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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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.
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A high-resolution map of active promoters in the human genome
Tae Hoon Kim,Leah O. Barrera,Ming Zheng,Chunxu Qu,Michael A. Singer,Todd Richmond,Ying Nian Wu,Roland Green,Bing Ren,Bing Ren +9 more
TL;DR: A genome-wide map of active promoters in human fibroblast cells, determined by experimentally locating the sites of PIC binding throughout the human genome is described, providing a global view of the functional relationships among transcriptional machinery, chromatin structure and gene expression in human cells.
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FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription
Mathieu Lupien,Jérôme Eeckhoute,Clifford A. Meyer,Qianben Wang,Yong Zhang,Wei Li,Jason S. Carroll,X. Shirley Liu,Myles Brown +8 more
TL;DR: It is demonstrated that genome-wide positional analyses suggest that methylation of histone H3 lysine 4 is part of the epigenetic signature that defines lineage-specific FoxA1 recruitment sites in chromatin.
Journal ArticleDOI
Signaling Pathways Downstream of Pattern-Recognition Receptors and Their Cross Talk
Myeong Sup Lee,Young Joon Kim +1 more
TL;DR: Signaling pathways downstream of PRRs and their cross talk control immune responses in effective manners and can be negatively regulated by negative feedback mechanisms and also by anti-inflammatory factors such as TGFbeta, interleukin (IL)-10, and steroids.
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Failure of B-cell differentiation in mice lacking the transcription factor EBF
Haishan Lin,Rudolf Grosschedl +1 more
TL;DR: It is shown that EBF is necessary for the generation of immunoglobulin-expressing B cells in EBF-deficient mice, and that various non-lymphoid tissues that express EBF are apparently normal in homozygous mutant mice, including olfactory neurons in which EBF was identified as Olf-1.
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Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation
Kairong Cui,Chongzhi Zang,Tae-Young Roh,Dustin E. Schones,Richard W. Childs,Weiqun Peng,Keji Zhao +6 more
TL;DR: The data suggest that gene expression changes during differentiation are programmed by chromatin modifications present at the HSC/HPC stage and provide a resource for enhancer and promoter identification.