Natural methylation epialleles correlate with gene expression in maize

Area of Science:

• Plant epigenetics
• Genomics
• Gene expression regulation

Background:

• DNA methylation in plants is generally absent in cis-regulatory regions but present in gene bodies.
• Gene body methylation (gbM) occurs in the CG context, while TE-like methylation (teM) involves both CG and non-CG contexts.
• The functional significance of these methylation patterns in gene regulation remains challenging to ascertain.

Purpose of the Study:

• To investigate patterns of DNA methylation in gene bodies and their relationship with gene expression in maize.
• To differentiate and characterize the roles of gbM and teM in maize gene regulation.
• To leverage genomic and transcriptomic data to refine gene annotations and identify potentially non-functional methylated genes.

Main Methods:

• Utilized maize genome assemblies, gene annotations, and methylome data.
• Quantified methylation patterns, specifically gbM and teM, across various maize stocks and tissues.
• Correlated methylation levels with gene expression data to assess functional associations.

Main Results:

• A continuum of CG methylation levels was observed in gbM genes, without a distinct boundary between methylated and unmethylated genes.
• A weak but significant positive correlation was found between gbM and gene expression across most tissues, with a ~3% increase in expression for gbM epialleles.
• teM genes, comprising ~12% of the genome, were found to be largely silent, poorly conserved, and potentially misannotated.

Conclusions:

• gbM is generally associated with active gene expression in maize, albeit with a modest effect size.
• teM genes are predominantly non-functional or misannotated, and their inclusion can complicate whole-genome analyses.
• These findings aid in refining maize gene annotations and understanding the regulatory roles of DNA methylation.