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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Differential DNA repair underlies mutation hotspots at active promoters in cancer genomes
TL;DR: It is shown that increased mutation density at gene promoters can be linked to promoter activity and differential nucleotide excision repair (NER), and it is observed that melanomas with an ultraviolet-induced DNA damage mutation signature show greatest enrichment of promoter mutations, whereas cancers that are not highly dependent on NER show no sign of such enrichment.
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Brown-adipose-tissue macrophages control tissue innervation and homeostatic energy expenditure
Yochai Wolf,Sigalit Boura-Halfon,Nina Cortese,Zhana Haimon,Hadas Sar Shalom,Yael Kuperman,Vyacheslav Kalchenko,Alexander Brandis,Eyal David,Yifat Segal-Hayoun,Louise Chappell-Maor,Avraham Yaron,Steffen Jung +12 more
TL;DR: A previously unappreciated homeostatic role for macrophages in the control of tissue innervation is reported, which might contribute to the phenotype by repulsion of sympathetic axons expressing the transmembrane semaphorin Sema6A.
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Comprehensive Profiling of an Aging Immune System Reveals Clonal GZMK+ CD8+ T Cells as Conserved Hallmark of Inflammaging
Denis A. Mogilenko,Oleg Shpynov,Oleg Shpynov,Prabhakar S. Andhey,Laura L. Arthur,Amanda Swain,Ekaterina Esaulova,Simone Brioschi,Irina Shchukina,Martina Kerndl,Monika Bambouskova,Zhangting Yao,Anwesha Laha,Konstantin Zaitsev,Samantha Burdess,Susan Gillfilan,Sheila A. Stewart,Marco Colonna,Maxim N. Artyomov +18 more
TL;DR: This work defined organ-specific and common immune alterations and identified a subpopulation of age-associated granzyme K-expressing CD8+ T (Taa) cells that are distinct from T effector memory (Tem) cells, a potential target to address age- associated dysfunctions of the immune system.
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Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs
TL;DR: Random displacement amplification sequencing (RamDA-seq) is described, the first full-length total RNA-sequencing method for single cells and shows high sensitivity to non-poly(A) RNA and near-complete full- lengths transcript coverage.
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Collagen density regulates the activity of tumor-infiltrating T cells
Dorota Ewa Kuczek,Anne Mette Hvid Larsen,Anne Mette Hvid Larsen,Marie-Louise Thorseth,Marco Carretta,Adrija Kalvisa,Majken S. Siersbæk,Ana Micaela Carnaz Simoes,Anne Roslind,Lars H. Engelholm,Elfriede Noessner,Marco Donia,Inge Marie Svane,Per thor Straten,Per thor Straten,Lars Grøntved,Daniel H. Madsen +16 more
TL;DR: Whole-transcriptome analysis of 3D-cultured T cells revealed that a high-density matrix induces downregulation of cytotoxic activity markers and upregulation of regulatory T cell markers that could be essential for suppression of T cell activity in the tumor microenvironment.
References
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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.