Seasonal Stability and Dynamics of DNA Methylation in Plants in a Natural Environment

Abstract

: DNA methylation has been considered a stable epigenetic mark but may respond to fluctuating environments. However, it is unclear how they behave in natural environments. Here, we analyzed seasonal patterns of genome-wide DNA methylation in a single clone from a natural population of the perennial Arabidopsis halleri. The genome-wide pattern of DNA methylation was primarily stable, and most of the repetitive regions were methylated across the year. Although the proportion was small, we detected seasonally methylated cytosines (SeMCs) in the genome. SeMCs in the CHH context were detected predominantly at repetitive sequences in intergenic regions. In contrast, gene-body CG methylation (gbM) itself was generally stable across seasons, but the levels of gbM were positively associated with seasonal stability of RNA expression of the genes. These results suggest the existence of two distinct aspects of DNA methylation in natural environments: sources of epigenetic variation and epigenetic marks for stable gene expression.

Genome-Wide DNA Methylation Analysis Reveals a Conserved Epigenetic Response to Seasonal Environmental Variation in the Staghorn Coral Acropora cervicornis

“…Moreover, epigenetic marks acquired throughout the lifespan of coral can be inherited intergenerationally, promoting acclimatized phenotypes in the offspring and thus increasing their fitness (Liew et al, 2020;Putnam et al, 2020). In addition, seasonal patterns of DNA methylation have been observed in vertebrates (Stevenson and Prendergast, 2013;Viitaniemi et al, 2019), invertebrates (Pegoraro et al, 2016;Suarez-Ulloa et al, 2019) and plants (Finnegan et al, 1998;Bastow et al, 2004;Ito et al, 2019). Based on these elements, it is not surprising that DNA methylation could play an active role during coral responses to seasonal variation.…”

“…In addition, seasonal changes in these parameters also drive subsequent variation in coral physiology (Scheufen et al, 2017). Contrary to the case of random environmental variation, the predictability of seasonal fluctuations can be conducive to the development and inheritance of plastic transcriptional profiles mediating phenotypic responses, regulated by epigenetic mechanisms [e.g., seasonal DNA methylation changes in bivalve mollusks (Suarez-Ulloa et al, 2019), plants (Ito et al, 2019) and birds (Viitaniemi et al, 2019)]. Indeed, seasonality produces dramatic physiological adjustments in corals, including changes in symbiont's abundance and pigmentation (Fitt et al, 2000;Thornhill et al, 2006), modifications of microbial community composition (Sharp et al, 2017), as well as the alteration of transcriptional profiles (Edge et al, 2008;Brady et al, 2011;Parkinson et al, 2018;Brener-Raffalli et al, 2019).…”

The contribution of transposable elements to transcriptional novelty in plants: theFLCaffair

“…An independent natural allele of FLC associated with variation in DNA methylation over an intronic SINE-like non-LTR retroelement has been identified in A. hallerii [56], which propagates clonally and has a perennial life-cycle [57]. Similarly to its role in other perennial Brassicaceae, such as A. alpina [58], FLC expression in A. hallerii is regulated seasonally and suppresses flowering when upregulated.…”

“…Similarly to its role in other perennial Brassicaceae, such as A. alpina [58], FLC expression in A. hallerii is regulated seasonally and suppresses flowering when upregulated. To assess the role of DNA methylation in seasonal responses, the authors collected samples from the same clonal plant acoss the year and produced whole-genome bisulfite sequencing (WGBS) [56]. Remarkably, the SINE-like insertion in the first intron of FLC showed a seasonal change in CHH methylation, with methylation levels in March and June being the highest and lowest, respectively.…”

Duration of cold exposure defines the rate of reactivation of a perennial FLC orthologue via H3K27me3 accumulation

“…www.nature.com/scientificreports/ halleri [20][21][22][23][24][25] , Arabidopsis lyrata 26 , and Arabis alpina [27][28][29] . H3K27me3 accumulates at perennial FLC orthologues under cold conditions and is removed from the locus in response to warm temperatures 24,25,27 .…”