Transcriptome-wide Cas13 guide RNA design for model organisms and viral RNA pathogens

• DOI: 10.1016/j.xgen.2021.100001
• Publication Date: 2021-09-03T07:27:22Z
• Authors: Xinyi Guo; Jahan A. Rahman; Hans-Hermann Wessels; Alejandro Méndez-...; Daniel Haro; Xinru Chen; Neville E. Sanjana
• Keywords: Guide RNA; Model Organism

The recent characterization of RNA-targeting CRISPR nucleases has enabled diverse transcriptome engineering and screening applications that depend crucially on prediction selection optimized guide RNAs (gRNAs). Previously, we developed a computational model to predict RfxCas13d gRNA activity for all human protein-coding genes. Here, extend this framework six organisms (human, mouse, zebrafish, fly, nematode, flowering plants) genes noncoding (ncRNAs) also four RNA virus families (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2], HIV-1, H1N1 influenza, Middle East [MERS]). We include experimental validation predictions by testing knockdown multiple ncRNAs (MALAT1, HOTAIRM1, Gas5, Pvt1) in mouse cells. freely available web-based platform (cas13design) with pre-scored gRNAs transcriptome-wide targeting several an interactive design tool optimal custom targets entered the user. This resource will facilitate CRISPR-Cas13 organisms, emerging viral threats health.