The role of epigenetic modifications in the transcriptional regulation of long noncoding RNAs in Brassica rapa vegetables

Plant transcriptome analyses have revealed RNAs devoid of protein-coding potential noncoding RNAs (ncRNAs). Long noncoding RNAs (lncRNAs) that are longer than 200 nucleotides (nt) are classified by their position and orientation of transcription. There are long intergenic noncoding RNAs (lincRNAs), intronic noncoding RNAs (incRNAs) derived from introns, and natural antisense transcripts (NATs) transcribed from the cDNA strand of their associated genes. Recent studies have shown that lncRNAs play crucial roles in abiotic and biotic stress responses. However, studies on the mechanism of lncRNA expression regulation are limited in plants. In this study, we identified lncRNAs with dimethylation of lysine 9 of histone H3 (H3K9me2) marks in their genomic region. There were fewer lncRNAs with H3K9me2 marks in their encoding regions than with the other histone modifications (H3K4me3, H3K36me3, H3K27me3). The encoding regions of lncRNAs with H3K9me2 marks tended to overlap inverted repeat regions (IRRs). LncRNAs with H3K9me2 marks in their encoding region showed no tendency to repress expression. The DNA methylation level in the encoding regions of lncRNAs with H3K9me2 marks was higher than that of lncRNAs with the other histone modifications, especially in lincRNAs encoding regions. This study presents a comprehensive analysis of the H3K9me2 in lncRNA encoding regions in Brassica rapa.