Modeling RNA dynamics without metabolic labeling

Transcript’s abundance is typically considered a proxy of the corresponding genes transcriptional activity. Yet, a poorly transcribed gene could see many of its RNA molecules accumulate just because they are highly stable. Conversely, if a gene is very actively transcribed but its transcripts are highly unstable, only a few copies of its RNAs are found in the cell. Indeed, RNA abundance and its variation arise from the combined action of cellular machineries responsible for the synthesis of novel transcripts, their processing into mature species, and the degradation of the latter. The quantification of the kinetic rates governing these key steps of RNA metabolism (henceforth RNA kinetic rates) is largely based on the integrative analysis of total and nascent transcription, the latter being quantified through RNA metabolic labeling. We previously developed a tool, the R/Bioconductor INSPEcT package, for the quantification of RNA kinetic rates at steady state and in time course.

We now developed INSPEcT-, which relies on the mathematical modeling of premature and mature RNA expression from time course total RNA-seq experiments for the temporal quantification of all RNA kinetic rates, without requiring any information on nascent transcripts. At the steady-state, INSPEcT- identifies genes that are candidate post-transcriptionally regulated, while it cannot disentangle the contribution of processing or degradation dynamics. INSPEcT- reduces the cost and complexity of the experiments, can be adopted to study experimental conditions where nascent transcription cannot be readily profiled, and discloses a fuller characterization of gene expression programs which goes beyond the mere quantification of absolute or differential gene expression.

Understanding how the combined modulation of RNA synthesis, processing and degradation impacts on premature and mature RNA is fascinating but can be complicated. To facilitate the exploration of the intricacy of RNA metabolism we developed the INSPEcT-GUI graphical user interface. INSPEcT-GUI allows visualizing and manipulating models inferred by INSPEcT without requiring computer science or math skills. Moreover, without requiring any experimental data, it allows defining functional forms of the kinetic rates to explore how the RNA kinetic rates shape the temporal profiles of premature and mature RNAs.

INSPEcT- and INSPEcT-GUI are available within the INSPEcT R/Bioconductor package, which can now unveil RNA dynamics from steady state or time course data, with or without the profiling of nascent RNA, and can be used through command line or a GUI.

Availability: The INSPEcT package, including INSPEcT- and INSPEcT-GUI, is available at https://bioconductor.org/packages/INSPEcT/

References:

• Furlan, M., Galeota, E., Del Gaudio, N., Dassi, E., Caselle, M., de Pretis, S., & Pelizzola, M. (2020). Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling. Genome Research, 1–17. http://doi.org/10.1101/gr.260984.120
• de Pretis, S., Furlan, M., & Pelizzola, M. (2020). INSPEcT-GUI Reveals the Impact of the Kinetic Rates of RNA Synthesis, Processing, and Degradation, on Premature and Mature RNA Species. Frontiers in Genetics, 11, 230. http://doi.org/10.3389/fgene.2020.00759