Transcriptomic and epigenomic analyses revealed that polycomb repressive complex 2 regulates not only developmental but also stress responsive metabolism in Brassica rapa

Abstract

Polycomb group proteins (PcG) play a crucial role in developmental programs in eukaryotic organisms, including plants. PcG-mediated gene repression is achieved by epigenetic histone modification on target chromatins. Loss of PcG components leads to severe developmental defects. CURLY LEAF (CLF), a PcG component in Arabidopsis, catalyzes the trimethylation of histone H3 on lysine 27 (H3K27me3), a repressive histone mark in numerous genes in Arabidopsis. In this study, we isolated a single homolog of Arabidopsis CLF, namely, BrCLF, in Brassica rapa ssp. trilocularis. Transcriptomic analysis revealed that BrCLF participated in B. rapa developmental processes, such as seed dormancy, leaf and flower organ development, and floral transition. BrCLF was also involved in stress signaling and stress-responsive metabolism, such as aliphatic and indolic glucosinolate metabolism in B. rapa. Epigenome analysis showed that H3K27me3 was substantially enriched in genes related to these developmental and stress-responsive processes. Thus, this study provided a basis for elucidating the molecular mechanism of the PcG-mediated regulation of development and stress responses in B. rapa.

Brassica rapa CURLY LEAF is a major H3K27 methyltransferase regulating flowering time

“…However, we also found a large number of upregulated and downregulated genes related to metabolism in braA.clf-1 (Supplementary Data S3 ). These results are consistent with a recent transcriptomic report suggesting that BraA.CLF may be regulating the expression of stress-response and metabolic genes (Nugroho et al 2023 ). These authors also proposed that BraA.CLF suppresses the expression of genes involved in the glucosinolate metabolism (Nugroho et al 2023 ).…”

“…These results are consistent with a recent transcriptomic report suggesting that BraA.CLF may be regulating the expression of stress-response and metabolic genes (Nugroho et al 2023 ). These authors also proposed that BraA.CLF suppresses the expression of genes involved in the glucosinolate metabolism (Nugroho et al 2023 ). However, our analysis only revealed five upregulated genes in braA.clf-1 related to the glucosinolate-pathway, compared to the 27 genes described by Nugroho and colleagues.…”

“…2 C). However, we could not observe any abnormally elongated pistil or severe reduction in plant height as described by Nugroho et al ( 2023 ). In our study, both braA.clf-1 and wild-type plants attained similar heights at the flowering stage (Fig.…”