Generalizable sgRNA design for improved CRISPR/Cas9 editing efficiency.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 05 2020
01 05 2020
Historique:
received:
23
07
2019
revised:
14
01
2020
accepted:
16
01
2020
pubmed:
24
1
2020
medline:
10
10
2020
entrez:
24
1
2020
Statut:
ppublish
Résumé
The development of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) technology has provided a simple yet powerful system for targeted genome editing. In recent years, this system has been widely used for various gene editing applications. The CRISPR editing efficacy is mainly dependent on the single guide RNA (sgRNA), which guides Cas9 for genome cleavage. While there have been multiple attempts at improving sgRNA design, there is a pressing need for greater sgRNA potency and generalizability across various experimental conditions. We employed a unique plasmid library expressed in human cells to quantify the potency of thousands of CRISPR/Cas9 sgRNAs. Differential sequence and structural features among the most and least potent sgRNAs were then used to train a machine learning algorithm for assay design. Comparative analysis indicates that our new algorithm outperforms existing CRISPR/Cas9 sgRNA design tools. The new sgRNA design tool is freely accessible as a web application, http://crispr.wustl.edu. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 31971562
pii: 5714741
doi: 10.1093/bioinformatics/btaa041
pmc: PMC7203743
doi:
Substances chimiques
RNA, Guide
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
2684-2689Subventions
Organisme : NIDCR NIH HHS
ID : R01 DE026471
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM089784
Pays : United States
Organisme : NIGMS NIH HHS
ID : R41 GM126682
Pays : United States
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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