Molecular Evolutionary and Population Genetics Studies on Regulatory Makorin1-derived Processed Pseudogenes

Processed pseudogenes are produced from the reverse transcription of mRNA followed<br />by integration into the genome. This process is mediated by enzymes encoded by <br />retrotransposable elements such as LINE-1 in mammals. In most cases, processed <br />pseudogenes can not produce transcripts because of lacking functional promoter. <br />Therefore, processed pseudogenes are treated as genomic `fossil records'. However, <br />recently, processed pseudogene has been shown to carry out biochemical function. In<br /> mice, the Makorinl-pl processed pseudogene regulates the mRNA stability of its<br /> homologous coding gene (Makorin 1) by competitive interaction for degradation<br />factors. In this thesis, molecular evolutionary and population genetics approaches are<br />used to investigate the origin and evolution of Makorin 1-derived processed<br />pseudogenes. <br />　　　　　It is shown that Makorin 1-p1 originated almost immediately before the<br />musculus and cervicolor species groups diverged from each other some 4 mi11ion years ago and that the Makorinl-pl orthologs in various Mus species are transcribed. <br />However,Mus caroli in the cervicolor species group transcribes not only Makorinl-pl,<br />but also another older Makorinl-derived processed pseudogene, demonstrating the<br />rapid generation and turnover of the pseudogenes in the subgenus Mus. Under this<br />circumstance, transcribed processed pseudogenes of Makorin1 evolve in a strictly<br />neutral fashion even with an enchanced substitution rate at CpG dinucleotide sites.<br />Makorin1-pl is divided into three regions by its function and the homology to<br />Makorin1; region A has no homology with Makorin1, region B has homology with<br />Makorin1 and includes the target region of degradation factors, and region C has<br />homology with Makorin1 but has no relationship with its mRNA stability. In mouse<br />Makorin1-p1orthologs, there is no difference at the nucleotide substitution rate<br />between regions. <br />　　　　　Extended analyses of Makorin1-derived processed pseudogenes in the genome <br />database and genomic PCRs show that rats have their own Makorin1-derived<br />processed pseudogene. Furthermore, RT-PCRs using testis tota1 RNA demonstrate the<br />cotranscription of Makorin1 and Makorinl-derived processed pseudogenes in rats.<br />These results suggest that the rat specific Makorin1-derived processed pseudogene can take over the role of Makorin1-p1 in the subgenus Mus. Extended analyses to other<br />mammals (dogs, cows, chimpanzees and humans) using genome databases also shows that each species has its own Makorin1-derived processed pseudogenes, except for chimpanzees and humans. In dogs, they have three relatively recently originated Makorin1-derived processed pseudogenes, suggesting that Makorin1-derived processed pseudogenes are rapidly generated in dogs as in mice. Thus, there is a possibility that Makorin1 mRNA stability has been maintained by its processed pseudogenes in dogs. In cows, chimpanzees and humans, however, relatively recent Makorin1-derived processed pseudogenes do not exist. In cows, due to incompleteness of the genome database, such newly emerged sequences may not be identified. In humans and chimpanzees, sevenMakorin1-derived processed pseudogenes exist, and all of them show the relatively old origin. For stability of Makorin1mRNA, the impormt featue is sequence similarity and transcription. RT-PCRs using testis total RNA demonstrate the cotranscription of Makorin1 and Makorin1-derived processed pseudogenes in humans too. If humans and chimpanzees do not have relatively recent Makorin1-derived processed pseudogenes, preexisting pseudogenes must be prevented from accumulating detrimental mutations by negative selection on functionally related region (B region). In fact, comparison between human and chimpanzee orthologs reveals that the B region in two Makorin1-derived processed pseudogenes,MKRN4 and MKRNP1, isconserved. <br />　　　　　To examine whether this conservation is general in primale lineage and human populations, extended analyses to simian primates and human populations using genomic PCRs and genome database searches were carried out. Prosimians have their own specific Makorin1-derived processed pseudogenes. Galagoides demidoff<br />(Demidoff’s galago) has one Makorinl-derived processed pseudogene which has high<br /> homology with Makorin1 in humans and mice, while Galago moholi(South African<br />galago) and Otolemur crassieaudatus(thick-tailed bush baby) have two pairs of<br />orthlogous Makorin1-derived processed pseudogenes and one of them indicates the<br />conservation of th ...

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