Erdei, Anna Laura
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences
- Eötvös Lóránd Research Network (ELKH)
Research article2025Peer reviewedOpen access
INCREASED DNA METHYLATION 3 forms a potential chromatin remodelling complex with HAIRPLUS to regulate DNA methylation and trichome development in tomato
Nyiko, Tunde; Gyula, Peter; Rath, Szilvia; Sos-Hegedus, Anita; Csorba, Tibor; Abbas, Syed Hussam; Boka, Karoly; Pettko-Szandtner, Aladar; Moricz, agnes M.; Molnar, Bela Peter; Erdei, Anna Laura; Szittya, Gyorgy
Abstract
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.
Keywords
DNA methylation; DNA demethylation; Epigenomics; Chromatin remodelling; Gene expression regulation; Trichomes; Plant; Tomato
Published in
Plant Journal
2025, volume: 121, number: 6, article number: e70085
Publisher: WILEY
SLU Authors
UKÄ Subject classification
Agricultural Science
Publication identifier
- DOI: https://doi.org/10.1111/tpj.70085
Permanent link to this page (URI)
https://res.slu.se/id/publ/141527