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From https://en.wikipedia.org/wiki/Recombination_hotspot#:~:text=Recombination%20hotspots%20are%20regions%20in,that%20of%20the%20surrounding%20region.

I understand that hotspots may arise when certain regions are enriched with particular repeats, or if certain loci are located in chromosome regions that facilitate recombination.

But I'm not sure I understand this paragraph and the implications it may have:

"Recombination hotspots do not seem to be solely caused by DNA sequence arrangements or chromosome structure. Alternatively, initiation sites of recombination hotspots can be coded for in the genome. Through the comparison of recombination between different mouse strains, locus Dsbc1 was identified as a locus that contributes to the specification of initiation sites in the genome in at least two recombination hotspot locations. Additional crossing over mapping located the Dsbc1 locus to the 12.2 to 16.7-Mb region of mouse chromosome 17, which contains the PRDM9 gene. The PRDM9 gene encodes a histone methyltransferase in the Dsbc1 region, providing evidence of a non-random, genetic basis for recombination initiation sites in mice. Rapid evolution of the PRDM9 gene explains the observation that human and chimpanzees share few recombination hotspots, despite a high level of sequence identity."

I interpret this as there is a locus "Dsbc1" that plays a role in determining which place in the genome gets to have a recombination site (or makes that site more prone to recombination), and that the PRDM9 gene difference between chimps and humans causes our recombination sites to be different to those of chimpanzees. If I'm correct here, does that mean mutations to this or similar genes can have downstream effects on the mutation rate and thus how conserved another gene is?

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    $\begingroup$ There are many examples of genes that impact DNA processing and thus mutation rate globally. See pol delta (ncbi.nlm.nih.gov/pmc/articles/PMC2169052), mutS (elifesciences.org/articles/22939), etc. $\endgroup$ Jun 14 at 23:29
  • $\begingroup$ @MaximilianPress Yes, I'm guessing genes encoding DNA repair proteins may have the same effect, but I was thinking more about genes that determine hotspots (or make an existing spot hotter), and how this may impact the "conservativeness" of gene regions. $\endgroup$
    – AnethOthbo
    Jun 14 at 23:41
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    $\begingroup$ Yes, there are such cases. Another example would be homology-directed repair (HDR) genes, where HDR targets rejoining of DNA breaks to regions sharing homology with each other. nature.com/articles/s41467-019-11105-z. This is one of the reasons why pericentromeric and other repetitive regions have high structural variability. $\endgroup$ Jun 14 at 23:58
  • $\begingroup$ Latin -us singular, -i plural (for the particular declension to which locus belongs). $\endgroup$
    – David
    Jun 15 at 16:16

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