dorsal/arxiv
View SchemaSubstantial regional variation in substitution rates in the human genome: importance of GC content, gene density and telomere-specific effects
| Authors | Peter F Arndt, Terence Hwa, Dmitri A Petrov |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0501020 |
| URL | https://arxiv.org/abs/q-bio/0501020 |
Abstract
This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements 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 2-fold among different regions. The rates of substitutions of C or G nucleotides with A or T nucleotides vary much more sharply than the reverse 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 Mbp's. Our analysis revealed that GC-content of surrounding sequences is the best predictor of the rates of substitution. The pattern of substitution appears 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 pattern of substitution is consistent with natural selection or biased gene conversion acting to increase the GC-content of the sequences that are within 10-15 Mbp away from the telomere.
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"abstract": "This study presents the first global, 1 Mbp level analysis of patterns of\nnucleotide substitutions along the human lineage. The study is based on the\nanalysis of a large amount of repetitive elements deposited into the human\ngenome since the mammalian radiation, yielding a number of results that would\nhave been difficult to obtain using the more conventional comparative method of\nanalysis. This analysis revealed substantial and consistent variability of\nrates of substitution, with the variability ranging up to 2-fold among\ndifferent regions. The rates of substitutions of C or G nucleotides with A or T\nnucleotides vary much more sharply than the reverse rates suggesting that much\nof that variation is due to differences in mutation rates rather than in the\nprobabilities of fixation of C/G vs. A/T nucleotides across the genome. For all\ntypes of substitution we observe substantially more hotspots than coldspots,\nwith hotspots showing substantial clustering over tens of Mbp\u0027s. Our analysis\nrevealed that GC-content of surrounding sequences is the best predictor of the\nrates of substitution. The pattern of substitution appears very different near\ntelomeres compared to the rest of the genome and cannot be explained by the\ngenome-wide correlations of the substitution rates with GC content or exon\ndensity. The telomere pattern of substitution is consistent with natural\nselection or biased gene conversion acting to increase the GC-content of the\nsequences that are within 10-15 Mbp away from the telomere.",
"arxiv_id": "q-bio/0501020",
"authors": [
"Peter F Arndt",
"Terence Hwa",
"Dmitri A Petrov"
],
"categories": [
"q-bio.GN"
],
"title": "Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density and telomere-specific effects",
"url": "https://arxiv.org/abs/q-bio/0501020"
},
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