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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Identification of Lineage-Specific Transcription Factors That Prevent Activation of Hepatic Stellate Cells and Promote Fibrosis Resolution
Xiao Liu,Jun Xu,Sara Brin Rosenthal,Ling-juan Zhang,Ling-juan Zhang,Ryan McCubbin,Nairika Meshgin,Linshan Shang,Yukinori Koyama,Hsiao-Yen Ma,Sonia Sharma,Sven Heinz,Christopher K. Glass,Christopher Benner,David A. Brenner,Tatiana Kisseleva +15 more
TL;DR: It is found GATA6 and PPARγ to be required for inactivation of human HSCs and regression of liver fibrosis in mice andMotif enrichment identified ETS1, ETS2, GATA4, Gata6, IRF1, and IRF2 transcription factors as regulators of the mouse andhuman HSC lineage.
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CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning.
TL;DR: Combining live-cell imaging, fluorescence recovery after photobleaching, and single molecule tracking showed that almost all CTCF chromatin binding is lost in prometaphase, which reveals that CTCf sites, key architectural cis-elements, display cell cycle stage-dependent dynamics in factor binding and nucleosome positioning.
Journal ArticleDOI
GenPipes: an open-source framework for distributed and scalable genomic analyses
Mathieu Bourgey,Rola Dali,Robert Eveleigh,Kuang Chung Chen,Louis Letourneau,Joel Fillon,Marc Michaud,Maxime Caron,Johanna Sandoval,Francois Lefebvre,Gary Leveque,Eloi Mercier,David Bujold,Pascale Marquis,Patrick Tran Van,David Anderson de Lima Morais,Julien Tremblay,Xiaojian Shao,Edouard Henrion,Emmanuel Gonzalez,Pierre-Olivier Quirion,B. Caron,Guillaume Bourque +22 more
TL;DR: GenPipes is a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for high-performance computing clusters and the cloud, and offers genomics researchers a simple method to analyze different types of data.
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SF3B1 Association with Chromatin Determines Splicing Outcomes
Nir Kfir,Galit Lev-Maor,Ohad Glaich,Adi Alajem,Arnab Datta,Siu Kwan Sze,Eran Meshorer,Gil Ast +7 more
TL;DR: These findings suggest that the association of SF3B1 with nucleosomes is functionally important for splice-site recognition and that SF3 B1 conveys splicing-relevant information embedded in chromatin structure.
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Comprehensive functional characterization of cancer-testis antigens defines obligate participation in multiple hallmarks of cancer.
Kimberly Maxfield,Patrick Taus,Patrick Taus,Kathleen Corcoran,Joshua Wooten,Jennifer Macion,Yunyun Zhou,Mark D. Borromeo,Rahul K. Kollipara,Jingsheng Yan,Yang Xie,Xian Jin Xie,Angelique W. Whitehurst +12 more
TL;DR: A multidimensional functional genomics approach is implemented that incorporates 7 different phenotypic assays in 11 distinct disease settings and discovers that Foetal and Adult Testis Expressed 1 (FATE1) is a key survival factor in multiple oncogenic backgrounds.
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.