S01 - Session O6 - The role of histone modification in gene expression in Brassica rapa vegetables

Authors: Saaya Shiraki *, Hasan Mehraj, Satoshi Takahashi, Ayasha Akter, Naomi Miyaji, Motoaki Seki, Elizabeth S Dennis, Ryo Fujimoto

Histone modification is an epigenetic regulatory mechanism, which affects transcriptional activity of chromatin without changing DNA sequence and is crucial for the development and adaptation of plants to changing environments. The application of high-throughput sequencing technologies provides an opportunity to identify genome-wide profiles of histone modification by a combination of chromatin immunoprecipitation (ChIP) and genome-wide sequencing (ChIP-seq). In this study, we investigated the distribution of two active histone marks (H3K4me3 and H3K36me3) and two repressive histone marks (H3K9me2 and H3K27me3) in Brassica rapa by ChIP-seq. H3K4me3 and H3K36me3 marks were enriched at the transcription start site of genes, and the transcription level of a gene was positively associated with the level of H3K4me3 and H3K36me3. Levels of H3K27me3 were associated with decreased gene expression and H3K27me3-marked genes tended to show tissue-specific expression. H3K9me2 showed moderate association with interspersed repeat regions including transposable elements. Bivalent active and repressive histone modifications such as H3K4me3 and H3K27me3 marks or antagonistic coexistence of H3K36me3 and H3K27me3 marks, were observed in some genes. Expression may be influenced by abiotic and biotic stresses in genes having both H3K4me3 and H3K27me3 marks. In the triplicated genome of B. rapa , the presence of H3K36me3 or H3K27me3 marks was associated with different levels of gene expression or tissue specificity between paralogous paired genes, suggesting that H3K36me3 and H3K27me3 marks might be involved in sub-functionalization of the subgenomes.