Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation
Justin J.-L. Wong,Justin J.-L. Wong,William Ritchie,William Ritchie,Olivia A. Ebner,Matthias Selbach,Jason W. H. Wong,Yizhou Huang,Dadi Gao,Dadi Gao,Natalia Pinello,Natalia Pinello,María Jesús González González,María Jesús González González,Kinsha Baidya,Kinsha Baidya,Annora Thoeng,Annora Thoeng,Teh-Liane Khoo,Teh-Liane Khoo,Charles G. Bailey,Charles G. Bailey,Jeff Holst,Jeff Holst,John E.J. Rasko,John E.J. Rasko,John E.J. Rasko +26 more
TLDR
Bioinformatic analyses of transcriptomic and proteomic data of normal white blood cell differentiation reveal IR as a physiological mechanism of gene expression control and establish that IR coupled with NMD is a conserved mechanism in normal granulopoiesis.About:
This article is published in Cell.The article was published on 2013-08-01 and is currently open access. It has received 411 citations till now. The article focuses on the topics: Intron & Gene expression.read more
Citations
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Journal ArticleDOI
Nonsense-mediated mRNA decay: an intricate machinery that shapes transcriptomes.
TL;DR: How NMD targets m RNAs, the types of mRNAs that are targeted, and the roles of NMD in cellular stress, differentiation and maturation processes are discussed.
Journal ArticleDOI
Widespread intron retention in mammals functionally tunes transcriptomes
Ulrich Braunschweig,Nuno L. Barbosa-Morais,Nuno L. Barbosa-Morais,Qun Pan,Emil N. Nachman,Babak Alipanahi,Thomas Gonatopoulos-Pournatzis,Brendan J. Frey,Manuel Irimia,Benjamin J. Blencowe +9 more
TL;DR: It is shown that intron retention acts widely to reduce the levels of transcripts that are less or not required for the physiology of the cell or tissue type in which they are detected, and this "transcriptome tuning" function of IR acts through both nonsense-mediated mRNA decay and nuclear sequestration and turnover of IR transcripts.
Journal ArticleDOI
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells
Lu Chen,Lu Chen,Bing Ge,Francesco Paolo Casale,Louella Vasquez,Tony Kwan,Diego Garrido-Martín,Stephen Watt,Ying Yan,Kousik Kundu,Kousik Kundu,Simone Ecker,Avik Datta,David J. Richardson,Frances Burden,Frances Burden,Daniel Mead,Alice L. Mann,José M. Fernández,Sophia Rowlston,Sophia Rowlston,Steven P. Wilder,Samantha Farrow,Samantha Farrow,Xiaojian Shao,John J. Lambourne,Adriana Redensek,Cornelis A. Albers,Vyacheslav Amstislavskiy,Sofie Ashford,Sofie Ashford,Kim Berentsen,Lorenzo Bomba,Guillaume Bourque,David Bujold,Stephan Busche,Maxime Caron,Shu-Huang Chen,Warren A. Cheung,Oliver Delaneau,Emmanouil T. Dermitzakis,Heather Elding,Irina Colgiu,Frederik Otzen Bagger,Frederik Otzen Bagger,Frederik Otzen Bagger,Paul Flicek,Ehsan Habibi,Valentina Iotchkova,Valentina Iotchkova,Eva M. Janssen-Megens,Bowon Kim,Hans Lehrach,Ernesto Lowy,Amit Mandoli,Filomena Matarese,Matthew T. Maurano,John A. Morris,Vera Pancaldi,Farzin Pourfarzad,Karola Rehnström,Karola Rehnström,Augusto Rendon,Thomas Risch,Nilofar Sharifi,Marie-Michelle Simon,Marc Sultan,Alfonso Valencia,Klaudia Walter,Shuang-Yin Wang,Mattia Frontini,Mattia Frontini,Mattia Frontini,Stylianos E. Antonarakis,Laura Clarke,Marie-Laure Yaspo,Stephan Beck,Roderic Guigó,Daniel Rico,Joost H.A. Martens,Willem H. Ouwehand,Taco W. Kuijpers,Taco W. Kuijpers,Dirk S. Paul,Dirk S. Paul,Hendrik G. Stunnenberg,Oliver Stegle,Kate Downes,Kate Downes,Tomi Pastinen,Nicole Soranzo +90 more
TL;DR: High-resolution genetic, epigenetic, and transcriptomic profiling in three major human immune cell types from up to 197 individuals yields insights into cell-type-specific correlation between diverse genomic inputs, more generalizable correlations between these inputs, and defines molecular events that may underpin complex disease risk.
Journal ArticleDOI
Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing
Bo Wang,Elizabeth Tseng,Michael Regulski,Tyson A. Clark,Ting Hon,Yinping Jiao,Zhenyuan Lu,Andrew Olson,Joshua C. Stein,Doreen Ware,Doreen Ware +10 more
TL;DR: The results show that characterization of the maize B73 transcriptome is far from complete, and that maize gene expression is more complex than previously thought.
Journal ArticleDOI
Quality and quantity control of gene expression by nonsense-mediated mRNA decay
TL;DR: This Review discusses how NMD serves multiple purposes in human cells by degrading both mutated mRNAs to protect the integrity of the transcriptome and normal m RNAs to control the quantities of unmutated transcripts.
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