识别与果成熟启动相关的谱系特定的 cis-trans 监管网络
Eriko Kuwada1, Kouki Takeshita2, Taiji Kawakatsu3
1Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan.
The Plant journal : for cell and molecular biology
|October 27, 2024
概括
深度学习发现了控制果成熟的新型基因调节网络. 这种方法揭示了水果成熟如何在物种之间演变为独特的遗传途径.
科学领域:
- 植物生物学 植物生物学
- 基因组学就是基因组学.
- 生物技术是生物技术.
背景情况:
- 果实成熟涉及复杂的遗传调节,具有跨物种基因表达网络的独立进化.
- 了解转录因子 (TF) 和 cis-regulatory element (CRE) 相互作用是破译这些网络的关键.
研究的目的:
- 通过使用可解释的深度学习 (DL) 来识别影响乙烯诱导基维果成熟的谱系特定的CRE-TF相互作用.
- 为了验证果实成熟的新型监管关系.
主要方法:
- 可解释的深度学习框架来预测在促进器序列中的CREs的基因表达.
- 在果成熟过程中选CRE-TF相互作用.
- 使用暂时报告测试和DNA亲和力净化测序 (DAP-Seq) 的验证.
主要成果:
- 确定了影响乙烯诱导果成熟的新型CRE-TF相互作用.
- 发现特定的TFs (ABI5类bZIP,G2类,MYB81类) 能够调节乙烯信号/生物合成基因.
- 基于DL的选确定了与共同表达模式不同的监管网络.
结论:
- 可解释的DL是一种强大的工具,用于发现新的CRE-TF相互作用在水果成熟.
- 果作物种类拥有独特的,特定于血统的 cis-trans 调节网络,控制成熟过程.
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