1. Homology-dependent methylation in primate repetitive DNA
- Author
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Julien Meunier, Laurent Duret, Adel Khelifi, Vincent Navratil, Baobab, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), and CCIN2P3
- Subjects
MESH: Short Interspersed Nucleotide Elements ,MESH: Selection, Genetic ,MESH: Pan troglodytes ,Genome ,Homology (biology) ,chemistry.chemical_compound ,MESH: DNA Methylation ,0302 clinical medicine ,MESH: Pseudogenes ,MESH: Animals ,MESH: Models, Genetic ,MESH: CpG Islands ,MESH: Evolution, Molecular ,Short Interspersed Nucleotide Elements ,MESH: Papio ,Genetics ,0303 health sciences ,Multidisciplinary ,MESH: DNA ,Methylation ,Biological Sciences ,MESH: Primates ,CpG site ,Pseudogenes ,Primates ,Transposable element ,[SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT] ,Pan troglodytes ,MESH: Sequence Alignment ,Biology ,MESH: Sequence Homology, Nucleic Acid ,Evolution, Molecular ,03 medical and health sciences ,Epigenetics of physical exercise ,Sequence Homology, Nucleic Acid ,Animals ,Humans ,Point Mutation ,Selection, Genetic ,Repeated sequence ,Repetitive Sequences, Nucleic Acid ,MESH: Point Mutation ,030304 developmental biology ,MESH: Repetitive Sequences, Nucleic Acid ,MESH: Humans ,Models, Genetic ,DNA ,DNA Methylation ,chemistry ,CpG Islands ,Sequence Alignment ,030217 neurology & neurosurgery ,Papio - Abstract
In mammals, several studies have suggested that levels of methylation are higher in repetitive DNA than in nonrepetitive DNA, possibly reflecting a genome-wide defense mechanism against deleterious effects associated with transposable elements (TEs). To analyze the determinants of methylation patterns in primate repetitive DNA, we took advantage of the fact that the methylation rate in the germ line is reflected by the transition rate at CpG sites. We assessed the variability of CpG substitution rates in nonrepetitive DNA and in various TE and retropseudogene families. We show that, unlike other substitution rates, the rate of transition at CpG sites is significantly (37%) higher in repetitive DNA than in nonrepetitive DNA. Moreover, this rate of CpG transition varies according to the number of repeats, their length, and their level of divergence from the ancestral sequence (up to 2.7 times higher in long, lowly divergent TEs compared with unique sequences). This observation strongly suggests the existence of a homology-dependent methylation (HDM) mechanism in mammalian genomes. We propose that HDM is a direct consequence of interfering RNA-induced transcriptional gene silencing.
- Published
- 2005
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