Screening for functional transcriptional and splicing regulatory variants with GenIE
| Autor: | Jeremy Schwartzentruber, Andrew R. Bassett, Erica Bello, Eve L. Coomber, Sarah Cooper |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
AcademicSubjects/SCI00010
Induced Pluripotent Stem Cells Single-nucleotide polymorphism Genome-wide association study Computational biology Biology Regulatory Sequences Nucleic Acid Genome Polymorphism Single Nucleotide Genome engineering 03 medical and health sciences 0302 clinical medicine Alzheimer Disease Genetics CRISPR Humans Gene Alleles 030304 developmental biology Gene Editing 0303 health sciences Intron Genetic Variation Narese/22 Alternative Splicing Clusterin Enhancer Elements Genetic RNA splicing Mutation Methods Online CRISPR-Cas Systems 030217 neurology & neurosurgery Genome-Wide Association Study |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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