CRISPRTE: A web-based tool to generate single guide RNA targets transposable elements

CRISPR/Cas systems have gained prominence as powerful tools for genome engineering. Recent investigations into the crucial role of transposable elements (TEs) have stimulated research interest in manipulating TEs to elucidate their functions. Nevertheless, designing single guide RNAs (sgRNAs) that are both specific and efficient for TE manipulation presents a formidable challenge, considering the repetitive nature and high copy numbers of TEs. Although various sgRNA design tools have been developed for gene editing, an optimized sgRNA designer explicitly for TE manipulation has yet to be established. To bridge this gap, we presented CRISPR-TE, a web-based application featuring an accessible graphical user interface, available at https://www.crisprte.cn. CRISPR-TE could identify all potential sgRNAs for TEs and offers a comprehensive solution for efficient TE targeting at both the single duplicate and subfamily levels. We also demonstrated that young TEs can be targeted with higher coverage at the subfamily level. Finally, we validated the overexpression of SVAD, a human-specific TE, using dCas9-VP64 activator incorporated with three sgRNAs designed by our tool. Collectively, our findings suggest that CRISPR-TE may serve as a versatile framework for designing sgRNAs aimed at TE targeting.