius,Peter Smibert,Rahul Satija +9 more
TL;DR: A strategy to "anchor" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities.
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deepTools2: a next generation web server for deep-sequencing data analysis
Fidel Ramírez,Devon Ryan,Björn Grüning,Vivek Bhardwaj,Fabian Kilpert,Andreas S. Richter,Steffen Heyne,Friederike Dündar,Thomas Manke +8 more
TL;DR: An update to the Galaxy-based web server deepTools, which allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches, is presented.
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Histone H3K27ac separates active from poised enhancers and predicts developmental state
Menno P. Creyghton,Albert W. Cheng,G. Grant Welstead,Tristan Kooistra,Bryce W. Carey,Eveline J. Steine,Jacob H. Hanna,Michael A. Lodato,Garrett M. Frampton,Phillip A. Sharp,Laurie A. Boyer,Richard A. Young,Rudolf Jaenisch +12 more
TL;DR: The epigenetic landscape of enhancer elements in embryonic stem cells and several adult tissues in the mouse is interrogated and it is found that histone H3K27ac distinguishes active enhancers from inactive/poised enhancers and poised enhancer networks provide clues to unrealized developmental programs.
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Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
Warren A. Whyte,David A. Orlando,Denes Hnisz,Brian J. Abraham,Charles Y. Lin,Charles Y. Lin,Michael H. Kagey,Peter B. Rahl,Tong Ihn Lee,Richard A. Young +9 more
TL;DR: In this article, the ESC master transcription factors form unusual enhancer domains at most genes that control the pluripotent state, called super-enhancers, which consist of clusters of enhancers that are densely occupied by the master regulators and Mediator.
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Regulatory T Cells: Mechanisms of Differentiation and Function
TL;DR: Cellular and molecular mechanisms in the differentiation and function of regulatory T cells and their role in autoimmune and autoinflammatory disorders, allergy, acute and chronic infections, cancer, and metabolic inflammation are discussed.
References
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Alan P. Boyle,Sean Davis,Hennady P. Shulha,Paul S. Meltzer,Elliott H. Margulies,Zhiping Weng,Terrence S. Furey,Gregory E. Crawford +7 more
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Control of Pancreas and Liver Gene Expression by HNF Transcription Factors
Duncan T. Odom,Nora Zizlsperger,D. Benjamin Gordon,George W. Bell,Nicola J. Rinaldi,Heather L. Murray,Tom L. Volkert,Jörg Schreiber,P. Alexander Rolfe,David K. Gifford,Ernest Fraenkel,Graeme I. Bell,Richard A. Young +12 more
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Identification of Flt3(+) lympho-myeloid stem cells lacking erythro-megakaryocytic potential: A revised road map for adult blood lineage commitment
Jörgen Adolfsson,Robert Månsson,Natalija Buza-Vidas,Anne Hultquist,Karina Liuba,Christina Jensen,David Bryder,Liping Yang,O J Borge,Lina Thorén,Kristina Anderson,Ewa Sitnicka,Yutaka Sasaki,Mikael Sigvardsson,Sten Eirik W. Jacobsen +14 more
TL;DR: Evidence is presented for a population of cells which, although sustaining a high proliferative and combined lympho-myeloid differentiation potential, have lost the ability to adopt erythroid and megakaryocyte lineage fates.
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Opening of Compacted Chromatin by Early Developmental Transcription Factors HNF3 (FoxA) and GATA-4
TL;DR: The ability of HNF3 to open chromatin is mediated by a high affinity DNA binding site and by the C-terminal domain of the protein, which binds histones H3 and H4.
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Dissecting self-renewal in stem cells with RNA interference
Natalia Ivanova,Radu Dobrin,Rong Lu,Iulia Kotenko,John Levorse,Christina DeCoste,Xenia Schafer,Yi Lun,Ihor R. Lemischka +8 more
TL;DR: This work uses short hairpin RNA (shRNA) loss-of-function techniques to downregulate a set of gene products whose expression patterns suggest self-renewal regulatory functions, and focuses on transcriptional regulators and identifies seven genes for which shRNA-mediated depletion negatively affects self-Renewal.