title: A computational algorithm to predict shRNA potency.
abstract: The strength of conclusions drawn from RNAi-based studies is heavily influenced by the quality of tools used to elicit knockdown. Prior studies have developed algorithms to design siRNAs. However, to date, no established method has emerged to identify effective shRNAs, which have lower intracellular abundance than transfected siRNAs and undergo additional processing steps. We recently developed a multiplexed assay for identifying potent shRNAs and used this method to generate ∼250,000 shRNA efficacy data points. Using these data, we developed shERWOOD, an algorithm capable of predicting, for any shRNA, the likelihood that it will elicit potent target knockdown. Combined with additional shRNA design strategies, shERWOOD allows the ab initio identification of potent shRNAs that specifically target the majority of each gene's multiple transcripts. We validated the performance of our shRNA designs using several orthogonal strategies and constructed genome-wide collections of shRNAs for humans and mice based on our approach.
authors.affiliation: Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
authors.forename: Simon R V
authors.initials: SRV
authors.lastname: Knott
authors.affiliation: Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
authors.forename: Ashley
authors.initials: A
authors.lastname: Maceli
authors.affiliation: Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Erard
authors.affiliation: Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Chang
authors.affiliation: Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
authors.forename: Krista
authors.initials: K
authors.lastname: Marran
authors.affiliation: Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
authors.forename: Xin
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
authors.forename: Assaf
authors.initials: A
authors.lastname: Gordon
authors.affiliation: Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
authors.forename: Osama El
authors.initials: OE
authors.lastname: Demerdash
authors.affiliation: Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
authors.forename: Elvin
authors.initials: E
authors.lastname: Wagenblast
authors.affiliation: Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
authors.forename: Sun
authors.initials: S
authors.lastname: Kim
authors.affiliation: Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
authors.forename: Christof
authors.initials: C
authors.lastname: Fellmann
authors.affiliation: Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.|Cancer Research UK Cambridge Insitute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB20RE, UK.
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Hannon
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D045744:Cell Line, Tumor; D003198:Computer Simulation; D016384:Consensus Sequence; D055785:Gene Knockdown Techniques; D006801:Humans; D035683:MicroRNAs / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D034741:RNA, Small Interfering / Q000235:genetics*; D012984:Software
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering