纳米孔测序和多组学揭示了可预测的非编码RNA激活在DNA甲基化缺陷的Arabidopsis thaliana中
Wanghong Shi1, Luyao Wang2, Na Zhou3
1Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
Communications biology
|December 31, 2025
概括
表观遗传变异,特别是DNA甲基化变化,可预测地激活了Arabidopsis中的长跨基因非编码RNA (lincRNAs). 这项研究为发现新型非编码RNA建立了框架.
科学领域:
- 基因组学就是基因组学.
- 表观遗传学 在表观遗传学中,表观遗传学是指表观遗传学.
- 在RNA生物学,RNA生物学.
背景情况:
- 长跨基因非编码RNAs (lincRNAs) 是具有多种表达模式的调节性RNA分子.
- 临界RNAs的可预测性和广泛激活,特别是对表观遗传变化的反应,仍然在很大程度上未被探索.
研究的目的:
- 为了研究DNA甲基化和lincRNA激活在Arabidopsis中的关系.
- 开发一种用于识别激活的lincRNAs的预测模型,使用多omics数据和机器学习.
主要方法:
- 利用牛津纳米孔技术在阿拉比多普西斯DNA甲基化突变体 (ddm1,met1) 和野生类型上进行直接RNA和DNA测序 (ONT DRS和DDS).
- 进行了差异表达分析,以识别上调的lincRNAs.
- 编译了50个多omics功能来训练6个机器学习模型,包括随机森林,用于lincRNA分类.
主要成果:
- 确定了340个上调的lincRNA和209个与DNA甲基化负相关的lincRNAs.
- 在天然的阿拉比多普西斯种群中观察到类似的激活模式.
- 随机森林模型在分类ddm1-激活的lincRNA中实现了0.96的高平均精度.
- 突出了DNA甲基化,RNA修饰和可转移元素作为lincRNA激活的关键预测因素.
结论:
- 表观遗传变异,特别是DNA甲基化,显著影响可预测的lincRNA激活.
- 开发了一个强大的机器学习框架,用于系统地发现和表征可表达的非编码RNA.
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