Comprehensive analysis of CCCH zinc-finger-type transcription factors in the Brassica rapa genome

The CCCH-type zinc finger proteins are characterized by their signature motif of three cysteine and one histidine residues. These proteins are RNA binding proteins that function in plant growth, developmental processes, and responses to various environmental stress conditions. In this study, a comprehensive analysis using computational methods allowed the identification of 63 functionally important CCCH genes in the Brassica rapa genome. Several analyses were carried out on the identified genes to understand their roles in this plant. Comparative phylogenetic analysis classified CCCH genes into six clusters, while motif and structural analyses revealed four unique CCCH motifs including different functional motifs and intron/exon variations unique to plants compared to those in other species. Real-time qRT-PCR analysis of 10 randomly selected genes indicated they function at the early stages rather than the later stages of cold and salt stress. This study provides a basic understanding of potential candidate CCCH genes in B. rapa, their structural variation, expression patterns, and their roles under different stress conditions.