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通过综合计算方法优先考虑与心血管疾病相关的改变NKX2-5和TBX5结合的变异
Edwin G Peña-Martínez1, Diego A Pomales-Matos1, Alejandro Rivera-Madera2
1Department of Biology, University of Puerto Rico Río Piedras Campus, San Juan, Puerto Rico.
The Journal of biological chemistry
|November 5, 2023
概括
研究人员开发了一种计算方法,以精确确定与心血管疾病 (CVD) 相关的遗传变异. 这种方法优先考虑影响转录因子结合的单核酸多态 (SNP),有助于识别导致心血管疾病的突变.
科学领域:
- 基因组学就是基因组学.
- 心血管遗传学 心血管遗传学
- 生物信息学是一种生物信息学.
背景情况:
- 心血管疾病 (CVD) 是全球主要的死亡原因.
- 大多数与心血管疾病相关的遗传变异都存在于非编码基因组中,影响着像转录因子 (TF) 结合部位这样的调节元件.
- 从全基因组关联研究中优先考虑数百万个单核酸多态 (SNP) 来进行功能验证是一个重大挑战.
研究的目的:
- 开发和验证用于识别和优先考虑CVD相关SNP的计算方法.
- 具体确定改变关键心脏转录因子NKX2-5和TBX5.5结合的SNP.
- 将组织特异表达量特征位点 (eQTL) 数据与TF绑定预测集成.
主要方法:
- 实施了基于支持矢量机 (SVM) 的TF绑定站点分类模型.
- 利用心脏表达量的特征位点 (eQTL) 分析来识别心脏组织中的基因型依赖基因表达.
- 在心肌细胞中使用ChIP-seq数据对NKX2-5和TBX5进行训练,训练了一个有间隙的k-mer SVM模型.
- 通过电泳性移动转移试验 (EMSA) 验证了SNP对TF结合的预测效应.
主要成果:
- 在TF足迹和假定的心脏增强剂中确定了1535种与心血管疾病相关的SNP.
- 发现了14218种与心脏基因表达的链接不平衡变异.
- 优先考虑五种特定变异 (rs59310144,rs6715570,rs61872084为NKX2-5;rs7612445,rs7790964为TBX5) 预测对TF结合和心脏eQTLs的影响.
- 证实所有五种优先变异都在体外改变了NKX2-5和TBX5的DNA结合.
结论:
- 开发的生物信息学方法有效地优先考虑了与心血管疾病相关的变异.
- 将组织特异性eQTL分析与基于SVM的TF结合位点分类相结合,是对变异优先级的强大策略.
- 该方法有助于对与心血管疾病有关的遗传变异进行功能验证.
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