Identifying and Understanding the Importance and Role of Bidirectional Promoters in Wheat

In the context of a changing climate, understanding gene regulation in the globally important Triticum asetivum (bread wheat) is becoming increasingly important to inform breeding programs and further techniques and resources in genetic manipulation. Bidirectional promoters are one such gene regulatory element. Bidirectional promoters are promoters that initiate the transcription of two diverging genes simultaneously. In bioinformatic analysis genes with transcription start sites within 1000 base pairs of one another and are located on opposite strands are considered to be bidirectionally arranged and under the control of the same promoter. I conducted a whole genome analysis in T. aestivum identifying 1,050 bidirectional promoters representing 1.95% of the protein coding genes in wheat. I also performed this analysis for Arabidopsis thaliana, Oryza sativa Japonica (rice), Avina sativa (oat), Zea mays (maize), Brassica Rapa (field mustard), Populus trichocarpa (black cottonwood), Solanum lycopersicum (cherry tomato) in which bidirectional genes represented 16.7, 5.6, 0.8, 2.5, 7.9, 2.6, and 3.2% of all protein coding genes, respectively. The bidirectional arrangement was conserved in wheat, rice, and Arabidopsis in twenty-two pairs. Like bidirectional genes in previous studies, wheat bidirectional genes were found to be located predominantly in CpG islands, highly coexpressed, and frequently involved in functions relating to cellular maintenance. Bidirectional genes in wheat can also respond to temperature, with one pair confirmed through qPCR to be expressed more highly at 25°C than 15°C. Bidirectional promoters are enriched for particular motifs, four of which are consensus sequences for four transcription factor families: MADSbox; MIKC, AP2; ERF, TCP, and NAC; NAM. The former is known to regulate genes in response to temperature, while the latter two are known to regulate genes in response to stress in plants. Extreme temperature is a source of stress in plants. Therefore, bidirectional genes, in addition to other regulatory elements such as non-coding and alternative splicing, may be important in responding to stress in plants. Furthermore, a new definition for bidirectional genes in plants is suggested, with a cut off of 560 rather than 1000 base pairs. In conclusion, bidirectional genes in wheat have the broad characteristics defined in animals for bidirectional genes, but may play a more important role in response to stress and temperature response than animal species.