Homology-dependent methylation in primate repetitive DNA.
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.
Meunier
Julien
J
Unité Mixte de Recherche 5558 Centre National de la Recherche Scientifique, Université Claude Bernard-Lyon I, 16 Rue Raphael Dubois, 69622 Villeurbanne Cedex, France.
Khelifi
Adel
A
Navratil
Vincent
V
Duret
Laurent
L
D000818:Animals; D018899:CpG Islands / Q000235:genetics; D004247:DNA / Q000235:genetics* / Q000378:metabolism*; D019175:DNA Methylation; D019143:Evolution, Molecular; D006801:Humans; D008957:Models, Genetic; D002679:Pan troglodytes / Q000235:genetics; D010215:Papio / Q000235:genetics; D017354:Point Mutation / Q000235:genetics; D011323:Primates / Q000235:genetics*; D011544:Pseudogenes / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D012641:Selection, Genetic; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D020086:Short Interspersed Nucleotide Elements / Q000235:genetics
D004247:DNA