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Volume 14
Issue 16
10.3390/plants14162543
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

RdDM-Associated Chromatin Remodelers in Soybean: Evolution and Stress-Induced Expression of CLASSY Genes

by
Paula Machado de Araújo
1,
Arthur Gruber
2,
Liliane Santana OIiveira
2,
Sara Sangi
3,
Geovanna Vitória Olimpio
1,
Felipe Cruz Paula
1 and
Clícia Grativol
1,*
1
Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes 28013-602, RJ, Brazil
2
Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil
3
Laboratório de Biologia Celular e Tecidual, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes 28013-602, RJ, Brazil
*
Author to whom correspondence should be addressed.
Plants 2025, 14(16), 2543; https://doi.org/10.3390/plants14162543
Submission received: 16 July 2025 / Revised: 3 August 2025 / Accepted: 12 August 2025 / Published: 15 August 2025
(This article belongs to the Special Issue Molecular Regulation of Plant Stress Responses)
Versions Notes

Abstract

RNA-directed DNA methylation (RdDM) is an epigenetic mechanism involved in several biological processes in plants, requiring complex machinery including the chromatin remodeling protein CLASSY (CLSY). The CLSY family regulates global and locus-specific DNA methylation and was initially identified in Arabidopsis thaliana. Despite reports in other plants, detailed knowledge about CLSY proteins in soybean is scarce. In this work, we used profile hidden Markov models (profile HMMs) specifically constructed for CLSY detection to identify new members in soybean and to analyze their phylogenetic relationships across bryophyte, basal angiosperm, basal eudicot, monocots, and eudicots. We identified two new candidates for CLSY1-2 and one for DRD1 in soybean and, for the first time, detected CLSY and DRD1 genes in Aquilegia coerulea. Phylogenetic analysis indicated two main CLSY groups: one similar to Arabidopsis CLSY1-2 and another to CLSY3-4. Gene duplication analysis demonstrated that whole-genome duplication/segmental duplication events contributed to CLSY family expansion in soybean. RT-qPCR analysis showed that CLSY and five other epigenetic regulator genes had stress-modulated expression during soybean germination under salt and osmotic stress, with variation among cultivars. Our findings enhance comprehension of the evolutionary dynamics of the CLSY family and furnish insights into their response to abiotic stress in soybean.
Keywords: epigenetic regulation; RNA-directed DNA methylation; CLSY1-4; phylogeny; profile hidden Markov models; Glycine max epigenetic regulation; RNA-directed DNA methylation; CLSY1-4; phylogeny; profile hidden Markov models; Glycine max

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MDPI and ACS Style

Araújo, P.M.d.; Gruber, A.; OIiveira, L.S.; Sangi, S.; Olimpio, G.V.; Paula, F.C.; Grativol, C. RdDM-Associated Chromatin Remodelers in Soybean: Evolution and Stress-Induced Expression of CLASSY Genes. Plants 2025, 14, 2543. https://doi.org/10.3390/plants14162543

AMA Style

Araújo PMd, Gruber A, OIiveira LS, Sangi S, Olimpio GV, Paula FC, Grativol C. RdDM-Associated Chromatin Remodelers in Soybean: Evolution and Stress-Induced Expression of CLASSY Genes. Plants. 2025; 14(16):2543. https://doi.org/10.3390/plants14162543

Chicago/Turabian Style

Araújo, Paula Machado de, Arthur Gruber, Liliane Santana OIiveira, Sara Sangi, Geovanna Vitória Olimpio, Felipe Cruz Paula, and Clícia Grativol. 2025. "RdDM-Associated Chromatin Remodelers in Soybean: Evolution and Stress-Induced Expression of CLASSY Genes" Plants 14, no. 16: 2543. https://doi.org/10.3390/plants14162543

APA Style

Araújo, P. M. d., Gruber, A., OIiveira, L. S., Sangi, S., Olimpio, G. V., Paula, F. C., & Grativol, C. (2025). RdDM-Associated Chromatin Remodelers in Soybean: Evolution and Stress-Induced Expression of CLASSY Genes. Plants, 14(16), 2543. https://doi.org/10.3390/plants14162543

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