RT Journal Article SR Electronic T1 Temperature-dependent small RNA expression depends on wild genetic backgrounds of Caenorhabditis briggsae JF bioRxiv FD Cold Spring Harbor Laboratory SP 2022.05.23.493161 DO 10.1101/2022.05.23.493161 A1 Daniel D. Fusca A1 Eesha Sharma A1 Jörg G. Weiss A1 Julie M. Claycomb A1 Asher D. Cutter YR 2022 UL http://biorxiv.org/content/early/2022/05/24/2022.05.23.493161.abstract AB Geographically distinct populations can adapt to the temperature conditions of their local environment, leading to temperature-dependent fitness differences between populations. Consistent with local adaptation, phylogeographically distinct Caenorhabditis briggsae nematodes show distinct fitness responses to temperature. The genetic mechanisms underlying local adaptation, however, remain unresolved. To investigate the potential role of small noncoding RNAs in genotype-specific responses to temperature, we quantified small RNA expression using high-throughput sequencing of C. briggsae nematodes from tropical and temperate strain genotypes reared under three temperature conditions (14°C, 20°C, 30°C). Strains representing both tropical and temperate regions showed significantly lower expression of PIWI-interacting RNAs (piRNAs) at high temperatures, primarily mapping to a large ∼7 Mb long piRNA cluster on chromosome IV. We also documented decreased expression of 22G-RNAs antisense to protein-coding genes and other genomic features at high rearing temperatures for the thermally-intolerant temperate strain genotype, but not for the tropical strain genotype. Reduced 22G-RNA expression was widespread along chromosomes and among feature types, indicative of a genome-wide response. Targets of the EGO-1/CSR-1 22G-RNA pathway were most strongly impacted compared to other 22G-RNA pathways, implicating the CSR-1 Argonaute and its RNA-dependent RNA polymerase EGO-1 in the genotype-dependent modulation of C. briggsae 22G-RNAs under chronic thermal stress. Our work suggests that gene regulation via small RNAs may be an important contributor to the evolution of local adaptations.Competing Interest StatementThe authors have declared no competing interest.