Small Nuclear RNA 3′ End Processing Factors in Transposon Silencing and piRNA Biogenesis

Abstract

In Drosophila, germline piRNAs derive from both strands of transposon-rich genomic clusters. Transcription of these “dual strand” clusters requires a fly-specific, heterochromatin protein 1 paralog, Rhino (Rhi), which binds the heterochromatin mark trimethylated lysine 9 on histone 3 (H3K9me3). Rhino facilitates the assembly of an RNA polymerase II (RNA pol II) transcriptional initiation complex, bypassing the need for promoter sequences. Rhi also collaborates with the protein Cutoff (Cuff) to suppress splicing and CPSF-mediated cleavage and polyadenylation of cluster transcripts. Like piRNA precursor transcripts, the small nuclear RNAs (snRNA) transcribed by RNA pol II are also not polyadenylated, relying on alternative mechanisms to generate their 3′ ends. Two complexes have been proposed to mediate snRNA 3′ end formation. First, the nuclear exosome targeting complex (NEXT) has been proposed to trigger exosome-mediated snRNA termination. Ars2, a core component of the complex, links NEXT to the cap binding complex, promoting the exosome to process the 3′ ends of snRNAs. Second, the Integrator complex (INT), a homolog of CPSF, has also been proposed to act in snRNA processing and transcription termination. Our studies implicate both the NEXT and INT complexes in female fertility and repression of transposons in ovaries. Depletion of NEXT or INT components by germline RNAi increases expression of transposons, including the somatic element, gypsy, producing virus-like particles in late developmental stages of oogenesis. Furthermore, loss of Rhi or Cuff generates unprocessed snRNA transcripts, suggesting shared mechanisms in the production or maturation of snRNAs and piRNAs.