Screening for functional transcriptional and splicing regulatory variants with GenIE.
Alleles
Alternative Splicing
/ genetics
Alzheimer Disease
/ genetics
CRISPR-Cas Systems
/ genetics
Clusterin
/ genetics
Enhancer Elements, Genetic
/ genetics
Gene Editing
Genetic Variation
/ genetics
Genome-Wide Association Study
Humans
Induced Pluripotent Stem Cells
/ metabolism
Mutation
Polymorphism, Single Nucleotide
/ genetics
Regulatory Sequences, Nucleic Acid
/ genetics
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
16 12 2020
16 12 2020
Historique:
accepted:
08
10
2020
revised:
22
09
2020
received:
28
07
2020
pubmed:
6
11
2020
medline:
14
1
2021
entrez:
5
11
2020
Statut:
ppublish
Résumé
Genome-wide association studies (GWAS) have identified numerous genetic loci underlying human diseases, but a fundamental challenge remains to accurately identify the underlying causal genes and variants. Here, we describe an arrayed CRISPR screening method, Genome engineering-based Interrogation of Enhancers (GenIE), which assesses the effects of defined alleles on transcription or splicing when introduced in their endogenous genomic locations. We use this sensitive assay to validate the activity of transcriptional enhancers and splice regulatory elements in human induced pluripotent stem cells (hiPSCs), and develop a software package (rgenie) to analyse the data. We screen the 99% credible set of Alzheimer's disease (AD) GWAS variants identified at the clusterin (CLU) locus to identify a subset of likely causal variants, and employ GenIE to understand the impact of specific mutations on splicing efficiency. We thus establish GenIE as an efficient tool to rapidly screen for the role of transcribed variants on gene expression.
Identifiants
pubmed: 33152068
pii: 5957169
doi: 10.1093/nar/gkaa960
pmc: PMC7736817
doi:
Substances chimiques
CLU protein, human
0
Clusterin
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e131Subventions
Organisme : Wellcome Trust
ID : 206194
Pays : United Kingdom
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
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