当前位置: X-MOL 学术Biol. Psychiatry › 论文详情
Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)
Functional genomics identify a regulatory risk variation rs4420550 in the 16p11.2 schizophrenia-associated locus
Biological Psychiatry ( IF 10.6 ) Pub Date : 2021-02-01 , DOI: 10.1016/j.biopsych.2020.09.016
Hong Chang 1 , Xin Cai 2 , Hui-Juan Li 2 , Wei-Peng Liu 2 , Li-Juan Zhao 2 , Chu-Yi Zhang 2 , Jun-Yang Wang 2 , Jie-Wei Liu 1 , Xiao-Lei Ma 1 , Lu Wang 1 , Yong-Gang Yao 3 , Xiong-Jian Luo 4 , Ming Li 3 , Xiao Xiao 1
Affiliation  

BACKGROUND Genome-wide association studies (GWASs) have reported hundreds of genomic loci associated with schizophrenia, yet identifying the functional risk variations is a key step in elucidating the underlying mechanisms. METHODS We applied multiple bioinformatics and molecular approaches, including expression quantitative trait loci analyses, epigenome signature identification, luciferase reporter assay, chromatin conformation capture, homology-directed genome editing by CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/Cas9), RNA sequencing and ATAC-Seq (assay for transposase-accessible chromatin using sequencing). RESULTS We found that the schizophrenia GWAS risk variations at 16p11.2 were significantly associated with messenger RNA levels of multiple genes in human brain, and one of the leading expression quantitative trait loci genes, MAPK3, is located ∼200 kb away from these risk variations in the genome. Further analyses based on the epigenome marks in human brain and cell lines suggested that a noncoding single nucleotide polymorphism, rs4420550 (p = 2.36 × 10-9 in schizophrenia GWAS), was within a DNA enhancer region, which was validated via in vitro luciferase reporter assays. The chromatin conformation capture experiment showed that the rs4420550 region physically interacted with the MAPK3 promoter and TAOK2 promoter. Precise CRISPR/Cas9 editing of a single base pair in cells followed by RNA sequencing further confirmed the regulatory effects of rs4420550 on the transcription of 16p11.2 genes, and ATAC-Seq demonstrated that rs4420550 affected chromatin accessibility at the 16p11.2 region. The rs4420550-[A/A] cells showed significantly higher proliferation rates compared with rs4420550-[G/G] cells. CONCLUSIONS These results together suggest that rs4420550 is a functional risk variation, and this study illustrates an example of comprehensive functional characterization of schizophrenia GWAS risk loci.

中文翻译:

功能基因组学确定 16p11.2 精神分裂症相关基因座中的调节风险变异 rs4420550

背景 全基因组关联研究 (GWAS) 已经报道了数百个与精神分裂症相关的基因组位点,但识别功能风险变异是阐明潜在机制的关键步骤。方法 我们应用了多种生物信息学和分子方法,包括表达数量性状位点分析、表观基因组特征识别、荧光素酶报告分析、染色质构象捕获、CRISPR/Cas9 同源定向基因组编辑(成簇规律间隔的短回文重复序列/Cas9)、RNA 测序和 ATAC-Seq(使用测序检测转座酶可及染色质)。结果 我们发现 16p11.2 的精神分裂症 GWAS 风险变异与人脑中多个基因的信使 RNA 水平显着相关,和主要表达数量性状位点基因之一,MAPK3,距离基因组中的这些风险变异约 200 kb。基于人脑和细胞系中的表观基因组标记的进一步分析表明,非编码单核苷酸多态性 rs4420550(在精神分裂症 GWAS 中 p = 2.36 × 10-9)位于 DNA 增强子区域内,通过体外荧光素酶报告基因得到验证化验。染色质构象捕获实验表明rs4420550区域与MAPK3启动子和TAOK2启动子物理相互作用。精确 CRISPR/Cas9 编辑细胞中的单个碱基对,然后进行 RNA 测序,进一步证实了 rs4420550 对 16p11.2 基因转录的调节作用,ATAC-Seq 证明 rs4420550 影响 16p11.2 区域的染色质可及性。与 rs4420550-[G/G] 细胞相比,rs4420550-[A/A] 细胞显示出显着更高的增殖率。结论 这些结果共同表明 rs4420550 是一种功能性风险变异,本研究举例说明了精神分裂症 GWAS 风险基因座的综合功能特征。
更新日期:2021-02-01
down
wechat
bug