The Progeny of Arabidopsis thaliana Plants Exposed to Salt Exhibit Changes in DNA Methylation, Histone Modifications and Gene Expression

Andriy Bilichak,Igor Kovalchuk,Jens Hollunder,Yaroslav Ilnystkyy,Frederic Berger

doi:10.1371/journal.pone.0030515

Andriy Bilichak, Igor Kovalchuk + Show 3 more

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https://doi.org/10.1371/journal.pone.0030515

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Abstract

Plants are able to acclimate to new growth conditions on a relatively short time-scale. Recently, we showed that the progeny of plants exposed to various abiotic stresses exhibited changes in genome stability, methylation patterns and stress tolerance. Here, we performed a more detailed analysis of methylation patterns in the progeny of Arabidopsis thaliana (Arabidopsis) plants exposed to 25 and 75 mM sodium chloride. We found that the majority of gene promoters exhibiting changes in methylation were hypermethylated, and this group was overrepresented by regulators of the chromatin structure. The analysis of DNA methylation at gene bodies showed that hypermethylation in the progeny of stressed plants was primarily due to changes in the 5′ and 3′ ends as well as in exons rather than introns. All but one hypermethylated gene tested had lower gene expression. The analysis of histone modifications in the promoters and coding sequences showed that hypermethylation and lower gene expression correlated with the enrichment of H3K9me2 and depletion of H3K9ac histones. Thus, our work demonstrated a high degree of correlation between changes in DNA methylation, histone modifications and gene expression in the progeny of salt-stressed plants.

Highlights

Living organisms are frequently influenced by abiotic and biotic environmental factors
We found a high degree of correlation among the levels of methylation, histone modification status, and the level of mRNA in SU(VAR)3-9 HOMOLOG 2 (SUVH2), SU(VAR)3-9 HOMOLOG 5 (SUVH5), SU(VAR)3-9 HOMOLOG 6 (SUVH6), SU(VAR)3-9 HOMOLOG 8 (SUVH8), UBIQUITIN-SPECIFIC PROTEASE 26 (UBP26), DSRNA-BINDING PROTEIN 2 (DRB2), WRKY22, ROS1, MUTS HOMOLOG 6 (MSH6), UVH3 homolog, Arabidopsis Pumilio 3 (APUM3) and MOS6 in the progeny of salt-stressed plants
There was a 2.5-fold higher percentage of hypermethylated genes compared to hypomethylated genes in the progeny of plants exposed to 25 mM NaCl (p = 0.045) and a 5-fold higher percentage – in the progeny of plants exposed to 75 mM NaCl (p = 0.003) (Figure 2A)

Summary

Introduction

Living organisms are frequently influenced by abiotic and biotic environmental factors. Apart from physiological changes in the exposed generation, stress alters epigenetic marks that can potentially persist in the progeny. Epigenetic factors can contribute to both short-term (mitotic) and long-term (meiotic) inheritance of an altered gene expression without changing the primary DNA sequences [1]. Slightly more than 20% of the Arabidopsis genome is methylated, with transposable elements (TEs) and DNA repeats representing the largest fraction of methylated sequences. Whereas TEs are heavily methylated throughout their whole sequence, non-TE genes that are expressed in a tissue-specific manner are primarily methylated at the gene promoter regions [6]. For the analysis of the promoter region, we used the 5 kb sequence 59 of a transcribed region. For the analysis of methylation at the transcribed region, we used the entire sequences of the transcribed region of each gene. We identified the number of methylated reporters (the region of 90 nt in length, see Materials and Methods for details) out of the total number of reporters which are present either in the

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