Dennis, E. S. | Search bioRxiv

bioRxiv2025

DECREASE IN DNA METHYLATION 1-mediated epigenetic regulation maintains gene expression balance required for heterosis in Arabidopsis thaliana

Heterosis, or hybrid vigor, is characterized by superior phenotypic performance in F hybrids compared to their parental lines, and its expression is influenced by both genetic and epigenetic factors. In this study, we investigated the role of epigenetic regulation, particularly DNA methylation mediated by DECREASE IN DNA METHYLATION 1 (DDM1), in early seedling biomass heterosis using hybrids between Arabidopsis thaliana accessions Columbia-0 and C24. Loss of DDM1 function in F hybrids resulted in a significant reduction of rosette diameter, confirming that DDM1 is essential for heterosis. Transcriptomic and epigenomic analyses revealed extensive genotype-specific changes in gene expression and DNA methylation patterns in ddm1 mutants. Notably, ddm1-F hybrids exhibited upregulation of genes categorized into xyloglucan:xyloglucosyl transferase activity and downregulation of genes categorized into circadian rhythm, which may contribute to reduced growth vigor. Whole-genome bisulfite sequencing showed widespread hypomethylation in ddm1 mutants, yet the overlap between differentially methylated and expressed genes was limited, suggesting indirect or context-dependent regulatory effects. Additionally, we examined the role of salicylic acid (SA) in heterosis using SA-deficient mutants and found that variations in endogenous SA levels did not correlate with biomass heterosis under normal conditions. Our findings suggest that heterosis in A. thaliana is dependent on the maintenance of parental epigenetic divergence, particularly in DNA methylation patterns mediated by DDM1. Disruption of DDM1 compromises this epigenetic complementarity, leading to transcriptomic imbalances that reduce heterosis. HighlightLoss of DDM1 reduces biomass heterosis in Arabidopsis thaliana hybrids by disrupting DNA methylation and transcriptome stability, revealing a novel salicylic acid-independent epigenetic mechanism.

plant biology↗

bioRxiv2020

Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa and related species

Long noncoding RNAs (lncRNAs) are RNA fragments that generally do not code for a protein but are involved in epigenetic gene regulation. In this study, lncRNAs of Brassica rapa were classified into long intergenic noncoding RNAs, natural antisense RNAs, and intronic noncoding RNAs and their expression were analyzed in relation to genome-wide 24-nt small interfering RNAs (siRNAs), DNA methylation, and histone H3 lysine 27 trimethylation marks (H3K27me3). More than 65% of the lncRNAs analyzed consisted of one exon, and more than 55% overlapped with inverted repeat regions (IRRs). Overlap of lncRNAs with IRRs or genomic regions encoding for 24-nt siRNAs resulted in increased DNA methylation levels and when both were present, there were further increase in DNA methylation levels. LncRNA did not overlap greatly with H3K27me3 marks, but the expression level of intronic noncoding RNAs that did coincide with H3K27me3 marks was higher than without H3K27me3 marks. The Brassica genus comprises important vegetables and oil seed crops grown across the world. Brassica rapa is a diploid (AA genome) thought to be one of the ancestral species of both B. juncea (AABB genome) and B. napus (AACC) through genome merging (allotetrapolyploidization). Complex genome restructuring and epigenetic alterations are thought to be involved in these allotetrapolyploidization events, but the detailed mechanism is not known. Comparison of lncRNAs between B. rapa and B. nigra, B. oleracea, B. juncea, and B. napus showed the highest conservation with B. oleracea. This study presents a comprehensive analysis of the epigenome structure of the B. rapa at multi-epigenetic levels (siRNAs, DNA methylation, H3K27me3, and lncRNAs) and offers insights into the function of lncRNA in the Brassica genus.

plant biology↗