High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies

Rabani, Michal and Raychowdhury, Raktima and Jovanovic, Marko and Rooney, Michael and Stumpo, Deborah J. and Pauli, Andrea and Hacohen, Nir and Schier, Alexander F. and Blackshear, Perry J. and Friedman, Nir and Amit, Ido and Regev, Aviv. (2014) High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies. Cell, 159 (7). pp. 1698-1710.

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Official URL: https://edoc.unibas.ch/74687/

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Cells control dynamic transitions in transcript levels by regulating transcription, processing, and/or degradation through an integrated regulatory strategy. Here, we combine RNA metabolic labeling, rRNA-depleted RNA-seq, and DRiLL, a novel computational framework, to quantify the level; editing sites; and transcription, processing, and degradation rates of each transcript at a splice junction resolution during the LPS response of mouse dendritic cells. Four key regulatory strategies, dominated by RNA transcription changes, generate most temporal gene expression patterns. Noncanonical strategies that also employ dynamic posttranscriptional regulation control only a minority of genes, but provide unique signal processing features. We validate Tristetraprolin (TTP) as a major regulator of RNA degradation in one noncanonical strategy. Applying DRiLL to the regulation of noncoding RNAs and to zebrafish embryogenesis demonstrates its broad utility. Our study provides a new quantitative approach to discover transcriptional and posttranscriptional events that control dynamic changes in transcript levels using RNA sequencing data.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Growth & Development > Cell and Developmental Biology (Schier)
UniBasel Contributors:Schier, Alexander F
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Cell Press
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:16 Dec 2020 15:36
Deposited On:16 Dec 2020 15:36

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