Temperature reshapes epigenomic diversity in Arabidopsis thaliana -- JSD and Methylator reveal RdDM-CMT2 plasticity

TL;DR

This study investigates how temperature influences DNA methylation diversity in Arabidopsis thaliana, revealing temperature-dependent plasticity, pathway interactions, and geographic variation in epigenomic landscapes.

Contribution

It demonstrates that temperature modulates methylation diversity, especially in non-CG contexts, and uncovers pathway interactions affecting transposable element regulation.

Findings

Temperature affects methylation diversity, especially at intermediate levels.

Non-CG methylation diversity increases at warmer temperatures.

Southern European accessions show higher non-CG diversity at 22°C.

Abstract

DNA methylation can be associated with phenotypic plasticity, yet how temperature shapes DNA methylation diversity in natural populations is unclear. Analyzing whole-genome bisulfite sequencing from 1075 Arabidopsis thaliana accessions grown at 10{\deg}C, 16{\deg}C, and 22{\deg}C, we quantified single-cytosine diversity using Jensen-Shannon Divergence (JSD). Diversity consistently peaked at intermediate methylation levels across the CpG, CHG, and CHH sequence contexts. Temperature modulated this diversity, primarily impacting intermediately methylated sites, with non-CG contexts (CHG and CHH) exhibiting increased diversity at warmer temperatures. Notably, at 22{\deg}C, CHH diversity patterns indicated altered balance between the RdDM and CMT2 pathways that regulate specific transposable element (TE) superfamilies. Furthermore, accessions from Southern Europe displayed higher non-CG diversity at 22{\deg}C compared to Northern European accessions. Our findings reveal that temperature influences the epigenomic diversity landscape, highlighting context-dependent plasticity, a dynamic interplay between silencing pathways, and potential geographic adaptation in response to environmental cues.