Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium

• Type of Material: Article
• Authors: Simen M. Kristoffersen, University of Oslo; Chad Haase, Emory University; M. Ryan Weil, Emory University; Karla D. Passalacqua, Emory University; Faheem Niazi, A Roche Company; Stephen K. Hutchison, A Roche Company; Brian Desany, A Roche Company; Anne-Brit Kolsto, University of Oslo; Nicolas J. Tourasse, University of Oslo; Timothy D Read, Emory University; Ole Andreas Okstad, University of Oslo
• Language: English
• Date: 2012-04-26
• Publisher: BioMed Central
• Publication Version: Final Published Version
• Copyright Statement: © 2012 Kristoffersen et al.; licensee BioMed Central Ltd.
• License: Creative Commons Attribution 2.0 Generic
• Final Published Version (URL): http://genomebiology.com/2012/13/4/R30
• Title of Journal or Parent Work: Genome Biology
• ISSN: 1465-6906
• Volume: 13
• Issue: R30
• Start Page: 1
• End Page: 21
• Grant/Funding Information: Sources of funding for equipment included the Georgia Research Alliance [94] and Atlanta Clinical & Translational Sciences Institute; This work was partially funded by project grants from the Norwegian Research Council [97], through a Strategic University Programme (SUP, project number 146534) and the FUGE II Programme (channel 3 grant; project number 183421).
• Research Categories: Health Sciences, Pharmacology; Biology, Genetics

Abstract

Background Recent years have shown a marked increase in the use of next-generation sequencing technologies for quantification of gene expression (RNA sequencing, RNA-Seq). The expression level of a gene is a function of both its rate of transcription and RNA decay, and the influence of mRNA decay rates on gene expression in genome-wide studies of Gram-positive bacteria is under-investigated. Results In this work, we employed RNA-Seq in a genome-wide determination of mRNA half-lives in the Gram-positive bacterium Bacillus cereus. By utilizing a newly developed normalization protocol, RNA-Seq was used successfully to determine global mRNA decay rates at the single nucleotide level. The analysis revealed positional degradation patterns, with mRNAs being degraded from both ends of the molecule, indicating that both 5' to 3' and 3' to 5' directions of RNA decay are present in B. cereus. Other operons showed segmental degradation patterns where specific ORFs within polycistrons were degraded at variable rates, underlining the importance of RNA processing in gene regulation. We determined the half-lives for more than 2,700 ORFs in B. cereus ATCC 10987, ranging from less than one minute to more than fifteen minutes, and showed that mRNA decay rate correlates globally with mRNA expression level, GC content, and functional class of the ORF. Conclusions To our knowledge, this study presents the first global analysis of mRNA decay in a bacterium at single nucleotide resolution. We provide a proof of principle for using RNA-Seq in bacterial mRNA decay analysis, revealing RNA processing patterns at the single nucleotide level.