Identifying HIV-1 host cell factors by genome-scale RNAi screening.
Advances in the application of RNA interference (RNAi) have facilitated the establishment of systematic cell-based loss-of-function screening platforms. Widespread implementation of this technology has enabled genome-wide genetic analysis of a diverse array of cellular phenotypes, including the identification of host cell factors involved in viral replication. Four recent studies employed whole-genome RNAi technologies to elucidate cellular genes important for the replication of HIV-1. While these four genome-scale screens shared a common objective, they differ in their scope and experimental design. In this review we explore alternative strategies for developing RNAi screens, and discuss potential pitfalls of the technology. Important technical considerations include the choice of silencing reagents, experimental systems, assay readout and analysis methods. We focus on experimental and computational parameters that can impact the outcome of high-throughput genetic screens, and provide guidelines for the development of reliable cell-based RNAi screens.
Pache
Lars
L
Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
König
Renate
R
Chanda
Sumit K
SK
D003627:Data Interpretation, Statistical; D055106:Genome-Wide Association Study; D057809:HEK293 Cells; D015658:HIV Infections / Q000378:metabolism* / Q000821:virology; D015497:HIV-1 / Q000235:genetics / Q000502:physiology*; D057166:High-Throughput Screening Assays; D058605:Host-Derived Cellular Factors / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000235:genetics; D014162:Transfection / Q000379:methods; D014779:Virus Replication
D058605:Host-Derived Cellular Factors; D034741:RNA, Small Interfering