Assessment of Bona Fide sRNAs in Staphylococcus aureus
Bacterial regulatory RNAs have been extensively studied for over a decade, and are progressively being integrated into the complex genetic regulatory network. Transcriptomic arrays, recent deep-sequencing data and bioinformatics suggest that bacterial genomes produce hundreds of regulatory RNAs. How...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-02-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fmicb.2018.00228/full |
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| author | Wenfeng Liu Tatiana Rochat Claire Toffano-Nioche Thao Nguyen Le Lam Philippe Bouloc Claire Morvan |
| author_facet | Wenfeng Liu Tatiana Rochat Claire Toffano-Nioche Thao Nguyen Le Lam Philippe Bouloc Claire Morvan |
| author_sort | Wenfeng Liu |
| collection | DOAJ |
| description | Bacterial regulatory RNAs have been extensively studied for over a decade, and are progressively being integrated into the complex genetic regulatory network. Transcriptomic arrays, recent deep-sequencing data and bioinformatics suggest that bacterial genomes produce hundreds of regulatory RNAs. However, while some have been authenticated, the existence of the others varies according to strains and growth conditions, and their detection fluctuates with the methodologies used for data acquisition and interpretation. For example, several small RNA (sRNA) candidates are now known to be parts of UTR transcripts. Accurate annotation of regulatory RNAs is a complex task essential for molecular and functional studies. We defined bona fide sRNAs as those that (i) likely act in trans and (ii) are not expressed from the opposite strand of a coding gene. Using published data and our own RNA-seq data, we reviewed hundreds of Staphylococcus aureus putative regulatory RNAs using the DETR'PROK computational pipeline and visual inspection of expression data, addressing the question of which transcriptional signals correspond to sRNAs. We conclude that the model strain HG003, a NCTC8325 derivative commonly used for S. aureus genetic regulation studies, has only about 50 bona fide sRNAs, indicating that these RNAs are less numerous than commonly stated. Among them, about half are associated to the S. aureus sp. core genome and a quarter are possibly expressed in other Staphylococci. We hypothesize on their features and regulation using bioinformatic approaches. |
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| format | Article |
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| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-16T10:01:32Z |
| publishDate | 2018-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-e0168d445731441e82188cc14aa4e9022022-12-21T22:35:47ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-02-01910.3389/fmicb.2018.00228313422Assessment of Bona Fide sRNAs in Staphylococcus aureusWenfeng Liu0Tatiana Rochat1Claire Toffano-Nioche2Thao Nguyen Le Lam3Philippe Bouloc4Claire Morvan5Institute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, FranceVIM, Institut National de la Recherche Agronomique, Université Paris-Saclay, Institut National de la Recherche Agronomique Centre Jouy-en-Josas, Jouy-en-Josas, FranceInstitute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, FranceInstitute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, FranceInstitute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, FranceInstitute for Integrative Biology of the Cell (I2BC), CEA, Centre National de la Recherche Scientifique, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, FranceBacterial regulatory RNAs have been extensively studied for over a decade, and are progressively being integrated into the complex genetic regulatory network. Transcriptomic arrays, recent deep-sequencing data and bioinformatics suggest that bacterial genomes produce hundreds of regulatory RNAs. However, while some have been authenticated, the existence of the others varies according to strains and growth conditions, and their detection fluctuates with the methodologies used for data acquisition and interpretation. For example, several small RNA (sRNA) candidates are now known to be parts of UTR transcripts. Accurate annotation of regulatory RNAs is a complex task essential for molecular and functional studies. We defined bona fide sRNAs as those that (i) likely act in trans and (ii) are not expressed from the opposite strand of a coding gene. Using published data and our own RNA-seq data, we reviewed hundreds of Staphylococcus aureus putative regulatory RNAs using the DETR'PROK computational pipeline and visual inspection of expression data, addressing the question of which transcriptional signals correspond to sRNAs. We conclude that the model strain HG003, a NCTC8325 derivative commonly used for S. aureus genetic regulation studies, has only about 50 bona fide sRNAs, indicating that these RNAs are less numerous than commonly stated. Among them, about half are associated to the S. aureus sp. core genome and a quarter are possibly expressed in other Staphylococci. We hypothesize on their features and regulation using bioinformatic approaches.http://journal.frontiersin.org/article/10.3389/fmicb.2018.00228/fullbona fide sRNAStaphylococcus aureus HG003RNA-seqtranscription factorsgene regulation |
| spellingShingle | Wenfeng Liu Tatiana Rochat Claire Toffano-Nioche Thao Nguyen Le Lam Philippe Bouloc Claire Morvan Assessment of Bona Fide sRNAs in Staphylococcus aureus Frontiers in Microbiology bona fide sRNA Staphylococcus aureus HG003 RNA-seq transcription factors gene regulation |
| title | Assessment of Bona Fide sRNAs in Staphylococcus aureus |
| title_full | Assessment of Bona Fide sRNAs in Staphylococcus aureus |
| title_fullStr | Assessment of Bona Fide sRNAs in Staphylococcus aureus |
| title_full_unstemmed | Assessment of Bona Fide sRNAs in Staphylococcus aureus |
| title_short | Assessment of Bona Fide sRNAs in Staphylococcus aureus |
| title_sort | assessment of bona fide srnas in staphylococcus aureus |
| topic | bona fide sRNA Staphylococcus aureus HG003 RNA-seq transcription factors gene regulation |
| url | http://journal.frontiersin.org/article/10.3389/fmicb.2018.00228/full |
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