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

Abstract

The bromodomain containing proteins (Brd-proteins) comprise a diverse family of 'epigenetic mark readers', which are an integral to epigenetic gene regulation, important for diverse cellular processes and environmental stress responses. The Brd-proteins harbour a conserved 'bromodomain (BRD)' that interacts with the acetylated histones in the chromatin. Presence of several additional domains enhances the structural-functional diversity and the associated functions of the Brd-proteins. Plants contains multiple Brd-proteins, however the extent of diversity and the molecular events responsible are relatively less understood. The present genome-wide analysis of Brd-members in A. thaliana and O. sativa showed extensive diversity in structure of gene and regulatory regions, expression dynamics, and domains/motifs, including bromodomain. More than 40% Brd-genes in both the species were affected by genomic duplication events, while, ~60% A. thaliana and ~40% O. sativa genes showed alternative splicing-mediated changes. These molecular events affected one or more features of the Brd-members (regulatory elements, untranslated regions, and coding regions), which could potentially alter their expression, and associated functions. The phylogenetic analysis divided the A. thaliana and O. sativa Brd-homologs into six major clusters, and displayed consistency with certain domain/motif combination architectures. Homology modelling of most A. thaliana and O. sativa Brd-homologs displayed typical BRD-fold. However, the duplicate/divergent sequences displayed important structural variations, which can potentially alter its interaction with the chromatin, and affect associated function. The results also suggested substantial contribution of various genome duplication events (predominantly block events) in the evolution and expansion of Brd-family among diverse plants, including both monocot and dicot species.

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“…The bromodomain proteins proceed with these functions via binding to acetylated histones and anchoring sequence-specific factors on the chromatin of target promoters. Further, bromodomain-containing proteins contain various families of ‘epigenetic mark readers’, which are basic to epigenetic gene regulation, and necessary for different environmental stress responses and cellular processes ( Abiraami et al., 2022 ). In Arabidopsis, the bromodomain-containing transcription factors, GTE9, and GTE11 convert specific factors as BT2 to control gene expression.…”