S01 - Session O2 - The role of epigenetic modifications in the transcriptional regulation of long noncoding RNAs in Brassica rapa vegetables

Authors: Yoshiki Kamiya *, Hasan Mehraj, Satoshi Takahashi, Ayasha Akter, Naomi Miyaji, Motoaki Seki, Elizabeth S. Dennis, Kenji Osabe, Ryo Fujimoto

Plant transcriptome analyses have revealed RNAs devoid of protein-coding potential, which are called noncoding RNAs (ncRNAs). Long ncRNAs (lncRNAs) that are longer than 200 nucleotides (nt), are classified by their position and orientation of transcription: long intergenic noncoding RNAs (lincRNAs), intronic noncoding RNAs (incRNAs) derived from introns, and natural antisense transcripts (NATs) transcribed from the complementary DNA 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 and examined the epigenetic modifications including DNA methylation and histone modifications in the genomic regions covering the lncRNAs. The average DNA methylation levels in regions covering lncRNAs were similar to those of the whole genome. The DNA methylation level in regions producing NATs was lower than in those producing any of the three types of lncRNAs. Overlap of lncRNAs with inverted repeat regions (IRRs) or genomic regions encoding for 24-nt small interfering RNAs (siRNAs) resulted in increased DNA methylation levels when both were present. The transcription level of lincRNAs was positively associated with the level of active histone marks (H3K4me3 and H3K36me3), while this association was not observed in NATs and incRNAs. LncRNA did not overlap greatly with repressive histone marks (H3K27me3), but the expression level of incRNAs that did coincide with H3K27me3 marks, was higher than without H3K27me3 marks. This study presents a comprehensive analysis of the epigenome structure in lncRNA-encoding regions in B. rapa .