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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Enhancers as information integration hubs in development: lessons from genomics
Christa Buecker,Joanna Wysocka +1 more
TL;DR: It is proposed that enhancers serve as information integration hubs, at which instructions encoded by the genome are read in the context of a specific cellular state, signaling milieu and chromatin environment, allowing for exquisitely precise spatiotemporal control of gene expression during embryogenesis.
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Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis
Michael N. Weedon,Inês Cebola,Ann-Marie Patch,Sarah E. Flanagan,Elisa De Franco,Richard Caswell,Santiago A. Rodríguez-Seguí,Charles Shaw-Smith,Candy H.-H. Cho,Hana Lango Allen,Jayne A L Houghton,Christian L. Roth,Rongrong Chen,Khalid Hussain,Phil Marsh,Ludovic Vallier,Anna Murray,Sian Ellard,Jorge Ferrer,Andrew T. Hattersley +19 more
TL;DR: This analysis uncovered six different recessive mutations in a previously uncharacterized ∼400-bp sequence located 25 kb downstream of PTF1A (encoding pancreas-specific transcription factor 1a) in ten families with pancreatic agenesis.
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Signaling by Nuclear Receptors
TL;DR: Nuclear receptors are activated by lipid-soluble signals (e.g., steroid hormones) that cross the plasma membrane and once activated, most function as transcription factors to control gene expression for numerous biological processes.
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Discrete functions of nuclear receptor Rev-erbα couple metabolism to the clock
Yuxiang Zhang,Bin Fang,Matthew J. Emmett,Manashree Damle,Zheng Sun,Zheng Sun,Dan Feng,Sean M. Armour,Jarrett R. Remsberg,Jennifer Jager,Raymond E. Soccio,David J. Steger,Mitchell A. Lazar +12 more
TL;DR: It is shown that Rev-erbα modulates the clock and metabolism by different genomic mechanisms, which provides a universal mechanism for self-sustained control of the molecular clock across all tissues.
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Synergistic Activation of Inflammatory Cytokine Genes by Interferon-γ-Induced Chromatin Remodeling and Toll-like Receptor Signaling
Yu Qiao,Eugenia G. Giannopoulou,Chun Hin Chan,Sung Ho Park,Shiaoching Gong,Janice Chen,Xiaoyu Hu,Xiaoyu Hu,Olivier Elemento,Lionel B. Ivashkiv,Lionel B. Ivashkiv +10 more
TL;DR: This work found that IFN-γ induced sustained occupancy of transcription factors STAT1, IRF-1, and associated histone acetylation at promoters and enhancers at the TNF, IL6, and IL12B loci and provided a synergy mechanism whereby IFN -γ creates a primed chromatin environment to augment TLR-induced gene transcription.
References
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High-resolution profiling of histone methylations in the human genome.
Artem Barski,Suresh Cuddapah,Kairong Cui,Tae-Young Roh,Dustin E. Schones,Zhibin Wang,Gang Wei,Iouri Chepelev,Keji Zhao +8 more
TL;DR: High-resolution maps for the genome-wide distribution of 20 histone lysine and arginine methylations as well as histone variant H2A.Z, RNA polymerase II, and the insulator binding protein CTCF across the human genome using the Solexa 1G sequencing technology are generated.
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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
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RAG-1-deficient mice have no mature B and T lymphocytes
Peter Mombaerts,John Iacomini,Randall S. Johnson,Karl Herrup,Susumu Tonegawa,Virginia E. Papaioannou +5 more
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
Xi Chen,Han Xu,Ping Yuan,Fang Fang,Fang Fang,Mikael Huss,Vinsensius B. Vega,Eleanor Wong,Yuriy L. Orlov,Weiwei Zhang,Weiwei Zhang,Jianming Jiang,Jianming Jiang,Yuin-Han Loh,Yuin-Han Loh,Hock Chuan Yeo,Zhen Xuan Yeo,Vipin Narang,Kunde R Govindarajan,Bernard Leong,Atif Shahab,Yijun Ruan,Guillaume Bourque,Wing-Kin Sung,Neil D. Clarke,Chia-Lin Wei,Huck-Hui Ng,Huck-Hui Ng +27 more
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.