Analysis of Conserved Domains in Promoters of Differentially Expressed Genes in Rice

Analysis of Conserved Domains in Promoters of Differentially Expressed Genes in Rice

Alvin Sherman Library

Plant responses to stress involve changes in gene expression, and understanding these changes is key to improving crop resilience. A critical step in this process is identifying "conserved domains" in the promoters of Differentially Expressed Genes (DEGs), as these domains often provide binding sites for transcription factors. In this study, we aim to identify the Cis-Regulatory Elements (CREs) in the promoters of DEGs associated with heat stress. Previously, we identified 149 DEGs from transcriptomic analyses of two rice varieties, Cypress (heat-tolerant) and LaGrue (heat-sensitive), both exposed to high night temperatures (HNT; 82.4 ± 1°F or 28 ± 1°C). We hypothesize that the DEGs, either up- or down-regulated under HNT stress, may share a set of common CREs or exhibit specific polymorphic patterns that correlate with distinct DEG expression patterns. To test this hypothesis, we analyzed the promoter sequences using two bioinformatics tools -- 'ElemeNT' and 'MEME' -- to identify core promoter motifs, their relative positions to the Transcription Start Site (TSS), and their statistical significance. These motifs were functionally annotated, revealing potential roles in the regulation of stress-responsive genes. The annotation indicated that certain motifs are enriched in promoters of up-regulated genes, while others are associated with down-regulated genes under heat stress. These findings will be further examined to determine how variations in these CREs correlate with gene expression patterns during heat stress.