ArticleGenome biology2003
Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates.
Article in Genome biology, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.
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90 citing papers in PubMed, 190 citations in OpenAlex.
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- Evolution and function of developmentally dynamic pseudogenes in mammals.Genome biology · 2022Article
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- The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology.International journal of molecular sciences · 2022Review
- Identification of multiple TAR DNA binding protein retropseudogene lineages during the evolution of primates.Scientific reports · 2022Article
- Particulate matter-induced hypomethylation of Alu and LINE1 in normal human bronchial epithelial cells and epidermal keratinocytes.Genes and environment : the official journal of the Japanese Environmental Mutagen Society · 2022Article
- Analysis of SINE Families B2, Dip, and Ves with Special Reference to Polyadenylation Signals and Transcription Terminators.International journal of molecular sciences · 2021Article
- Nuku, a family of primate retrocopies derived from KU70.G3 (Bethesda, Md.) · 2021Article
- The mutational load in natural populations is significantly affected by high primary rates of retroposition.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- RetroScan: An Easy-to-Use Pipeline for Retrocopy Annotation and Visualization.Frontiers in genetics · 2021Article
- Pseudogenes: A Novel Source of Trans-Acting Antisense RNAs.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Transcriptional activity and strain-specific history of mouse pseudogenes.Nature communications · 2020Article
- LINE-1 ORF1p does not determine substrate preference for human/orangutan SVA and gibbon LAVA.Mobile DNA · 2020Article
- Inflammation-induced DNA damage, mutations and cancer.DNA repair · 2019Review
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- Impact of non-LTR retrotransposons in the differentiation and evolution of anatomically modern humans.Mobile DNA · 2018Article
- Review
30 more citing papers are in PubMed but not listed here.
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6 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAbundant 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.
resultsThe 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.
conclusionsWe 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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