piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode
Abstract The small RNA (sRNA) pathways identified in the model organism Caenorhabditis elegans are not widely conserved across nematodes. For example, the PIWI pathway and PIWI-interacting RNAs (piRNAs) are involved in regulating and silencing transposable elements (TE) in most animals but have been...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-06-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-14247-1 |
| _version_ | 1818236903720222720 |
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| author | Mona Suleiman Asuka Kounosu Ben Murcott Mehmet Dayi Rebecca Pawluk Akemi Yoshida Mark Viney Taisei Kikuchi Vicky L. Hunt |
| author_facet | Mona Suleiman Asuka Kounosu Ben Murcott Mehmet Dayi Rebecca Pawluk Akemi Yoshida Mark Viney Taisei Kikuchi Vicky L. Hunt |
| author_sort | Mona Suleiman |
| collection | DOAJ |
| description | Abstract The small RNA (sRNA) pathways identified in the model organism Caenorhabditis elegans are not widely conserved across nematodes. For example, the PIWI pathway and PIWI-interacting RNAs (piRNAs) are involved in regulating and silencing transposable elements (TE) in most animals but have been lost in nematodes outside of the C. elegans group (Clade V), and little is known about how nematodes regulate TEs in the absence of the PIWI pathway. Here, we investigated the role of sRNAs in the Clade IV parasitic nematode Strongyloides ratti by comparing two genetically identical adult stages (the parasitic female and free-living female). We identified putative small-interfering RNAs, microRNAs and tRNA-derived sRNA fragments that are differentially expressed between the two adult stages. Two classes of sRNAs were predicted to regulate TE activity including (i) a parasite-associated class of 21–22 nt long sRNAs with a 5′ uridine (21-22Us) and a 5′ monophosphate, and (ii) 27 nt long sRNAs with a 5′ guanine/adenine (27GAs) and a 5′ modification. The 21-22Us show striking resemblance to the 21U PIWI-interacting RNAs found in C. elegans, including an AT rich upstream sequence, overlapping loci and physical clustering in the genome. Overall, we have shown that an alternative class of sRNAs compensate for the loss of piRNAs and regulate TE activity in nematodes outside of Clade V. |
| first_indexed | 2024-12-12T12:17:16Z |
| format | Article |
| id | doaj.art-1f12358eb5734e7bbbc5101afc2e3657 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-12T12:17:16Z |
| publishDate | 2022-06-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-1f12358eb5734e7bbbc5101afc2e36572022-12-22T00:24:45ZengNature PortfolioScientific Reports2045-23222022-06-0112111710.1038/s41598-022-14247-1piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematodeMona Suleiman0Asuka Kounosu1Ben Murcott2Mehmet Dayi3Rebecca Pawluk4Akemi Yoshida5Mark Viney6Taisei Kikuchi7Vicky L. Hunt8Department of Biology and Biochemistry, University of BathParasitology, Department of Infectious Dieses, Faculty of Medicine, University of MiyazakiDepartment of Biology and Biochemistry, University of BathParasitology, Department of Infectious Dieses, Faculty of Medicine, University of MiyazakiDepartment of Biology and Biochemistry, University of BathLaboratory of Genomics, Frontier Science Research Center, University of MiyazakiDepartment of Evolution, Ecology and Behaviour, University of LiverpoolParasitology, Department of Infectious Dieses, Faculty of Medicine, University of MiyazakiDepartment of Biology and Biochemistry, University of BathAbstract The small RNA (sRNA) pathways identified in the model organism Caenorhabditis elegans are not widely conserved across nematodes. For example, the PIWI pathway and PIWI-interacting RNAs (piRNAs) are involved in regulating and silencing transposable elements (TE) in most animals but have been lost in nematodes outside of the C. elegans group (Clade V), and little is known about how nematodes regulate TEs in the absence of the PIWI pathway. Here, we investigated the role of sRNAs in the Clade IV parasitic nematode Strongyloides ratti by comparing two genetically identical adult stages (the parasitic female and free-living female). We identified putative small-interfering RNAs, microRNAs and tRNA-derived sRNA fragments that are differentially expressed between the two adult stages. Two classes of sRNAs were predicted to regulate TE activity including (i) a parasite-associated class of 21–22 nt long sRNAs with a 5′ uridine (21-22Us) and a 5′ monophosphate, and (ii) 27 nt long sRNAs with a 5′ guanine/adenine (27GAs) and a 5′ modification. The 21-22Us show striking resemblance to the 21U PIWI-interacting RNAs found in C. elegans, including an AT rich upstream sequence, overlapping loci and physical clustering in the genome. Overall, we have shown that an alternative class of sRNAs compensate for the loss of piRNAs and regulate TE activity in nematodes outside of Clade V.https://doi.org/10.1038/s41598-022-14247-1 |
| spellingShingle | Mona Suleiman Asuka Kounosu Ben Murcott Mehmet Dayi Rebecca Pawluk Akemi Yoshida Mark Viney Taisei Kikuchi Vicky L. Hunt piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode Scientific Reports |
| title | piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode |
| title_full | piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode |
| title_fullStr | piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode |
| title_full_unstemmed | piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode |
| title_short | piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode |
| title_sort | pirna like small rnas target transposable elements in a clade iv parasitic nematode |
| url | https://doi.org/10.1038/s41598-022-14247-1 |
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