通过新型转录因子结合模型揭示了DNA甲基化和内基因依赖的广泛影响
Jan Grau1, Florian Schmidt2,3,4,5, Marcel H Schulz2,3,6,7
1Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle 06120, Germany.
Nucleic acids research
|August 31, 2023
概括
DNA甲基化会影响转录因子 (TF) 的结合. 我们的新工具MeDeMo模拟了这一点,揭示了甲基化往往会降低TF结合,并突出了因子内依赖性对准确分析的重要性.
科学领域:
- 分子生物学分子生物学
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 基因甲基化是影响基因表达的关键表观遗传调节剂.
- 以前的研究表明,DNA甲基化可以改变转录因子 (TF) 的结合亲和力.
- 甲基化对结合的精确机制和TF特异性影响仍然不完全理解.
研究的目的:
- 开发和验证一个计算工具箱 (MeDeMo),用于分析由于DNA甲基化导致的TF动机变化.
- 研究DNA甲基化对大量TF结合行为的全基因组影响.
- 评估内基因依赖在建模甲基化对TF结合的影响中的作用.
主要方法:
- 开发MeDeMo工具箱,将DNA甲基化数据与TF图案模型集成在一起.
- 对335个TF的ChIP-seq数据进行大规模分析,以确定甲基化相关的结合模式.
- 模型的比较分析,并没有考虑因子内依赖关系.
主要成果:
- 识别表现出甲基化相关的结合行为的新型TFs.
- 证明CpG甲基化通常会降低大多数已识别的TF的TF结合可能性.
- 证据表明,对于精确建模甲基化对TF结合的影响来说,内基因依赖关系对于一个重要的TF子集至关重要.
结论:
- MeDeMo为甲基化意识TF结合分析提供了一个新的框架.
- 考虑到DNA甲基化和内基因依赖性,可以改善TF结合模型.
- 忽视这些因素会导致分析甲基化相关TFs的表现不佳.
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