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.
BMC Genomics. 2012 Aug 28;13:429. doi: 10.1186/1471-2164-13-429.
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.
基因融合在进化过程中普遍存在。它通过嵌合序列片段或改变调节，预计会增加转录组和蛋白质组的多样性和复杂性。然而，猪的嵌合 mRNA 仍然不清楚。在这里，我们在猪中鉴定了一些嵌合 mRNA，并使用 RNA-seq 数据分析了它们在个体和品种之间的表达。
本研究在猪中鉴定了 669 个推定的嵌合 mRNA，其中 251 个嵌合候选物在一组 RNA-seq 数据中被检测到。618 个候选物有明确的跨剪接位点，其中 537 个符合典型的 GU-AG 剪接规则。只发现了两个推定的猪嵌合变异体，其融合接头与已知的人类嵌合 mRNA 重叠。一组独特的嵌合事件被认为是个体和品种之间表达的中间变异，并且在性别之间没有发现显著差异。此外，5'伙伴基因的基因组区域与 458 个推定的嵌合 mRNA 的 3'伙伴基因的 DNA 序列有相似之处。其中 81 个共享 DNA 序列与 JASPAR CORE 数据库中已知的 DNA 结合基序显著匹配。在亲本基因组区域共享的四个 DNA 基序与已知的人类 CTCF 结合位点有显著的相似性。
本研究提供了一些猪嵌合 mRNA 的详细信息。我们提出了一个模型，即反式作用因子，如 CTCF，诱导亲本基因的空间组织到相同的转录工厂，从而使亲本基因协调转录产生嵌合 mRNA。
