2. Academic Validation
  3. Decoding post-transcriptional regulatory networks by RNA-linked CRISPR screening in human cells

Decoding post-transcriptional regulatory networks by RNA-linked CRISPR screening in human cells

  • Nat Methods. 2025 Jun;22(6):1237-1246. doi: 10.1038/s41592-025-02702-6.
Patrick J Nugent 1 2,  Heungwon Park 1,  Cynthia L Wladyka 3,  James N Yelland 1,  Sayantani Sinha 4,  Katharine Y Chen 1 2,  Christine Bynum 1 5,  Grace Quarterman 1 5,  Stanley C Lee 4,  Andrew C Hsieh 3 6,  Arvind Rasi Subramaniam 7 8
Affiliations

Affiliations

  • 1 Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
  • 2 Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA.
  • 3 Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
  • 4 Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
  • 5 Department of Biology, Spelman College, Atlanta, GA, USA.
  • 6 Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA, USA.
  • 7 Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA. rasi@fredhutch.org.
  • 8 Department of Biochemistry and Department of Genome Sciences, University of Washington, Seattle, WA, USA. rasi@fredhutch.org.
PMID: 40442371 DOI: 10.1038/s41592-025-02702-6
Abstract

RNAs undergo a complex choreography of metabolic processes that are regulated by thousands of RNA-associated proteins. Here we introduce ReLiC, a scalable and high-throughput RNA-linked CRISPR approach to measure the responses of diverse RNA metabolic processes to knockout of 2,092 human genes encoding all known RNA-associated proteins. ReLiC relies on an iterative strategy to integrate genes encoding Cas9, single-guide RNAs (sgRNAs) and barcoded reporter libraries into a defined genomic locus. Combining ReLiC with polysome fractionation reveals key regulators of ribosome occupancy, uncovering links between translation and proteostasis. Isoform-specific ReLiC captures differential regulation of intron retention and exon skipping by SF3B complex subunits. Chemogenomic ReLiC screens decipher translational regulators upstream of messenger RNA (mRNA) decay and identify a role for the ribosome collision sensor GCN1 during treatment with the anti-leukemic drug homoharringtonine. Our work demonstrates ReLiC as a powerful framework for discovering and dissecting post-transcriptional regulatory networks in human cells.

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