Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion.

Pulido-Quetglas, Carlos; Aparicio-Prat, Estel; Arnan, Carme; Polidori, Taisia; Hermoso, Toni; Palumbo, Emilio; Ponomarenko, Julia; Guigo, Roderic; Johnson, Rory Baldwin (2017). Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion. PLoS computational biology, 13(3), e1005341. Public Library of Science 10.1371/journal.pcbi.1005341

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CRISPR-Cas9 technology can be used to engineer precise genomic deletions with pairs of single guide RNAs (sgRNAs). This approach has been widely adopted for diverse applications, from disease modelling of individual loci, to parallelized loss-of-function screens of thousands of regulatory elements. However, no solution has been presented for the unique bioinformatic design requirements of CRISPR deletion. We here present CRISPETa, a pipeline for flexible and scalable paired sgRNA design based on an empirical scoring model. Multiple sgRNA pairs are returned for each target, and any number of targets can be analyzed in parallel, making CRISPETa equally useful for focussed or high-throughput studies. Fast run-times are achieved using a pre-computed off-target database. sgRNA pair designs are output in a convenient format for visualisation and oligonucleotide ordering. We present pre-designed, high-coverage library designs for entire classes of protein-coding and non-coding elements in human, mouse, zebrafish, Drosophila melanogaster and Caenorhabditis elegans. In human cells, we reproducibly observe deletion efficiencies of ≥50% for CRISPETa designs targeting an enhancer and exonic fragment of the MALAT1 oncogene. In the latter case, deletion results in production of desired, truncated RNA. CRISPETa will be useful for researchers seeking to harness CRISPR for targeted genomic deletion, in a variety of model organisms, from single-target to high-throughput scales.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Department of Haematology, Oncology, Infectious Diseases, Laboratory Medicine and Hospital Pharmacy (DOLS) > Clinic of Medical Oncology
04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR)

UniBE Contributor:

Johnson, Rory Baldwin

Subjects:

600 Technology > 610 Medicine & health

ISSN:

1553-734X

Publisher:

Public Library of Science

Language:

English

Submitter:

Nicole Corminboeuf

Date Deposited:

23 May 2018 12:54

Last Modified:

23 Oct 2019 00:50

Publisher DOI:

10.1371/journal.pcbi.1005341

PubMed ID:

28253259

BORIS DOI:

10.7892/boris.116569

URI:

https://boris.unibe.ch/id/eprint/116569

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