Abstract
BackgroundUnderstanding the DNA methylome and its relationship with non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), is essential for elucidating the molecular mechanisms underlying key biological processes in plants. Few studies have examined the functional roles of the DNA methylome in grass species with highly heterozygous polyploid genomes.ResultsWe performed genome-wide DNA methylation profiling in the tetraploid switchgrass (Panicum virgatum L.) cultivar ‘Alamo’ using bisulfite sequencing. Single-base-resolution methylation patterns were observed in switchgrass leaf and root tissues, which allowed for characterization of the relationship between DNA methylation and mRNA, miRNA, and lncRNA populations. The results of this study revealed that siRNAs positively regulate DNA methylation of the mCHH sites surrounding genes, and that DNA methylation interferes with gene and lncRNA expression in switchgrass. Ninety-six genes covered by differentially methylated regions (DMRs) were annotated by GO analysis as being involved in stimulus-related processes. Functionally, 82% (79/96) of these genes were found to be hypomethylated in switchgrass root tissue. Sequencing analysis of lncRNAs identified two lncRNAs that are potential precursors of miRNAs, which are predicted to target genes that function in cellulose biosynthesis, stress regulation, and stem and root development.ConclusionsThis study characterized the DNA methylome in switchgrass and elucidated its relevance to gene and non-coding RNAs. These results provide valuable genomic resources and references that will aid further epigenetic research in this important biofuel crop.
Highlights
Understanding the DNA methylome and its relationship with non-coding RNAs, including microRNAs and long non-coding RNAs, is essential for elucidating the molecular mechanisms underlying key biological processes in plants
DNA methylation studies in model plants, such as Arabidopsis thaliana, rice, and B. distachyon, have generated several conserved rules: (1) mCG is dominating among the three methylated contexts; (2) methylation may act as a mechanism for controlling gene expression, but the methylation variation depends on types of contexts and gene region; and (3) RNA-dependent DNA methylation (RdDM) pathways are highly associated with mCHH [17, 26, 27, 29, 30]
Our results revealed that siRNAs positively regulated DNA methylation at the mCHH sites surrounding genes and that DNA methylation may interfere with both gene and long non-coding RNAs (lncRNAs) expression in the polyploid switchgrass genome
Summary
Single‐base resolution landscapes of DNA methylation in switchgrass Whole-genome bisulfite sequencing was applied to genomic DNA of switchgrass extracted from leaves and roots. DNA methylation differences between leaf and root tissues in switchgrass To identify global differentially methylated DNA between leaf and root tissues, the methylation levels of both genic and TE regions were compared The analysis of these two genomic components was further divided into upstream, body, and downstream regions (Fig. 2c; Additional file 9: Table S4). In the gene body and downstream flanking regions, the non-expressed group exhibited the highest methylation levels, and the highand middle-expressed lncRNAs displayed similar methylation patterns (Fig. 7a). The mCHG sites of lncRNAs had comparable patterns with mRNAs, and the mCHG levels in both the flanking and body regions were found to be negatively associated with gene expression For all three methylation contexts, these two different statistical approaches both
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