Comparative Single-Cell Profiling of CRISPR Knockout and Interference Defines Modality-Specific Strengths in Functional Genomics
- 1Cancer Research Horizons, Cambridge, United Kingdom
Abstract
Pooled CRISPR screens coupled with single-cell RNA sequencing enable high-throughput functional interrogation of gene regulatory networks, yet systematic comparisons of CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) remain limited. We established a single-cell CRISPRko workflow and benchmarked it against CRISPRi using 87 sgRNAs targeting 29 unfolded protein response genes. CRISPRko generated transcriptional phenotypes highly concordant with CRISPRi, and induced comparable pathway-level responses albeit with distinct on-target and off-target effects between modalities. While CRISPRi allows direct assessment of target gene repression, CRISPRko provides an effective complementary approach for complete loss-of-function studies, expanding the toolkit for single-cell functional genomics.
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BibTeX
@misc{gupta2026comparative,
title = {{Comparative Single-Cell Profiling of CRISPR Knockout and Interference Defines Modality-Specific Strengths in Functional Genomics}},
author = {N. Gupta and A. Sayer and M. Prater and C. Mastrokalou and K. Saeed and C. Company and C. Hart and R. Miragaia and A. Trehan and Functional Genomics Centre and U. McDermott and M. E. Strauss and D. Ross-Thriepland and D. Walter and A. Kalinka},
howpublished = {bioRxiv},
year = {2026},
month = aug,
doi = {10.64898/2026.08.26.747303},
url = {https://www.biorxiv.org/content/10.64898/2026.08.26.747303v2},
note = {CC BY},
}
RIS
TY - UNPB
TI - Comparative Single-Cell Profiling of CRISPR Knockout and Interference Defines Modality-Specific Strengths in Functional Genomics
AU - N. Gupta
AU - A. Sayer
AU - M. Prater
AU - C. Mastrokalou
AU - K. Saeed
AU - C. Company
AU - C. Hart
AU - R. Miragaia
AU - A. Trehan
AU - Functional Genomics Centre
AU - U. McDermott
AU - M. E. Strauss
AU - D. Ross-Thriepland
AU - D. Walter
AU - A. Kalinka
PY - 2026
DA - 2026/08/26
PB - bioRxiv
DO - 10.64898/2026.08.26.747303
UR - https://www.biorxiv.org/content/10.64898/2026.08.26.747303v2
AB - Pooled CRISPR screens coupled with single-cell RNA sequencing enable high-throughput functional interrogation of gene regulatory networks, yet systematic comparisons of CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) remain limited. We established a single-cell CRISPRko workflow and benchmarked it against CRISPRi using 87 sgRNAs targeting 29 unfolded protein response genes. CRISPRko generated transcriptional phenotypes highly concordant with CRISPRi, and induced comparable pathway-level responses albeit with distinct on-target and off-target effects between modalities. While CRISPRi allows direct assessment of target gene repression, CRISPRko provides an effective complementary approach for complete loss-of-function studies, expanding the toolkit for single-cell functional genomics.
ER -