Seasonal stability and dynamics of DNA methylation in plants in a natural environment

Abstract

20Organisms survive in naturally fluctuating environments by responding to 21 long-term signals, such as seasonality, by filtering out short-term noise. DNA 22 methylation (gbM) itself was generally stable across seasons, but the levels of 36 gbM were positively associated with seasonal stability of RNA expression of the 37 genes. These results suggest the existence of two distinct aspects of DNA 38 methylation in natural environments: sources of epigenetic variation and 39 epigenetic marks for stable gene expression. 40Keywords: Arabidopsis halleri, DNA methylation, Natural environment, 41 seasonal changes, seasonally methylated cytosines 42 6 manner (15, 16). Therefore, it is difficult to predict whether DNA methylation is 59 stable or dynamic under natural conditions. Recently the need for 'in natura' 60 studies has been highlighted in order to understand how organisms respond to 61 environmental signals by filtering out innumerable fluctuations and noise (17, 18). 62In the temperate regions, seasonality is the most prominent cause of 63 environment fluctuations. However, we still do not understand how DNA 64 methylation behaves across seasons. 65In order to reveal the seasonal dynamics of DNA methylation, here, we 66 conducted an "in natura" study on genome-wide DNA methylation using a single 67 clone growing in a population of Arabidopsis halleri (L.) O'Kane & Al-Shehbaz 68 subsp. gemmifera (Matsum.) O'Kane & Al-Shehbaz (hereafter referred to as A. 69 haleri), a close relative of Arabidopsis thaliana. Its clonal propagation and 70 perennial life-cycle allowed us to sample leaves all year round from the single 71 clonal individual (19). We studied seasonal dynamics of key flowering-time 72genes and whole transcriptome previously in the site (20, 21). In this study, to 73 understand the dynamics of DNA methylation, we performed whole-genome 74

Integrated analysis of the methylome and transcriptome of twin almonds (Prunus dulcis[Mill.] D.A.Webb) reveals genomic features associated with non-infectious bud failure

“…Of these DMR-gene associations, permutation testing revealed significantly more DMRs in the up-and downstream proximity classes and significantly fewer in the intragenic proximity class relative to a gene. This result supports previous findings showing gene body methylation in plants tends to be stable over time (and even across multiple generations [Luo et al, 2020]), while methylation occurring up-or downstream of genes tends to exhibit greater dynamism, particularly in response to stressors (Bewick and Schmitz, 2017;Picard and Gehring, 2017;Ito et al, 2019). Empirical evidence suggests a relationship between dormancy processes in the summer (i.e.…”

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.…”