Promoter Specificity and Transcription Levels Modulate Trans-Splicing Efficiency at the mod(mdg4) Locus in Drosophila

Unlike canonical cis-splicing, trans-splicing combines exons from two distinct transcripts, creating chimeric mRNAs. One striking example is the mod(mdg4) locus in Drosophila, where all mRNAs, encompassing over 30 isoforms, are exclusively generated via trans-splicing, which integrates common constitutive exons with one of the alternative 3' exons transcribed from independent promoters. This study analyzed the roles of the promoter, exons, and introns in trans-splicing, including in the constitutive part of the mod(mdg4) gene, using a previously validated model in the heterogeneous 22A genomic locus. We found that trans-splicing efficiency was significantly greater with the mod(mdg4) promoter compared to unrelated promoters with the similar transcription level. Trans-splicing efficiency correlates positively with transcriptional strength only at low transcription levels, and it does not change with further increases in mod(mdg4) transcription in the model system. The last common exon and the preceding intron of mod(mdg4) also play a minor role in enhancing trans-splicing. However, low levels of trans-splicing are maintained even when all sequences of the mod(mdg4) gene are replaced, except for the proximal part of the last intron, where trans-splicing is initiated.