TransCRISPR-sgRNA design tool for CRISPR/Cas9 experiments targeting specific sequence motifs

Tomasz Woźniak; Weronika Sura; Marta Kazimierska; Marta Elżbieta Kasprzyk; Marta Podralska; Agnieszka Dzikiewicz-Krawczyk

doi:10.1093/nar/gkad355

TransCRISPR-sgRNA design tool for CRISPR/Cas9 experiments targeting specific sequence motifs

Nucleic Acids Res. 2023 Jul 5;51(W1):W577-W586. doi: 10.1093/nar/gkad355.

Authors

Tomasz Woźniak¹, Weronika Sura¹, Marta Kazimierska¹, Marta Elżbieta Kasprzyk¹, Marta Podralska¹, Agnieszka Dzikiewicz-Krawczyk¹

Affiliation

¹ Institute of Human Genetics, Polish Academy of Sciences, Poznań, Poland.

Abstract

Eukaryotic genomes contain several types of recurrent sequence motifs, e.g. transcription factor motifs, miRNA binding sites, repetitive elements. CRISPR/Cas9 can facilitate identification and study of crucial motifs. We present transCRISPR, the first online tool dedicated to search for sequence motifs in the user-provided genomic regions and design optimal sgRNAs targeting them. Users can obtain sgRNAs for chosen motifs, for up to tens of thousands of target regions in 30 genomes, either for the Cas9 or dCas9 system. TransCRISPR provides user-friendly tables and visualizations, summarizing features of identified motifs and designed sgRNAs such as genomic localization, quality scores, closest transcription start sites and others. Experimental validation of sgRNAs for MYC binding sites designed with transCRISPR confirmed efficient disruption of the targeted motifs and effect on expression of MYC-regulated genes. TransCRISPR is available from https://transcrispr.igcz.poznan.pl/transcrispr/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Binding Sites / genetics
CRISPR-Cas Systems* / genetics
Genome
Genomics* / instrumentation
Genomics* / methods
Internet
Molecular Conformation
RNA, Guide, CRISPR-Cas Systems

Substances

RNA, Guide, CRISPR-Cas Systems