PT  - JOURNAL ARTICLE
AU  - Xinyi Guo
AU  - Hans-Hermann Wessels
AU  - Alejandro Méndez-Mancilla
AU  - Daniel Haro
AU  - Neville E. Sanjana
TI  - Transcriptome-wide Cas13 guide RNA design for model organisms and viral RNA pathogens
AID  - 10.1101/2020.08.20.259762
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.08.20.259762
4099  - http://biorxiv.org/content/early/2020/08/21/2020.08.20.259762.short
4100  - http://biorxiv.org/content/early/2020/08/21/2020.08.20.259762.full
AB  - CRISPR-Cas13 mediates robust transcript knockdown in human cells through direct RNA targeting. Compared to DNA-targeting CRISPR enzymes like Cas9, RNA targeting by Cas13 is transcript- and strand-specific: It can distinguish and specifically knock-down processed transcripts, alternatively spliced isoforms and overlapping genes, all of which frequently serve different functions. Previously, we identified optimal design rules for RfxCas13d guide RNAs (gRNAs), and developed a computational model to predict gRNA efficacy for all human protein-coding genes. However, there is a growing interest to target other types of transcripts, such as noncoding RNAs (ncRNAs) or viral RNAs, and to target transcripts in other commonly-used organisms. Here, we predicted relative Cas13-driven knock-down for gRNAs targeting messenger RNAs and ncRNAs in six model organisms (human, mouse, zebrafish, fly, nematode and flowering plants) and four abundant RNA virus families (SARS-CoV-2, HIV-1, H1N1 influenza and MERS). To allow for more flexible gRNA efficacy prediction, we also developed a web-based application to predict optimal gRNAs for any RNA target entered by the user. Given the lack of Cas13 guide design tools, we anticipate this resource will facilitate CRISPR-Cas13 RNA targeting in common model organisms, emerging viral threats to human health, and novel RNA targets.Competing Interest StatementThe New York Genome Center and New York University have applied for patents relating to the work in this article. N.E.S. is an adviser to Vertex.