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

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...

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Bibliographic Details
Published inbioRxiv
Main Authors Suleiman, Mona, Kohnosu, Asuka, Murcott, Ben, Dayi, Mehmet, Pawluk, Rebecca, Yoshida, Akemi, Viney, Mark, Kikuchi, Taisei, Hunt, Vicky L
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 22.02.2022
Subjects
Adenine
Caenorhabditis elegans
Genomes
Guanine
miRNA
Nematodes
Nucleotide sequence
tRNA
Uracil
Worms
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Summary: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 Caenorhabditis 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' uracil (21-22Us) and monophosphate modification, and (ii) 27 nt long sRNAs with a 5' guanine/adenine (27GAs) and polyphosphate 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. Competing Interest Statement The authors have declared no competing interest.
DOI:10.1101/2022.02.21.481297