Genome-wide identification, phylogenetic and co-expression analysis of OsSET gene family in rice.

Zhanhua Lu,Yidan Ouyang,Xiaolong Huang,Jialing Yao,Xiaoyu Zhang

doi:10.1371/journal.pone.0065426

Abstract

BackgroundSET domain is responsible for the catalytic activity of histone lysine methyltransferases (HKMTs) during developmental process. Histone lysine methylation plays a crucial and diverse regulatory function in chromatin organization and genome function. Although several SET genes have been identified and characterized in plants, the understanding of OsSET gene family in rice is still very limited.Methodology/Principal FindingsIn this study, a systematic analysis was performed and revealed the presence of at least 43 SET genes in rice genome. Phylogenetic and structural analysis grouped SET proteins into five classes, and supposed that the domains out of SET domain were significant for the specific of histone lysine methylation, as well as the recognition of methylated histone lysine. Based on the global microarray, gene expression profile revealed that the transcripts of OsSET genes were accumulated differentially during vegetative and reproductive developmental stages and preferentially up or down-regulated in different tissues. Cis-elements identification, co-expression analysis and GO analysis of expression correlation of 12 OsSET genes suggested that OsSET genes might be involved in cell cycle regulation and feedback.Conclusions/SignificanceThis study will facilitate further studies on OsSET family and provide useful clues for functional validation of OsSETs.

Highlights

SET domain, named after the three Drosophila proteins SUPPRESSOR OF VARIEGATION 3–9 [SU(VAR)3–9], ENHANCER OF ZESTE [E(Z)] and TRITHORAX (TRX) [1], has been known to be involved in the biochemical process of the histone lysine methyltransferases (HKMTs) [2]
Based on the update Pfam and ChromDB database and MSU data, 43 SET family genes in rice were identified in our study
These 43 OsSET genes were named from OsSET1 to OsSET43 according to their positions on chromosomes

Summary

Introduction

SET domain, named after the three Drosophila proteins SUPPRESSOR OF VARIEGATION 3–9 [SU(VAR)3–9], ENHANCER OF ZESTE [E(Z)] and TRITHORAX (TRX) [1], has been known to be involved in the biochemical process of the histone lysine methyltransferases (HKMTs) [2]. It contains an approximately 130-amino acid, presenting as an evolutionarily conserved motif in chromosome proteins from yeast to mammals and higher plants [3]. Springer et al identified 32 SET domain genes in Arabidopsis and 22 ones in Zea mays, and classified the SET domain proteins into five subfamilies, on the basis of phylogenetic analyses and domain organization [9]. Several SET genes have been identified and characterized in plants, the understanding of OsSET gene family in rice is still very limited

Methods

Results

Conclusion