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Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling
Genome Research ( IF 7 ) Pub Date : 2020-10-01 , DOI: 10.1101/gr.260984.120
Mattia Furlan 1, 2 , Eugenia Galeota 1 , Nunzio Del Gaudio 1 , Erik Dassi 3 , Michele Caselle 2 , Stefano de Pretis 1 , Mattia Pelizzola 1
Affiliation  

The quantification of the kinetic rates of RNA synthesis, processing, and degradation are largely based on the integrative analysis of total and nascent transcription, the latter being quantified through RNA metabolic labeling. We developed INSPEcT−, a computational method based on the mathematical modeling of premature and mature RNA expression that is able to quantify kinetic rates from steady-state or time course total RNA-seq data without requiring any information on nascent transcripts. Our approach outperforms available solutions, closely recapitulates the kinetic rates obtained through RNA metabolic labeling, improves the ability to detect changes in transcript half-lives, reduces the cost and complexity of the experiments, and can be adopted to study experimental conditions in which nascent transcription cannot be readily profiled. Finally, we applied INSPEcT− to the characterization of post-transcriptional regulation landscapes in dozens of physiological and disease conditions. This approach was included in the INSPEcT Bioconductor package, which can now unveil RNA dynamics from steady-state or time course data, with or without the profiling of nascent RNA.

中文翻译:

没有 RNA 代谢标记的 RNA 合成、加工和降解的全基因组动态

RNA 合成、加工和降解的动力学速率的量化主要基于对总转录和新生转录的综合分析,后者通过 RNA 代谢标记进行量化。我们开发了 INSPEcT−,这是一种基于过早和成熟 RNA 表达的数学模型的计算方法,能够从稳态或时间过程总 RNA-seq 数据中量化动力学速率,而无需任何关于新生转录本的信息。我们的方法优于现有的解决方案,密切概括了通过 RNA 代谢标记获得的动力学速率,提高了检测转录半衰期变化的能力,降低了实验的成本和复杂性,并可用于研究新生转录的实验条件不能容易地进行剖析。最后,我们将 INSPEcT− 应用于数十种生理和疾病条件下的转录后调控景观的表征。这种方法包含在 INSPEcT Bioconductor 软件包中,它现在可以从稳态或时间过程数据中揭示 RNA 动力学,无论是否对新生 RNA 进行分析。
更新日期:2020-10-02
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