Abstract
BackgroundPolyploidy, or whole-genome duplication (WGD) promotes genetic diversification in plants. However, whether WGD is accompanied by epigenetic regulation especially DNA methylation remains yet elusive. Methylation of different region in genomic DNA play discrete role in gene regulation and developmental processes in plants.ResultsIn our study, we used an apomictic rice line (SARII-628) that produces twin seedlings of different ploidy for methylated DNA immunoprecipitation sequencing (MeDIP-seq). We compared the level of methylation and mRNA expression in three different (CG, CHG, and CHH) sequence contexts of promoter region among haploid (1X), diploid (2X), and triploid (3X) seedling. We used MeDIP-Seq analysis of 14 genes to investigate whole genome DNA methylation and found that relative level of DNA methylation across different ploidy was in following order e.g. diploid > triploid > haploid. GO functional classification of differentially methylated genes into 9 comparisons group of promoter, intergenic and intragenic region discovered, these genes were mostly enriched for cellular component, molecular function, and biological process. By the comparison of methylome data, digital gene expression (DGE), mRNA expression profile, and Q-PCR findings LOC_ Os07g31450 and LOC_ Os01g59320 were analyzed for BS-Seq (Bisulphite sequencing).ConclusionsWe found that (1) The level of the promoter DNA methylation is negatively correlated with gene expression within each ploidy level. (2) Among all ploidy levels, CG sequence context had highest methylation frequency, and demonstrated that the high CG methylation did reduce gene expression change suggesting that DNA methylation exert repressive function and ensure genome stability during WGD. (3) Alteration in ploidy (from diploid to haploid, or diploid to triploid) reveals supreme changes in methylation frequency of CHH sequence context. Our finding will contribute an understanding towards lower stability of CHH sequence context and educate the effect of promoter region methylation during change in ploidy state in rice.
Highlights
Polyploidy, or whole-genome duplication (WGD) promotes genetic diversification in plants
(2) Among all ploidy levels, CG sequence context had highest methylation frequency, and demonstrated that the high CG methylation did reduce gene expression change suggesting that DNA methylation exert repressive function and ensure genome stability during WGD. (3) Alteration in ploidy reveals supreme changes in methylation frequency of CHH sequence context
Our finding will contribute an understanding towards lower stability of CHH sequence context and educate the effect of promoter region methylation during change in ploidy state in rice
Summary
Polyploidy, or whole-genome duplication (WGD) promotes genetic diversification in plants. Methylation of different region in genomic DNA play discrete role in gene regulation and developmental processes in plants. Methylated cytosine ( known as fifth nucleotide) is one of known epigenetic mark that is extensively found in genome of eukaryotes [1, 2]. Methylated cytosine (mCs) plays an important role in gene regulation in order to control growth and developmental processes in plants [3]. Methylated cytosine in plants comprised of three sequence contexts: symmetric (CG and CHG) and asymmetric (CHH) methylation depending on the composition of base (where, H refers to A/T/C). Methylation is believed to be primarily catalyzed by a specific families of DNA METHYLTRANSFERASES; MET1 (homologous to animal DNMT1) for CG, plant-specific CHROMOMETHYLTRANSFERASE (CMT3 and CMT2) for CHG, and DRM2 (homologous to animal DNMT3) for CHH sequence context. CMT2 is found to be involved in the maintenance of DNA methylation in CHH sequence context [12,13,14,15,16,17,18,19]
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