Replication-independent mutations: a universal signature ?
The quiescent X, the replicative Y and the Autosomes
Mutations are the primary source of genetic variation, and there is an obvious interest in characterizing and understanding the processes by which they appear. One particularly important question is the relative abundance, and nature, of replication-dependent and replication-independent mutations - the former arise as cells replicate due to DNA polymerization errors, whereas the latter are unrelated to the cell cycle. A recent experimental study in fission yeast identified a signature of mutations in quiescent (=non-replicating) cells: the spectrum of such mutations is characterized by an enrichment in insertions and deletions (indels) compared to point mutations, and an enrichment of deletions compared to insertions .
What Achaz et al.  report here is that the very same signature is detectable in humans. This time the approach is indirect and relies on two key aspects of mammalian reproduction biology: (1) oocytes remain quiescent over most of a female's lifespan, whereas spermatocytes keep dividing after male puberty, and (2) X chromosome, Y chromosome and autosomes spend different amounts of time in a female vs. male context. In agreement with the yeast study, Achaz et al. show that in humans the male-associated Y chromosome, for which quiescence is minimal, has by far the lowest ratios of indels to point mutations and of deletions to insertions, whereas the female-associated X chromosome has the highest. This is true both of variants that are polymorphic among humans and of fixed differences between humans and chimpanzees.
So we appear to be here learning about an important and general aspect of the mutation process. The authors suggest that, to a large extent, chromosomes tend to break in pieces at a rate that is proportional to absolute time - because indels in quiescent stage presumably result from double-strand DNA breaks. A very recent analysis of numerous mother-father-child trios in humans confirms this prediction in demonstrating an effect of maternal age, but not of paternal age, on the recombination rate . This result also has important implications with respect to the interpretation of substitution rate variation among taxa and genomic compartments, particularly mitochondrial vs. nuclear, and their relationship with the generation time and longevity of organisms (e.g. ).
 Achaz, G., Gangloff, S., and Arcangioli, B. (2019). The quiescent X, the replicative Y and the Autosomes. BioRxiv, 351288, ver. 3 peer-reviewed and recommended by PCI Evol Biol. doi: 10.1101/351288
 Gangloff, S., Achaz, G., Francesconi, S., Villain, A., Miled, S., Denis, C., and Arcangioli, B. (2017). Quiescence unveils a novel mutational force in fission yeast. eLife, 6:e27469. doi: 10.7554/eLife.27469
 Halldorsson, B. V., Palsson, G., Stefansson, O. A., Jonsson, H., Hardarson, M. T., Eggertsson, H. P., … Stefansson, K. (2019). Characterizing mutagenic effects of recombination through a sequence-level genetic map. Science, 363: eaau1043. doi: 10.1126/science.aau1043
 Saclier, N., François, C. M., Konecny-Dupré, L., Lartillot, N., Guéguen, L., Duret, L., … Lefébure, T. (2019). Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods. Molecular Biology and Evolution, in press. doi: 10.1093/molbev/msy247
Nicolas Galtier (2019) Replication-independent mutations: a universal signature ? . Peer Community in Evolutionary Biology, 100066. 10.24072/pci.evolbiol.100066
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.1101/351288
Version of the preprint: 1
Author's Reply, 29 Jan 2019
Decision by Nicolas Galtier, 08 Nov 2018
Achaz et al. report a simple but highly meaningful observation: the ratio of indels to point mutations, and of deletions over insertions, differ between X, Y and autosomes in humans. Why is this meaningful? Because (1) the results are fully consistent with the hypothesis that indels are more frequent than point mutations in quiescent oocytes (hence the X>autosomes>Y ranking), and (2) this very pattern has been experimentally demonstrated to occur in yeast. So we appear to be here learning about an important and general aspect of the mutation process. The two reviewers agree that this is an important result. They provide a number of useful suggestions, which should help improve the manuscript further. In particular, the authors should cite and take into account the last publications in this rapidly moving field (I take this opportunity to insert my and PCI Evol Biol's apologies about the slowness of the process), and make sure they provide a reliable, long-term public distribution of their source code.
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