Abstract
BackgroundGene fusion is ubiquitous over the course of evolution. It is expected to increase the diversity and complexity of transcriptomes and proteomes through chimeric sequence segments or altered regulation. However, chimeric mRNAs in pigs remain unclear. Here we identified some chimeric mRNAs in pigs and analyzed the expression of them across individuals and breeds using RNA-sequencing data.ResultsThe present study identified 669 putative chimeric mRNAs in pigs, of which 251 chimeric candidates were detected in a set of RNA-sequencing data. The 618 candidates had clear trans-splicing sites, 537 of which obeyed the canonical GU-AG splice rule. Only two putative pig chimera variants whose fusion junction was overlapped with that of a known human chimeric mRNA were found. A set of unique chimeric events were considered middle variances in the expression across individuals and breeds, and revealed non-significant variance between sexes. Furthermore, the genomic region of the 5′ partner gene shares a similar DNA sequence with that of the 3′ partner gene for 458 putative chimeric mRNAs. The 81 of those shared DNA sequences significantly matched the known DNA-binding motifs in the JASPAR CORE database. Four DNA motifs shared in parental genomic regions had significant similarity with known human CTCF binding sites.ConclusionsThe present study provided detailed information on some pig chimeric mRNAs. We proposed a model that trans-acting factors, such as CTCF, induced the spatial organisation of parental genes to the same transcriptional factory so that parental genes were coordinatively transcribed to give birth to chimeric mRNAs.
Highlights
Gene fusion is ubiquitous over the course of evolution
Following the hypothesis that a fusion transcription is derived by two non-continuously genomic loci, the present study revealed a list of pig chimeric mRNAs validated by the RNA-Seq and expressed sequence tag (EST) data (Figure 5)
Similar DNA sequences that share in the upstream regions of both partners significantly matched the known transcription factor binding sites in the JASPAR CORE database, suggesting the potential coordinated transcription of the parental genes
Summary
Gene fusion is ubiquitous over the course of evolution. It is expected to increase the diversity and complexity of transcriptomes and proteomes through chimeric sequence segments or altered regulation. Chimeric mRNAs fused by two previously separate genes located on different genomic loci may allow a limited number of genes to encode a substantially large number of mRNAs and proteins. They are expected to increase proteomic diversity through chimeric proteins or altered regulation. A low amount of a chimeric RNA (JAZF1-JJAZ1) was detected in normal endometrial tissues, joining the JAZF1 gene on chromosome band 7p15 to the JJAZ1/SUZ12 gene on chromosome band 17q21 [5]. Chimeric RNAs and proteins are identical to those produced from a chromosomal rearrangement found in human endometrial stromal tumours [5]. After incubation of mixed extracts from a human endometrial stromal cell line and from a rhesus monkey fibroblast cell line, rhesus JAZF1 exons were joined to human JJAZ1 exons, implying that the JAZF1JJAZ1 RNA is a result of trans-splicing [5]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
