INCREASED DNA METHYLATION 3 forms a potential chromatin remodelling complex with HAIRPLUS to regulate DNA methylation and trichome development in tomato

Sammanfattning

DNA methylation, a dynamic epigenetic mark influencing gene expression, is regulated by DNA demethylases that remove methylated cytosines at genomic regions marked by the INCREASED DNA METHYLATION (IDM) complex. In Arabidopsis, IDM3, a small alpha-crystalline domain-containing protein, stabilises the IDM complex. To investigate its role in tomato, we generated slidm3 mutants using genome editing. These mutants displayed a 'hairy' phenotype with increased glandular trichomes, resembling the hairplus (hap) mutant. Affinity purification of SlIDM3-GFP associated proteins identified several chromatin remodelling factors, including HAP. Genome-wide DNA methylation analysis revealed sequence context dependent alterations in the slidm3-1 plants, similar to the hap mutant. CHH methylation was predominantly increased, while CG methylation, particularly in intergenic regions, was decreased in both mutants. This imbalanced methylation suggests the presence of a 'methylstat' mechanism attempting to restore methylation levels at abnormally demethylated sites in the mutants. Comparative functional analysis of differentially methylated regions in the slidm3-1 and hap mutants identified potential methylation-regulated genes that could be linked to the hairy phenotype. Our findings indicate that SlIDM3 may form a chromatin remodelling complex with HAP, epigenetically regulating trichome development.

Nyckelord

DNA methylation; DNA demethylation; Epigenomics; Chromatin remodelling; Gene expression regulation; Trichomes; Plant; Tomato

Publicerad i

Plant Journal
2025, volym: 121, nummer: 6, artikelnummer: e70085
Utgivare: WILEY

SLU författare

• Erdei, Anna Laura

  • Institutionen för växtskyddsbiologi, Sveriges lantbruksuniversitet
    
  • Eötvös Lóránd Kutatási Hálózat (ELKH)

UKÄ forskningsämne

Jordbruksvetenskap

Publikationens identifierare

• DOI: https://doi.org/10.1111/tpj.70085

Permanent länk till denna sida (URI)

https://res.slu.se/id/publ/141527