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Identification and analysis of pig chimeric mRNAs using RNA sequencing data

Lei Ma12, Shulin Yang1, Weiming Zhao1, Zhonglin Tang1, Tingting Zhang2 and Kui Li1*

Author Affiliations

1 The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China

2 College of Life Science, Shihezi University, Xinjiang, 832000, P. R. China

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BMC Genomics 2012, 13:429  doi:10.1186/1471-2164-13-429

Published: 28 August 2012



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. 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.


The 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.


The 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.

Chimeric mRNA; Trans-splicing; RNA-sequencing; CTCF; Pig