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

Nat Biotechnol. 2024 Aug;42(8):1218-1223. doi: 10.1038/s41587-023-01948-9. Epub 2023 Sep 25.

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.

MeSH terms

  • CRISPR-Cas Systems / genetics
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics
  • Gene Expression Profiling / methods
  • Gene Expression Regulation
  • Humans
  • Kinetics
  • RNA / genetics
  • RNA / metabolism
  • RNA, Guide, CRISPR-Cas Systems / genetics
  • Single-Cell Analysis* / methods
  • Transcriptome* / genetics

Substances

  • RNA, Guide, CRISPR-Cas Systems
  • RNA