A polyclonal allelic expression assay for detecting regulatory effects of transcript variants

We present an assay to experimentally test the regulatory effects of genetic variants within transcripts using CRISPR/Cas9 followed by targeted sequencing. We applied the assay to 32 premature stop-gained variants across the genome and in two Mendelian disease genes, 33 putative causal variants of e...

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Autores principales: Brandt, Margot, Gokden, Alper, Ziosi, Marcello, Lappalainen, Tuuli
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7488413/
https://www.ncbi.nlm.nih.gov/pubmed/32912286
http://dx.doi.org/10.1186/s13073-020-00777-8
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author Brandt, Margot
Gokden, Alper
Ziosi, Marcello
Lappalainen, Tuuli
author_facet Brandt, Margot
Gokden, Alper
Ziosi, Marcello
Lappalainen, Tuuli
author_sort Brandt, Margot
collection PubMed
description We present an assay to experimentally test the regulatory effects of genetic variants within transcripts using CRISPR/Cas9 followed by targeted sequencing. We applied the assay to 32 premature stop-gained variants across the genome and in two Mendelian disease genes, 33 putative causal variants of eQTLs, and 62 control variants in HEK293T cells, replicating a subset of variants in HeLa cells. We detected significant effects in the expected direction (in 60% of variants), demonstrating the ability of the assay to capture regulatory effects of eQTL variants and nonsense-mediated decay triggered by premature stop-gained variants. The results suggest a utility for validating transcript-level effects of genetic variants.
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spelling pubmed-74884132020-09-16 A polyclonal allelic expression assay for detecting regulatory effects of transcript variants Brandt, Margot Gokden, Alper Ziosi, Marcello Lappalainen, Tuuli Genome Med Method We present an assay to experimentally test the regulatory effects of genetic variants within transcripts using CRISPR/Cas9 followed by targeted sequencing. We applied the assay to 32 premature stop-gained variants across the genome and in two Mendelian disease genes, 33 putative causal variants of eQTLs, and 62 control variants in HEK293T cells, replicating a subset of variants in HeLa cells. We detected significant effects in the expected direction (in 60% of variants), demonstrating the ability of the assay to capture regulatory effects of eQTL variants and nonsense-mediated decay triggered by premature stop-gained variants. The results suggest a utility for validating transcript-level effects of genetic variants. BioMed Central 2020-09-11 /pmc/articles/PMC7488413/ /pubmed/32912286 http://dx.doi.org/10.1186/s13073-020-00777-8 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Brandt, Margot
Gokden, Alper
Ziosi, Marcello
Lappalainen, Tuuli
A polyclonal allelic expression assay for detecting regulatory effects of transcript variants
title A polyclonal allelic expression assay for detecting regulatory effects of transcript variants
title_full A polyclonal allelic expression assay for detecting regulatory effects of transcript variants
title_fullStr A polyclonal allelic expression assay for detecting regulatory effects of transcript variants
title_full_unstemmed A polyclonal allelic expression assay for detecting regulatory effects of transcript variants
title_short A polyclonal allelic expression assay for detecting regulatory effects of transcript variants
title_sort polyclonal allelic expression assay for detecting regulatory effects of transcript variants
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7488413/
https://www.ncbi.nlm.nih.gov/pubmed/32912286
http://dx.doi.org/10.1186/s13073-020-00777-8
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