Abstract
Cytosine methylation plays vital roles in regulating gene expression and plant development. However, the function of DNA methylation in the development of macroalgae remains unclear. Through the genome-wide bisulfite sequencing of cytosine methylation in holdfast, stipe and blade, we obtained the complete 5-mC methylation landscape of Saccharina japonica sporophyte. Our results revealed that the total DNA methylation level of sporophyte was less than 0.9%, and the content of CHH contexts was dominant. Moreover, the distribution of CHH methylation within the genes exhibited exon-enriched characteristics. Profiling of DNA methylation in three parts revealed the diverse methylation pattern of sporophyte development. These pivotal DMRs were involved in cell motility, cell cycle and cell wall/membrane biogenesis. In comparison with stipe and blade, hypermethylation of mannuronate C5-epimerase in holdfast decreased the transcript abundance, which affected the synthesis of alginate, the key component of cell walls. Additionally, 5-mC modification participated in the regulation of blade and holdfast development by the glutamate content respectively via glutamine synthetase and amidophosphoribosyl transferase, which may act as the epigenetic regulation signal. Overall, our study revealed the global methylation characteristics of the well-defined holdfast, stipe and blade, and provided evidence for epigenetic regulation of sporophyte development in brown macroalgae.
Highlights
DNA methylation in eukaryotes can be divided into three forms: 5-methylcytosine
To describe the whole-genome methylation landscape of S. japonica sporophytes, the bisulfite-converted genome DNA fragments from the holdfast, stipe and blade were respectively sequenced by whole genome bisulfite sequencing (WGBS)
We found that the potential differentially methylated regions (DMRs) included cell motility, cell cycle and cell wall/membrane biogenesis, suggesting that these cell behaviors were under the regulation of cytosine methylation during sporophyte development
Summary
DNA methylation in eukaryotes can be divided into three forms: 5-methylcytosine (5-mC), 6-methyladenine (6-mA), and 7-methylguanine (7-mG) [1,2]. The 5-mC DNA methylation that transfers the methyl group from S-adenosyl-L-methionine to the C5 position of cytosine residues is one of the most conserved epigenetic modifications. It plays important roles in silencing of transposon proliferation [3], the control of genomic imprinting [4], and the regulation of transcript expression [5]. The occurrence of DNA methylation in transposon regions could inhibit the transcription and movement of transposons, protect the genome from uncontrolled insertion, prevent the invasion of foreign. DNA methylation in the promoter region with high tissue-specific expression could influence the transcription patterns by preventing the binding of regulatory proteins [9]
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