The effects of methylation on gene expression are mostly local, with positive associations for gbM and negative for teM, many of which remain significant after accounting for genetic variation, underscoring an epigenetic contribution.

Both gbM and teM explain a substantial portion of gene expression variance, with gbM effects increasing in genes with higher population frequency, while teM effects are more prominent in genes with lower conservation and expression entropy.

Analysis of nearly a thousand Arabidopsis accessions confirms that gbM and teM are largely independent, with distinct gene associations and conservation patterns, and do not originate from each other.

A recent study on Arabidopsis populations reveals that gene body methylation (gbM) and transposable element methylation (teM) are largely independent epigenetic phenomena, each with distinct effects on gene expression and phenotypic diversity.

The research highlights that gbM plays a significant role in regulating gene expression and contributing to phenotypic variation, which may be important for adaptation and evolution, separate from the influence of teM.

Importantly, the study emphasizes that gbM's impact on transcription is primarily epigenetic and independent of genetic variation, while teM often correlates with underlying genetic changes.

Data shows that gbM levels tend to be higher in genes with lower expression and are more likely to be preserved through natural selection, indicating their functional importance, whereas teM is mostly negatively associated and linked to genetic polymorphisms.

Mathematical models support the idea that gbM is maintained by self-reinforcing epigenetic dynamics, rather than being a by-product of teM or a driver of teM transition.