Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens

Zihan Xu; Andras Sziraki; Jasper Lee; Wei Zhou; Junyue Cao

doi:10.1038/s41587-023-01948-9

Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens

Nat Biotechnol. 2023 Sep 25:10.1038/s41587-023-01948-9. doi: 10.1038/s41587-023-01948-9. Online ahead of print.

Authors

Zihan Xu^{1

2}, Andras Sziraki^{1

2}, Jasper Lee¹, Wei Zhou^#¹, Junyue Cao^#³

Affiliations

¹ Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
² The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA.
³ Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA. jcao@rockefeller.edu.

^# Contributed equally.

PMID: 37749268
PMCID: PMC10961254 (available on 2025-03-25)
DOI: 10.1038/s41587-023-01948-9

Abstract

We present a combinatorial indexing method, PerturbSci-Kinetics, for capturing whole transcriptomes, nascent transcriptomes and single guide RNA (sgRNA) identities across hundreds of genetic perturbations at the single-cell level. Profiling a pooled CRISPR screen targeting various biological processes, we show the gene expression regulation during RNA synthesis, processing and degradation, miRNA biogenesis and mitochondrial mRNA processing, systematically decoding the genome-wide regulatory network that underlies RNA temporal dynamics at scale.

Abstract

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