ABSTRACT
DNA methylation (5-methylcytosine) represses transposon activity and contributes to inaccessible chromatin structure of repetitive DNA in plants. It is depleted from cis regulatory elements in and near genes, but in some genes it is present in the gene body including exons. Methylation in exons solely in the CG context is called gene body methylation (gbM). Methylation in exons in both CG and non-CG contexts is called TE-like methylation (teM). To develop a broader understanding of methylation in maize genes, we utilized recent genome assemblies, gene annotations, transcription data, and methylome data to decipher common patterns of gene methylation. To compare between genomes, we analyzed each data source relative to its own genome assembly rather than the easier but less accurate method of using one assembly as reference for all. We found that teM genes are mainly silent across plant tissues, are limited to specific maize stocks, and exhibit evidence of annotation errors. We used these data to flag all teM genes in the 26 NAM founder genome assemblies (on average 3,693 genes, 9% of total). In contrast to teM, gbM genes are broadly expressed across tissues. We found that they exist in a continuum of CG methylation levels without a clear demarcation between unmethylated genes and gbM genes. Analysis of expression levels across diverse maize stocks revealed a weak but highly significant positive correlation between gbM and gene expression. gbM epialleles were associated with an approximately 3% increase in steady-state expression level relative to unmethylated epialleles. We hypothesize based on these data that gbM can contribute toward broad and robust gene expression.
Competing Interest Statement
The authors have declared no competing interest.
