title: From experimental setup to bioinformatics: an RNAi screening platform to identify host factors involved in HIV-1 replication.
abstract: RNA interference (RNAi) has emerged as a powerful technique for studying loss-of-function phenotypes by specific down-regulation of gene expression, allowing the investigation of virus-host interactions by large-scale high-throughput RNAi screens. Here we present a robust and sensitive small interfering RNA screening platform consisting of an experimental setup, single-cell image and statistical analysis as well as bioinformatics. The workflow has been established to elucidate host gene functions exploited by viruses, monitoring both suppression and enhancement of viral replication simultaneously by fluorescence microscopy. The platform comprises a two-stage procedure in which potential host factors are first identified in a primary screen and afterwards re-tested in a validation screen to confirm true positive hits. Subsequent bioinformatics allows the identification of cellular genes participating in metabolic pathways and cellular networks utilised by viruses for efficient infection. Our workflow has been used to investigate host factor usage by the human immunodeficiency virus-1 (HIV-1), but can also be adapted to other viruses. Importantly, we expect that the description of the platform will guide further screening approaches for virus-host interactions. The ViroQuant-CellNetworks RNAi Screening core facility is an integral part of the recently founded BioQuant centre for systems biology at the University of Heidelberg and will provide service to external users in the near future.
authors.affiliation: Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany.
authors.forename: Kathleen
authors.initials: K
authors.lastname: Börner
authors.forename: Johannes
authors.initials: J
authors.lastname: Hermle
authors.forename: Christoph
authors.initials: C
authors.lastname: Sommer
authors.forename: Nigel P
authors.initials: NP
authors.lastname: Brown
authors.forename: Bettina
authors.initials: B
authors.lastname: Knapp
authors.forename: Bärbel
authors.initials: B
authors.lastname: Glass
authors.forename: Julian
authors.initials: J
authors.lastname: Kunkel
authors.forename: Gloria
authors.initials: G
authors.lastname: Torralba
authors.forename: Jürgen
authors.initials: J
authors.lastname: Reymann
authors.forename: Nina
authors.initials: N
authors.lastname: Beil
authors.forename: Jürgen
authors.initials: J
authors.lastname: Beneke
authors.forename: Rainer
authors.initials: R
authors.lastname: Pepperkok
authors.forename: Reinhard
authors.initials: R
authors.lastname: Schneider
authors.forename: Thomas
authors.initials: T
authors.lastname: Ludwig
authors.forename: Michael
authors.initials: M
authors.lastname: Hausmann
authors.forename: Fred
authors.initials: F
authors.lastname: Hamprecht
authors.forename: Holger
authors.initials: H
authors.lastname: Erfle
authors.forename: Lars
authors.initials: L
authors.lastname: Kaderali
authors.forename: Hans-Georg
authors.initials: HG
authors.lastname: Kräusslich
authors.forename: Maik J
authors.initials: MJ
authors.lastname: Lehmann
mesh_terms: D019295:Computational Biology / Q000379:methods*; D015497:HIV-1 / Q000235:genetics*; D006367:HeLa Cells; D006801:Humans; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D014779:Virus Replication / Q000235:genetics*
chemical_list: D012333:RNA, Messenger