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内容記述 |
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 <i>Makorinl-pl</i> processed pseudogene regulates the mRNA stability of its<br /> homologous coding gene (<i>Makorin 1</i>) 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 <i>Makorin 1</i>-derived processed<br />pseudogenes. <br /> It is shown that <i>Makorin 1-p1</i> originated almost immediately before the<br /><i>musculus</i> and <i>cervicolor</i> species groups diverged from each other some 4 mi11ion years ago and that the <i>Makorinl-pl</i> orthologs in various Mus species are transcribed. <br />However,<i>Mus caroli</i> in the <i>cervicolor</i> species group transcribes not only <i>Makorinl-pl,</i><br />but also another older <i>Makorinl</i>-derived processed pseudogene, demonstrating the<br />rapid generation and turnover of the pseudogenes in the subgenus <i>Mus</i>. Under this<br />circumstance, transcribed processed pseudogenes of <i>Makorin1</i> evolve in a strictly<br />neutral fashion even with an enchanced substitution rate at CpG dinucleotide sites.<br /><i>Makorin1-pl</i> is divided into three regions by its function and the homology to<br /><i>Makorin1</i>; region A has no homology with <i>Makorin1</i>, region B has homology with<br /><i>Makorin1</i> and includes the target region of degradation factors, and region C has<br />homology with <i>Makorin1</i> but has no relationship with its mRNA stability. In mouse<br /><i>Makorin1-p1</i>orthologs, there is no difference at the nucleotide substitution rate<br />between regions. <br /> Extended analyses of <i>Makorin1</i>-derived processed pseudogenes in the genome <br />database and genomic PCRs show that rats have their own <i>Makorin1</i>-derived<br />processed pseudogene. Furthermore, RT-PCRs using testis tota1 RNA demonstrate the<br />cotranscription of <i>Makorin1</i> and <i>Makorinl</i>-derived processed pseudogenes in rats.<br />These results suggest that the rat specific <i>Makorin1</i>-derived processed pseudogene can take over the role of <i>Makorin1-p1</i> in the subgenus <i>Mus.</i> Extended analyses to other<br />mammals (dogs, cows, chimpanzees and humans) using genome databases also shows that each species has its own <i>Makorin1</i>-derived processed pseudogenes, except for chimpanzees and humans. In dogs, they have three relatively recently originated <i>Makorin1</i>-derived processed pseudogenes, suggesting that <i>Makorin1</i>-derived processed pseudogenes are rapidly generated in dogs as in mice. Thus, there is a possibility that <i>Makorin1</i> mRNA stability has been maintained by its processed pseudogenes in dogs. In cows, chimpanzees and humans, however, relatively recent <i>Makorin1</i>-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, seven<i>Makorin1</i>-derived processed pseudogenes exist, and all of them show the relatively old origin. For stability of <i>Makorin1</i>mRNA, the impormt featue is sequence similarity and transcription. RT-PCRs using testis total RNA demonstrate the cotranscription of <i>Makorin1</i> and <i>Makorin1</i>-derived processed pseudogenes in humans too. If humans and chimpanzees do not have relatively recent <i>Makorin1</i>-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 <i>Makorin1</i>-derived processed pseudogenes,<i>MKRN4</i> and <i>MKRNP1</i>, 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 <i>Makorin1</i>-derived processed pseudogenes. <i>Galagoides demidoff</i><br />(Demidoff’s galago) has one <i>Makorinl</i>-derived processed pseudogene which has high<br /> homology with <i>Makorin1</i> in humans and mice, while <i>Galago moholi</i>(South African<br />galago) and <i>Otolemur crassieaudatus</i>(thick-tailed bush baby) have two pairs of<br />orthlogous <i>Makorin1</i>-derived processed pseudogenes and one of them indicates the<br />conservation of the B region. New World monkeys and Catarrhini have orthologous<br />pairs of human Makorin1-derived processed pseudogenes. Unlike rodents,<br /><i>Makorin1</i>-derived processed pseudogenes occur rather infrequently in simian primates.<br />Under this circumstance, it is hypothesized that preexisting transcribed processed<br />pseudogenes must be prevented from accumulating detrimental mutations by negative<br />selection. Comparison of <i>MKRN4</i>orthologous pairs shows that the conservation of the<br />B region is limited to humans and chimpanzees. In contrast to <i>MKRN4</i>, comparison of<br /><i>MKRNP1</i> orthlogous pairs shows that the conservation of the B region is general, and<br />especially, the strict conservation is observed in hominoids. In human populations,<br /> both <i>MKRN4</i> and <i>MKRNPI1</i>show the reduction of the nucleotide diversity in the B<br /> region, compared with other region. <br /> From the above observation it is concluded as follows: 1) The transcription of<br /><i>Makorinl</i>-derived processed pseudogene is not limited to mice. The phenomenon is<br />rather general in mammals. 2) The rate of emergence of these pseudogenes is, however, different from species to species. And 3) The evolutionary rate and pattern of<br /><i>Makorin1</i>-derived processed pseudogenes depend heavily on how frequently they are<br />disseminated in the genome. |
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