piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode.

Suleiman, Mona, Kounosu, Asuka, Murcott, Ben, Dayi, Mehmet, Pawluk, Rebecca, Yoshida, Akemi, Viney, Mark, Kikuchi, Taisei and Hunt, Vicky L ORCID: 0000-0002-7094-044X
(2022) piRNA-like small RNAs target transposable elements in a Clade IV parasitic nematode. Scientific reports, 12 (1). 10156-.

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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.

Item Type: Article
Uncontrolled Keywords: Animals, Nematoda, Caenorhabditis elegans, MicroRNAs, RNA, Small Interfering, DNA Transposable Elements, Female
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences
Depositing User: Symplectic Admin
Date Deposited: 18 Oct 2022 09:55
Last Modified: 18 Jan 2023 20:36
DOI: 10.1038/s41598-022-14247-1
Open Access URL: https://doi.org/10.1038/s41598-022-14247-1
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3165580