DNA methylation dynamics during stress response in woodland strawberry (Fragaria vesca)

Abstract

Summary Environmental stresses can result in a wide range of physiological and molecular responses in plants. These responses can also impact epigenetic information in genomes, especially at the level of DNA methylation (5-methylcytosine). DNA methylation is the hallmark heritable epigenetic modification and plays a key role in silencing transposable elements (TEs). Although DNA methylation is an essential epigenetic mechanism, fundamental aspects of its contribution to stress responses and adaptation remain obscure. We investigated epigenome dynamics of wild strawberry (Fragaria vesca) in response to variable ecologically relevant environmental conditions at the DNA methylation level. F. vesca methylome responded with great plasticity to ecologically relevant abiotic and hormonal stresses. Thermal stress resulted in substantial genome-wide loss of DNA methylation. Notably, all tested stress conditions resulted in marked hot spots of differential DNA methylation near centromeric or pericentromeric regions, particularly in the non-symmetrical DNA methylation context. Additionally, we identified differentially methylated regions (DMRs) within promoter regions of transcription factor (TF) superfamilies involved in plant stress-response and assessed the effects of these changes on gene expression. These findings improve our understanding on stress-response at the epigenome level by highlighting the correlation between DNA methylation, TEs and gene expression regulation in plants subjected to a broad range of environmental stresses.

Transcriptome Analysis Reveals Long-Term Somatic Memory of Stress in The Woody Perennial Crop, GrapevineVitis Viniferacv. Cabernet Sauvignon

“…Moreover, only around 2% of the DMGs were differentially expressed (23/1160, and 23/971 for ST4 2 00vsST4 2 33 and ST4 2 00vsST4 2 03, respectively) (Figure 5). A similar portion and no correlation between methylation changes and transcriptional patterns has been observed in previous studies (López et al, 2022;Rambani et al, 2020). Taken together, our results suggest that stress-induced transcriptional regulation might be, at least partially, independent of DNA methylation.…”

The plant response to highCO2levels is heritable and orchestrated byDNAmethylation

“…To investigate the molecular mechanisms responsible for the heritable response to high CO 2 levels, we used the reference plant Arabidopsis in order to take advantage of the available and well‐characterized mutants in the DNA methylation pathways (Stroud et al ., 2013; Panda et al ., 2016). Methylation of cytosine DNA bases is known to respond to the environment, pests, or other external stimuli (Baulcombe & Dean, 2014; Annacondia et al ., 2021; López et al ., 2022). For example, DNA methylation has been found to change in response to high CO 2 levels in Plantago lanceolata (Saban et al ., 2020).…”

Epigenetic differences between wild and cultivated grapevines highlight the contribution of DNA methylation during crop domestication

“…Ethylene is a critical hormone in plants, mediating various stress responses and developmental processes 40 . and ethylene responsive genes have been shown to change methylation status under abiotic stress 41 . The unique category of genes that showed both hyper and hypomethylated cytosines in both types of accessions, albeit being the smallest group, associated with defense response.…”