SUGP1 Deficiency Leads to Splicing Dysregulation and Reduced piRNA Abundance in Insects

Abstract

SUGP1 (SURP and G-patch domain containing 1) participates in splice-site recognition through its interaction with SF3B1, and loss of this factor leads to aberrant splicing. While its role in pre-mRNA splicing is well-documented, its impact on small RNA pathways remains poorly understood. Here, we used CRISPR/Cas9-mediated SUGP1 editing in Bombyx mori BmE cell populations and RNAi to systemically knock down SUGP1 in Drosophila melanogaster. SUGP1 loss caused widespread splicing abnormalities in both species and reduced transposon-derived piRNA abundance as shown by small RNA-seq. Notably, the expression and splicing patterns of known piRNA pathway genes remained largely unchanged. Integrating silkworm transcriptomic data with the Flag-SUGP1 Co-IP/MS interactome revealed no direct association with the components of the piRNA biogenesis pathway, but identified a physical interaction with the Y-box protein (YBX), suggesting a potential link connecting splicing surveillance to RNA metabolism and proteostasis. Collectively, these correlative findings suggest that SUGP1 depletion perturbs global RNA processing, and piRNA reduction may represent a secondary outcome associated with cellular stress or dysregulated RNA metabolism within these two tested insect systems. These results suggest a potential indirect link between SUGP1-dependent splicing regulation and piRNA abundance in the tested insect models.