Article

Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes

Japan Biological Information Research Center, Japan Biological Informatics Consortium, AIST Bio-IT Research Bldg 7F, 2-42 Aomi, Tokyo, Japan.
Gene (Impact Factor: 2.08). 04/2007; 389(2):196-203. DOI: 10.1016/j.gene.2006.11.007
Source: PubMed

ABSTRACT Despite the wide distribution of processed pseudogenes in mammalian genomes, such as those of human and mouse, relatively little is known about their roles in genomic evolution. While gene duplications are recognized as one of the major driving forces in genome evolution, processed pseudogenes, which are retrotransposed copies of mRNAs, have been regarded as junk or selfish DNA for a long time. In order to elucidate the quantitative and qualitative contribution of processed pseudogenes to the mammalian genome evolution, we attempted to detect processed pseudogenes by extensively mapping the mRNAs to both the human and mouse genomes, and then we estimated the rate of their emergence. As a result, we revealed that the rate of pseudogene emergence was about 1-2% per gene per million years, which was as high as the rate (0.9%) of gene duplication in the human genome, although the rate of pseudogene emergence was found to drastically decrease in the hominid lineage. Furthermore, 1% of the processed pseudogenes seemed to be reinvigorated by post-retrotransposition transcription, many of them preserving the intact coding regions. Since the expression patterns of transcribed pseudogenes in various tissues were quite different between human and mouse, their emergence might have led to species-specific evolution. Our results indicate that the generation of processed pseudogenes was not wholly futile but instead has been an indispensable resource, driving dynamic evolution of the mammalian genomes.

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    • "MBE " dead on arrival. " However, as a number of studies shows, many of them do acquire new functions (Burki and Kaessmann 2004; Krasnov et al. 2005; Sakai et al. 2007; Kaessmann et al. 2009). These new functions, usually different from the functions of parental genes, may come from the gain of new spatiotemporal expression patterns, imposed by the content of the genomic sequence surrounding inserted cDNA. "
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    • "Recently , several intriguing examples of primate retrogenes have been reported. For example, the human brain-specific isotype of the glutamate dehydrogenase (GLUD2) gene (Burki and Kaessmann 2004) and the brain-and testisspecific CDC14Bretro gene, which has evolved from the CDC14B cell cycle gene (Rosso et al. 2008), emerged by retroposition in a hominoid ancestor (Harrison et al. 2005; Marques et al. 2005; Vinckenbosch et al. 2006; Sakai et al. 2007; Baertsch et al. 2008; Kojima and Okada 2009). "
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