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

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.

Genetic and Physiological Responses to Heat Stress in Brassica napus

“…Different types of epigenetic mechanisms exist and the most common are DNA methylation, histone modifications and small RNAs. Along with its vital role in maintaining genome integrity, increasing evidence indicates that epigenetic mechanisms in plants play a substantial part in modulating gene expression under different environmental conditions, including salinity, drought, extreme temperatures and exposure to heavy metals ( Gao et al, 2014 ; Fan et al, 2020 ; Ueda and Seki, 2020 ).…”

“…These enzymes are classified into different categories depending on their protein structure and function ( Liu G. et al, 2018 ). Fan et al (2020) identified 22 methylase genes and six demethylase genes through studying two varieties of B. napus (YN171 and 93275; Table 1 ). In addition to the variations in methylation patterns detected at different sequence locations (gene regions and up/downstream regions) and contexts (CHG, CHH, and CG), analysis of gene expression in 22 tissues across different developmental stages showed that these genes have different regulatory roles in plant growth and development.…”

Genome-Wide Identification and Coexpression Network Analysis of DNA Methylation Pathway Genes and Their Differentiated Functions in Ginkgo biloba L.

“…DNA methylation is involved in various aspects of plant growth and development; even sex determination [2,50]. To investigate the expression pattern of DNA methylation pathway genes at different growth and development stages of various tissues, we collected root, stem, leaf, flower, and fruit samples from seedlings or adult plants of G. biloba for the transcriptomic analysis.…”

“…Cytosine DNA methylation is an epigenetic modification that regulates gene expression [1,2]. In the plant kingdom, 5mC is usually methylated in three cytosine contexts: CG, CHG, and CHH (H = A|T|C).…”

Genome-wide identification and analysis of DNA methyltransferase and demethylase gene families in Dendrobium officinale reveal their potential functions in polysaccharide accumulation

“…Additionally, OsROS1-mediated DNA demethylation in the rice endosperm restricts the number of aleurone cell layers, and thus the OsROS1 mutant contains more non-starch polysaccharides, lipids, proteins, vitamins, and minerals than the wild type [ 20 ]. Given that DNA methylation and demethylation are essential for many biological processes in plants, C5-MTase and dMTase genes have already been identified and characterized in several plant species, such as thale cress ( Arabidopsis thaliana ) [ 21 ], peanut ( Arachis hypogaea ) [ 22 ], rapeseed ( Brassica napus ) [ 23 ], castor bean ( Ricinus communis ) [ 24 ], tomato ( Solanum lycopersicum ) [ 25 ], and tea plant ( Camellia sinensis ) [ 26 ]. However, to date, no research has yet focused on the identification and analysis of C5-MTase and dMTase genes in the orchid, Dendrobium officinale Kimura et Migo, based on genome-wide analyses.…”