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 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-Se...

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Autores principales:	Grace Hui Ting Yeo, Oscar Juez, Qing Chen, Budhaditya Banerjee, Lendy Chu, Max W Shen, May Sabry, Ive Logister, Richard I Sherwood, David K Gifford
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/caf6d122ce4e4d598a6d62fc160301d9
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spelling	oai:doaj.org-article:caf6d122ce4e4d598a6d62fc160301d92021-12-02T19:57:37ZDetection of gene cis-regulatory element perturbations in single-cell transcriptomes.1553-734X1553-735810.1371/journal.pcbi.1008789https://doaj.org/article/caf6d122ce4e4d598a6d62fc160301d92021-03-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1008789https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358We 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.Grace Hui Ting YeoOscar JuezQing ChenBudhaditya BanerjeeLendy ChuMax W ShenMay SabryIve LogisterRichard I SherwoodDavid K GiffordPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 3, p e1008789 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Grace Hui Ting Yeo Oscar Juez Qing Chen Budhaditya Banerjee Lendy Chu Max W Shen May Sabry Ive Logister Richard I Sherwood David K Gifford Detection of gene cis-regulatory element perturbations in single-cell transcriptomes.
description	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.
format	article
author	Grace Hui Ting Yeo Oscar Juez Qing Chen Budhaditya Banerjee Lendy Chu Max W Shen May Sabry Ive Logister Richard I Sherwood David K Gifford
author_facet	Grace Hui Ting Yeo Oscar Juez Qing Chen Budhaditya Banerjee Lendy Chu Max W Shen May Sabry Ive Logister Richard I Sherwood David K Gifford
author_sort	Grace Hui Ting Yeo
title	Detection of gene cis-regulatory element perturbations in single-cell transcriptomes.
title_short	Detection of gene cis-regulatory element perturbations in single-cell transcriptomes.
title_full	Detection of gene cis-regulatory element perturbations in single-cell transcriptomes.
title_fullStr	Detection of gene cis-regulatory element perturbations in single-cell transcriptomes.
title_full_unstemmed	Detection of gene cis-regulatory element perturbations in single-cell transcriptomes.
title_sort	detection of gene cis-regulatory element perturbations in single-cell transcriptomes.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/caf6d122ce4e4d598a6d62fc160301d9
work_keys_str_mv	AT gracehuitingyeo detectionofgenecisregulatoryelementperturbationsinsinglecelltranscriptomes AT oscarjuez detectionofgenecisregulatoryelementperturbationsinsinglecelltranscriptomes AT qingchen detectionofgenecisregulatoryelementperturbationsinsinglecelltranscriptomes AT budhadityabanerjee detectionofgenecisregulatoryelementperturbationsinsinglecelltranscriptomes AT lendychu detectionofgenecisregulatoryelementperturbationsinsinglecelltranscriptomes AT maxwshen detectionofgenecisregulatoryelementperturbationsinsinglecelltranscriptomes AT maysabry detectionofgenecisregulatoryelementperturbationsinsinglecelltranscriptomes AT ivelogister detectionofgenecisregulatoryelementperturbationsinsinglecelltranscriptomes AT richardisherwood detectionofgenecisregulatoryelementperturbationsinsinglecelltranscriptomes AT davidkgifford detectionofgenecisregulatoryelementperturbationsinsinglecelltranscriptomes
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Detection of gene cis-regulatory element perturbations in single-cell transcriptomes.

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