Abstract
BackgroundThe presence of methyl groups on cytosine nucleotides across an organism’s genome (methylation) is a major regulator of genome stability, crossing over, and gene regulation. The capacity for DNA methylation to be altered by environmental conditions, and potentially passed between generations, makes it a prime candidate for transgenerational epigenetic inheritance. Here we conduct the first analysis of the Mimulus guttatus methylome, with a focus on the relationship between DNA methylation and gene expression.ResultsWe present a whole genome methylome for the inbred line Iron Mountain 62 (IM62). DNA methylation varies across chromosomes, genomic regions, and genes. We develop a model that predicts gene expression based on DNA methylation (R2 = 0.2). Post hoc analysis of this model confirms prior relationships, and identifies novel relationships between methylation and gene expression. Additionally, we find that DNA methylation is significantly depleted near gene transcriptional start sites, which may explain the recently discovered elevated rate of recombination in these same regions.ConclusionsThe establishment here of a reference methylome will be a useful resource for the continued advancement of M. guttatus as a model system. Using a model-based approach, we demonstrate that methylation patterns are an important predictor of variation in gene expression. This model provides a novel approach for differential methylation analysis that generates distinct and testable hypotheses regarding gene expression.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1668-0) contains supplementary material, which is available to authorized users.
Highlights
The presence of methyl groups on cytosine nucleotides across an organism’s genome is a major regulator of genome stability, crossing over, and gene regulation
Mapping to unmethylated lambda DNA confirmed that our PBAT treatment achieved 99.4 % conversion of unmethylated cytosines to thymine
The percent of genome methylation found in M. guttatus is higher in all contexts than Oryza sativa [20], Arabiopsis thaliana [8], Brachypodium distachyiom [27], lower in all contexts than Solanum lycopersicum [22], and both higher or lower than Zea mays [26] and Glycine max [52] depending on context (Fig. 1)
Summary
The presence of methyl groups on cytosine nucleotides across an organism’s genome (methylation) is a major regulator of genome stability, crossing over, and gene regulation. DNA methylation appears to alter mutation rates [6] and to decrease rates of recombination [7]. It is found in organisms spanning the eukaryotic phylogeny [8, 9], and can occur in many sequence contexts. Cytosine methylation can be found in CG, CHG, or CHH contexts, where H is any nucleotide besides G [10] It appears that much of the methylome is stable within an individual; the methylome does exhibit predictable plastic responses to developmental and environmental cues [11, 12]. Recent work has greatly expanded our knowledge of the mechanisms involved in maintaining and modifying DNA methylation in plants [13,14,15,16,17,18], yet we still do not Colicchio et al BMC Genomics (2015) 16:507 in regulating transposable elements through pre- and post-transcriptional silencing [25]
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