ArticleBMC genomics2013
A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 27 citations in OpenAlex.
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- Genome-Wide Transcription Start Sites Mapping inMicroorganisms · 2022Article
- TruNeo: an integrated pipeline improves personalized true tumor neoantigen identification.BMC bioinformatics · 2020Article
- Review
- Determination of the Genome and Primary Transcriptome of Syngas Fermenting Eubacterium limosum ATCC 8486.Scientific reports · 2017Article
- Article
- Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome.PloS one · 2017Article
- Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315.BMC genomics · 2015Article
- Quantitative bacterial transcriptomics with RNA-seq.Current opinion in microbiology · 2015Review
- Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli.Journal of bacteriology · 2015Article
- Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli.Nucleic acids research · 2014Article
- A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing.Molecular microbiology · 2014Article
- Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing.mBio · 2014Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundSequencing of the genome of Propionibacterium acnes produced a catalogue of genes many of which enable this organism to colonise skin and survive exposure to the elements. Despite this platform, there was little understanding of the gene regulation that gives rise to an organism that has a major impact on human health and wellbeing and causes infections beyond the skin. To address this situation, we have undertaken a genome-wide study of gene regulation using a combination of improved differential and global RNA-sequencing and an analytical approach that takes into account the inherent noise within the data.
resultsWe have produced nucleotide-resolution transcriptome maps that identify and differentiate sites of transcription initiation from sites of stable RNA processing and mRNA cleavage. Moreover, analysis of these maps provides strong evidence for 'pervasive' transcription and shows that contrary to initial indications it is not biased towards the production of antisense RNAs. In addition, the maps reveal an extensive array of riboswitches, leaderless mRNAs and small non-protein-coding RNAs alongside vegetative promoters and post-transcriptional events, which includes unusual tRNA processing. The identification of such features will inform models of complex gene regulation, as illustrated here for ribonucleotide reductases and a potential quorum-sensing, two-component system.
conclusionsThe approach described here, which is transferable to any bacterial species, has produced a step increase in whole-cell knowledge of gene regulation in P. acnes. Continued expansion of our maps to include transcription associated with different growth conditions and genetic backgrounds will provide a new platform from which to computationally model the gene expression that determines the physiology of P. acnes and its role in human disease.
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