Identification and analysis of pig chimeric mRNAs using RNA sequencing data

<p>Abstract</p> <p>Background</p> <p>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...

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Main Authors: Ma Lei, Yang Shulin, Zhao Weiming, Tang Zhonglin, Zhang Tingting, Li Kui
Format: Article
Language:English
Published: BMC 2012-08-01
Series:BMC Genomics
Subjects:
Online Access:http://www.biomedcentral.com/1471-2164/13/429
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author Ma Lei
Yang Shulin
Zhao Weiming
Tang Zhonglin
Zhang Tingting
Li Kui
author_facet Ma Lei
Yang Shulin
Zhao Weiming
Tang Zhonglin
Zhang Tingting
Li Kui
author_sort Ma Lei
collection DOAJ
description <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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<sup>′</sup> partner gene shares a similar DNA sequence with that of the 3<sup>′</sup> 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.</p> <p>Conclusions</p> <p>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.</p>
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spelling doaj.art-2116201e12794eb89d4a89e6a52c86c22022-12-21T21:19:53ZengBMCBMC Genomics1471-21642012-08-0113142910.1186/1471-2164-13-429Identification and analysis of pig chimeric mRNAs using RNA sequencing dataMa LeiYang ShulinZhao WeimingTang ZhonglinZhang TingtingLi Kui<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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<sup>′</sup> partner gene shares a similar DNA sequence with that of the 3<sup>′</sup> 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.</p> <p>Conclusions</p> <p>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.</p>http://www.biomedcentral.com/1471-2164/13/429Chimeric mRNATrans-splicingRNA-sequencingCTCFPig
spellingShingle Ma Lei
Yang Shulin
Zhao Weiming
Tang Zhonglin
Zhang Tingting
Li Kui
Identification and analysis of pig chimeric mRNAs using RNA sequencing data
BMC Genomics
Chimeric mRNA
Trans-splicing
RNA-sequencing
CTCF
Pig
title Identification and analysis of pig chimeric mRNAs using RNA sequencing data
title_full Identification and analysis of pig chimeric mRNAs using RNA sequencing data
title_fullStr Identification and analysis of pig chimeric mRNAs using RNA sequencing data
title_full_unstemmed Identification and analysis of pig chimeric mRNAs using RNA sequencing data
title_short Identification and analysis of pig chimeric mRNAs using RNA sequencing data
title_sort identification and analysis of pig chimeric mrnas using rna sequencing data
topic Chimeric mRNA
Trans-splicing
RNA-sequencing
CTCF
Pig
url http://www.biomedcentral.com/1471-2164/13/429
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AT tangzhonglin identificationandanalysisofpigchimericmrnasusingrnasequencingdata
AT zhangtingting identificationandanalysisofpigchimericmrnasusingrnasequencingdata
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