Characterization of Histone H3 Lysine 4 and 36 Tri-methylation in Brassica rapa L.

Hasan Mehraj,Yutaka Suzuki,Ayasha Akter,Satoshi Takahashi,Motoaki Seki,Elizabeth S Dennis,Ryo Fujimoto,Naomi Miyaji

doi:10.3389/fpls.2021.659634

Abstract

Covalent modifications of histone proteins act as epigenetic regulators of gene expression. We report the distribution of two active histone marks (H3K4me3 and H3K36me3) in 14-day leaves in two lines of Brassica rapa L. by chromatin immunoprecipitation sequencing. Both lines were enriched with H3K4me3 and H3K36me3 marks at the transcription start site, and the transcription level of a gene was associated with the level of H3K4me3 and H3K36me3. H3K4me3- and H3K36me3-marked genes showed low tissue-specific gene expression, and genes with both H3K4me3 and H3K36me3 had a high level of expression and were constitutively expressed. 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 susceptible to changes by abiotic and biotic stresses in genes having both H3K4me3 and H3K27me3 marks. We showed that the presence of H3K36me3 marks was associated with different gene expression levels or tissue specificity between paralogous paired genes, suggesting that H3K36me3 might be involved in subfunctionalization of the subgenomes.

Highlights

Brassica rapa L. encompasses commercially important cultivars of vegetables, oilseeds, condiments, and fodder and is a crop closely related to Arabidopsis thaliana (Cheng et al, 2014, 2016a; Lv et al, 2020)
We found that H3K36me3marked genes and genes having both H3K4me3 and H3K36me3 marks showed significantly lower average T-values compared with the total genes (Figure 5), suggesting that H3K36me3 has a role in constitutive gene expression
We examined the genomic locations of H3K4me3 and H3K36me3 using two B. rapa lines

Summary

Introduction

Brassica rapa L. encompasses commercially important cultivars of vegetables, oilseeds, condiments, and fodder and is a crop closely related to Arabidopsis thaliana (Cheng et al, 2014, 2016a; Lv et al, 2020). In addition to its agronomic significance, B. rapa is important for genomic studies, because it has the first complete genome sequence to be determined within the genus Brassica (Wang et al, 2011). The whole-genome triplication results in multiple copies of paralogous genes and generates three subgenomes, the least. After the whole genome triplication, subfunctionalization such as different expression levels or DNA methylation levels among three subgenomes or paralogous genes has been observed (Parkin et al, 2014; Chen et al, 2015)

Methods

Results

Conclusion