Transcriptome meta-analysis-based identification of hub transcription factors and RNA-binding proteins potentially orchestrating gene regulatory cascades and crosstalk in response to abiotic stresses in Arabidopsis thaliana.

Abstract

Deteriorating climatic conditions and increasing human population necessitate the development of robust plant varieties resistant to harsh environments. Manipulation of regulatory proteins such as transcription factors (TFs) and RNA-binding proteins (RBPs) would be a beneficial strategy in this regard. Further, understanding the complex interconnections between different classes of regulatory molecules would be essential for the identification of candidate genes/proteins for trait improvement. Most studies to date have analysed the roles of TFs or RBPs individually, in conferring stress resilience. However, it would be important to identify dominant/upstream TFs and RBPs inducing widespread transcriptomic alterations through other regulators (i.e., other TFs/RBPs targeted by the upstream regulators). To this end, the present study employed a transcriptome meta-analysis and computational approaches to obtain a comprehensive overview of regulatory interactions. This work identified dominant TFs and RBPs potentially influencing stress-mediated differential expression of other regulators, which could in turn influence gene expression, and consequently, physiological responses. Twenty transcriptomic studies [related to (i) UV radiation, (ii) wounding, (iii) salinity, (iv) cold, and (v) drought stresses in Arabidopsis thaliana] were analysed for differential gene expression, followed by the identification of differentially expressed TFs and RBPs. Subsequently, other TFs and RBPs which could be influencing these regulators were identified, and their interaction networks and hub nodes were analysed. As a result, an interacting module of Basic Leucine Zipper (bZIP) family TFs as well as Heterogeneous nuclear ribonucleoproteins (hnRNP) and Glycine-rich protein (GRP) family RBPs (among other TFs and RBPs) were shown to potentially influence the stress-induced differential expression of other TFs and RBPs under all the considered stress conditions. Some of the identified hub TFs and RBPs are known to be of major importance in orchestrating stress-induced transcriptomic changes influencing a variety of physiological processes from seed germination to senescence. This study highlighted the gene/protein candidates that could be considered for multiplexed genetic manipulation - a promising approach to develop robust, multi-stress-resilient plant varieties.