Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates.
BACKGROUND
Abundant pseudogenes are a feature of mammalian genomes. Processed pseudogenes (PPs) are reverse transcribed from mRNAs. Recent molecular biological studies show that mammalian long interspersed element 1 (L1)-encoded proteins may have been involved in PP reverse transcription. Here, we present the first comprehensive analysis of human PPs using all known human genes as queries.


RESULTS
The human genome was queried and 3,664 candidate PPs were identified. The most abundant were copies of genes encoding keratin 18, glyceraldehyde-3-phosphate dehydrogenase and ribosomal protein L21. A simple method was developed to estimate the level of nucleotide substitutions (and therefore the age) of PPs. A Poisson-like age distribution was obtained with a mean age close to that of the Alu repeats, the predominant human short interspersed elements. These data suggest a nearly simultaneous burst of PP and Alu formation in the genomes of ancestral primates. The peak period of amplification of these two distinct retrotransposons was estimated to be 40-50 million years ago. Concordant amplification of certain L1 subfamilies with PPs and Alus was observed.


CONCLUSIONS
We suggest that a burst of formation of PPs and Alus occurred in the genome of ancestral primates. One possible mechanism is that proteins encoded by members of particular L1 subfamilies acquired an enhanced ability to recognize cytosolic RNAs in trans.
Ohshima
Kazuhiko
K
School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
Hattori
Masahira
M
Yada
Tetsusi
T
Gojobori
Takashi
T
Sakaki
Yoshiyuki
Y
Okada
Norihiro
N
D000465:Algorithms; D020087:Alu Elements / Q000235:genetics*; D000818:Animals; D001482:Base Composition; D002874:Chromosome Mapping; D018076:DNA, Complementary / Q000235:genetics; D019143:Evolution, Molecular; D005787:Gene Frequency; D015894:Genome, Human; D006801:Humans; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics*; D009154:Mutation; D011323:Primates / Q000235:genetics*; D011544:Pseudogenes / Q000235:genetics*
D018076:DNA, Complementary