title: Impact of RNA-guided technologies for target identification and deconvolution.
abstract: For well over a decade, RNA interference (RNAi) has provided a powerful tool for investigators to query specific gene targets in an easily modulated loss-of-function setting, both in vitro and in vivo. Hundreds of publications have demonstrated the utility of RNAi in arrayed and pooled-based formats, in a wide variety of cell-based systems, including clonal, stem, transformed, and primary cells. Over the years, there have been significant improvements in the design of target-specific small-interfering RNA (siRNA) and short-hairpin RNA (shRNA), expression vectors, methods for mitigating off-target effects, and accurately interpreting screening results. Recent developments in RNAi technology include the Sensor assay, high-efficiency miR-E shRNAs, improved shRNA virus production with Pasha (DRGC8) knockdown, and assessment of RNAi off-target effects by using the C9-11 method. An exciting addition to the arsenal of RNA-mediated gene modulation is the clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas) system for genomic editing, allowing for gene functional knockout rather than knockdown.
authors.affiliation: RNAi Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
authors.forename: Myles
authors.initials: M
authors.lastname: Fennell
authors.affiliation: RNAi Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
authors.forename: Qing
authors.initials: Q
authors.lastname: Xiang
authors.affiliation: RNAi Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
authors.forename: Alexia
authors.initials: A
authors.lastname: Hwang
authors.affiliation: Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
authors.forename: Chong
authors.initials: C
authors.lastname: Chen
authors.affiliation: Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
authors.forename: Chun-Hao
authors.initials: CH
authors.lastname: Huang
authors.affiliation: Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
authors.forename: Chi-Chao
authors.initials: CC
authors.lastname: Chen
authors.affiliation: Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
authors.forename: Raphael
authors.initials: R
authors.lastname: Pelossof
authors.affiliation: RNAi Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA garippar@mskcc.org.
authors.forename: Ralph J
authors.initials: RJ
authors.lastname: Garippa
mesh_terms: D000818:Animals; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D029721:Drosophila Proteins / Q000235:genetics; D023281:Genomics / Q000379:methods*; D057166:High-Throughput Screening Assays / Q000379:methods*; D006801:Humans; D008322:Mammals / Q000235:genetics; D034622:RNA Interference; D000094704:RNA, Guide, CRISPR-Cas Systems; D034741:RNA, Small Interfering; D016601:RNA-Binding Proteins / Q000235:genetics
chemical_list: D029721:Drosophila Proteins; C534610:Pasha protein, Drosophila; D000094704:RNA, Guide, CRISPR-Cas Systems; D034741:RNA, Small Interfering; D016601:RNA-Binding Proteins
keywords: CRISPR/Cas9; HCS; OTE; RNAi; deconvolution; functional genomics; pooled shRNA; review; screening; viral vectors