Substantial regional variation in substitution rates in the human genome: Importance of GC content, gene density, and telomere-specific

Abstract. This study presents the first global, 1-Mbp-level analysis of patterns of nucleotide substi-tutions along the human lineage. The study is based on the analysis of a large amount of repetitive ele-ments deposited into the human genome since the mammalian radiation, yielding a number of results that would have been difficult to obtain using the more conventional comparative method of analysis. This analysis revealed substantial and consistent variability of rates of substitution, with the variability ranging up to twofold among different regions. The rates of substitutions of C or G nucleotides with A or T nucleotides vary much more sharply than the re-verse rates, suggesting that much of that variation is due to differences in mutation rates rather than in the probabilities of fixation of C/G vs. A/T nucleotides across the genome. For all types of substitution we observe substantially more hotspots than coldspots, with hotspots showing substantial clustering over tens of Mbps. Our analysis revealed that GC-content of surrounding sequences is the best predictor of the rates of substitution. The pattern of substitution ap-pears very different near telomeres compared to the rest of the genome and cannot be explained by the genome-wide correlations of the substitution rates with GC content or exon density. The telomere pat-tern of substitution is consistent with natural selec-tion or biased gene conversion acting to increase the GC-content of the sequences that are within 10–15 Mbp away from the telomere