Members of several animal phyla (nematodes, flatworms, an ascidian, and Hydra) and members of one phylum of unicellular eukaryotes (Trypanosomes and Euglena) have been found to carry out an RNA trans-splicing process in which a small leader sequence is added to the 5' end of some fraction of mRNAs.

To download the PDF file of the paper by Stover and Steele on trans-spliced leader addition in Hydra, click here.

In addition to being an interesting biological phenomenon, spliced leader addition is of practical value. Identification of the 5' end of a cDNA can be difficult. The presence of a spliced leader sequence indicates that the 5' end has, indeed, been obtained. Thus for Hydra cDNAs for which you are trying to get the 5' end, it would be worth trying RT PCR using primers for SL-A and SL-B. If spliced leader addition occurs on the gene, such an RT PCR approach should easily yield the 5' end of the cDNA. At this point we don't have a good idea of how many mRNAs in Hydra get spliced leaders. A PCR experiment carried out by Nick Stover (UC Irvine) using combinations of spliced leader primers and vector primers and DNA from a Hydra cDNA library as template yielded a product which migrated as a smear ranging in size from 200-2000 base pairs. This result suggests that the fraction of Hydra mRNAs that get spliced leaders may be quite large. No one has yet tested a given gene by RT PCR with spliced leader primers to determine whether there are genes in Hydra that do not receive spliced leaders. However, the location of the transcriptional start site in a Hydra actin gene (Fisher and Bode, Gene 84: 55-64, 1989) suggests that this gene does not receive a spliced leader. One can conclude this because the putative start site does not coincide with a potential splice acceptor sequence (as would be the case if nuclease protection mapping had actually identified the point of divergence between the genomic sequence and the spliced leader in the mRNA).

The table below lists the Hydra genes in the public domain for which spliced leader addition has been demonstrated (a number of additional cases have been found by various labs, but these have not yet been published or deposited in GenBank). If you have identified Hydra genes which have spliced leaders which you would like included in this table, please contact Rob Steele (resteele@uci.edu).

Notes: For some genes, only SL-A or SL-B containing forms have been identified. Whether this indicates exclusive use of one or the other spliced leader for those genes is unknown. For these cases, a question mark is entered in the column for the spliced leader which hasn't yet been found.