Stefano de Pretis1, Theresia Kress1, Marco J Morelli1, Giorgio E M Melloni1, Laura Riva1, Bruno Amati2, Mattia Pelizzola1. 1. Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milano, Italy and. 2. Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milano, Italy and Department of Experimental Oncology, European Institute of Oncology (IEO), 20139, Milano, Italy.
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. AVAILABILITY AND IMPLEMENTATION: INSPEcT is submitted to Bioconductor and is currently available as Supplementary Additional File S1. CONTACT: mattia.pelizzola@iit.it SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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. AVAILABILITY AND IMPLEMENTATION: INSPEcT is submitted to Bioconductor and is currently available as Supplementary Additional File S1. CONTACT: mattia.pelizzola@iit.it SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Johannes Meisig; Nadine Dreser; Marion Kapitza; Margit Henry; Tamara Rotshteyn; Jörg Rahnenführer; Jan G Hengstler; Agapios Sachinidis; Tanja Waldmann; Marcel Leist; Nils Blüthgen Journal: Nucleic Acids Res Date: 2020-12-16 Impact factor: 16.971
Authors: Hua-Bing Li; Jiyu Tong; Shu Zhu; Pedro J Batista; Erin E Duffy; Jun Zhao; Will Bailis; Guangchao Cao; Lina Kroehling; Yuanyuan Chen; Geng Wang; James P Broughton; Y Grace Chen; Yuval Kluger; Matthew D Simon; Howard Y Chang; Zhinan Yin; Richard A Flavell Journal: Nature Date: 2017-08-09 Impact factor: 49.962