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.
Journal ArticleDOI
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.
Journal ArticleDOI
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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Journal ArticleDOI
A two-step, PU.1-dependent mechanism for developmentally regulated chromatin remodeling and transcription of the c-fms gene.
Hanna Krysinska,Maarten Hoogenkamp,Richard Ingram,Nicola K. Wilson,Hiromi Tagoh,Peter Laslo,Harinder Singh,Constanze Bonifer +7 more
TL;DR: The two-step mechanism of developmental gene activation that is described here may be utilized to regulate gene activity in a variety of developmental pathways.
Journal ArticleDOI
C/EBPα:AP-1 leucine zipper heterodimers bind novel DNA elements, activate the PU.1 promoter and direct monocyte lineage commitment more potently than C/EBPα homodimers or AP-1
TL;DR: It is demonstrated that C/EBPα also zippers with AP-1 proteins and that this interaction allows contact with novel DNA elements and induction of monocyte lineage commitment in myeloid progenitors.
Journal ArticleDOI
Transcriptomic profiling identifies a PU.1 regulatory network in macrophages.
TL;DR: A multi-levelPU.1 transcriptional network with novel validated PU.1 target genes in macrophages and microglia is presented and an alternative transcript of the novel PU.
Journal ArticleDOI
Transcription Factor PU.1 Controls Transcription Start Site Positioning and Alternative TLR4 Promoter Usage
TL;DR: A detailed in vivo and in vitro study of the murine Tlr4 gene, including analysis of transcription start site location, transcription factor occupancy, and activities of its proximal regulatory sequences identified a PU.1-dependent myeloid promoter, which is conserved between humans and mouse.
Book ChapterDOI
Gene regulatory networks orchestrating B cell fate specification, commitment, and differentiation.
Kay L. Medina,Harinder Singh +1 more
TL;DR: A comprehensive developmental model is proposed that invokes sequentially acting regulatory networks which dictate the generation of B cells from multipotential hematopoietic progenitors.