Integrating expression data and genomic sequences to investigate the transcriptional regulation in barley in response to abiotic stress

• Main Authors: Azar Delavari, Zahra Zinati, Sima Sazegari, Ahmad Tahmasebi
• Format: Article
• Language: English
• Published: Termedia Publishing House 2021-03-01
• Series: BioTechnologia
• Subjects: barley; abiotic stress; transcriptomics analysis; motif discovery; motif enrichment; regulatory gene set
• Online Access: https://www.termedia.pl/Integrating-expression-data-and-genomic-sequences-to-investigate-the-transcriptional-regulation-in-barley-in-response-to-abiotic-stress,85,43334,1,1.html

Abiotic stress responses are regulated critically at the transcriptional level. Clarifying the intricate mechanisms that regulate gene expression in response to abiotic stress is crucial and challenging. For this purpose, the factors that regulate gene expression and their binding sites in DNA should be determined. By using bioinformatics tools, the differentially expressed probe sets were studied. A meta-analysis of transcriptomic responses to several abio¬tic stresses in barley was performed. Motif enrichments revealed that AP2/ERF (APETALA2/Ethylene-Res¬pon¬sive Factor) has the most frequent binding sites. We found that the bHLH transcription factor family has the high¬est number of transcription factor members. Moreover, network construction revealed that AP2 has the highest number of connections with other genes, which indicates its critical role in abiotic stress responses. The present research further predicted 49 miRNAs belonging to 23 miRNA families. This study identified the probable conserved and enriched motifs, which might have a role in the regulation of differentially expressed genes under abiotic stresses. In addition to shedding light on gene expression regulation, a toolbox of available promoters for genetic engineering of crop plants under such abiotic stresses was developed.