Detection of gene cis-regulatory element perturbations in single-cell transcriptomes
Author(s)Yeo, Grace Hui Ting; Juez, Oscar; Chen, Qing; Banerjee, Budhaditya; Chu, Lendy; Shen, Max Walt; Sabry, May; Logister, Ive; Sherwood, Richard I.; Gifford, David K; ... Show more Show less
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We introduce poly-adenine CRISPR gRNA-based single-cell RNA-sequencing (pAC-Seq), a method that enables the direct observation of guide RNAs (gRNAs) in scRNA-seq. We use pAC-Seq to assess the phenotypic consequences of CRISPR/Cas9 based alterations of gene cis-regulatory regions. We show that pAC-Seq is able to detect cis-regulatory-induced alteration of target gene expression even when biallelic loss of target gene expression occurs in only ~5% of cells. This low rate of biallelic loss significantly increases the number of cells required to detect the consequences of changes to the regulatory genome, but can be ameliorated by transcript-targeted sequencing. Based on our experimental results we model the power to detect regulatory genome induced transcriptomic effects based on the rate of mono/biallelic loss, baseline gene expression, and the number of cells per target gRNA.
DepartmentMassachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory; Massachusetts Institute of Technology. Computational and Systems Biology Program
PLoS Computational Biology
Public Library of Science (PLoS)
Yeo, Grace Hui Ting et al. "Detection of gene cis-regulatory element perturbations in single-cell transcriptomes." PLoS Computational Biology 17, 3 (March 2021): e1008789. © 2021 Yeo et al.
Final published version