Genome-wide Analysis of Bromodomain Gene Family in Arabidopsis and Rice

The bromodomain containing proteins (Brd-proteins) belongs to family of ‘epigenetic mark readers’, integral to epigenetic regulation. The Brd-members contain a conserved ‘bromodomain’ (BRD/BRD-fold: interacts with acetylated-lysine in histones), and several additional domains, making them structurally/functionally diverse. Like animals, plants also contain multiple Brd-homologs, however the extent of their diversity and impact of molecular events (genomic duplications, alternative splicing, AS) therein, is relatively less explored. The present genome-wide analysis of Brd -families of Arabidopsis thaliana and Oryza sativa showed extensive diversity in structure of genes/proteins, regulatory elements, expression pattern, domains/motifs, and the bromodomain (length/sequence, location) among Brd-members. Orthology analysis identified 13 ortholog groups, three paralog groups and four singleton members. While more than 40% Brd -genes were affected by genomic duplication events in both plants, AS-events affected 60% A . thaliana and 40% O . sativa genes. These molecular events affected various regions (promoters, untranslated regions, exons) of different Brd -members with potential impact on expression/structure-function characteristics. RNA-Seq data analysis of Brd -members, and RT-qPCR of duplicate Brd -genes showed differences in tissue-specificity and response to salinity. Phylogenetic analysis based on conserved BRD-region placed the A . thaliana and O . sativa homologs into clusters/sub-clusters, consistent with ortholog/paralog groups. The bromodomain-region displayed conserved signatures in key BRD-fold elements (α-helices, loops), and variations (1-20 sites) including indels among the Brd-duplicates. Homology modeling and superposition identified structural variations in BRD-folds of divergent and duplicate Brd-members, which might affect their interaction with chromatin and associated functions. The study also showed contribution of various duplication events in Brd -family expansion among diverse plants, including monocots and dicots.