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. 2003;4(11):R74.
doi: 10.1186/gb-2003-4-11-r74. Epub 2003 Oct 28.

Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates

Kazuhiko Ohshima  1 , Masahira Hattori, Tetsusi Yada, Takashi Gojobori, Yoshiyuki Sakaki, Norihiro Okada
Affiliations

Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates

Kazuhiko Ohshima et al. Genome Biol. 2003.

Abstract

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.

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Figures

Figure 1
Figure 1
Difference between the profiles of the PP parental genes and PPs in the human genome. (a) Classifications of the PP parental genes. (b) Classifications of the PPs. Gene classes were based on the functional annotation of the NCBI Reference Sequence collection [61] for the respective genes (see Table 1) and were further integrated into four main classes. Ligand-binding proteins, transcription factors, RNA-binding proteins, zinc finger protein, ring finger proteins, nuclear ribonucleoproteins and splicing factors were classified as 'Ligand binding'.
Figure 2
Figure 2
GC content of the PP parental genes and the number of PP copies of those genes. The total number of PP parental genes having a given GC content is shown as individual bars in increments of 4%. The PP-generation rate (the PP number/gene) is shown as a line that connects averages for respective groups. The vertical error bars indicate standard error of the mean.
Figure 3
Figure 3
Chromosomal origins of human PPs. Individual bars indicate the total number of PPs in each chromosome. The different colors represent the chromosomal origins of the PPs.
Figure 4
Figure 4
PP and gene density within each chromosome. For each chromosome, the number of PPs per megabase is plotted against the number of genes per megabase.
Figure 5
Figure 5
Age distribution of human retroposons represented by the level of nucleotide substitutions. (a) Human PPs. The number of nucleotide substitutions per 100 bases (except CpG sites) was calculated for each PP, and the total number of PPs having a given number of substitutions is shown as individual bars in one-nucleotide increments. For comparison, the line shows a Poisson distribution of the same average values for PPs. (b) Alu repeats, calculated and presented as in (a). The line shows a Poisson distribution of the same average values for Alus. (c) Alu subfamilies, calculated as in (a). The curves connect apices of respective bars calculated as in (a). For simplicity, subfamilies that contain less than 5,000 Alus, such as Alu Ya and Yb, are not shown. (d) L1s, calculated and presented as in (a). (e) L1 subfamilies, calculated and presented as in (c). For simplicity, subfamilies that contain less than 1,000 L1s, such as L1PA1 (L1Hs) and L1P1, are not shown. L1PA6, L1PA7 and L1PA8 are shown as bold blue lines.
Figure 6
Figure 6
Phylogenetic relationships between L1 subfamilies. Amino-acid substitutions within the 'C domain' at particular stages of L1 evolution are denoted in boxes. The phylogenetic tree was constructed using the neighbor-joining method [62] based on the last 900 bp of the consensus sequences of respective subfamilies.
Figure 7
Figure 7
Timing of the retrotranspositional explosion during primate evolution. Phylogenetic relationships among primates and the estimated timeframes are based on data from references [34,36] and [37], and references therein.
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