Down the Penrose stairs, or how selection for fewer recombination hotspots maintains their existence
Abstract
In many species, meiotic recombination events tend to occur in narrow intervals of the genome, known as hotspots. In humans and mice, double strand break (DSB) hotspot locations are determined by the DNA-binding specificity of the zinc finger array of the PRDM9 protein, which is rapidly evolving at residues in contact with DNA. Previous models explained this rapid evolution in terms of the need to restore PRDM9 binding sites lost to gene conversion over time, under the assumption that more PRDM9 binding always leads to more DSBs. This assumption, however, does not align with current evidence. Recent experimental work indicates that PRDM9 binding on both homologs facilitates DSB repair, and that the absence of sufficient symmetric binding disrupts meiosis. We therefore consider an alternative hypothesis: that rapid PRDM9 evolution is driven by the need to restore symmetric binding because of its role in coupling DSB formation and efficient repair. To this end, we model the evolution of PRDM9 from first principles: from its binding dynamics to the population genetic processes that govern the evolution of the zinc finger array and its binding sites. We show that the loss of a small number of strong binding sites leads to the use of a greater number of weaker ones, resulting in a sharp reduction in symmetric binding and favoring new PRDM9 alleles that restore the use of a smaller set of strong binding sites. This decrease, in turn, drives rapid PRDM9 evolutionary turnover. Our results therefore suggest that the advantage of new PRDM9 alleles is in limiting the number of binding sites used effectively, rather than in increasing net PRDM9 binding. By extension, our model suggests that the evolutionary advantage of hotspots may have been to increase the efficiency of DSB repair and/or homolog pairing.
Data availability
All modeling code, as well as code used to generate the figures, is available at https://github.com/sellalab/PRDM9_model. Source Data files have been provided for Figures 2-6 and their associated figure supplements, as well as for Figures in appendices 4-5.
Article and author information
Author details
Funding
National Institute of Health (R01 GM83098)
- Molly Przeworski
National Institute of Health (R01 GM115889)
- Guy Sella
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Bernard de Massy, CNRS UM, France
Version history
- Preprint posted: September 28, 2022 (view preprint)
- Received: September 28, 2022
- Accepted: October 12, 2023
- Accepted Manuscript published: October 13, 2023 (version 1)
- Version of Record published: December 6, 2023 (version 2)
Copyright
© 2023, Baker et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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