Identification, Evolution, and Expression Profiling of Histone Lysine Methylation Moderators in Brassica rapa.

Gaofeng Liu,Xiaoqing Ma,Nadeem Khan,Xilin Hou

doi:10.3390/plants8120526

Abstract

Histone modifications, such as methylation and demethylation, are vital for regulating chromatin structure, thus affecting its expression patterns. The objective of this study is to understand the phylogenetic relationships, genomic organization, diversification of motif modules, gene duplications, co-regulatory network analysis, and expression dynamics of histone lysine methyltransferases and histone demethylase in Brassica rapa. We identified 60 SET (HKMTases), 53 JmjC, and 4 LSD (HDMases) genes in B. rapa. The domain composition analysis subcategorized them into seven and nine subgroups, respectively. Duplication analysis for paralogous pairs of SET and JmjC (eight and nine pairs, respectively) exhibited variation. Interestingly, three pairs of SET exhibited Ka/Ks > 1.00 values, signifying positive selection, whereas the remaining underwent purifying selection with values less than 1.00. Furthermore, RT-PCR validation analysis and RNA-sequence data acquired on six different tissues (i.e., leaf, stem, callus, silique, flower, and root) revealed dynamic expression patterns. This comprehensive study on the abundance, classification, co-regulatory network analysis, gene duplication, and responses to heat and cold stress of SET and JmjC provides insights into the structure and diversification of these family members in B. rapa. This study will be helpful to reveal functions of these putative SET and JmjC genes in B. rapa.

Highlights

IntroductionThe role of histone methylation in transcription regulation was first reported in the 1960s [1]
The role of histone methylation in transcription regulation was first reported in the 1960s [1].It was not until 15 years later that a catalytic SET domain (Su(var)3–9, enhancer of zeste and trithorax) the first histone methyltransferase (SUV39H1), was identified [2]
We identified 60 BraSET, 53 BraJmjC, and 4 BraLSD genes in B. rapa

Summary

Introduction

The role of histone methylation in transcription regulation was first reported in the 1960s [1]. It was not until 15 years later that a catalytic SET domain (Su(var), enhancer of zeste and trithorax) the first histone methyltransferase (SUV39H1), was identified [2]. This discovery led to a number of SET-domain homologous searches [3]. Histone methylation and demethylation play fundamental roles in various biological processes, in regulating transcription, genome integrity, and epigenetic inheritance [5,6]. Mass spectroscopy and liquid chromatography were used to identify the histone modification profile in Arabidopsis thaliana, Plants 2019, 8, 526; doi:10.3390/plants8120526 www.mdpi.com/journal/plants

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