重建尼安德特人的3D基因组组织揭示了染色质折叠形成的表型和序列分歧
Evonne McArthur1,2,3, David C Rinker4, Yang Cheng5
1Department of Medicine, University of Washington, Seattle, WA.
bioRxiv : the preprint server for biology
|September 15, 2025
概括
我们使用深度学习来重建古人类的3D基因组折叠,揭示了与人类进化相关的基因调节差异. 这种3D基因组结构影响了古老的侵入现代人类.
科学领域:
- 基因组学就是基因组学.
- 进化生物学 进化生物学
- 计算生物学 计算生物学
背景情况:
- 基因调节的变化导致了人类的分歧.
- 3D基因组折叠对于基因表达至关重要,但在古老的原始人 (AHs) 中尚未探索.
- 古代DNA降解阻止了AHs的实验3D基因组折叠确定.
研究的目的:
- 推断和分析尼安德特人,丹尼索瓦人和现代人类 (MHs) 的3D基因组组织.
- 为了确定AHs和MHs之间3D基因组组织分化的区域.
- 探索3D基因组折叠在人类进化和内进化的作用.
主要方法:
- 应用深度学习从DNA序列推断出3D基因组组织.
- 为尼安德特人,丹尼索瓦人和MH基因组生成3D接触地图.
- 识别了分离的3D基因组区域,并分析了基因丰富和内进化模式.
主要成果:
- 确定了167个区域,AHs和MHs之间的3D基因组组织不同.
- 分离的基因位点为与眼睛,头发,肺部,免疫和认知功能相关的基因进行丰富.
- AH和MH3D基因组比序列分歧表明的更相似,表明了约束.
- 3D基因组组织影响了现代欧亚人AH祖先的景观.
- 在现代欧亚人中确定了具有新AH 3D折叠模式的内进位位.
结论:
- 深度学习可以推断古老的3D基因组组织,从古老的DNA中揭示分子表型.
- 3D基因组结构在限制人类序列进化的过程中发挥了重要作用.
- 3D基因组折叠模式影响了基因调节和人类群体之间的表型差异.
- 了解3D基因组组织为古老的侵入及其功能后果提供了洞察力.
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