Cross-validated methods for promoter/transcription start site mapping in SL trans-spliced genes, established using the Ciona intestinalis troponin I gene.

In conventionally-expressed eukaryotic genes, transcription start sites (TSSs) can be identified by mapping the mature mRNA 5'-terminal sequence onto the genome. However, this approach is not applicable to genes that undergo pre-mRNA 5'-leader trans-splicing (SL trans-splicing) because the original 5'-segment of the primary transcript is replaced by the spliced leader sequence during the trans-splicing reaction and is discarded. Thus TSS mapping for trans-spliced genes requires different approaches.

SL RNA genes of the ascidian tunicates Ciona intestinalis and Ciona savignyi.

We characterized by bioinformatics the trans-spliced leader donor RNA (SL RNA) genes of two ascidians, Ciona intestinalis and Ciona savignyi. The Ciona intestinalis genome contains approximately 670 copies of the SL RNA gene, principally on a 264-bp tandemly repeated element. Fluorescent in-situ hybridization mapped most of the repeats to a single site on the short arm of chromosome 8.