transCRISPR

transCRISPR designs single-guide RNAs to target sequence motifs in eukaryotic genomes for CRISPR/Cas9 and dCas9 experiments investigating transcription factor binding sites, miRNA binding sites, and repetitive elements.

Key Features:

• Motif Identification: Searches for specific sequence motifs within user-provided genomic regions across up to 30 genomes.
• Supported Motif Types: Targets transcription factor binding sites, miRNA binding sites, and repetitive elements.
• sgRNA Design: Designs single-guide RNAs for both Cas9 and dCas9 systems that target identified motifs.
• High-throughput Design: Generates sgRNAs for tens of thousands of target regions to support large-scale studies.
• Annotation and Scoring: Reports genomic localization, quality scores, and proximity to transcription start sites for designed sgRNAs.

Scientific Applications:

• Motif-targeted CRISPR experiments: Enables precise targeting and disruption of sequence motifs to study their regulatory and functional roles.
• Transcription factor site validation: Facilitates disruption of TF binding sites, exemplified by sgRNAs used to disrupt MYC binding sites and assess effects on MYC-regulated gene expression.

Methodology:

Users input genomic regions to identify sequence motifs, and the tool applies algorithms to design sgRNAs targeting those motifs with attention to specificity and efficiency.