Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq

Hans Hermann Wessels, Alejandro Méndez-Mancilla, Yuhan Hao, Efthymia Papalexi, William M. Mauck, Lu Lu, John A. Morris, Eleni P. Mimitou, Peter Smibert, Neville E. Sanjana, Rahul Satija

Research output: Contribution to journalArticlepeer-review


Pooled CRISPR screens coupled with single-cell RNA-sequencing have enabled systematic interrogation of gene function and regulatory networks. Here, we introduce Cas13 RNA Perturb-seq (CaRPool-seq), which leverages the RNA-targeting CRISPR–Cas13d system and enables efficient combinatorial perturbations alongside multimodal single-cell profiling. CaRPool-seq encodes multiple perturbations on a cleavable CRISPR array that is associated with a detectable barcode sequence, allowing for the simultaneous targeting of multiple genes. We compared CaRPool-seq to existing Cas9-based methods, highlighting its unique strength to efficiently profile combinatorially perturbed cells. Finally, we apply CaRPool-seq to perform multiplexed combinatorial perturbations of myeloid differentiation regulators in an acute myeloid leukemia (AML) model system and identify extensive interactions between different chromatin regulators that can enhance or suppress AML differentiation phenotypes.

Original languageEnglish (US)
Pages (from-to)86-94
Number of pages9
JournalNature methods
Issue number1
StatePublished - Jan 2023

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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