ArticleGenome biology2012
Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium.
Article in Genome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 57 citations in OpenAlex.
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- Genome-Wide Analysis of RNA Decay in the CyanobacteriummSystems · 2020Article
- Dynamic insights on transcription initiation and RNA processing during bacterial adaptation.RNA (New York, N.Y.) · 2020Article
- Biofilm formation displays intrinsic offensive and defensive features ofNPJ biofilms and microbiomes · 2020Article
- Regulation of mRNA Stability During Bacterial Stress Responses.Frontiers in microbiology · 2020Review
- Highly variable mRNA half-life time within marine bacterial taxa and functional genes.Environmental microbiology · 2019Article
- Bacillus cereusApplied and environmental microbiology · 2019Article
- Article
- Role of CsrA in stress responses and metabolism important for Salmonella virulence revealed by integrated transcriptomics.PloS one · 2019Article
- Genome-wide analysis shows that RNase G plays a global role in the stability of mRNAs in Stenotrophomonas maltophilia.Scientific reports · 2017Article
- Global survey of mRNA levels and decay rates ofHeliyon · 2017Article
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Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRecent 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.
resultsIn 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.
conclusionsTo 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.
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