构建一个神经网络模型来定义V(D) J重组的DNA序列特异性
Justin C Harris1, Jennifer N Byrum2, Cooper B McKinney2
1Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences, Oklahoma City, OK 73104, United States.
Nucleic acids research
|June 23, 2025
概括
V(D) J重组使用特定的DNA序列称为重组信号序列 (RSSs) 组装抗原受体基因. 我们的研究揭示了RSS七度和非亚美体区域的核酸变化如何影响这一关键的基因组装过程.
科学领域:
- 免疫学 免疫学 免疫学
- 分子生物学分子生物学
- 遗传学 是一个遗传学.
背景情况:
- V(D) J重组组合在发育中的淋巴细胞中组装抗原受体基因.
- 重组信号序列 (RSS) 引导这一过程,但其精确的选择机制尚不清楚.
- RSSs由由间隔器分隔的heptamer和nonamer动图组成,侧面的基因段是重排的目标.
研究的目的:
- 阐明在V(D) J重组中管理RSS选择的基于序列的规则.
- 了解RSS中特定的核酸位置如何影响重组效率.
- 为了研究RSS七度和非亚米区域之间的协同作用和相互依赖的效应.
主要方法:
- 开发了一个神经网络模型,使用V(D) J重组效率数据随机选择的12个RSS.
- 应用了夏普利添加式解释 (SHAP) 来解释神经网络的预测.
- 训练了第二个神经网络,结合了非amer序列来分析heptamer-nonamer相互作用.
主要成果:
- 在RSS七度体中确定了特定的核酸位置,这些位置显著影响了重组效率.
- 在SHAP分析中,发现了核酸对在heptamer中的协同贡献.
- 发现了体和非体区域之间的相互依赖作用,对V(D) J重组效率产生影响.
结论:
- 在RSS heptamer中的特定位置的序列变化对于V(D) J重组效率至关重要.
- 在RSS七度体内以及七度体与非三度体之间的核酸相互作用有助于调节V(D) J重组.
- 这项研究提供了在适应性免疫受体基因组装过程中对RSS选择的更深入的机制理解.
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