Detection of gene cis-regulatory element perturbations in single-cell transcriptomes

We introduce poly-adenine CRISPR gRNA-based single cell RNA-sequencing (pAC-Seq), a method enabling simultaneous observation of mutagenic guide RNAs (gRNAs) and their transcriptional consequences in single cell RNA sequencing (scRNA-seq) data. We have made gRNAs robustly visible in scRNA-seq data while maintaining full activity by modifying them with a hardcoded poly-adenine tract. We apply pAC-Seq to study the transcriptomic effects of non-coding CRISPR/Cas9-induced mutations in a pooled screening format. pAC-Seq is a simple, robust, and broadly applicable method of measuring the global effects of genomic mutation. Overall design: Pooled screening of transcriptomic effects of CRISPR/Cas9-induced non-coding mutations