Genome-wide analysis of bromodomain gene family in Arabidopsis and Rice

V., A. T.; Sanyal, R. P.; Misra, H. S.; Saini, A.

doi:10.1101/2022.02.08.479518

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bioRxiv · 10.1101/2022.02.08.479518

Genome-wide analysis of bromodomain gene family in Arabidopsis and Rice

V., A. T.·Sanyal, R. P.·Misra, H. S.·Saini, A.

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Abstract

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 (-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.

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V., A. T., Sanyal, R. P., Misra, H. S., Saini, A.. 2022-02-10. Genome-wide analysis of bromodomain gene family in Arabidopsis and Rice. https://doi.org/10.1101/2022.02.08.479518

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