Open AccessDetection of gene cis-regulatory element perturbations in single-cell transcriptomes
Author(s) -
Grace Hui Ting Yeo,
Oscar Juez,
Qing Chen,
Budhaditya Banerjee,
Lendy Chu,
Max Shen,
May Sabry,
Ive Logister,
Richard I. Sherwood,
David K. Gifford
Publication year - 2021
Publication title -
plos computational biology/plos computational biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.628
H-Index - 182
eISSN - 1553-7358
pISSN - 1553-734X
DOI - 10.1371/journal.pcbi.1008789
Subject(s) - crispr , guide rna , transcriptome , biology , gene , cas9 , gene expression , regulation of gene expression , computational biology , genome , rna , genetics , regulatory sequence , gene expression profiling , phenotype
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.