The Methylation Inhibitor 5-Aza-2′-Deoxycytidine Induces Genome-Wide Hypomethylation in Rice

Abstract

DNA methylation is a conserved epigenetic modification which is vital for regulating gene expression and maintaining genome stability in both mammals and plants. Homozygous mutation of rice methyltransferase 1 (met1) gene can cause host death in rice, making it difficult to obtain plant material needed for hypomethylation research. To circumvent this challenge, the methylation inhibitor, 5-Aza-2′-deoxycytidine (AzaD), is used as a cytosine nucleoside analogue to reduce genome wide hypomethylation and is widely used in hypomethylation research. However, how AzaD affects plant methylation profiles at the genome scale is largely unknown. Here, we treated rice seedlings with AzaD and compared the AzaD treatment with osmet1-2 mutants, illustrating that there are similar CG hypomethylation and distribution throughout the whole genome. Along with global methylation loss class I transposable elements (TEs) which are farther from genes compared with class II TEs, were more significantly activated, and the RNA-directed DNA Methylation (RdDM) pathway was activated in specific genomic regions to compensate for severe CG loss. Overall, our results suggest that AzaD is an effective DNA methylation inhibitor that can influence genome wide methylation and cause a series of epigenetic variations.

DNA methylation and expression of the egfr gene are associated with worker size in monomorphic ants

“…For instance, in C. floridanus, worker larvae fed 5-Aza-dC exhibited both genome-wide hypomethylation and local-level egfr hypermethylation 30 . A hypermethylating effect of 5-Aza-dC was also reported in plants 50 . This inverse relationship is thought to be mediated by crosstalk with other epigenetic mechanisms, such as histone post-translational modifications 51 or non-coding RNAs 52 .…”

Interplay of phytohormones and epigenetic regulation: A recipe for plant development and plasticity

“…5‐aza and hydroxyurea were used as hypo‐ or hyper‐methylating agents to study the relationship between SL and DNA methylation in a parasitic plant branched broomrape ( Phelipanche ramosa ) (Lechat et al, 2015). Liu et al (2022) examined the effects of 5‐aza‐2’‐deoxycytidine (AzaD) as a methylation inhibitor in rice and found that AzaD‐treated seedlings display similar CG hypomethylation and distribution with that of osmet1‐2 mutant. Interestingly, the application of 5‐aza increased the contents of tanshinones in Chinese sage ( Salvia miltiorrhiza ) (Yang et al, 2022a), highlighting the potential of using CREs in Chinese medicine to improve the contents of effective components.…”