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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Cooperativity and equilibrium with FOXA1 define the androgen receptor transcriptional program
TL;DR: It is shown that AR directly binds chromatin through the androgen-response elements (AREs), which is not required for AR-chromatin interaction, but instrumental in recruiting AR to low-affinity half-AREs by opening local chromatin around adjacent FKHD sites.
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Transcription elongation factors represent in vivo cancer dependencies in glioblastoma
Tyler E. Miller,Tyler E. Miller,Brian B. Liau,Brian B. Liau,Lisa C. Wallace,Andrew R. Morton,Andrew R. Morton,Qi Xie,Deobrat Dixit,Daniel C. Factor,Leo J.Y. Kim,Leo J.Y. Kim,James J. Morrow,Qiulian Wu,Stephen C. Mack,Stephen C. Mack,Christopher G. Hubert,Christopher G. Hubert,Shawn M. Gillespie,Shawn M. Gillespie,William A. Flavahan,William A. Flavahan,Thomas Hoffmann,Rohit Thummalapalli,Rohit Thummalapalli,Michael T. Hemann,Patrick J. Paddison,Craig Horbinski,Johannes Zuber,Peter C. Scacheri,Bradley E. Bernstein,Bradley E. Bernstein,Paul J. Tesar,Jeremy N. Rich,Jeremy N. Rich,Jeremy N. Rich +35 more
TL;DR: In this article, the authors adapted pooled RNA interference (RNAi) screening technology for use in orthotopic patient-derived xenograft models, creating a high-throughput negative-selection screening platform in a functional in vivo tumour microenvironment.
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Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors.
Darko Barišić,Michael B. Stadler,Michael B. Stadler,Mario Iurlaro,Dirk Schübeler,Dirk Schübeler +5 more
TL;DR: Genetic deletion of mammalian chromatin remodelling complexes reveals that mammalian ISWI is critical for nucleosomal periodicity and nuclear organization and that transcription factors rely on specific remodelling pathways for correct genomic binding.
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Fragile X mental retardation protein modulates the stability of its m6A-marked messenger RNA targets.
Feiran Zhang,Yunhee Kang,Mengli Wang,Yujing Li,Tianlei Xu,Wei Yang,Hongjun Song,Hao Wu,Qiang Shu,Peng Jin +9 more
TL;DR: Biochemical analyses indicate that FMRP regulates the stability of its m6A‐marked mRNA targets through YTHDF2, which could potentially contribute to the molecular pathogenesis of FXS, and transcriptome‐wide gene expression profiling suggests that M6A is a widespread epitranscriptomic modification in brain.
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An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease.
Raffaella Nativio,Yemin Lan,Greg Donahue,Simone Sidoli,Simone Sidoli,Amit Berson,Ananth R. Srinivasan,Oksana Shcherbakova,Alexandre Amlie-Wolf,Ji Nie,Xiaolong Cui,Chuan He,Li-San Wang,Benjamin A. Garcia,John Q. Trojanowski,Nancy M. Bonini,Shelley L. Berger +16 more
TL;DR: It is suggested that Alzheimer’s disease involves a reconfiguration of the epigenome, where H3K27ac and H3k9ac impact disease pathways by dysregulating transcription- and chromatin-gene feedback loops and highlights potential epigenetic strategies for early-stage disease treatment.
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
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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.