Screening for functional regulatory variants in open chromatin using GenIE-ATAC

Understanding the effects of genetic variation in gene regulatory elements is crucial to interpreting genome function. This is particularly pertinent for the hundreds of thousands of disease-associated variants that have been identified by genome-wide association studies (GWAS), which often sit within gene regulatory elements but whose functional effect is challenging to establish. Current methods are limited in terms of their scalability and ability to assay regulatory variants in their endogenous context, independently of other tightly linked variants. Here we present a new medium-throughput screening system, genome engineering based interrogation of enhancers assay for transposase accessible chromatin (GenIE-ATAC), that measures the effects of individual variants on chromatin accessibility in their endogenous genomic and chromatin context. We employ this assay to screen for the effects of putative regulatory variants in human induced pluripotent stem cells (hiPSCs), validating a subset of causal variants, and extend our software package (rgenie) to analyse these new data. We demonstrate that this methodology can also be used to understand the impact of defined deletions and point mutations within transcription factor binding sites on binding efficiency. We thus establish GenIE-ATAC as a method to rapidly screen for the effect of gene regulatory element variation, which can be used to identify and prioritise causal variants from GWAS for functional follow-up and understand the mechanisms of regulatory element function.