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

PLoS One. 2013 Jun 7;8(6):e65426. doi: 10.1371/journal.pone.0065426. Print 2013.

Abstract

Background: SET 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 findings: In 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/significance: This study will facilitate further studies on OsSET family and provide useful clues for functional validation of OsSETs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Arabidopsis / genetics
  • Base Sequence
  • Cell Cycle / genetics
  • Chromosomes, Plant / genetics
  • Conserved Sequence / genetics
  • Gene Duplication
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant*
  • Gene Ontology
  • Gene Regulatory Networks / genetics
  • Genes, Plant / genetics*
  • Histones / metabolism
  • Molecular Sequence Data
  • Multigene Family*
  • Oligonucleotide Array Sequence Analysis
  • Oryza / cytology
  • Oryza / genetics*
  • Phylogeny*
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • Promoter Regions, Genetic / genetics
  • Protein Processing, Post-Translational / genetics
  • Protein Structure, Tertiary
  • Reproduction / genetics
  • Segmental Duplications, Genomic

Substances

  • Histones
  • Plant Proteins

Grants and funding

This research was supported by grants from the National Natural Science Foundation of China (http://www.nsfc.gov.cn/e_nsfc/desktop/zn/0101.htm; grant number 30971551), the Fundamental Research Funds for the Central Universities (http://www.dost.moe.edu.cn/; grant number 2012MBDX012), and the Specialized Research Fund for the Doctoral Program of Higher Education (http://www.cutech.edu.cn/cn/index.htm; grant number 20100146120034). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.