Genome-wide methylation landscape during somatic embryogenesis in Medicago truncatula reveals correlation between Tnt1 retrotransposition and hyperactive methylation regions

Authors: Nandety, Raja Sekhar; OH, SUNHEE - Noble Research Institute; LEE, HEE-KYUNG - Noble Research Institute; KROM, NICK - Noble Research Institute; Gupta, Rajeev; MYSORE, KIRANKUMAR - Oklahoma State University

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/14/2024
Publication Date: 4/16/2024
Citation: Nandety, R.S., Oh, S., Lee, H., Krom, N., Gupta, R., Mysore, K. 2024. Genome-wide methylation landscape during somatic embryogenesis in Medicago truncatula reveals correlation between Tnt1 retrotransposition and hyperactive methylation regions. Plant Journal. https://doi.org/10.1111/tpj.16744.
DOI: https://doi.org/10.1111/tpj.16744

Interpretive Summary: During life cycle of higher plants, various biological processes involve programming of several genes that control the development process in a dynamic way. These genes can also be turned on or off based on genetics and/or its interaction with environment. In our study, we identified gene expression patterns and DNA modifications which helped us to understand the gene regulation through which genes can be turned on and off depending on the external factors. The knowledge generated from this study could help in understanding of complex traits and their regulation in plants.

Technical Abstract: Medicago truncatula is a model legume for fundamental research on legume biology and symbiotic nitrogen fixation (SNF). Tnt1, a retrotransposon from tobacco, was used to generate insertion mutants in M. truncatula R108. Approximately 21,000 insertion lines have been generated and publicly available. Tnt1 retro-transposition event occurs during somatic embryogenesis, a pivotal process that triggers massive methylation changes. We studied the somatic embryogenesis of M. truncatula R108 using leaf explants and explored the dynamic shifts in the methylation landscape from leaf explants to callus formation and finally embryogenesis. Robust cytosine methylation in all three contexts of CG, CHG and CHH patterns was observed during somatic embryogenesis compared to the controls. Higher methylation patterns were observed in promoters of the genes, while lowest was recorded in the untranslated regions (UTRs). Differentially methylated promoter region analysis showed a stronger CHH methylation in embryogenesis samples when compared to CG and CHG methylation. Strong correlation (89.71 %) was identified between the differentially methylated regions and the site of Tnt1 insertions in M. truncatula R108 and stronger hypermethylation of genes correlated with higher number of Tnt1 insertions in all contexts of CG, CHG and CHH methylation. GO enrichment and KEGG pathway enrichment analysis identified genes and pathways enriched in the signal peptide processing, ATP hydrolysis, RNA polymerase activity, transport, secondary metabolites and nitrogen metabolism pathways. Our results show that a dynamic shift in methylation happens during the embryogenesis process in the context of CG, CHH and CHG methylation and the Tnt1 retrotransposition correlates with the hyperactive methylation regions.