Poster abstracts

Poster number 33 submitted by Hieu Nguyen

Comparative analysis of piRNA pathways and transposons in C. elegans and sibling species

Hieu Nguyen (Department of Biological Chemistry and Pharmacology, The Ohio State University), Benjamin Pastore (Department of Biological Chemistry and Pharmacology, The Ohio State University), Wen Tang (Department of Biological Chemistry and Pharmacology, The Ohio State University)

Abstract:
Piwi-interacting RNAs (piRNAs) are an ancient class of small non-coding RNAs that suppress transposable elements (TEs) in animal germlines, thereby maintaining genome integrity and fertility (Ozata et al., 2019). While piRNA biogenesis and function have been extensively studied, the mechanisms driving piRNA evolution remain poorly understood (Pastore et al., 2022). To address this gap, I investigated piRNA evolution through comparative genomics of three Caenorhabditis nematodes: C. elegans, C. briggsae, and the recently described C. inopinata (Kanzaki et al., 2018), spanning distinct evolutionary distances (~100 million years and ~10 million years from C. elegans, respectively). Using small RNA sequencing, I identified over 11000 piRNA genes and defined 3 piRNA clusters in C. inopinata. By comparing piRNA sequences, genomic organization, and targets across all three species, I discovered that piRNA clusters remain largely syntenic despite extensive chromosomal rearrangements, suggesting cluster organization is selectively maintained. This analysis also revealed that piRNA sequences diverge far more rapidly than other types of non-coding RNAs including miRNAs or tRNAs. To test whether this sequence turnover also occurs within a species, I analyzed whole-genome sequencing data from over 1,000 C. elegans wild isolates (Crombie et al., 2024) and found that while upstream promoter regions are conserved, piRNA sequences accumulate SNPs at rates comparable to non-coding regions, indicating rapid evolution even on short timescales. Finally, de novo TE annotation (Ou et al., 2019) uncovered a striking expansion of LTR transposons in C. inopinata, accompanied by reduced silencing at these elements. Together, these findings reveal that piRNA sequences evolve rapidly within conserved cluster architectures, potentially in response to dynamic TE landscapes. My ongoing research, utilizing comparative genomics and CRISPR-based genetic approaches in C. elegans and C. inopinata, aims to uncover the molecular mechanisms that drive rapid piRNA sequence turnover.

References:
Ozata, D. M., Gainetdinov, I., Zoch, A., O'Carroll, D., & Zamore, P. D. (2019). PIWI-interacting RNAs: Small RNAs with big functions. Nature Reviews Genetics, 20(2), 89–108.
Pastore, B., Hertz, H. L., & Tang, W. (2022). Comparative analysis of piRNA sequences, targets and functions in nematodes. RNA Biology, 19(1), 1276–1292.
Kanzaki, N., Tsai, I. J., Tanaka, R., et al. (2018). Biology and genome of a newly discovered sibling species of Caenorhabditis elegans. Nature Communications, 9, 3216.
Crombie, T. A., McKeown, R., Moya, N. D., et al. (2024). CaeNDR, the Caenorhabditis Natural Diversity Resource. Nucleic Acids Research, 52(D1), D850–D858.
Ou, S., Su, W., Liao, Y., et al. (2019). Benchmarking transposable element annotation methods. Genome Biology, 20, 275.

Keywords: piRNA, nematodes, transposon