Analysis of rice Snf2 family proteins and their potential roles in epigenetic regulation

Abstract

Snf2 family proteins are ATP-dependent chromatin remodeling factors that control many aspects of DNA events such as transcription, replication, homologous recombination and DNA repair. In animals several members in this family have been revealed to control gene expression in concert with other epigenetic mechanisms including histone modification, histone variants and DNA methylation. Their function in regulating genome expression in plant has hardly been disclosed before except in Arabidopsis. Here we identified 40 members of this family in the rice (Oryza Sativa) genome and constructed a phylogenetic tree together with Arabidopsis 41 Snf2 proteins. Sequence alignment of the Snf2 helicase regions revealed conserved motifs and blocks in most proteins. Expression profile analysis indicates that many rice Snf2 family genes show a tissue-specific expression pattern and some of them respond to abiotic stresses including drought, salt and cold. The results provide a basis for further analysis of their roles in epigenetic regulation to control rice development.

Keywords: Abitotic stress; Arabidopsis thaliana BRAHMA; AtBRM; BPTF; CHD3; DDM1; DRD1; Epigenetic regulation; Expression profile; H3K27me3; H3K4me3; H3K79; H3K9; HP1; ING2; MOM1; Morpheus molecule 1; PC; PIE1; Rice development; SPLAYED; SYD; Snf2; Snf2 family; bromodomain PHD finger transcription factor; chromodomain helicase DNA binding protein3; decrease in DNA methylation 1; defective in RNA-directed DNA methylation 1; heterochromatin protein 1; histone H3 lysine 79; histone H3 lysine 9; inhibitor of growth 2; photoperiod-independent early flowering 1; polycomb; sucrose nonfermentable; trimethylated histone H3 lysine 27; trimethylated histone H3 lysine 4.