High-throughput characterization of genetic effects on DNA-protein binding and gene transcription
High-throughput characterization of genetic effects on DNA-protein binding and gene transcription
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DOI：
10.1101/gr.237354.118
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发表时间：
2018-11-01
期刊：
影响因子：
7
通讯作者：
Luca, Francesca
中科院分区：
文献类型：
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作者：
Kalita, Cynthia A.;Brown, Christopher D.;Luca, Francesca
许多与复杂性状相关的变异位于非编码区，并通过扰乱调控序列来影响表型。为了表征这些变体，我们开发了一种简化的高通量报告分析方法，即双等位基因靶向Starr-seq(bit-starr-seq)，它识别等位基因特异性表达(ASE)，同时通过唯一的分子识别符来解释PCR重复。我们检测了75,501个寡核苷酸(43,500个SNPs)，发现了2720个具有显著ASE的SNPs(FDR<；10%)。为了验证结合中断是ASE的机制之一，我们建立了一种新的高通量NFKB1等位基因特异性结合试验。我们发现了2684个具有等位基因特异性结合(ASB)的SNPs(Fdr<；10%)，其中256个SNPs也有ASE(OR=1.97，P值=0.0006)。在与复杂性状相关的变异中，1531个导致ASE，1662个导致ASB。例如，我们的特征是rs3810936的克罗恩病风险变体增加了NFKB1的结合并导致基因表达改变。
Many variants associated with complex traits are in noncoding regions and contribute to phenotypes by disrupting regulatory sequences. To characterize these variants, we developed a streamlined protocol for a high-throughput reporter assay, Biallelic Targeted STARR-seq (BiT-STARR-seq), that identifies allele-specific expression (ASE) while accounting for PCR duplicates through unique molecular identifiers. We tested 75,501 oligos (43,500 SNPs) and identified 2720 SNPs with significant ASE (FDR < 10%). To validate disruption of binding as one of the mechanisms underlying ASE, we developed a new high-throughput allele-specific binding assay for NFKB1. We identified 2684 SNPs with allele-specific binding (ASB) (FDR < 10%); 256 of these SNPs also had ASE (OR = 1.97, P-value = 0.0006). Of variants associated with complex traits, 1531 resulted in ASE, and 1662 showed ASB. For example, we characterized that the Crohn's disease risk variant for rs3810936 increases NFKB1 binding and results in altered gene expression.