Center for Genomic Science, Fondazione Istituto Italiano di Tecnologia, 20139 Milan, Italy.
Physics Department and INFN, University of Turin, 10125 Turin, Italy.
Genome Res. 2020 Oct;30(10):1492-1507. doi: 10.1101/gr.260984.120. Epub 2020 Sep 25.
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.
RNA 合成、加工和降解的动力学速率的定量分析在很大程度上基于总转录物和新生转录物的综合分析,后者通过 RNA 代谢标记进行定量。我们开发了 INSPEcT-,这是一种基于不成熟和成熟 RNA 表达的数学模型的计算方法,能够从稳态或时间过程的总 RNA-seq 数据中定量动力学速率,而不需要任何关于新生转录物的信息。我们的方法优于现有解决方案,紧密再现通过 RNA 代谢标记获得的动力学速率,提高检测转录物半衰期变化的能力,降低实验的成本和复杂性,并可用于研究新生转录物不易分析的实验条件。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。该方法被包含在 INSPEcT Bioconductor 包中,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。