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

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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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Acknowledgements

We thank Katsuhiko Murakami (RIKEN-GSC) for helpful discussions and Kei-ichi Kuma and Takashi Miyata (Kyoto University) for providing the data on the average nucleotide substitution rates of 31 pairs of human PPs. This work was partially supported by the Ministry of Education, Culture, Sports, Science and Technology of Japan, Grant-in-Aid for Scientific Research. This work was also supported by a grant from BIRD of Japan Science and Technology Corporation (JST) for K.O.

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Authors and Affiliations

  1. School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan

    Kazuhiko Ohshima & Norihiro Okada

  2. RIKEN Genomic Sciences Center, 1-7-22, Suehiro Tsurumi, Yokohama, Kanagawa, 230-0045, Japan

    Masahira Hattori & Yoshiyuki Sakaki

  3. Laboratory of Genome Information, Kitasato Institute for Life Science, Kitasato University, 1-15-1, Kitasato, Sagamihara, Kanagawa, 228-8555, Japan

    Masahira Hattori

  4. Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan

    Tetsusi Yada & Yoshiyuki Sakaki

  5. Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan

    Takashi Gojobori

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  1. Kazuhiko Ohshima
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Correspondence to Norihiro Okada.

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Ohshima, K., Hattori, M., Yada, T. et al. Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol 4, R74 (2003). https://doi.org/10.1186/gb-2003-4-11-r74

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