AI Article Synopsis

  • - The study investigates single-nucleotide variants (SNVs) within segmental duplications (SDs) across 102 human haplotypes, revealing that SNVs are 60% more prevalent in SDs than in unique regions, largely due to interlocus gene conversion (IGC).
  • - Researchers created a genome-wide map detailing IGC hotspots, identifying 498 acceptor and 454 donor regions impacting approximately 800 protein-coding genes, with some genes having "relocated" an average of 1.61 megabase pairs.
  • - The findings highlight that the mutational patterns in SDs differ from unique DNA, showing a higher ratio of specific transition mutations and a lower frequency of CpG mutations, which

Article Abstract

Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data. Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 102 human haplotypes and compared the pattern of SNVs between unique and duplicated regions. We find that human SNVs are elevated 60% in SDs compared to unique regions and estimate that at least 23% of this increase is due to interlocus gene conversion (IGC) with up to 4.3 megabase pairs of SD sequence converted on average per human haplotype. We develop a genome-wide map of IGC donors and acceptors, including 498 acceptor and 454 donor hotspots affecting the exons of about 800 protein-coding genes. These include 171 genes that have 'relocated' on average 1.61 megabase pairs in a subset of human haplotypes. Using a coalescent framework, we show that SD regions are slightly evolutionarily older when compared to unique sequences, probably owing to IGC. SNVs in SDs, however, show a distinct mutational spectrum: a 27.1% increase in transversions that convert cytosine to guanine or the reverse across all triplet contexts and a 7.6% reduction in the frequency of CpG-associated mutations when compared to unique DNA. We reason that these distinct mutational properties help to maintain an overall higher GC content of SD DNA compared to that of unique DNA, probably driven by GC-biased conversion between paralogous sequences.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10172114PMC
http://dx.doi.org/10.1038/s41586-023-05895-yDOI Listing

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