THE RATE OF CPG MUTATION IN ALU REPETITIVE ELEMENTS WITHIN THE P53 TUMOR-SUPPRESSOR GENE IN THE PRIMATE GERMLINE

Cytosine to thymine transition mutations at the CpG dinucleotide are t he most common point mutations in cancer and genetic disease. We calcu lated the in vivo rate of CpG mutation in the primate germline by deri ving a primordial consensus sequence for an Alu repetitive element whi ch inserted into intron 6 of the primate p53 gene 35 to 55 million yea rs ago. Comparison of this primordial sequence to the Alu sequence in intron 6 of present-day primates was used to determine the nature and rate of mutations which occurred during evolution. We estimate the hal f-life of a CpG nucleotide to be 24 to 60 million years, and the rate constant for mutation at this dinucleotide to be 1.2 x 10(-8) to 2.9 x 10(-8) years(-1). These results were confirmed by the analysis of a s econd Alu sequence in intron 10 of the p53 gene. The in vitro mutation rate is at least 1250-fold slower than the in vitro chemical rate of 5-methylcytosine deamination in double-stranded DNA, showing that curr ent estimates of CpG mutation repair have been significantly underesti mated. Furthermore, the mutability of the CpG dinucleotide has led to the depletion of this dinucleotide from the vertebrate genome, and cal culations in this study suggest that current levels of the CpG dinucle otide in the primate genome are very close to a steady state equilibri um in which the rate of CpG mutation is equal to the rate of CpG forma tion by random mutation. (C) 1996 Academic Press Limited