Generation and characterization of inducible KRAB-dCas9 iPSCs from primates for cross-species CRISPRi

Comparisons of molecular phenotypes across primates provide unique information to understand human biology and evolution, and single-cell RNA-seq CRISPR interference (CRISPRi) screens are a powerful approach to analyze them. Here, we generate and validate three human, three gorilla, and two cynomolgus iPS cell lines that carry a dox-inducible KRAB-dCas9 construct at the AAVS1 locus. We show that despite variable expression levels of KRAB-dCas9 among lines, comparable downregulation of target genes and comparable phenotypic effects are observed in a single-cell RNA-seq CRISPRi screen. Hence, we provide valuable resources for performing and further extending CRISPRi in human and non-human primates. [Display omitted] •Generation and validation of eight primate iPSC lines for dox-inducible CRISPRi•Comparable knockdowns despite variable KRAB-dCas9 levels among cells•Quantitative association between SOX2 knockdown and transcriptome profile•Single-cell CRISPRi screen for 24 transcription factors in human and cynomolgus Molecular biology