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Open Access Research article

Newly evolved introns in human retrogenes provide novel insights into their evolutionary roles

Li-Fang Kang1, Zheng-Lin Zhu1*, Qian Zhao1, Li-Yong Chen2* and Ze Zhang1

Author affiliations

1 College of Life Sciences, Chongqing University, Chongqing, 400044, China

2 Department of Anesthesiology, Research Institute of Surgery, Daping Hospital, Third Military Medical University, 10 Changjiang Zhilu, Chongqing, 400042, China

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Citation and License

BMC Evolutionary Biology 2012, 12:128  doi:10.1186/1471-2148-12-128

Published: 28 July 2012

Abstract

Background

Retrogenes generally do not contain introns. However, in some instances, retrogenes may recruit internal exonic sequences as introns, which is known as intronization. A retrogene that undergoes intronization is a good model with which to investigate the origin of introns. Nevertheless, previously, only two cases in vertebrates have been reported.

Results

In this study, we systematically screened the human (Homo sapiens) genome for retrogenes that evolved introns and analyzed their patterns in structure, expression and origin. In total, we identified nine intron-containing retrogenes. Alignment of pairs of retrogenes and their parents indicated that, in addition to intronization (five cases), retrogenes also may have gained introns by insertion of external sequences into the genes (one case) or reversal of the orientation of transcription (three cases). Interestingly, many intronizations were promoted not by base substitutions but by cryptic splice sites, which were silent in the parental genes but active in the retrogenes. We also observed that the majority of introns generated by intronization did not involve frameshifts.

Conclusions

Intron gains in retrogenes are not as rare as previously thought. Furthermore, diverse mechanisms may lead to intron creation in retrogenes. The activation of cryptic splice sites in the intronization of retrogenes may be triggered by the change of gene structure after retroposition. A high percentage of non-frameshift introns in retrogenes may be because non-frameshift introns do not dramatically affect host proteins. Introns generated by intronization in human retrogenes are generally young, which is consistent with previous findings for Caenorhabditis elegans. Our results provide novel insights into the evolutionary role of introns.