A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci. A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci

Genome-wide association studies (GWAS) have been highly informative in discovering disease-associated loci, but are not designed to capture all structural variations in the human genome. Using long-read sequencing data, we discovered widespread structural variation within SVA (Sine-VNTR-Alu) elements, a class of great-ape specific transposable elements with gene-regulatory roles, which represents a major source of structural variability in the human population. We highlight the presence of structurally variable SVAs (SV-SVAs) in neurological disease-associated loci, and further associate SV-SVAs to disease-associated SNPs and differential gene expression using luciferase assays and expression quantitative trait loci data. Finally, we genetically deleted SV-SVAs in the BIN1 and CD2AP Alzheimer-associated risk loci and in the BCKDK Parkinson disease-associated risk locus and assessed multiple aspects of their gene-regulatory influence in a human neuronal context. Together, this study reveals a novel layer of genetic variation in transposable elements that may contribute to identification of the structural variants that are the actual drivers of disease-associations of GWAS loci. Overall design: RNA and ChIP-seq analysis of CRISPR/Cas9 SVA-KO and wild type hESC-derived cortical organoids.

全基因组关联分析（Genome-wide association studies, GWAS）在发掘疾病关联位点方面极具价值，但该方法无法捕获人类基因组中的全部结构变异。本研究借助长读长测序数据，发现SVA（Sine-VNTR-Alu）元件中存在广泛的结构变异：这类类人猿特异性转座元件兼具基因调控功能，是人类群体中结构变异性的主要来源。我们证实了神经系统疾病关联位点中存在结构变异型SVA（SV-SVAs），并通过荧光素酶报告基因实验与表达数量性状位点（expression quantitative trait loci, eQTL）数据，将SV-SVAs与疾病关联单核苷酸多态性（Single Nucleotide Polymorphism, SNP）及基因表达差异建立了关联。最后，我们分别在阿尔茨海默病相关风险位点BIN1、CD2AP以及帕金森病相关风险位点BCKDK中敲除SV-SVAs，并在人类神经元环境中评估了其对基因调控的多方面影响。综上，本研究揭示了转座元件中一层全新的遗传变异维度，或有助于识别驱动GWAS位点疾病关联的真正结构变异。整体实验设计：对CRISPR/Cas9介导的SVA敲除（SVA-KO）与野生型人胚胎干细胞（human embryonic stem cell, hESC）来源的皮层类器官开展RNA及染色质免疫共沉淀测序（ChIP-seq）分析。