Systematic Analysis of the DNA Methylase and Demethylase Gene Families in Rapeseed (Brassica napus L.) and Their Expression Variations After Salt and Heat stresses.

Shihang Fan,Jing Liu,Shouming Xu,Wei Hua,Hongfang Liu,Jun Li

doi:10.3390/ijms21030953

Abstract

DNA methylation is a process through which methyl groups are added to the DNA molecule, thereby modifying the activity of a DNA segment without changing the sequence. Increasing evidence has shown that DNA methylation is involved in various aspects of plant growth and development via a number of key processes including genomic imprinting and repression of transposable elements. DNA methylase and demethylase are two crucial enzymes that play significant roles in dynamically maintaining genome DNA methylation status in plants. In this work, 22 DNA methylase genes and six DNA demethylase genes were identified in rapeseed (Brassica napus L.) genome. These DNA methylase and DNA demethylase genes can be classified into four (BnaCMTs, BnaMET1s, BnaDRMs and BnaDNMT2s) and three (BnaDMEs, BnaDML3s and BnaROS1s) subfamilies, respectively. Further analysis of gene structure and conserved domains showed that each sub-class is highly conserved between rapeseed and Arabidopsis. Expression analysis conducted by RNA-seq as well as qRT-PCR suggested that these DNA methylation/demethylation-related genes may be involved in the heat/salt stress responses in rapeseed. Taken together, our findings may provide valuable information for future functional characterization of these two types of epigenetic regulatory enzymes in polyploid species such as rapeseed, as well as for analyzing their evolutionary relationships within the plant kingdom.

Highlights

Epigenetics is the study of heritable phenotypic changes that do not involve changes in the DNA sequence
DNA methylation mainly occurs as modifications of cytosine into 5-methylcytosine (5-meC), in sequence targets such as CG, CHG, CHH, and as conversion of purines into N6-methyladenine (N6-mA) and 7-methylguanine (7-mG) [8,9]
DNA-MTase is essential for DNA methylation, and the enzymes belonging this family could be sorted into four categories based on the protein structure and function, respectively: methyltransferase 1 (MET1), chromomethylase (CMT), domains rearranged methyltransferase (DRM) and DNA methyltransferase-2 (DNMT2) [10,11]

Summary

Introduction

Epigenetics is the study of heritable phenotypic changes that do not involve changes in the DNA sequence. The actual DNA methylation patterns and levels are related to the function of DNA methyltransferase (DNA-MTase) and DNA demethylase (DNA-deMTase). DNA-MTase is essential for DNA methylation, and the enzymes belonging this family could be sorted into four categories based on the protein structure and function, respectively: methyltransferase 1 (MET1), chromomethylase (CMT), domains rearranged methyltransferase (DRM) and DNA methyltransferase-2 (DNMT2) [10,11]. MET1 functions to maintain the DNA methylation level of CG during DNA replication [12,13]. CMT, which is known to be unique in plants, helps to maintain DNA methylation of CHG, CHH and heterochromatin status [14,15]. DRM mediates the de novo methylation of the asymmetric site CHH sequences of DNA. DNA-MTase have already been identified and characterized in several plant species, including Arabidopsis [19], Oryza sativa [20], Daucus carota [21], Hordeum vulgare [22], Zea mays [23] and Lycopersicon esculentum [24]

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Conclusion