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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Transcriptional elongation requires DNA break-induced signalling
Heeyoun Bunch,Brian Lawney,Yu Fen Lin,Aroumougame Asaithamby,Ayesha Murshid,Yaoyu E. Wang,Benjamin P C Chen,Stuart K. Calderwood +7 more
TL;DR: It is proposed that DDR signalling is required for effective Pol II pause release and transcriptional elongation through a novel mechanism involving TRIM28, DNA-PK and topoisomerase II.
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Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement
Guangshuai Jia,Jens Preussner,Xi Chen,Stefan Guenther,Xuejun Yuan,Michail Yekelchyk,Carsten Kuenne,Mario Looso,Yonggang Zhou,Sarah A. Teichmann,Sarah A. Teichmann,Thomas P. Braun +11 more
TL;DR: It is shown that CPC fate transitions are associated with distinct open chromatin states critically depending on Isl1 and Nkx2-5, and provides a model of transcriptional and epigenetic regulations during cardiac progenitor cell fate decisions at single-cell resolution.
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Efficient derivation of stable primed pluripotent embryonic stem cells from bovine blastocysts.
Y. S. Bogliotti,Jun Wu,Jun Wu,Jun Wu,Marcela Vilarino,Daiji Okamura,Delia Alba Soto,Cuiqing Zhong,Masahiro Sakurai,Masahiro Sakurai,Masahiro Sakurai,R. V. Sampaio,Keiichiro Suzuki,Juan Carlos Izpisua Belmonte,Pablo J. Ross +14 more
TL;DR: It is reported that stable bovine ESCs can be efficiently derived in a culture condition based on Wnt-pathway inhibition and these well-characterized ESC lines will enrich the understanding of pluripotency programs in the ungulate species but also will provide a useful resource for the creation of transgenic ungulates models of human diseases.
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SCALE method for single-cell ATAC-seq analysis via latent feature extraction.
Lei Xiong,Kui Xu,Kang Tian,Yanqiu Shao,Lei Tang,Ge Gao,Michael Q. Zhang,Tao Jiang,Qiangfeng Cliff Zhang +8 more
TL;DR: SCALE substantially outperforms the other tools in all aspects of scATAC-seq data analysis, including visualization, clustering, and denoising and imputation, and generates interpretable features that directly link to cell populations, and can potentially reveal batch effects in scATac-seq experiments.
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RNA Interactions Are Essential for CTCF-Mediated Genome Organization
Ricardo Saldaña-Meyer,Javier Rodriguez-Hernaez,Thelma M. Escobar,Mayilaadumveettil Nishana,Karina Jácome-López,Elphège P. Nora,Benoit G. Bruneau,Aristotelis Tsirigos,Mayra Furlan-Magaril,Jane A. Skok,Danny Reinberg +10 more
TL;DR: Two independent features that disrupt CTCF association with chromatin are reported: inhibition of transcription and disruption of C TCF-RNA interactions through mutations of 2 of its 11 zinc fingers that are not required for CTCf binding to its cognate DNA site.
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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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.