RNA Sequencing Unveils Very Small RNAs With Potential Regulatory Functions in Bacteria Article Swipe
Idrissa Diallo
,
Jeffrey Ho
,
David Lalaouna
,
Éric Massé
,
Patrick Provost
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.3389/fmolb.2022.914991
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.3389/fmolb.2022.914991
RNA sequencing (RNA-seq) is the gold standard for the discovery of small non-coding RNAs. Following a long-standing approach, reads shorter than 16 nucleotides (nt) are removed from the small RNA sequencing libraries or datasets. The serendipitous discovery of an eukaryotic 12 nt-long RNA species capable of modulating the microRNA from which they derive prompted us to challenge this dogma and, by expanding the window of RNA sizes down to 8 nt, to confirm the existence of functional very small RNAs (vsRNAs <16 nt). Here we report the detailed profiling of vsRNAs in Escherichia coli , E. coli -derived outer membrane vesicles (OMVs) and five other bacterial strains ( Pseudomonas aeruginosa PA7, P. aeruginosa PAO1, Salmonella enterica serovar Typhimurium 14028S, Legionella pneumophila JR32 Philadelphia-1 and Staphylococcus aureus HG001). vsRNAs of 8–15 nt in length [RNAs (8-15 nt)] were found to be more abundant than RNAs of 16–30 nt in length [RNAs (16–30 nt)]. vsRNA biotypes were distinct and varied within and across bacterial species and accounted for one third of reads identified in the 8–30 nt window. The tRNA-derived fragments (tRFs) have appeared as a major biotype among the vsRNAs, notably Ile-tRF and Ala-tRF, and were selectively loaded in OMVs. tRF-derived vsRNAs appear to be thermodynamically stable with at least 2 G-C basepairs and stem-loop structure. The analyzed tRF-derived vsRNAs are predicted to target several human host mRNAs with diverse functions. Bacterial vsRNAs and OMV-derived vsRNAs could be novel players likely modulating the intricate relationship between pathogens and their hosts.
Related Topics
Concepts
Small RNA
RNA
Biology
Escherichia coli
Non-coding RNA
Pseudomonas aeruginosa
Deep sequencing
Salmonella enterica
Bacteria
Microbiology
Genetics
Gene
Computational biology
Genome
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.3389/fmolb.2022.914991
- https://www.frontiersin.org/articles/10.3389/fmolb.2022.914991/pdf
- OA Status
- gold
- Cited By
- 20
- References
- 88
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4281666631
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4281666631Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.3389/fmolb.2022.914991Digital Object Identifier
- Title
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RNA Sequencing Unveils Very Small RNAs With Potential Regulatory Functions in BacteriaWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2022Year of publication
- Publication date
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2022-06-03Full publication date if available
- Authors
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Idrissa Diallo, Jeffrey Ho, David Lalaouna, Éric Massé, Patrick ProvostList of authors in order
- Landing page
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https://doi.org/10.3389/fmolb.2022.914991Publisher landing page
- PDF URL
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https://www.frontiersin.org/articles/10.3389/fmolb.2022.914991/pdfDirect link to full text PDF
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YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
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https://www.frontiersin.org/articles/10.3389/fmolb.2022.914991/pdfDirect OA link when available
- Concepts
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Small RNA, RNA, Biology, Escherichia coli, Non-coding RNA, Pseudomonas aeruginosa, Deep sequencing, Salmonella enterica, Bacteria, Microbiology, Genetics, Gene, Computational biology, GenomeTop concepts (fields/topics) attached by OpenAlex
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20Total citation count in OpenAlex
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2025: 2, 2024: 8, 2023: 8, 2022: 2Per-year citation counts (last 5 years)
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88Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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