TY - JOUR
T1 - Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes
AU - Sakai, Hiroaki
AU - Koyanagi, Kanako O.
AU - Imanishi, Tadashi
AU - Itoh, Takeshi
AU - Gojobori, Takashi
N1 - Funding Information:
We thank T. Habara, Y. Mimiura, A. Matsuya and Y. Fujii for their technical supports in computation, and C. Gough and P. B. Hilton for proofreading the manuscript. This research was financially supported in part by the Ministry of Economy, Trade and Industry of Japan (METI) and the Japan Biological Informatics Consortium (JBIC).
PY - 2007/3/15
Y1 - 2007/3/15
N2 - 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.
AB - 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.
KW - Expression profile
KW - Processed pseudogene
KW - Substitution rate
UR - http://www.scopus.com/inward/record.url?scp=33846665251&partnerID=8YFLogxK
U2 - 10.1016/j.gene.2006.11.007
DO - 10.1016/j.gene.2006.11.007
M3 - Article
C2 - 17196768
AN - SCOPUS:33846665251
SN - 0378-1119
VL - 389
SP - 196
EP - 203
JO - GENE
JF - GENE
IS - 2
ER -