Yeo, GHT;
Juez, O;
Chen, Q;
Banerjee, B;
Chu, L;
Shen, MW;
Sabry, M;
... Gifford, DK; + view all
(2021)
Detection of gene cis-regulatory element perturbations in single-cell transcriptomes.
PLoS Computational Biology
, 17
(3)
, Article e1008789. 10.1371/journal.pcbi.1008789.
(In press).
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Abstract
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.
| Type: | Article |
|---|---|
| Title: | Detection of gene cis-regulatory element perturbations in single-cell transcriptomes |
| Location: | United States |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1371/journal.pcbi.1008789 |
| Publisher version: | https://doi.org/10.1371/journal.pcbi.1008789 |
| Language: | English |
| Additional information: | © 2021 Yeo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/). |
| Keywords: | Guide RNA, Gene expression, Transcriptome analysis, Flow cytometry, Polymerase chain reaction, Human genomics, Gene regulation, Mutation |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Haematology |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10125242 |
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