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

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Eukaryotic genomes feature diverse sequence motifs like transcription factor binding sites and repetitive elements.
• CRISPR/Cas9 technology offers powerful capabilities for identifying and investigating these crucial genomic motifs.

Purpose of the Study:

• To introduce transCRISPR, the first online platform for searching genomic sequence motifs and designing optimal single-guide RNAs (sgRNAs) for CRISPR/Cas9 applications.
• To enable users to obtain sgRNAs for specific motifs across numerous genomes using either Cas9 or dCas9 systems.

Main Methods:

• Development of an online tool, transCRISPR, for motif searching within user-defined genomic regions.
• Design of sgRNAs targeting identified motifs for both Cas9 and dCas9 systems, supporting large-scale analyses across 30 genomes.
• Implementation of user-friendly tables and visualizations for motif and sgRNA feature summarization.

Main Results:

• Experimental validation confirmed that transCRISPR-designed sgRNAs efficiently disrupt MYC binding sites.
• Targeted motif disruption led to observable effects on the expression of MYC-regulated genes.
• The tool facilitates the analysis of motif localization, quality scores, and proximity to transcription start sites.

Conclusions:

• transCRISPR is a valuable resource for researchers studying genomic motifs and gene regulation using CRISPR/Cas9.
• The platform simplifies the process of designing and validating sgRNAs for motif-targeted experiments.
• Successful experimental validation underscores the utility of transCRISPR in functional genomics research.