Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq.
Nat Methods
; 20(1): 86-94, 2023 01.
Article
em En
| MEDLINE
| ID: mdl-36550277
ABSTRACT
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.
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1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
RNA
/
Cromatina
Idioma:
En
Revista:
Nat Methods
Ano de publicação:
2023
Tipo de documento:
Article