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

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