The Dynamic Changes of DNA Methylation and Histone Modifications of Salt Responsive Transcription Factor Genes in Soybean

Abstract

Epigenetic modification contributes to the regulation of gene expression and plant development under salinity stress. Here we describe the identification of 49 soybean transcription factors by microarray analysis as being inducible by salinity stress. A semi-quantitative RT-PCR-based expression assay confirmed the salinity stress inducibility of 45 of these 49 transcription factors, and showed that ten of them were up-regulated when seedlings were exposed to the demethylation agent 5-aza-2-deoxycytidine. Salinity stress was shown to affect the methylation status of four of these ten transcription factors (one MYB, one b-ZIP and two AP2/DREB family members) using a combination of bisulfite sequencing and DNA methylation-sensitive DNA gel blot analysis. ChIP analysis indicated that the activation of three of the four DNA methylated transcription factors was correlated with an increased level of histone H3K4 trimethylation and H3K9 acetylation, and/or a reduced level of H3K9 demethylation in various parts of the promoter or coding regions. Our results suggest a critical role for some transcription factors' activation/repression by DNA methylation and/or histone modifications in soybean tolerance to salinity stress.

Global DNA methylation changes in Cucurbitaceae inter-species grafting

“…Open and closed chromatin states are associated with gene activation and gene silencing, respectively, and govern proper onset of gene expression programmes during development and in response to changing environmental conditions (Bennetzen and Zhu 2011). Locus-specific and mainly genome-wide studies analyzing entire methylomes have well established that DNA methylation depends on a number of endogenous and exogenous factors including genotype, cell type, developmental stage and environmental stimulus (Cokus et al 2008, Feng et al 2010, Karan et al 2012, Song et al 2012. Since grafting engages most of these factors it is conceivable that DNA methylation changes will be evidenced in the grafting partners, that is, the rootstock and the scion of grafted plants.…”

Epigenomics of Plant Responses to Environmental Stress

“…However, histone modifications are reversible and cross-talk between histone acetylation and cytosine methylation makes the plant responses more complex. These may have a combined effect on stress-inducible gene, as it was reported in soybean to affect the expression of transcription factors [99]. Histone deacetylase HDA6 was found to be crucial for H3K4me3-mediated gene activation and mutation in HDA6 resulted in its hypersensitivity to salt stress in the model plant [98].…”

Immediate and Transgenerational Regulation of Plant Stress Response through DNA Methylation

“…A significant correlation was observed between shift in DNA methylation pattern under salt stress and gene expression of four genes in this species. The expression profile of one MYB (Myeloblastosis), one b-ZIP (basic leucine zipper) and two AP2/DREB genes showed differential expression associated with DNA hypomethylation in promoter or coding region under salt stress conditions (Song et al, 2012).…”