Detection of human interchromosomal trans-splicing in sequence databanks

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.

Mechanism of alternative splicing and its regulation

“…Trans-splicing is a common phenomenon in trypanosomes, nematodes, Drosophila and even humans, and refers to the novel and unusual splicing of exons from independent pre-mRNAs (62,63). The phenomenon has been explored as a therapeutic option for a variety of genetic diseases, particularly in the treatment of cancer (64).…”

Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency

“…Generally, trans-splicing is detected by comparing the reference genomes with ESTs/mRNAs (Shao et al 2006;Li et al 2009;Herai and Yamagishi 2010;Kim et al 2010) or by next-generation sequencing (NGS) of mRNAs (RNA-seq) (McManus et al 2010;Zhang et al 2010;Al-Balool et al 2011;Fang et al 2012). Transsplicing events detected by such means may, however, include a considerable number of false positives that arise from experimental artifacts, such as template switching (McManus et al 2010;Ozsolak and Milos 2011).…”

Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts

“…Chimeric mRNAs are distinct from conventionally spliced mRNA isoforms as they are produced by joining exons from two or more different gene loci (Pirrotta 2002;Horiuchi and Aigaki 2006;Robertson et al 2007;Li et al 2008;Gingeras 2009;Douris et al 2010;Herai and Yamagishi 2010;McManus et al 2010a,b;Pettitt et al 2010;Allen et al 2011). In humans, chimeric transcripts are generated in several ways: trans-splicing of pre-mRNAs (Gingeras 2009;Li et al 2009c), RNA transcription runoff (Akiva et al 2006;Parra et al 2006), from other errors in RNA transcription processing (Gingeras 2009), or represent artifacts of RNA sequencing.…”

“…In humans, chimeric transcripts are generated in several ways: trans-splicing of pre-mRNAs (Gingeras 2009;Li et al 2009c), RNA transcription runoff (Akiva et al 2006;Parra et al 2006), from other errors in RNA transcription processing (Gingeras 2009), or represent artifacts of RNA sequencing. Alternatively, chimeric transcripts can be the products of gene fusion following inter-chromosomal translocations or intra-chromosomal rearrangements (Gingeras 2009;Maher et al 2009b;Herai and Yamagishi 2010). Specific cellular phenotypes are characterized by expression of chimeric transcripts, for example, the fused BCR/ABL, FUS/ERG, MLL/AF6, and MOZ/CBP genes are expressed in acute myeloid leukemia (AML) (Panagopoulos et al 2003;Nambiar et al 2008), and the TMPRSS2/ETS chimera is associated with overexpression of the oncogene in prostate cancer (Nambiar et al 2008).…”