Intronic transposon insertion within the MYB transcription factor gene BjPur disturbs anthocyanin accumulation by inducing epigenetic modification in Brassica juncea

Transposable elements (TEs) account for about 50.36% of the Brassica juncea (B. juncea) genome, playing an important role in gene expression and genome evolution. However, the mechanisms by which host genes are influenced by TEs remain poorly understood. Our previous study revealed that the insertion of a 1268-bp DNA sequence into the intron of a MYB (BjPur) gene converts leaf color from purple to green in B. juncea. Here, we demonstrated that this insertion corresponds to a short interspersed nuclear element (SINE) retrotransposon, designated as Bjpur-SINE, which suppresses the expression of the Bjpur gene in green-leaved plants. Further analysis revealed that the insertion of Bjpur-SINE leads to increased DNA methylation at the BjPur locus, and the application of a DNA methylation inhibitor attenuated this transcriptional repression. Moreover, the knockout of two pivotal DNA methylation factors, BjDRM2 and BjAGO4, abolished Bjpur-SINE-mediated suppression and resulted in enhanced anthocyanin accumulation. Additionally, we observed alterations in repressive histone modifications at the BjPur locus in green-leaved B. juncea. Overall, our results confirmed that DNA and histone methylations synergistically participated in retrotransposon-mediated epigenetic silencing and provided insight into the mechanism by which intronic TEs regulated the expression of host genes.