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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Stromal cues regulate the pancreatic cancer epigenome and metabolome.
Mara H. Sherman,Ruth T. Yu,Tiffany W. Tseng,Cristovão M. Sousa,Sihao Liu,Morgan L. Truitt,Nanhai He,Ning Ding,Christopher Liddle,Annette R. Atkins,Mathias Leblanc,Eric A. Collisson,John M. Asara,Alec C. Kimmelman,Alec C. Kimmelman,Michael Downes,Ronald M. Evans +16 more
TL;DR: This work suggests the existence of a molecular “AND-gate” such that tumor activation is the consequence of mutant Kras and stromal cues, providing insight into the role of the tumor microenvironment in the origin and treatment of Ras-driven tumors.
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PU.1 Level-Directed Chromatin Structure Remodeling at the Irf8 Gene Drives Dendritic Cell Commitment
Jörg Schönheit,Christiane Kuhl,Marie Luise Gebhardt,Francisco Fernández Klett,Pia Riemke,Marina Scheller,Gang Huang,Ronald Naumann,Achim Leutz,Carol Stocking,Josef Priller,Miguel A. Andrade-Navarro,Frank Rosenbauer,Frank Rosenbauer +13 more
TL;DR: PU.1 is delineated as a concentration-dependent rheostat of myeloid lineage selection by controlling long-distance contacts between regulatory elements and suggested that specific higher-order chromatin remodeling at the Irf8 gene determines DC differentiation.
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LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome.
Alaguraj Veluchamy,Teddy Jégu,Federico Ariel,David Latrasse,Kiruthiga Mariappan,Soon-Kap Kim,Martin Crespi,Heribert Hirt,Catherine Bergounioux,Cécile Raynaud,Moussa Benhamed +10 more
TL;DR: A general role of LHP1 is revealed from local to higher conformation levels of chromatin configuration to determine its accessibility to define gene expression patterns to control transcriptional co-regulation in Arabidopsis thaliana.
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Anti-inflammatory Chromatinscape Suggests Alternative Mechanisms of Glucocorticoid Receptor Action
Kyu-Seon Oh,Heta Patel,Rachel A. Gottschalk,Wai Shing Lee,Songjoon Baek,Iain D. C. Fraser,Gordon L. Hager,Myong-Hee Sung +7 more
TL;DR: Monitoring the epigenomic landscape of macrophages found that the gene‐inducing activity of GR is crucial for boosting inhibitors of inflammatory factors, and cautions the idea that GR ligands selectively promoting trans‐repression should improve therapeutic outcome.
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Genome-wide prediction of cis-regulatory regions using supervised deep learning methods
TL;DR: The predicted annotations of cis-regulatory regions will provide broad utility for genome interpretation from functional genomics to clinical applications and inspires the development of other advanced neural network models for further improvement of genome annotations.
References
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RAG-1-deficient mice have no mature B and T lymphocytes
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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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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.