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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

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...

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Autores principales: Ohshima, Kazuhiko, Hattori, Masahira, Yada, Tetsusi, Gojobori, Takashi, Sakaki, Yoshiyuki, Okada, Norihiro
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2003
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC329124/
https://www.ncbi.nlm.nih.gov/pubmed/14611660
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author Ohshima, Kazuhiko
Hattori, Masahira
Yada, Tetsusi
Gojobori, Takashi
Sakaki, Yoshiyuki
Okada, Norihiro
author_facet Ohshima, Kazuhiko
Hattori, Masahira
Yada, Tetsusi
Gojobori, Takashi
Sakaki, Yoshiyuki
Okada, Norihiro
author_sort Ohshima, Kazuhiko
collection PubMed
description 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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spelling pubmed-3291242004-02-05 Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates Ohshima, Kazuhiko Hattori, Masahira Yada, Tetsusi Gojobori, Takashi Sakaki, Yoshiyuki Okada, Norihiro Genome Biol Research 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. BioMed Central 2003 2003-10-28 /pmc/articles/PMC329124/ /pubmed/14611660 Text en Copyright © 2003 Ohshima et al.; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.
spellingShingle Research
Ohshima, Kazuhiko
Hattori, Masahira
Yada, Tetsusi
Gojobori, Takashi
Sakaki, Yoshiyuki
Okada, Norihiro
Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates
title Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates
title_full Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates
title_fullStr Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates
title_full_unstemmed Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates
title_short Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates
title_sort whole-genome screening indicates a possible burst of formation of processed pseudogenes and alu repeats by particular l1 subfamilies in ancestral primates
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC329124/
https://www.ncbi.nlm.nih.gov/pubmed/14611660
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