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Computational prediction of functional abortive RNA in E. coli

Marcus, Jeremy I., Hassoun, Soha, Nair, Nikhil U.
Genomics 2017 v.109 no.3-4 pp. 196-203
DNA, DNA-directed RNA polymerase, Escherichia coli, Gibbs free energy, RNA, bacteriophages, binding sites, genetic models, hybridization, prediction
Failure by RNA polymerase to break contacts with promoter DNA results in release of bound RNA and re-initiation of transcription. These abortive RNAs were assumed to be non-functional but have recently been shown to affect termination in bacteriophage T7. Little is known about the functional role of these RNA in other genetic models. Using a computational approach, we investigated whether abortive RNA could exert function in E. coli. Fragments generated from 3780 transcription units were used as query sequences within their respective transcription units to search for possible binding sites. Sites that fell within known regulatory features were then ranked based upon the free energy of hybridization to the abortive. We further hypothesize about mechanisms of regulatory action for a select number of likely matches. Future experimental validation of these putative abortive-mRNA pairs may confirm our findings and promote exploration of functional abortive RNAs (faRNAs) in natural and synthetic systems.