The DNA Methylome and Association of Differentially Methylated Regions with Differential Gene Expression during Heat Stress in Brassica rapa

Gaofeng Liu,Yudong Xia,Tongkun Liu,Shaojun Dai,Xilin Hou

doi:10.3390/ijms19051414

Abstract

Cytosine DNA methylation is a critical epigenetic mechanism in the silencing of transposable elements, imprinting and regulating gene expression. However, little is known about the potential role of mC in response to heat stress. To determine and explore the functions of the dynamic DNA methylome during heat stress, we characterized single-base resolution methylome maps of Brassica rapa and assessed the dynamic changes of mC under heat stress using whole genome bisulfite sequencing. On average, the DNA methylation levels of CG, CHG and CHH are 39.3%, 15.38% and 5.24% in non-heading Chinese cabbage (NHCC), respectively. We found that the patterns of methylation are similar to other eudicot plants, but with higher CHH methylation levels. Further comparative analysis revealed varying patterns for three sequence contexts (mCG, mCHG and mCHH) under heat stress indicating context- and position-dependent methylation regulation. DNA methylation near the TSS and TES may be closely associated with methylation-dependent transcriptional silencing. Association analysis of differential methylation and differential gene expression revealed a different set of methDEGs involved at early and late stages under heat stress. The systemic characterization of the dynamic DNA methylome during heat stress will improve our understanding of the mechanism of epigenetic regulation under heat stress.

Highlights

As sessile organisms, plants encounter a wide range of environmental stimuli and stresses
Methyltransferase Inhibitor Decreases the Heat Tolerance To test whether DNA methylation changes in the genome influence plant heat stress resistance, we analyTzoetdestthwe hheetahte-rtoDleNraAncmeedthifyflearteinoncechbaentwgeeseninptlhaengtsen(NomHeCiCnf0l0u1e)ntcreepatleadntwheitaht 5st-raezsascryetsiidstiannecaen, d a cownetraonl aglryozuedp.tWheehoebaste-trovleedratnhcaetdthifefegreronwcethbeotfwtereenatepdlapntlsan(NtsHwCaCs 0o0b1v)iotruesaltyedrewpritehss5e-daz(aFciygtuidrein1ea)
We found that the B. rapa genome contains at least one copy of most key factors involved in DNA methylation control, including CMT2, CHROMOMETHYLASE 3 (CMT3), DRM2 and methyltransferase 1 (MET1) (Table S4)

Summary

Introduction

Plants encounter a wide range of environmental stimuli and stresses. Heat stress responses have been studied for decades, including signal transduction, accumulation of heat stress proteins (HSP), and transcription factors for gene expression regulation, amongst others [4,5,6]. Increasing evidence indicates that DNA methylation and histone modification play critical roles in the regulation of gene expression in the response of plants to environmental stresses, including pathogens, drought, salinity, extreme temperatures and heavy metals [7,8,9,10,11,12,13]. A recent study showed that cold-induced flavor loss of tomato is associated with transient changes in DNA methylation [18]

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Results

Conclusion