Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
OpenTargets, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Nucleic Acids Res. 2023 Jun 23;51(11):e64. doi: 10.1093/nar/gkad332.
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 identified by GWAS, which frequently sit within gene regulatory elements but whose functional effects are often unknown. Current methods are limited in 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 effect of individual variants on chromatin accessibility in their endogenous genomic and chromatin context. We employ this assay to screen for the effects of regulatory variants in human induced pluripotent stem cells, validating a subset of causal variants, and extend our software package (rgenie) to analyse these new data. We demonstrate that this methodology can be used to understand the impact of defined deletions and point mutations within transcription factor binding sites. We thus establish GenIE-ATAC as a method to screen for the effect of gene regulatory element variation, allowing identification and prioritisation of causal variants from GWAS for functional follow-up and understanding the mechanisms of regulatory element function.
了解基因调控元件中遗传变异的影响对于解释基因组功能至关重要。这对于通过 GWAS 鉴定的数十万种与疾病相关的变异尤其重要，这些变异通常位于基因调控元件内，但它们的功能影响通常未知。目前的方法在其可扩展性和在其内源性环境中检测调控变异的能力方面存在局限性，无法独立于其他紧密连锁的变异进行检测。在这里，我们提出了一种新的高通量筛选系统：基于基因组工程的增强子转座酶可及染色质检测分析（GenIE-ATAC），该系统可测量单个变异在其内源基因组和染色质环境中对染色质可及性的影响。我们利用该检测方法在人类诱导多能干细胞中筛选调控变异的影响，验证了一部分因果变异，并扩展了我们的软件包（rgenie）来分析这些新数据。我们证明，该方法可用于理解转录因子结合位点内定义的缺失和点突变的影响。因此，我们确立了 GenIE-ATAC 作为筛选基因调控元件变异影响的方法，可用于从 GWAS 中鉴定和优先考虑因果变异，进行功能后续研究，并理解调控元件功能的机制。
