Allele-specific DNA methylation analyses associated with siRNAs in Arabidopsis hybrids

Accumulating evidence has suggested that epigenetic marks including DNA methylation, small RNA and histone modification may involve hybrid vigor in plants. However, knowledge about how epigenetic marks in hybrids regulate gene expression is still limited. Based on genome-wide DNA methylation landscapes of Arabidopsis thaliana Ler and C24 ecotypes and their reciprocal F1 hybrids which were obtained in our previous work, we analyzed allele-specific DNA methylation and distinguished cis- and trans-regulated DNA methylation in hybrids. Our study indicated that both cis- and trans-regulated DNA methylation played roles in hybrids, when cis-regulation played a major role in CG methylation and trans-regulation played major roles in CHG and CHH methylation. In addition, we observed correlations between trans-regulated DNA methylation and siRNA densities. Enriched siRNA regions were significantly concurrent with highly trans-regulated DNA methylation regions. Our results illustrated DNA methylation regulation patterns integrated with siRNAs in Arabidopsis hybrids, and shed light on understanding the mechanism of epigenetic reprogramming for hybrid vigor.