AUTHOR=Abiraami T. V. , Sanyal Ravi Prakash , Misra Hari Sharan , Saini Ajay 

TITLE=Genome-wide analysis of bromodomain gene family in Arabidopsis and rice

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1120012

DOI=10.3389/fpls.2023.1120012

ISSN=1664-462X

ABSTRACT=<p>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 <italic>Brd</italic>-gene families of <italic>Arabidopsis thaliana</italic> and <italic>Oryza sativa</italic> showed extensive diversity in structure of genes/proteins, regulatory elements, expression pattern, domains/motifs, and the bromodomain (w.r.t. length, sequence, location) among the Brd-members. Orthology analysis identified thirteen ortholog groups (OGs), three paralog groups (PGs) and four singleton members (STs). While more than 40% <italic>Brd</italic>-genes were affected by genomic duplication events in both plants, AS-events affected 60% <italic>A. thaliana</italic> and 41% <italic>O</italic>. <italic>sativa</italic> genes. These molecular events affected various regions (promoters, untranslated regions, exons) of different Brd-members with potential impact on expression and/or structure-function characteristics. RNA-Seq data analysis indicated differences in tissue-specificity and stress response of Brd-members. Analysis by RT-qPCR revealed differential abundance and salt stress response of duplicate <italic>A. thaliana</italic> and <italic>O</italic>. <italic>sativa Brd</italic>-genes. Further analysis of <italic>AtBrd</italic> gene, <italic>AtBrdPG1b</italic> showed salinity-induced modulation of splicing pattern. Bromodomain (BRD)-region based phylogenetic analysis placed the <italic>A. thaliana</italic> and <italic>O</italic>. <italic>sativa</italic> homologs into clusters/sub-clusters, mostly consistent with ortholog/paralog groups. The bromodomain-region displayed several conserved signatures in key BRD-fold elements (α-helices, loops), along with variations (1-20 sites) and 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 the chromatin histones, and associated functions. The study also showed contribution of various duplication events in <italic>Brd</italic>-gene family expansion among diverse plants, including several monocot and dicot plant species.</p>