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de Pretis S, Kress T, Morelli MJ, Melloni GEM, Riva L, Amati B, Pelizzola M. INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments. Bioinformatics 2015; 31:2829-35. [PMID: 25957348 DOI: 10.1093/bioinformatics/btv288] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/03/2015] [Indexed: 11/15/2022] Open
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.
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Affiliation(s)
- Stefano de Pretis
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milano, Italy and
| | - Theresia Kress
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milano, Italy and
| | - Marco J Morelli
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milano, Italy and
| | - Giorgio E M Melloni
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milano, Italy and
| | - Laura Riva
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milano, Italy and
| | - Bruno Amati
- 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
| | - Mattia Pelizzola
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milano, Italy and
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Jovanovic M, Rooney MS, Mertins P, Przybylski D, Chevrier N, Satija R, Rodriguez EH, Fields AP, Schwartz S, Raychowdhury R, Mumbach MR, Eisenhaure T, Rabani M, Gennert D, Lu D, Delorey T, Weissman JS, Carr SA, Hacohen N, Regev A. Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens. Science 2015; 347:1259038. [PMID: 25745177 DOI: 10.1126/science.1259038] [Citation(s) in RCA: 336] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein expression is regulated by the production and degradation of messenger RNAs (mRNAs) and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics so as to build a quantitative genomic model of the differential regulation of gene expression in lipopolysaccharide-stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for more than half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction for newly activated cellular functions and by protein life-cycle changes for remodeling of preexisting functions.
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Affiliation(s)
- Marko Jovanovic
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael S Rooney
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Philipp Mertins
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Nicolas Chevrier
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Harvard Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rahul Satija
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Edwin H Rodriguez
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alexander P Fields
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Schraga Schwartz
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Thomas Eisenhaure
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michal Rabani
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dave Gennert
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Diana Lu
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Toni Delorey
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA. Howard Hughes Medical Institute (HHMI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nir Hacohen
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA 02114, USA. Harvard Medical School, Boston, MA 02115, USA.
| | - Aviv Regev
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA. HHMI, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA.
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