In Silico Analysis of CCGAC and CATGTG Cis-regulatory Elements Across Genomes Reveals their Roles in Gene Regulation under Stress

Abstract

Background: Plant yield closely depends on its environment and is negatively affected by abiotic stress conditions like drought, salinity, heat, and cold. Analysis of the stress-inducible genes in Arabidopsis has previously shown that CCGAC and CATGTG play a crucial role in controlling the gene expression through the binding of DREB/CBF and NAC TFs under various stress conditions, mainly drought and salinity. Methods: The pattern of these motifs is conserved, which has been analyzed in this study to find the mechanism of gene expression through spacer specificity, inter motif distance preference, functional analysis, and statistical analysis for four different plants, namely Oryza sativa, Triticum aestivum, Arabidopsis thaliana, and Glycine max. Results: The spacer frequency analysis has shown a preference for particular spacer lengths among four genomes. The spacer specificity at all the spacer lengths which predicts dominance of particular base pairs over others, was analyzed to find the preference of the sequences in the flanking region. Functional analysis on stress-regulated genes for saline, osmotic, and heat stress clearly shows that these motif frequencies with inter motif distance (0-30) in the promoter region of Arabidopsis are highest in genes which are upregulated by saline and osmotic stress and downregulated by heat stress. Conclusion: Microarray data were analyzed to confirm the role of both motifs in stress response pathways. Transcription factors seem to prefer larger motif size with repeated CCGAC and CATGTG elements. The common preference for one spacer was further validated through Box and Whisker’s statistical analysis.

Genomic insights into CKX genes: key players in cotton fibre development and abiotic stress responses

“…In addition, the GhCKX genes consisted of several cis -elements in their promoter region associated with circadian control, light response, auxin response, abscisic acid response, phytochrome regulatory elements, zein metabolism, low temperature, anaerobic induction, meristem and endosperm expression, elements responding to gibberellin, MeJA, and salicylic acid. Earlier studies identified the light-induced cis-elements GT1 motif, G-box, I-box and AT-rich regions ( Sun et al, 2023 ), AuxRE, DR5, the cis-elements induced by auxin ( Li et al, 2022 ), and the cis-elements CATGTG and CACG induced by cold ( Bhadouriya et al, 2021 ). The abundance of elements in the promoter region of GhCKX genes suggests the functional diversity of these genes in cotton.…”

Artificially designed synthetic promoter for a high level of salt induction using a cis-engineering approach

“…WRKY TFs are involved in drought, salt, and heat response 36 . CCGAC and CAT GTG functions in drought and salinity stress 37 . GT1 and TGA motifs function in response to salt-induced stress 38,39 .…”