title: Computational prediction of functional abortive RNA in E. coli.
abstract: 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.
authors.affiliation: Department of Computer Science, Tufts University, Medford, MA 02155, United States.
authors.forename: Jeremy I
authors.initials: JI
authors.lastname: Marcus
authors.affiliation: Department of Computer Science, Tufts University, Medford, MA 02155, United States; Department of Chemical and Biological Engineering, Tufts University, Medford, MA 02155, United States.
authors.forename: Soha
authors.initials: S
authors.lastname: Hassoun
authors.affiliation: Department of Chemical and Biological Engineering, Tufts University, Medford, MA 02155, United States. Electronic address: nikhil.nair@tufts.edu.
authors.forename: Nikhil U
authors.initials: NU
authors.lastname: Nair
mesh_terms: D019295:Computational Biology; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D012329:RNA, Bacterial / Q000378:metabolism; D022661:RNA, Untranslated / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D012329:RNA, Bacterial; D022661:RNA, Untranslated; D012321:DNA-Directed RNA Polymerases
keywords: Abortives; E. coli; Noncoding; RNA; Regulation; Transcription