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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A Single-Cell Transcriptomic Atlas of Human Neocortical Development during Mid-gestation.
Damon Polioudakis,Luis de la Torre-Ubieta,Justin Langerman,Andrew G. Elkins,Xu Shi,Jason L. Stein,Celine K. Vuong,Susanne Nichterwitz,Melinda Gevorgian,Melinda Gevorgian,Carli K. Opland,Daning Lu,William Connell,Elizabeth K. Ruzzo,Jennifer K. Lowe,Tarik Hadzic,Flora I. Hinz,Shan Sabri,William E. Lowry,Mark Gerstein,Kathrin Plath,Daniel H. Geschwind +21 more
TL;DR: This work ties cell-cycle progression with early cell fate decisions during neurogenesis, demonstrating that differentiation occurs on a transcriptomic continuum; rather than only expressing a few transcription factors that drive cell fates, differentiating cells express broad, mixed cell-type transcriptomes before telophase.
Journal ArticleDOI
cis-regulatory requirements for tissue-specific programs of the circadian clock.
Antonio C. A. Meireles-Filho,Anaïs F. Bardet,J. Omar Yáñez-Cuna,Gerald Stampfel,Alexander Stark +4 more
TL;DR: The results reveal how universal clock circuits can regulate tissue-specific rhythms and provide insights into the mechanism by which universal TFs can be modulated to drive tissue- specific programs of gene expression.
Journal ArticleDOI
High-density lipoprotein mediates anti-inflammatory reprogramming of macrophages via the transcriptional regulator ATF3
Dominic De Nardo,Larisa I. Labzin,Hajime Kono,Reiko Seki,Susanne Schmidt,Marc Beyer,Dakang Xu,Sebastian Zimmer,Catharina Lahrmann,Frank A. Schildberg,Johanna Vogelhuber,Michael Kraut,Thomas Ulas,Anja Kerksiek,Wolfgang Krebs,Niklas Bode,Alena Grebe,Michael L. Fitzgerald,Nicholas J. Hernandez,Bryan R.G. Williams,Percy A. Knolle,Manfred Kneilling,Martin Röcken,Dieter Lütjohann,Samuel D. Wright,Joachim L. Schultze,Eicke Latz +26 more
TL;DR: The transcriptional regulator ATF3 is identified, as an HDL-inducible target gene in macrophages that downregulates the expression of Toll-like receptor (TLR)-induced proinflammatory cytokines and may explain the broad anti-inflammatory and metabolic actions of HDL.
Journal ArticleDOI
Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding.
Tsung-Han S. Hsieh,Claudia Cattoglio,Elena Slobodyanyuk,Anders S. Hansen,Oliver J. Rando,Robert Tjian,Xavier Darzacq +6 more
TL;DR: This study uncovers previously obscured finer-scale genome organization, establishing functional links between chromatin folding and gene regulation by using high-resolution Micro-C to probe links between 3D genome organization and transcriptional regulation in mouse stem cells.
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Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking.
Joachim Weischenfeldt,Joachim Weischenfeldt,Taronish D. Dubash,Alexandros P. Drainas,Balca R. Mardin,Yuanyuan Chen,Adrian M. Stütz,Sebastian M. Waszak,Graziella Bosco,Ann Rita Halvorsen,Benjamin Raeder,Theocharis Efthymiopoulos,Serap Erkek,Serap Erkek,Christine Siegl,Hermann Brenner,Odd Terje Brustugun,Sebastian M. Dieter,Paul A. Northcott,Iver Petersen,Stefan M. Pfister,Martin Schneider,Steinar Solberg,Erik Thunissen,Wilko Weichert,Wilko Weichert,Thomas Zichner,Roman K. Thomas,Martin Peifer,Åslaug Helland,Claudia R. Ball,Martin Jechlinger,Rocio Sotillo,Hanno Glimm,Jan O. Korbel +34 more
TL;DR: A framework for inferring cancer-related gene overexpression resulting from CRE reorganization by integrating SCNAs, gene expression data and information on topologically associating domains (TADs) is presented and enables systematic inference of CRE rearrangements mediating dysregulation in cancer.
References
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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.