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Methylation in the CHH context allows to predict recombination in rice

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Title Methylation in the CHH context allows to predict recombination in rice
 
Creator Peñuela, Mauricio
Gallo-Franco, Jenny Johana
Finke, Jorge
Rocha, Camilo
Gkanogiannis, Anestis
Ghneim-Herrera, Thaura
Lorieux, Mathias
 
Subject methylation
epigenetics
machine learning
modelling
metilación
epigenético
aprendizaje automático
 
Description DNA methylation is the most studied epigenetic trait. It is considered a key factor in regulating plant development and physiology, and has been associated with the regulation of several genomic features, including transposon silencing, regulation of gene expression, and recombination rates. Nonetheless, understanding the relation between DNA methylation and recombination rates remains a challenge. This work explores the association between recombination rates and DNA methylation for two commercial rice varieties. The results show negative correlations between recombination rates and methylated cytosine counts for all contexts tested at the same time, and for CG and CHG contexts independently. In contrast, a positive correlation between recombination rates and methylated cytosine count is reported in CHH contexts. Similar behavior is observed when considering only methylated cytosines within genes, transposons, and retrotransposons. Moreover, it is shown that the centromere region strongly affects the relationship between recombination rates and methylation. Finally, machine learning regression models are applied to predict recombination using the count of methylated cytosines in the CHH context as the entrance feature. These findings shed light on the understanding of the recombination landscape of rice and represent a reference framework for future studies in rice breeding, genetics, and epigenetics.
 
Date 2022-10-19
2023-02-16T11:18:12Z
2023-02-16T11:18:12Z
 
Type Journal Article
 
Identifier Peñuela, M.; Gallo-Franco, J.J.; Finke, J.; Rocha, C.; Gkanogiannis, A.; Ghneim-Herrera, T.; Lorieux, M. (2022) Methylation in the CHH context allows to predict recombination in rice. International Journal of Molecular Sciences 23(20):12505 14 p. ISSN: 1661-6596
1661-6596
https://hdl.handle.net/10568/128722
https://doi.org/10.3390/ijms232012505
 
Language en
 
Rights CC-BY-4.0
Open Access
 
Format 14 p.
application/pdf
 
Publisher MDPI AG
 
Source International Journal of Molecular Sciences