Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion

Pulido-Quetglas, Carlos; Aparicio i Prat, Estel, 1986-; Arnan Ros, Carme; Polidori, Taisia; Hermoso Pulido, Antonio; Palumbo, Emilio; Ponomarenko, Julia; Guigó Serra, Roderic; Johnson, Rory

Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion

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dc.contributor.author Pulido-Quetglas, Carlosca
dc.contributor.author Aparicio i Prat, Estel, 1986-ca
dc.contributor.author Arnan Ros, Carmeca
dc.contributor.author Polidori, Taisiaca
dc.contributor.author Hermoso Pulido, Antonioca
dc.contributor.author Palumbo, Emilioca
dc.contributor.author Ponomarenko, Juliaca
dc.contributor.author Guigó Serra, Rodericca
dc.contributor.author Johnson, Roryca
dc.date.accessioned 2017-03-10T11:13:56Z
dc.date.available 2017-03-10T11:13:56Z
dc.date.issued 2017
dc.description.abstract 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.
dc.description.sponsorship This work was financially supported by the following grants: CSD2007-00050 from the Spanish Ministry of Science (http://www.mineco.gob.es/portal/site/mineco/idi), grant SGR-1430 from the Catalan Government (http://web.gencat.cat/ca/temes/tecnologia/), grant ERC-2011-AdG-294653-RNA-MAPS from the European Community financial support under the FP7 (https://erc.europa.eu/) and grant R01MH101814 by the National Human Genome Research Institute of the National Institutes of Health (https://www.genome.gov/), to RG. Ramón y Cajal RYC-2011-08851 and Plan Nacional BIO2011-27220, both from the Spanish Ministry of Science (http://www.mineco.gob.es/portal/site/mineco/idi), to RJ. We also acknowledge support of the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-0208 (http://www.mineco.gob.es/portal/site/mineco/idi). We also acknowledge the support of the CERCA Programme / Generalitat de Catalunya (http://web.gencat.cat/ca/temes/tecnologia/). This research was partly supported by the NCCR RNA & Disease funded by the Swiss National Science Foundation (http://www.nccr-rna-and-disease.ch/).
dc.format.mimetype application/pdfca
dc.identifier.citation Pulido-Quetglas C, Aparicio-Prat E, Arnan C, Polidori T, Hermoso Pulido A, Palumbo E, Ponomarenko J, Guigo Serra R, Johnson R. Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion. Plos Computational Biology. 2017;13(3):e1005341. DOI: 10.1371/journal.pcbi.1005341
dc.identifier.doi http://dx.doi.org/10.1371/journal.pcbi.1005341
dc.identifier.issn 1553-734X
dc.identifier.uri http://hdl.handle.net/10230/28203
dc.language.iso eng
dc.publisher Public Library of Science (PLoS)ca
dc.relation.ispartof Plos Computational Biology. 2017;13(3):e1005341
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/CSD2007-00050
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/294653
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2011-27220
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SEV2012-0208
dc.rights © 2017 Pulido-Quetglas et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.rights.uri https://creativecommons.org/licenses/by/4.0/
dc.subject.keyword Genomic databases
dc.subject.keyword Invertebrate genomics
dc.subject.keyword Mammalian genomics
dc.subject.keyword Genomic library screening
dc.subject.keyword CRISPR
dc.subject.keyword Genomic libraries
dc.subject.keyword Sequence databases
dc.subject.keyword Genome analysis
dc.title Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletionca
dc.type info:eu-repo/semantics/article
dc.type.version info:eu-repo/semantics/publishedVersion

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