The Small RNA Universe of Capitella teleta

Abstract

RNAi is an evolutionarily fluid mechanism with dramatically different activities across animal phyla. One major group where there has been little investigation is annelid worms. Here, the small RNAs of the polychaete developmental model Capitella teleta are profiled across development. As is seen with nearly all animals, nearly 200 microRNAs were found with 58 high-confidence novel species. Greater miRNA diversity was associated with later stages consistent with differentiation of tissues. Outside miRNA, a distinct composition of other small RNA pathways was found. Unlike many invertebrates, an endogenous siRNA pathway was not observed, indicating pathway loss relative to basal planarians. No processively generated siRNA-class RNAs could be found arising from dsRNA precursors. This has a significant impact on RNAi technology development for this group of animals. Unlike the apparent absence of siRNAs, a significant population of piRNAs was observed. For many piRNAs, phasing and ping-pong biogenesis pathways were identified. Interestingly, piRNAs were found to be highly expressed during early development, suggesting a potential role in regulation in metamorphosis. Critically, the configuration of RNAi factors in C. teleta is found in other annelids and mollusks, suggesting that similar biology is likely to be present in the wider clade. This study is the first in providing comprehensive analysis of small RNAs in annelids.

The Evolution and Characterization of the RNA Interference Pathways in Lophotrochozoa

“…DICER2 generally processes double-stranded RNAs producing two 21 bases siRNA duplexes that overlap by 19 bases. Similarly, piRNAs produced by the ping-pong cycle go in pairs that overlap by 10 bases ( Antoniewski 2014 ; Khanal et al 2022 ). Thus, siRNAs and piRNAs have a unique signature that can be identified in sncRNA libraries by looking for overlapping pairs of reads.…”

“…Outside those phyla, few data have been published. The endo-siRNA pathway seems absent in the Annelida Capitella teleta ( Khanal et al 2022 ) and the annotation of miRNA families is restricted to one Syndermata, one Brachiopoda, and two Annelida species ( Fromm et al 2022 ).…”

Annelid methylomes reveal ancestral developmental and ageing-associated epigenetic erosion across Bilateria

“…Indeed, TE load does not correlate well with global 5mC levels and TE methylation in annelids: the deep-sea species Paraescarpia echinospica has a higher TE burden than O. fusiformis but does not show TE methylation [29, 42, 75]. Alternative pathways to control TE activity, such as PIWI-interacting RNAs (piRNAs) [76, 77], are more broadly conserved in annelids and molluscs [78, 79]. In addition, although the mechanism of how DNMTs target gene bodies is quite well understood (the PWWP domain in DNMT3 orthologues binds to histone lysine 36 trimethylated residues typical of gene bodies) [80], how invertebrate DNMTs might target TEs remains unresolved.…”

MiSiPi-Rna: an integrated tool for characterizing small regulatory RNA processing

“…This may increase deployment of RNAi for in recently sequenced or unannotated species. Indeed, while small RNA biology is well characterized in model species studies highlight the diversity of biogenesis between even related organisms (Flynt, 2021;Mondal et al, 2021) (Khanal et al, 2022). Notably, MiSiPi-RNA is one of the only tools available thus far which can classify siRNA loci.…”

“…To facilitate overall small assessment the final function of MiSiPi-Rna is to output tables of values for phasing (both for siRNA and piRNA), dicer signatures (dual strand and across a hairpin), and pingpong signatures. Such tables are amendable to plotting with heatmaps and for clustering loci (Khanal et al, 2022).…”