Abstract
BackgroundAs a well-known epigenomic modification, DNA methylation is found to be common in plants and plays an important role in many biological processes. Relying on the unique feature of methylation-dependent digestion, the family of methylation-requiring restriction-like endonuclease, such as MspJI and its homologs, was suggested for a potential usage in methylation detection.ResultsIn this study, we combine MspJI digestion and electrophoretic band selection with next generation high-throughput sequencing technology to detect 5-methylcytosines in Arabidopsis genome. By developing a bioinformatics workflow to attribute the CNNR sites recognized by MspJI to the reference genome, we fulfilled the systematic assessment of this method.ConclusionsAccording to the assessment, here we provide the method for generating a detailed map of plant methylome that could be feasible, reliable and economical in methylation investigation.
Highlights
As a well-known epigenomic modification, DNA methylation is found to be common in plants and plays an important role in many biological processes
Simulation of enzymatic digestion on Arabidopsis thaliana by methylation- dependent restriction endonuclease MspJI Based on the former study in recognition specificities of the MspJI enzyme [7], we performed in silico analysis to simulate MspJI digestion on the Arabidopsis genome
We calculated the number of potential MspJI recognition sites and found that at least 10.72 M cytosines in fragments ranging from 28 bp to 35 bp can be extracted from the genomic DNA of Arabidopsis by MspJI digestion (Twoway cleavage, Additional file 1E, 1F), representing 25.03% of the total 42.86 M cytosines in Arabidopsis genome (Table 1)
Summary
As a well-known epigenomic modification, DNA methylation is found to be common in plants and plays an important role in many biological processes. DNA methylation occurs in all domains of life, from viruses to cellular organisms, serving for DNA protection in prokaryotes and regulation of gene expression in plants and animals [1,2,3]. Methylation mainly occurs on the cytosines in CpG context, nonCpG methylation is prevalent in embryonic stem cells as well [4]. Methylation occurs in both CpG and non-CpG contexts [5]. Plant genomes are normally much larger than mammalian ones and contain a lot of repetitive sequences. The gold standard method whole genome bisulfite sequencing (WGBS) can be used to examine DNA methylation in single-base resolution, it requires large volume of sequencing data for confident DNA methylation calling.
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