Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities

By Kendall R. Sanson, Ruth E. Hanna, Mudra Hegde, Katherine F. Donovan, Christine Strand, Meagan E. Sullender, Emma Vaimberg, A. Goodale, D. Root, F. Piccioni and 1 more. Nature Communications, 2018

858 citations recorded by the source corpus.

The creation of genome-wide libraries for CRISPR knockout (CRISPRko), interference (CRISPRi), and activation (CRISPRa) has enabled the systematic interrogation of gene function. Here, we show that our recently-described CRISPRko library (Brunello) is more effective than previously published libraries at distinguishing essential and non-essential genes, providing approximately the same perturbation-level performance improvement over GeCKO libraries as GeCKO provided over RNAi. Additionally, we present genome-wide libraries for CRISPRi (Dolcetto) and CRISPRa (Calabrese), and show in negative selection screens that Dolcetto, with fewer sgRNAs per gene, outperforms existing CRISPRi libraries and achieves comparable performance to CRISPRko in detecting essential genes. We also perform positive selection CRISPRa screens and demonstrate that Calabrese outperforms the SAM approach at identifying vemurafenib resistance genes. We further compare CRISPRa to genome-scale libraries of open reading frames (ORFs). Together, these libraries represent a suite of genome-wide tools to efficiently interrogate gene function with multiple modalities. Genome-wide libraries for CRISPR knockout, interference, and activation have allowed the systemic interrogation of gene function. Here, the authors evaluate the Brunello CRISPRko library and introduce Dolcetto and Calabrese for CRISPRi and CRISPRa, respectively.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/19a0bf6fe3f4f03c0898e0e4f7558f6347dc6482

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In Molecular Biology

1. Joy Y. Wang
2. Jennifer A. Doudna
3. Feng Zhang
4. Lei S. Qi
5. Rodolphe Barrangou

Citations in the corpus

• CRISPR technology: A decade of genome editing is only the beginning (2023, background): “The ease of designing and cloning guide RNA (gRNAs) has enabled the development of gRNA libraries up to genome-wide scales, allowing researchers to perturb every gene in the human genome (47, 48).”