TransCRISPR - sgRNA design tool for CRISPR/Cas9 experiments targeting transcription factor motifs

ABSTRACT Transcription factors (TFs) regulate gene expression via binding to specific sequence motifs in promoters or enhancers. They are involved in various biological processes and their aberrant action may lead to multiple pathological states. To better understand the function of a given TF, it is necessary to identify its crucial binding sites and target genes, which is not a trivial task. CRISPR/Cas9 has been recently successfully applied in the study of TFs. Here, we present an online tool, transCRISPR, created to search for TF binding motifs in the user-provided query and design optimal sgRNAs targeting them. Users can obtain sgRNAs for chosen TFs motifs, for up to tens of thousands of target regions in the human or mouse genome, 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. TransCRISPR is available at https://transcrispr.igcz.poznan.pl/transcrispr/.