Identification and characterization of the SET domain gene family in maize

Histone lysine methylation plays a pivotal role in a variety of developmental and physiological processes through modifying chromatin structure and thereby regulating eukaryotic gene transcription. The SET domain proteins represent putative candidates for lysine methyltransferases containing the evolutionarily-conserved SET domain, and important epigenetic regulators present in eukaryotes. In recent years, increasing evidence reveals that SET domain proteins are encoded by a large multigene family in plants and investigation of the SET domain gene family will serve to elucidate the epigenetic mechanism diversity in plants. Although the SET domain gene family has been thoroughly characterized in multiple plant species including two model plant systems, Arabidopsis and rice, through their sequenced genomes, analysis of the entire SET domain gene family in maize was not completed following maize (B73) genome sequencing project. Here, we performed a genome-wide structural and evolutionary analysis of maize SET domain genes from the latest version of the maize (B73) genome. A complete set of 43 SET domain genes (Zmset1-43) were identified in the maize genome using Blast search tools and categorized into seven classes (Class I-VII) based on phylogeny. Chromosomal location of these genes revealed that they are unevenly distributed on all ten chromosomes with seven segmental duplication events, suggesting that segmental duplication played a key role in expansion of the maize SET domain gene family. EST expression data mining revealed that these newly identified genes had temporal and spatial expression pattern and suggested that many maize SET domain genes play functional developmental roles in multiple tissues. Furthermore, the transcripts of the 18 genes (the Class V subfamily) were detected in the leaves by two different abiotic stress treatments using semi-quantitative RT-PCR. The data demonstrated that these genes exhibited different expression levels in stress treatments. Overall, our study will serve to better understand the complexity of the maize SET domain gene family and also be beneficial for future experimental research to further unravel the mechanisms of epigenetic regulation in plants.