The role of histone modification in gene expression in Brassica rapa vegetables
Histone modification is an epigenetic regulatory mechanism, which affects the transcriptional activity of chromatin without changing the 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). We investigated the distribution of two active histone marks, trimethylation of lysine 4 of histone H3 (H3K4me3) and trimethylation of lysine 36 of histone H3 (H3K36me3), in Brassica rapa L. 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. In this study, we compared H3K4me3 and H3K36me3 levels between the two Chinese cabbage inbred lines in B. rapa var. pekinensis. Most H3K4me3-marked and H3K36me3-marked genes overlapped between the two lines, while 5 and 6% of genes showed a difference in H3K4me3 and H3K36me3 levels between the two lines. Among these genes showing a difference of H3K4me3 or H3K36me3 levels between the lines, 30 and 37% of genes showed a positive association between the level of H3K4me3 or H3K36me3 and the level of transcription. These results suggest that differences in the level of H3K4me3 and H3K36me3 between the lines determine the difference in the transcriptional levels, but did not account for the high percentage of differentially expressed genes seen between the two lines. It will be interesting to examine how histone modifications, which have been found to differ between the lines, are inherited in an F1 or cross-segregating population of these two lines.
Shiraki, S., Kamiya, Y., Mehraj, H., Takahashi, S., Seki, M., Dennis, E.S. and Fujimoto, R. (2023). The role of histone modification in gene expression in Brassica rapa vegetables. Acta Hortic. 1362, 107-112
epigenetics, trimethylation of lysine 4 of histone H3, trimethylation of lysine 36 of histone H3, chromatin immunoprecipitation sequencing, Chinese cabbage