کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
2035182 1072143 2014 13 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies
موضوعات مرتبط
علوم زیستی و بیوفناوری بیوشیمی، ژنتیک و زیست شناسی مولکولی بیوشیمی، ژنتیک و زیست شناسی مولکولی (عمومی)
پیش نمایش صفحه اول مقاله
High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies
چکیده انگلیسی


• High resolution temporal map of newly transcribed and total RNA in mouse DCs
• Genomic quantification of dynamic RNA production, processing, and degradation rates
• Four key regulatory strategies are dominated by RNA production changes
• Minor strategies add posttranscriptional regulation for unique signal processing

SummaryCells 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.

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ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: - Volume 159, Issue 7, 18 December 2014, Pages 1698–1710
نویسندگان
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