| Full text | |
| Author(s): |
Total Authors: 2
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| Affiliation: | [1] Univ Estadual Campinas, Inst Biol, Dept Genet & Mol Biol, BR-13083862 Campinas, SP - Brazil
[2] Brazilian Agr Res Corp, Agr Informat Subdiv, Appl Bioinformat Lab, Campinas, SP - Brazil
Total Affiliations: 2
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| Document type: | Journal article |
| Source: | BRIEFINGS IN BIOINFORMATICS; v. 11, n. 2, p. 198-209, MAR 2010. |
| Web of Science Citations: | 25 |
| Abstract | |
Trans-splicing is a common phenomenon in nematodes and kinetoplastids, and it has also been reported in other organisms, including humans. Up to now, all in silico strategies to find evidence of trans-splicing in humans have required that the candidate sequences follow the consensus splicing site rules (spliceosome-mediated mechanism). However, this criterion is not supported by the best human experimental evidence, which, except in a single case, do not follow canonical splicing sites. Moreover, recent findings describe a novel alternative tRNA mediated trans-splicing mechanism, which prescinds the spliceosome machinery. In order to answer the question, `Are there hybrid mRNAs in sequence databanks, whose characteristics resemble those of the best human experimental evidence?', we have developed a methodology that successfully identified 16 hybrid mRNAs which might be instances of interchromosomal trans-splicing. Each hybrid mRNA is formed by a trans-spliced region (TSR), which was successfully mapped either onto known genes or onto a human endogenous retrovirus (HERV-K) transcript which supports their transcription. The existence of these hybrid mRNAs indicates that trans-splicing may be more widespread than believed. Furthermore, non-canonical splice site patterns suggest that infrequent splicing sites may occur under special conditions, or that an alternative trans-splicing mechanism is involved. Finally, our candidates are supposedly from normal tissue, and a recent study has reported that trans-splicing may occur not only in malignant tissues, but in normal tissues as well. Our methodology can be applied to 5'-UTR, coding sequences and 3'-UTR in order to find new candidates for a posteriori experimental confirmation. (AU) | |
| FAPESP's process: | 08/02647-3 - Inverted repeats study in mammals and plant genomes |
| Grantee: | Roberto Hirochi Herai |
| Support Opportunities: | Scholarships in Brazil - Doctorate |