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染色体折叠和转录组中由凝聚素和相关因素引起的上下文依赖性扰动
Ryuichiro Nakato1, Toyonori Sakata2,3,4, Jiankang Wang5
1Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-0032, Japan. rnakato@iqb.u-tokyo.ac.jp.
Nature communications
|September 19, 2023
概括
凝聚蛋白通过染色体折叠影响基因表达. 新的计算工具分析了凝聚和相关因素如何影响3D基因组结构和基因活性,揭示了TAD分裂和表达变化之间的联系.
科学领域:
- 基因组学就是基因组学.
- 分子生物学分子生物学
- 计算生物学 计算生物学
背景情况:
- 凝聚蛋白对于通过染色体折叠来调节基因表达至关重要,包括增强剂-促进剂循环和拓关联域 (TAD) 形成.
- 凝聚素与凝聚素加载器和CTCF等因素合作,建立特定的3D基因组结构.
研究的目的:
- 开发和验证一个计算工作流 (CustardPy) 用于系统地比较多omics数据集.
- 研究凝聚和相关因素如何集体或单独调节3D基因组结构和基因表达.
主要方法:
- 在凝聚和相关因素耗尽之前和之后生成3D基因组,转录组和表观组数据.
- 使用CustardPy计算工作流程对多omics数据集进行系统比较.
- 分析3D基因组变化,表观基因组状态和基因表达变化之间的相关性.
主要成果:
- 观察到3D基因组和转录组在凝聚力和相关因子耗尽后产生不同的影响.
- 在基因表达变化和TADs在凝聚性损失时的分裂之间证明了相关性.
- 识别了TAD与其表观基因组状态相关的长距离相互作用的变异.
结论:
- 开发的计算工具和数据集为3D基因组和表观基因组研究提供了宝贵的资源.
- 凝聚素耗尽显著影响3D基因组组织和基因表达,TAD分裂是关键机制.
- 表观基因组状态影响TAD内部的长距离相互作用,突出显示了基因组结构和表观基因调节之间的相互作用.
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