Screening for functional regulatory variants in open chromatin using GenIE-ATAC
Sarah Cooper1,2, Jeremy Schwartzentruber1,2, Eve L Coomber1
1Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Nucleic Acids Research
|May 1, 2023
Summary
We developed GenIE-ATAC, a new method to screen genetic variants in gene regulatory elements. This assay measures variant effects on chromatin accessibility, aiding in understanding disease associations.
Area of Science:
- Genomics
- Molecular Biology
- Epigenetics
Background:
- Interpreting genome function requires understanding genetic variation in gene regulatory elements.
- Genome-Wide Association Studies (GWAS) identify numerous disease-associated variants in regulatory regions, but their functional impact remains largely unknown.
- Existing methods for assaying regulatory variants are limited in scalability and their ability to assess variants in their endogenous genomic context.
Purpose of the Study:
- To develop a scalable, medium-throughput screening system to assay the functional effects of individual genetic variants within gene regulatory elements.
- To measure the impact of variants on chromatin accessibility in their native genomic and chromatin environment.
- To enable the identification and prioritization of causal variants from GWAS for further functional investigation.
Main Methods:
- Development of the genome engineering based interrogation of enhancers assay for transposase accessible chromatin (GenIE-ATAC) system.
- Application of GenIE-ATAC to screen regulatory variants in human induced pluripotent stem cells.
- Extension of the rgenie software package for analyzing GenIE-ATAC data.
- Validation of the method by assessing the impact of defined deletions and point mutations within transcription factor binding sites.
Main Results:
- GenIE-ATAC successfully measures the effect of individual variants on chromatin accessibility in their endogenous context.
- The assay validated a subset of causal regulatory variants in human induced pluripotent stem cells.
- The rgenie software was updated to effectively analyze the generated data.
- The methodology demonstrated the ability to discern the impact of specific mutations within transcription factor binding sites.
Conclusions:
- GenIE-ATAC is an effective method for screening the effects of genetic variation in gene regulatory elements.
- This system facilitates the identification and prioritization of causal variants from GWAS.
- GenIE-ATAC aids in elucidating the mechanisms underlying regulatory element function and its role in disease.
