# Genome-Wide DNA Methylation and Transcription Analysis Reveal the Potential Epigenetic Mechanism of Heat–Light Stress Response in the Green Macro Algae Ulva prolifera

## TL;DR

This study explores how the green algae Ulva prolifera uses DNA methylation to adapt to heat and light stress, revealing key epigenetic and metabolic responses.

## Contribution

The study identifies specific DNA methylation patterns and gene expression changes in Ulva prolifera under stress, linking them to adaptive and regenerative mechanisms.

## Key findings

- CG methylation decreases under stress, correlating with increased gene expression.
- CHG and CHH methylation in transposable elements and intergenic regions may stabilize the genome.
- Glycolysis-related genes are upregulated, suggesting a key role in stress adaptation.

## Abstract

Ulva prolifera (Chlorophyta), a pivotal species in green tide generation, is particularly vulnerable to abiotic stressors, including variations in temperature and light intensity, requiring specific regulatory frameworks for survival. Epigenetic modification is recognized as a molecular mechanism contributing to the flexible adaptability to environmental alterations. In this study, using DNA methylation pattern analysis, we investigated abiotic stress responsive methylation events, as well as gene and pathway expression patterns, in green macroalgae U. prolifera cultured under elevated temperature–light stress (30 °C and 300 µmol photons m−2 s−1) and identified a negative correlation between CG methylation and gene expression patterns which indicated that abiotic stress caused CG demethylation and afterwards provoked the transcription response. CHG and CHH methylation exhibited an increased mutability and were preeminently found in transposable elements and intergenic regions, possibly contributing to genetic stability by restricting transposon activity. Furthermore, a rapid regeneration through spore ejection and the formation of new thalli was observed, which emphasized its tenacity capacity for stress memory. Our study also revealed an upregulation of genes associated with the glycolysis pathway and highlighted the critical roles of hexokinase, 6-phosphofructokinase-1, and fructose-6-phosphate in triggering glycolysis as a significant stress-adaptive pathway. Overall, these findings suggested that DNA methylation functions as a potential regulatory mechanism, maintaining environmental adaptability, genomic integrity, and underpinning regenerative capacity in U. prolifera. The findings elucidated the molecular resilience of U. prolifera, highlighting its feasibility for sustainable development and biotechnological applications.