从序列中预测调节元素的预测准确性因功能测序技术而异
Ronald J Nowling1, Kimani Njoya2, John G Peters1
1Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, WI, United States.
Frontiers in cellular and infection microbiology
|August 21, 2023
概括
机器学习模型使用DNA序列预测cis-regulatory元素. 与ChIP-seq方法不同,DNase-seq和STARR-seq数据准确地预测了监管活动,突出了基于序列的预测潜力.
科学领域:
- 基因组学就是基因组学.
- 计算生物学 计算生物学
- 分子生物学分子生物学
背景情况:
- * 识别 cis 调节元件 (CREs) 对于理解基因组调节至关重要.
- *使用各种测序技术 (ChIP-seq,ATAC-seq,DNase-seq,STARR-seq),取决于直接序列或间接标记.
- *CRE活性取决于DNA序列和二次表观遗传过程.
研究的目的:
- * 通过使用机器学习,仅基于DNA序列来评估CREs的预测准确性.
- * 要区分由序列驱动的监管活动与由次要过程影响的监管活动.
- * 为了比较不同测序数据集对训练基于序列的预测模型的适用性.
主要方法:
- *机器学习模型在D. melanogaster*的cis调节元素序列上进行了训练和评估.
- *数据集包括DNase-seq,STARR-seq和各种ChIP-seq (H3K4me1,H3K4me3,H3K27ac),FAIRE-seq和ATAC-seq的数据.
- *使用化酶试验进行实验验证,对比了所选序列的增强剂活性.
主要成果:
- *在DNase-seq和STARR-seq数据上训练的模型显示出比使用ChIP-seq,FAIRE-seq或ATAC-seq的模型更高的准确性.
- *DNase-seq和STARR-seq活动在很大程度上是由DNA序列解释的,独立于二次表观遗传标记.
- * 路西法酶试验证实STARR-seq序列对增强剂活性进行了丰富,而DNase-seq和H3K4me1 ChIP-seq序列则没有.
结论:
- *DNase-seq识别了广泛的监管元素,适用于基于序列的一般活动预测.
- *STARR-seq数据是训练模型预测增强剂特定序列的最佳选择.
- * H3K4me1 ChIP-seq数据不适合训练基于序列的模型进行CRE预测.
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