Maximizing CRISPRi efficacy and accessibility with dual-sgRNA libraries and optimal effectors
- University of California, San Francisco, United States
- Whitehead Institute for Biomedical Research, United States
- Harvard Medical School, United States
- National Institutes of Health, United States
- National Institute of Neurological Disorders and Stroke, United States
Abstract
CRISPR interference (CRISPRi) enables programmable, reversible, and titratable repression of gene expression (knockdown) in mammalian cells. Initial CRISPRi-mediated genetic screens have showcased the potential to address basic questions in cell biology, genetics, and biotechnology, but wider deployment of CRISPRi screening has been constrained by the large size of single guide RNA (sgRNA) libraries and challenges in generating cell models with consistent CRISPRi-mediated knockdown. Here, we present next-generation CRISPRi sgRNA libraries and effector expression constructs that enable strong and consistent knockdown across mammalian cell models. First, we combine empirical sgRNA selection with a dual-sgRNA library design to generate an ultra-compact (1-3 elements per gene), highly active CRISPRi sgRNA library. Next, we compare CRISPRi effectors to show that the recently published Zim3-dCas9 provides an excellent balance between strong on-target knockdown and minimal nonspecific effects on cell growth or the transcriptome. Finally, we engineer a suite of cell lines with stable expression of Zim3-dCas9 and robust on-target knockdown. Our results and publicly available reagents establish best practices for CRISPRi genetic screening.
Data availability
Sequencing data are available on NCBI GEO under accession number GSE205310 (Perturb-seq) and GSE205147 (bulk RNA-seq). sgRNA counts from CRISPRi screens are included as supplemental tables. All data generated or analyzed during this study are included in the manuscript and supporting files.
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Comparison of dual sgRNA library versus Dolcetto by Perturb-seqNCBI Gene Expression Omnibus, GSE205310.
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Comparison of non-specific transcriptional effects of CRISPRi effector proteins by RNA-seqNCBI Gene Expression Omnibus, GSE205147.
Article and author information
Author details
Michael Emmerson Ward
Funding
National Institutes of Health (R00GM130964)
- Marco Jost
National Institutes of Health (T32AI132120)
- Baylee J Russell
Human Frontier Science Program (2019L/LT000858)
- Alina Guna
Chan Zuckerberg Initiative (Ben Barres Early Career Acceleration Award)
- Martin Kampmann
Howard Hughes Medical Institute (Investigator)
- Jonathan S Weissman
National Institutes of Health (RM1HG009490-01)
- Jonathan S Weissman
Springer Nature Global Grant for Gut Health (1772808)
- Marco Jost
Charles H. Hood Foundation (Child Health Research Award)
- Marco Jost
Defense Advanced Research Projects Agency (HR0011-19-2-0007)
- Jonathan S Weissman
Ludwig Center for Molecular Oncology (NA)
- Jonathan S Weissman
Chan Zuckerberg Initiative (NA)
- Jonathan S Weissman
National Institutes of Health (F31NS115380)
- Joseph M Replogle
National Institutes of Health (F30AG066418)
- Kun Leng
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Jan E Carette, Stanford University School of Medicine, United States
Version history
- Preprint posted: July 13, 2022 (view preprint)
- Received: July 13, 2022
- Accepted: December 23, 2022
- Accepted Manuscript published: December 28, 2022 (version 1)
- Version of Record published: January 9, 2023 (version 2)
Copyright
This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.
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Maximizing CRISPRi efficacy and accessibility with dual-sgRNA libraries and optimal effectors
eLife 11:e81856.
https://doi.org/10.7554/eLife.81856
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