INSPEcT: A computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments

Stefano De Pretis, Theresia Kress, Marco J. Morelli, Giorgio E M Melloni, Laura Riva, Bruno Amati, Mattia Pelizzola

Research output: Contribution to journalArticlepeer-review

Abstract

Motivation: Cellular mRNA levels originate from the combined action of multiple regulatory processes, which can be recapitulated by the rates of pre-mRNA synthesis, pre-mRNA processing and mRNA degradation. Recent experimental and computational advances set the basis to study these intertwined levels of regulation. Nevertheless, software for the comprehensive quantification of RNA dynamics is still lacking. Results: INSPEcT is an R package for the integrative analysis of RNA- and 4sU-seq data to study the dynamics of transcriptional regulation. INSPEcT provides gene-level quantification of these rates, and a modeling framework to identify which of these regulatory processes are most likely to explain the observed mRNA and pre-mRNA concentrations. Software performance is tested on a synthetic dataset, instrumental to guide the choice of the modeling parameters and the experimental design.

Original languageEnglish
Pages (from-to)2829-2835
Number of pages7
JournalBioinformatics
Volume31
Issue number17
DOIs
Publication statusPublished - Feb 6 2015

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability

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