SUGP1 associates Y-box protein to regulate piRNA biogenesis in Bombyx mori

PIWI-interacting RNAs (piRNAs) are critical for transposon silencing and genome integrity, as well as gene expression regulation and antiviral immunity in metazoans, yet the molecular mechanisms governing their biogenesis remain incompletely understood. The participation of the splicing-associated process in piRNA biogenesis has been emphasized in multiple species, but the key factors and mechanisms remain elusive. Here, we identified SUGP1 (SURP and G-Patch Domain Containing 1) in BmE (a unique model cell system with a complete piRNA biogenesis pathway) as a key splicing factor that functions in piRNA biogenesis. Through CRISPR-Cas9-mediated gene knockdown in cultured cells combined with RNA-seq, small RNA-seq, and IP-mass spectrometry (IP-MS), our results reveal that SUGP1 deficiency disrupts piRNA accumulation, alters mature piRNA length distributions, and activates transposon expression. Immunofluorescence and Western blot (WB) analyses further demonstrate that SUGP1 interacts with Y-box protein (YBP), which is key regulators of RNA metabolism. Functional validation in Drosophila SUGP1-RNAi lines highlights evolutionary conserved and species-specific roles of SUGP1 in piRNA maturation. Collectively, our data uncover a dual role for silkworm SUGP1 in coordinating YBP-dependent piRNA biogenesis, thus elucidating a novel mechanistic framework for piRNA pathway regulation. Our work also underscores the silkworm as a unique model for studying non-canonical piRNA biogenesis mechanisms, with implications for treating transposon dysregulation-linked diseases. Author summaryDisruption of piRNA synthesis leads to abnormal consequences such as transposon de-repression, posing a significant threat to genomic stability. It is therefore essential to in-depth analysis of the piRNA biosynthetic mechanism. Previous studies have highlighted the involvement of splicing-related processes in piRNA biosynthesis, yet key factors and mechanisms remain poorly understood. This study employed the silkworm cell system, which possesses a complete piRNA biosynthetic pathway. Utilizing CRISPR-Cas9-mediated gene knockout technology combined with RNA sequencing, small RNA sequencing, and immunoprecipitation-mass spectrometry (IP-MS), we discovered that SUGP1 deficiency disrupts piRNA accumulation, alters the length distribution of mature piRNAs, and activates transposon expression. Furthermore, immunofluorescence and Western blot analyses confirmed an interaction between SUGP1 and Y-box proteins (YBPs), key regulators of RNA metabolism. Functional validation using Drosophila SUGP1-RNAi lines revealed that SUGP1 plays dual roles in piRNA maturation. Our study reveals that the silkworm scissor-related factor SUGP1 has dual functions in coordinating YBP-dependent piRNA biosynthesis.