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

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dc.authoridHunt, Vicky/0000-0002-7094-044X
dc.authorwosidDayı, Mehmet/GQP-8056-2022
dc.contributor.authorSuleiman, Mona
dc.contributor.authorKounosu, Asuka
dc.contributor.authorMurcott, Ben
dc.contributor.authorDayı, Mehmet
dc.contributor.authorPawluk, Rebecca
dc.contributor.authorYoshida, Akemi
dc.contributor.authorViney, Mark
dc.date.accessioned2023-07-26T11:51:05Z
dc.date.available2023-07-26T11:51:05Z
dc.date.issued2022
dc.departmentDÜ, Ormancılık Meslek Yüksekokulu, Ormancılık Bölümüen_US
dc.description.abstractThe 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.en_US
dc.description.sponsorshipElizabeth Blackwell Institute fellowship; Japanese Society for the Promotion of Science Fellowship [PE16024]; Wellcome Trust Sir Henry Dale Fellowship [211227/Z/18/Z]; URSA University of Bath PhD studentship; Japan Society for the Promotion of Science (JSPS) KAKENHI Grant [19H03212, 17KT0013]; JST CREST Grant [JPMJCR18S7]; Grants-in-Aid for Scientific Research [19H03212, 17KT0013] Funding Source: KAKENen_US
dc.description.sponsorshipVLH was funded by an Elizabeth Blackwell Institute fellowship, a Japanese Society for the Promotion of Science Fellowship (PE16024) and a Wellcome Trust Sir Henry Dale Fellowship (211227/Z/18/Z). For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. MS was funded by a URSA University of Bath PhD studentship. TK was funded by Japan Society for the Promotion of Science (JSPS) KAKENHI Grant Numbers 19H03212 and 17KT0013, and JST CREST Grant Number JPMJCR18S7.en_US
dc.identifier.doi10.1038/s41598-022-14247-1
dc.identifier.issn2045-2322
dc.identifier.issue1en_US
dc.identifier.pmid35710810en_US
dc.identifier.scopus2-s2.0-85132079583en_US
dc.identifier.scopusqualityQ1en_US
dc.identifier.urihttps://doi.org/10.1038/s41598-022-14247-1
dc.identifier.urihttps://hdl.handle.net/20.500.12684/12489
dc.identifier.volume12en_US
dc.identifier.wosWOS:000812562700003en_US
dc.identifier.wosqualityQ2en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakPubMeden_US
dc.indekslendigikaynakScopusen_US
dc.institutionauthorDayı, Mehmet
dc.language.isoenen_US
dc.publisherNature Portfolioen_US
dc.relation.ispartofScientific Reportsen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.snmz$2023V1Guncelleme$en_US
dc.subjectDifferential Expression Analysis; Piwi; Pathway; Germ; Annotation; Evolution; Proteins; 21u-Rnas; Insights; Packageen_US
dc.titlepiRNA-like small RNAs target transposable elements in a Clade IV parasitic nematodeen_US
dc.typeArticleen_US

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