Frequency of intron loss correlates with processed pseudogene abundance: a novel strategy to test the reverse transcript
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RESEARCH ARTICLE
Open Access
Frequency of intron loss correlates with processed pseudogene abundance: a novel strategy to test the reverse transcriptase model of intron loss Tao Zhu1,2 and Deng-Ke Niu1,2*
Abstract Background: Although intron loss in evolution has been described, the mechanism involved is still unclear. Three models have been proposed, the reverse transcriptase (RT) model, genomic deletion model and double-strandbreak repair model. The RT model, also termed mRNA-mediated intron loss, suggests that cDNA molecules reverse transcribed from spliced mRNA recombine with genomic DNA causing intron loss. Many studies have attempted to test this model based on its predictions, such as simultaneous loss of adjacent introns, 3’-side bias of intron loss, and germline expression of intron-lost genes. Evidence either supporting or opposing the model has been reported. The mechanism of intron loss proposed in the RT model shares the process of reverse transcription with the formation of processed pseudogenes. If the RT model is correct, genes that have produced more processed pseudogenes are more likely to undergo intron loss. Results: In the present study, we observed that the frequency of intron loss is correlated with processed pseudogene abundance by analyzing a new dataset of intron loss obtained in mice and rats. Furthermore, we found that mRNA molecules of intron-lost genes are mostly translated on free cytoplasmic ribosomes, a feature shared by mRNA molecules of the parental genes of processed pseudogenes and long interspersed elements. This feature is likely convenient for intron-lost gene mRNA molecules to be reverse transcribed. Analyses of adjacent intron loss, 3’-side bias of intron loss, and germline expression of intron-lost genes also support the RT model. Conclusions: Compared with previous evidence, the correlation between the abundance of processed pseudogenes and intron loss frequency more directly supports the RT model of intron loss. Exploring such a correlation is a new strategy to test the RT model in organisms with abundant processed pseudogenes. Keywords: Free cytoplasmic ribosomes, genomic deletion model, intron loss, long interspersed element, Muridae, processed pseudogene, reverse transcription
Background The loss of spliceosomal introns in eukaryotic evolution has been well documented [1-11]. However, the molecular mechanism of intron loss is still a matter of debate. Three models have been proposed. The first is the reverse transcriptase (RT) model, also termed mRNAmediated intron loss [12,13]. This model assumes that a * Correspondence: [email protected] 1 Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Xinjiekouwai Street 19, Beijing 100875, China Full list of author information is available at the end of the article
cDNA molecule reverse transcribed from mature mRNA recombines with the intron-present genomic DNA, resulting in the precise deletion of one or several introns from t
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