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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Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming.
TL;DR: During transcriptionally quiescent gametic and embryonic stages, an H2A.Z(FV)/H3K4me1-containing Placeholder nucleosome deters DNA methylation, poising parental genes for either gene-specific activation or facultative repression.
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Next generation transcriptomics and genomics elucidate biological complexity of microglia in health and disease
TL;DR: In this review, insights obtained from isolated microglia transcriptome studies are presented, and compared to studies using other genome‐wide approaches, as well as the role ofmicroglia in the aging brain and in neurodegenerative conditions are discussed.
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In the loop: promoter–enhancer interactions and bioinformatics
TL;DR: This review provides a comprehensive background for future PEI studies and critically review different types of bioinformatics analysis methods and tools related to representation and visualization of PEI data, raw data processing and PEI prediction.
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Genome-wide analysis of STAT3 binding in vivo predicts effectors of the anti-inflammatory response in macrophages
TL;DR: The genomic targets of STAT3 are reported and it is shown that STAT3's transcriptional program during the AIR is highly specific to IL-10-stimulated macrophages, thatSTAT3 is a positive transcriptional regulator, and the authors predict severalputative AIR factors that merit further investigation.
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Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors.
Paloma Cejas,Yotam Drier,Yotam Drier,Yotam Drier,Koen M.A. Dreijerink,Lodewijk A.A. Brosens,Vikram Deshpande,Charles B. Epstein,Elfi B. Conemans,Folkert H.M. Morsink,Mindy K. Graham,Gerlof D. Valk,Menno R. Vriens,Carlos Fernandez-del Castillo,Cristina R. Ferrone,Tomer Adar,Michaela Bowden,Holly Whitton,Annacarolina da Silva,Alba Font-Tello,Henry W. Long,Elizabeth Gaskell,Noam Shoresh,Christopher M. Heaphy,Ewa Sicinska,Matthew H. Kulke,Matthew H. Kulke,Daniel C. Chung,Bradley E. Bernstein,Bradley E. Bernstein,Ramesh A. Shivdasani,Ramesh A. Shivdasani +31 more
TL;DR: A robust molecular stratification provides insight into cell lineage correlates of non-functional PNETs, accurately predicts disease course and can inform postoperative clinical decisions, and defines clinically relevant markers for stratification of patients with pancreatic neuroendocrine cancer.
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.