A high-throughput, streamlined cloning protocol to generate guide RNAs for CRISPR activation.

Abstract

Caenorhabditis elegans is a powerful model for studying gene function and disease pathogenesis. While RNA interference effectively suppresses gene expression, CRISPR activation (CRISPRa) provides a robust tool for upregulating endogenous gene expression in C. elegans . Compared with traditional injection-based methods, feeding-based CRISPRa, similar to RNA interference, is easy, cost-effective and efficient. However, the traditional cloning workflows remain a bottleneck for high-throughput gene screening. Here, we present a pooled, one-step dual gRNA cloning protocol that enables rapid and efficient construction of gRNA expression vectors for CRISPRa. In a test case, by designing 55-mer and 54-mer primers, each containing one gRNA, we amplified and pooled 126 gRNA inserts in a single reaction pipeline. The 126 gRNA clones were completed in three pooled rounds, achieving 42%-56% coverage for each round, with remaining clones processed individually. This protocol dramatically reduces time, labor, and reagent consumption, while increasing scalability and maintaining reproducibility. It is particularly well suited for high-throughput screening of gene libraries or pathways and supports downstream applications such as phenotypic screening and lifespan analysis. This work advances CRISPRa-based functional genomics in C. elegans by providing a practical tool for large-scale gene activation studies.