Coarsening dynamics can explain meiotic crossover patterning in both the presence and absence of the synaptonemal complex
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During meiotic prophase I, protein complexes essential for crossover recombination are distributed non-randomly along chromosomes. With mathematical modelling and based on results from super-resolution microscopy, the authors introduce a second type of coarsening of protein ensembles between chromosome axes and nucleoplasm between chromosomes and nucleoplasm to support the random distribution of the complexes in the synapsis-defective mutant. The new model is interesting and may be applied to other chromosomal events accompanied by the formation of large protein ensembles on the chromosomes. The work is of interest to colleagues studying recombination and meiosis.
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Abstract
The shuffling of genetic material facilitated by meiotic crossovers is a critical driver of genetic variation. Therefore, the number and positions of crossover events must be carefully controlled. In Arabidopsis, an obligate crossover and repression of nearby crossovers on each chromosome pair are abolished in mutants that lack the synaptonemal complex (SC), a conserved protein scaffold. We use mathematical modelling and quantitative super-resolution microscopy to explore and mechanistically explain meiotic crossover pattering in Arabidopsis lines with full, incomplete, or abolished synapsis. For zyp1 mutants, which lack an SC, we develop a coarsening model in which crossover precursors globally compete for a limited pool of the pro-crossover factor HEI10, with dynamic HEI10 exchange mediated through the nucleoplasm. We demonstrate that this model is capable of quantitatively reproducing and predicting zyp1 experimental crossover patterning and HEI10 foci intensity data. Additionally, we find that a model combining both SC- and nucleoplasm-mediated coarsening can explain crossover patterning in wild-type Arabidopsis and in pch2 mutants, which display partial synapsis. Together, our results reveal that regulation of crossover patterning in wild-type Arabidopsis and SC-defective mutants likely acts through the same underlying coarsening mechanism, differing only in the spatial compartments through which the pro-crossover factor diffuses.
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Author Response
Reviewer #2 (Public Review):
The ability of the model to recreate one non-trivial aspect of the crossover distribution is not sufficient to rule out other possible models, which would be necessary to consider this work a significant advance. However, if the authors are able to provide additional, non-trivial predictions relating to this and to other experimental conditions, this would dramatically elevate their ability to claim that a coarsening-based mechanism is indeed the most plausible one to explain crossover distribution. Some of these conditions could involve experimental perturbation of key parameters in the model: HEI10 levels, the number of DSBs or recombination intermediates (the 'substrate' that ends up resulting in crossovers), the length of time coarsening is allowed to proceed, or the volume of the …
Author Response
Reviewer #2 (Public Review):
The ability of the model to recreate one non-trivial aspect of the crossover distribution is not sufficient to rule out other possible models, which would be necessary to consider this work a significant advance. However, if the authors are able to provide additional, non-trivial predictions relating to this and to other experimental conditions, this would dramatically elevate their ability to claim that a coarsening-based mechanism is indeed the most plausible one to explain crossover distribution. Some of these conditions could involve experimental perturbation of key parameters in the model: HEI10 levels, the number of DSBs or recombination intermediates (the 'substrate' that ends up resulting in crossovers), the length of time coarsening is allowed to proceed, or the volume of the nucleus.
As discussed above, we have now included additional experiments and modelling investigating the patterning of late-HEI10 foci in a pch2 mutant, which exhibits partial synapsis. We have also demonstrated that the nucleoplasmic coarsening model can explain the recently published massive elevation of COs in zyp1 + HEI10 overexpressor lines (Durand et al., 2022). We hope that these additional results, explaining other non-trivial aspects of CO patterning, sufficiently elevates this work to be considered as a significant advance within the field.
Reviewer #3 (Public Review):
The new model assumes the possibility of loading HEI10 directly from the nucleoplasm, which of course is logical considering the phenotype of the zyp1 mutant in Arabidopsis. However, in a situation where the SC is fully functional, should not we expect some level of nucleoplasmic coarsening in addition to the dominant SC-mediated coarsening? Should the original model not be corrected, and if it is not necessary (e.g., because it included this effect from the very beginning, or the effect is too weak and therefore negligible), the authors should discuss it. With reference to this observation, it would be worthwhile to compare different characteristics of both types of coarsening (e.g., time course).
We agree with this reviewer that it seems intuitive and likely that some small amount of nucleoplasmic coarsening will persist even in the wild-type situation. As mentioned above, we have now explicitly modelled a combined version of the coarsening model than incorporates aspects of SC and nucleoplasm-mediated coarsening and compared this to simulation outputs from our original coarsening model (which did not incorporate nucleoplasmic recycling). The effects and implications of combining the two models on coarsening dynamics are now discussed.
Recently, a preprint from the Raphael Mercier group has been released, in which the authors show a massive increase in crossover frequency in zyp1 mutants overexpressing HEI10. I think this is a great opportunity to check to what extent the parameters adopted by the authors in the nucleoplasmic coarsening model are universal and can correctly simulate such an experimental set-up. Therefore, can the authors perform such a simulation and validate it against the experimental data in Durand et al. doi.org/10.1101/2022.05.11.491364? Can CO sites identified by Durand et al. be used instead of MLH1 foci for the modeling?
As mentioned above, we have now incorporated additional modelling demonstrating that the nucleoplasmic coarsening model can reproduce the massive increase in COs observed in zyp1 + HEI10 overexpressor lines (Durand et al., 2022). We have compared our model simulations against cytological data from this study (MLH1 counts from male Col-0 plants) as we feel this is the most appropriate data to compare our model against. The remaining CO patterning data in the Durand et al., paper is from genetic experiments, which are not optimal for comparing model simulations against for two main reasons. Firstly, the metric of interference (and coarsening) is microns of axis/SC length and not, for example, Mbp and we feel that (due to the non-uniform compaction of chromatin along pachytene chromosomes) the coarsening model cannot currently be reliably used to explain genetic mapping data. Secondly, genetic CO data includes both class I and class II COs, whereas the coarsening model only simulates class I CO patterning. Therefore, we strongly feel that, for now, it is better to exclusively rely on cytological data to fit our model against.
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eLife assessment
During meiotic prophase I, protein complexes essential for crossover recombination are distributed non-randomly along chromosomes. With mathematical modelling and based on results from super-resolution microscopy, the authors introduce a second type of coarsening of protein ensembles between chromosome axes and nucleoplasm between chromosomes and nucleoplasm to support the random distribution of the complexes in the synapsis-defective mutant. The new model is interesting and may be applied to other chromosomal events accompanied by the formation of large protein ensembles on the chromosomes. The work is of interest to colleagues studying recombination and meiosis.
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Reviewer #1 (Public Review):
In this study, the authors introduced a new mathematical model of coarsening of protein ensembles between chromosome axes and nucleoplasm to explain the random distribution of the complexes including Hei10 in a chromosome synapsis-defective, zyp1a/zyp1b double mutant. Although the modeling of the new regulatory mechanism of the crossover (CO) control during meiosis (nucleoplasmic coarsening model and/or trans-interference), which seems to be validated by the super-resolution imaging results, is intriguing, it incrementally contributes to our understanding of the molecular mechanism of CO control during "wild-type" meiosis, since the new model only explains the distribution of COs only in the synapsis-defective mutant (little implication of CO patterning in wild-type).
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Reviewer #2 (Public Review):
The authors address a very old question: what is the mechanism that controls genetic exchanges (crossovers) between the maternal and paternal chromosomes during sexual reproduction (meiosis). Specifically, what could account for two crucial aspects of the non-random distribution of crossovers: the lower-than-expected rate of non-exchange chromosomes, and the larger-than-expected distance between adjacent crossovers on the same chromosome. Despite the great progress that was made in the last few decades in understanding the molecular details crossover formation, the mechanism accounting for their non-random distribution remains a matter of heated debate. Hence, an ability to provide new insight into this question will be of interest to the wide chromosome biology community.
In this work, the authors combine …
Reviewer #2 (Public Review):
The authors address a very old question: what is the mechanism that controls genetic exchanges (crossovers) between the maternal and paternal chromosomes during sexual reproduction (meiosis). Specifically, what could account for two crucial aspects of the non-random distribution of crossovers: the lower-than-expected rate of non-exchange chromosomes, and the larger-than-expected distance between adjacent crossovers on the same chromosome. Despite the great progress that was made in the last few decades in understanding the molecular details crossover formation, the mechanism accounting for their non-random distribution remains a matter of heated debate. Hence, an ability to provide new insight into this question will be of interest to the wide chromosome biology community.
In this work, the authors combine two important findings/resources. The first is their own modeling of a biophysical framework called 'coarsening'. Coarsening relates to the well-described behavior of liquid compartments, which tend to get larger with time, at the expense of smaller compartments. As the authors note, their coarsening work builds on research by many labs, and on the recent understanding of the role of condensates in cell biology in general, and the liquid nature of the synaptonemal complex - a conserved meiotic chromosomal interface. In their previous paper, the authors found that coarsening could account for multiple cytological aspects of crucial regulators of crossovers - a conserved protein called HEI10. Their modeling was able to recapitulate temporal changes in HEI10 distribution and to account for changes that occur upon changes to HEI10 expression levels (halving of expression and over-expression). The second is the recent analysis of plant strains lacking the synaptonemal complex (zyp1). In that mutant, crossovers do occur (this is different than in some organisms), but the non-random distribution of crossovers is mostly lost: both crossover interference and the paucity of non-exchange chromosomes fit mostly random distribution.
Here, the authors combine these resources and adjust their modeling to account for the lack of the synaptonemal complex. A crucial difference is that instead of diffusing inside the SC (which spans each chromosome pair end-to-end), HEI10 now diffuses in the nucleoplasm. With this modified simulation they mostly account for crossover distribution in zyp1 mutants, using both published and new data they have acquired.
Despite the very limited amount of new data included in this manuscript, the clever combination of these two sources of data manages to add yet another layer of evidence to the idea that coarsening can explain crossover distribution. The main concern regarding the manuscript is that most of the aspects of crossover distribution that the model reproduces are quite trivial - for example, the resulting random distribution of the number of crossovers per chromosome. Some of the non-trivial aspects of the distribution - for example, the telomere enrichment - were built into the simulation as an explicit parameter. The only aspect that would be considered truly non-trivial is the narrower-than-expected number of total crossovers, despite the random distribution of crossovers per chromosome (Fig. 2A). Indeed, the modeling recapitulates this parameter, albeit to a much stronger degree than the in vivo data.
The ability of the model to recreate one non-trivial aspect of the crossover distribution is not sufficient to rule out other possible models, which would be necessary to consider this work a significant advance. However, if the authors are able to provide additional, non-trivial predictions relating to this and to other experimental conditions, this would dramatically elevate their ability to claim that a coarsening-based mechanism is indeed the most plausible one to explain crossover distribution. Some of these conditions could involve experimental perturbation of key parameters in the model: HEI10 levels, the number of DSBs or recombination intermediates (the 'substrate' that ends up resulting in crossovers), the length of time coarsening is allowed to proceed, or the volume of the nucleus.
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Reviewer #3 (Public Review):
Fozard et al. presented a new model explaining the distribution of the pro-crossover factor HEI10 and its effect on the formation of crossovers in the absence of a functional synaptonemal complex (SC). The creation of such a model is important considering recent results showing that in Arabidopsis and possibly many other plants (perhaps all plants), the major crossover pathway may function independently of the SC. Crossover modeling can help to better understand crossover formation dynamics and facilitate the prediction of crossover distribution.
The new model assumes the possibility of loading HEI10 directly from the nucleoplasm, which of course is logical considering the phenotype of the zyp1 mutant in Arabidopsis. However, in a situation where the SC is fully functional, should not we expect some level of …
Reviewer #3 (Public Review):
Fozard et al. presented a new model explaining the distribution of the pro-crossover factor HEI10 and its effect on the formation of crossovers in the absence of a functional synaptonemal complex (SC). The creation of such a model is important considering recent results showing that in Arabidopsis and possibly many other plants (perhaps all plants), the major crossover pathway may function independently of the SC. Crossover modeling can help to better understand crossover formation dynamics and facilitate the prediction of crossover distribution.
The new model assumes the possibility of loading HEI10 directly from the nucleoplasm, which of course is logical considering the phenotype of the zyp1 mutant in Arabidopsis. However, in a situation where the SC is fully functional, should not we expect some level of nucleoplasmic coarsening in addition to the dominant SC-mediated coarsening? Should the original model not be corrected, and if it is not necessary (e.g., because it included this effect from the very beginning, or the effect is too weak and therefore negligible), the authors should discuss it. With reference to this observation, it would be worthwhile to compare different characteristics of both types of coarsening (e.g., time course).
Recently, a preprint from the Raphael Mercier group has been released, in which the authors show a massive increase in crossover frequency in zyp1 mutants overexpressing HEI10. I think this is a great opportunity to check to what extent the parameters adopted by the authors in the nucleoplasmic coarsening model are universal and can correctly simulate such an experimental set-up. Therefore, can the authors perform such a simulation and validate it against the experimental data in Durand et al. doi.org/10.1101/2022.05.11.491364? Can CO sites identified by Durand et al. be used instead of MLH1 foci for the modeling?
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