Some abstracts do not have video files because ASAS was denied recording rights.
414
Recurrent chimeric transcripts in human and mouse
The formation of chimeric transcripts (chimeras) has been widely reported [1,2,3]. Some of them reflect underlying chromosomal rearrangements [4], or are the results of the propensity of reverse transcriptase to engage in template switching [5], however, a proportion of cases genuinely appear to correspond to trans-splicing of RNAs, as has previously been described [6,7].
Here we use ENCODE and mouse ENCODE deeply sequenced and bio-replicated RNAseq data from 18 human and 30 mouse samples, and the ChimPipe program, to identify chimeras occurring in multiple biological samples (recurrent), and between the same pairs of genes in human and mouse, since they are more likely to be transcriptionally induced and functional.
Recurrent common chimeras tend to connect gene pairs located on the same chromosome and relatively near to each other (<100kb), therefore pointing to polymerase read-through, however interchromosomal chimeras are also observed, pointing to trans-splicing. Importantly, these recurrent chimeras tend to maintain an open reading frame, and could therefore generate chimeric proteins. We also observe that not only the gene-to-gene connection is conserved, but strikingly so are specific junction sites. The genes connected in common chimeras tend to be involved in morphogenesis and body plan formation, and consistently tend to be detected in cell lines of embryonic origin.
Validation of human chimeras by RT-PCR yielded a success rate of 50%, and subsequent cloning and sequencing revealed novel transcript structures, of which some preserve the domains from the two parent genes. Applying this method to multiple animal species and breeds will help us understanding chimera evolution as well as reveal some links between genotype and phenotype.
[1] Gingeras, T.R. Implications of chimaeric non-co-linear transcripts. Nature, 2009.
[2] Kaessmann, H. Origins, evolution, and phenotypic impact of new genes. Genome Re, 2010.
[3] Djebali, S. et al. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One, 2012.
[4] Mitelman F., Johansson B. & Mertens F., The impact of translocations and gene fusions on cancer causation, Nature Rev Cancer, 2007
[5] Houseley, J. & Tollervey, D. Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro. PLoS One, 2010.
[6] Li, H., Wang, J., Mor, G. & Sklar, J. A neoplastic gene fusion mimics trans-splicing of RNAs in normal human cells. Science, 2008.
[7] Wu, C.S. et al. Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency. Genome Res, 2013.
Keywords: chimeras, transcripts, trans-splicing