生物
全基因组关联研究
遗传学
增强子
单核苷酸多态性
基因座(遗传学)
连锁不平衡
等位基因
诱导多能干细胞
基因
基因表达
基因型
胚胎干细胞
作者
Shilpa Sonti,Sheridan H. Littleton,Matthew C. Pahl,Amber Zimmerman,Alessandra Chesi,Justin Palermo,Chiara Lasconi,Elizabeth Brown,James A. Pippin,Andrew D. Wells,Fusun Doldur-Balli,Allan I Pack,Phillip R. Gehrman,Alex C. Keene,Struan F.A. Grant
出处
期刊:Sleep
[Oxford University Press]
日期:2024-04-04
卷期号:47 (7)
被引量:1
标识
DOI:10.1093/sleep/zsae085
摘要
Abstract Although genome-wide association studies (GWAS) have identified loci for sleep-related traits, they do not directly uncover the underlying causal variants and corresponding effector genes. The majority of such variants reside in non-coding regions and are therefore presumed to impact cis-regulatory elements. Our previously reported ‘variant-to-gene mapping’ effort in human induced pluripotent stem cell (iPSC)-derived neural progenitor cells (NPCs), combined with validation in both Drosophila and zebrafish, implicated phosphatidyl inositol glycan (PIG)-Q as a functionally relevant gene at the insomnia “WDR90” GWAS locus. However, importantly that effort did not characterize the corresponding underlying causal variant. Specifically, our previous 3D genomic datasets nominated a shortlist of three neighboring single nucleotide polymorphisms (SNPs) in strong linkage disequilibrium within an intronic enhancer region of WDR90 that contacted the open PIG-Q promoter. We sought to investigate the influence of these SNPs collectively and then individually on PIG-Q modulation to pinpoint the causal “regulatory” variant. Starting with gross level perturbation, deletion of the entire region in NPCs via CRISPR-Cas9 editing and subsequent RNA sequencing revealed expression changes in specific PIG-Q transcripts. Results from individual luciferase reporter assays for each SNP in iPSCs revealed that the region with the rs3752495 risk allele (RA) induced a ~2.5-fold increase in luciferase expression. Importantly, rs3752495 also exhibited an allele-specific effect, with the RA increasing the luciferase expression by ~2-fold versus the non-RA. In conclusion, our variant-to-function approach and in vitro validation implicate rs3752495 as a causal insomnia variant embedded within WDR90 while modulating the expression of the distally located PIG-Q.
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