Epigenetic Regulation of Subgenomic Gene Expression in Allotetraploid <i>Brassica napus</i>

The allotetraploid <i>Brasscia napus</i> has now been extensively utilized to reveal the genetic processes involved in hybridization and polyploidization. Here, transcriptome, WGBS, and Chip-Seq sequencing data were obtained to explore the regulatory consequences of DNA methylation and histone modifications on gene expression in <i>B. napus</i>. When compared with diploid parents, the expression levels of 14,266 (about 32%) and 17,054 (about 30%) genes were altered in the A_n and C_n subgenomes, respectively, and a total of 4982 DEGs were identified in <i>B. napus</i>. Genes with high or no expression in diploid parents often shifted to medium or low expression in <i>B. napus</i>. The number of genes with elevated methylation levels in gene promoters and gene body regions has increased in A_n and C_n subgenomes. The peak number of H3K4me3 modification increased, while the peak number of H3K27ac and H3K27me3 decreased in A_n and C_n subgenomes, and more genes that maintained parental histone modifications were identified in C_n subgenome. The differential multiples of DEGs in <i>B. napus</i> were positively correlated with DNA methylation levels in promoters and the gene body, and the differential multiples of these DEGs were also affected by the degree of variation in DNA methylation levels. Further analysis revealed that about 99% of DEGs were of DNA methylation, and about 68% of DEGs were modified by at least two types of DNA methylation and H3K4me3, H3K27ac, and H3K27me3 histone modifications. These results demonstrate that DNA methylation is crucial for gene expression regulation, and different epigenetic modifications have an essential function in regulating the differential expression of genes in <i>B. napus</i>.