Prediction of new abiotic stress genes in Arabidopsis thaliana and Oryza sativa according to enumeration-based statistical analysis

Abstract

Plants undergo an extensive change in gene regulation during abiotic stress. It is of great agricultural importance to know which genes are affected during stress response. The genome sequence of a number of plant species has been determined, among them Arabidopsis and Oryza sativa, whose genome has been annotated most completely as of yet, and are well-known organisms widely used as experimental systems. This paper applies a statistical algorithm for predicting new stress-induced motifs and genes by analyzing promoter sets co-regulated by abiotic stress in the previously mentioned two species. After identifying characteristic putative regulatory motif sequence pairs (dyads) in the promoters of 125 stress-regulated Arabidopsis genes and 87 O. sativa genes, these dyads were used to screen the entire Arabidopsis and O. sativa promoteromes to find related stress-induced genes whose promoters contained a large number of these dyads found by our algorithm. We were able to predict a number of putative dyads, characteristic of a large number of stress-regulated genes, some of them newly discovered by our algorithm and serve as putative transcription factor binding sites. Our new motif prediction algorithm comes complete with a stand-alone program. This algorithm may be used in motif discovery in the future in other species. The more than 1,200 Arabidopsis and 1,700 Orzya sativa genes found by our algorithm are good candidates for further experimental studies in abiotic stress.

Motifome comparison between modern human, Neanderthal and Denisovan

“…Assuming a random background nucleotide distribution, we would expect that motifs which occur in higher numbers than expected do so because they have experienced positive selective pressure due to the functionality they convey. Using the same reasoning, motifs which occur at the expected frequency or lower are considered biologically irrelevant [ 26 ]. The present work defines the motifomes of the three hominin subspecies—human, Neanderthal, and Denisovan—and predicts motifs which may take part in the regulation of gene sets that could cause phenotypic differences between the three subspecies.…”