单细胞水平上定量研究基因表达异质性的DNA表观调控机制

Thanks to biological noise, a clonal population of cells can display a surprisingly high degree of gene expression heterogeneity. Such heterogeneity often results in metastable and plastic cell states and plays key roles in crucial cellular processes, including fate decisions of stem cells and heterogeneity of cancer cells. Despite the importance, how key gene regulatory mechanisms, such as DNA epigenetic regulation, influence gene expression heterogeneity is not yet well understood, which is essential for understanding cell state control. Here, we integrate systems and synthetic biology approaches and address this question in two separate model organisms. One the one hand, by analyzing intrinsic and extrinsic noises as well as noise propagation mechanisms, we aim to quantitatively dissect how DNA methylation-based epigenetic mechanism regulates the heterogeneity of stemness-related genes in mouse embryonic stem cells. One the other hand, we aim to reconstruct a mammalian-sourced DNA methylation-based epigenetic regulatory system in budding yeast, which lacks endogenous DNA methylation systems. This approach allows investigating the influences of DNA epigenetic regulation on gene expression heterogeneity in an orthogonal cellular environment. Overall, the unique integration of “top-down” and “bottom-up” approaches can not only provide insights into DNA epigenetic mechanism-based cell state control strategy, but can also enable us to artificially perturb and control cell states. Furthermore, this project may have important implications for drug designs that target cell state heterogeneity.

由于生物噪音的存在,具有相同基因组的不同细胞之间往往表现出惊人的基因表达异质性，该异质性常常赋予了细胞状态的亚稳性及可塑性，对干细胞命运决策、肿瘤细胞异质性等有着深远影响。虽然基因表达异质性的生物学意义已被广泛研究，但是，包括DNA表观遗传调控等重要基因调控机制如何影响基因表达异质性，仍然是从根本上理解细胞状态调控的关键性问题。本项目拟结合系统与合成生物学研究方法，在小鼠胚胎干细胞内通过解析内外源噪音、研究噪音传递规律，定量阐明DNA甲基化调控机制如何影响干性基因的表达异质性；并在酵母细胞内通过嫁接小鼠DNA甲基化修饰系统，在正交的细胞环境内系统性解析基因表达异质性的DNA表观调控机制。这种“从自上而下法”与“自下而上法”相融合的研究思路，不仅帮助我们深入理解基于DNA表观修饰的细胞状态调控机制，更将赋予我们对细胞状态进行定向干扰的能力，并为针对细胞状态异质性的药物设计提供全新思路。

具有相同基因型的细胞常常展示出惊人的细胞状态异质性，越来越多的研究表明，这种异质性在肿瘤发生发展、胚胎发育、免疫应答等关键生物学过程中均发挥了关键的作用。然而，我们对非基因型细胞异质性的机制理解仍然很有限，对异质性的表现模式也知之甚少。本项目围绕非基因型异质性这一关键科学问题，针对异质性的表现模式及产生机制开展了一系列定量单细胞研究，产出了若干项成果，其中一些成果已发表在专业期刊上或已申请国家发明专利，一些成果在审稿阶段，另一些成果尚在整理中。代表性成果及其科学意义主要有：提出了基于时间平均的哺乳动物细胞外源噪音过滤机制，为理解非基因型异质性提供了新的视角；开发了基于荧光比例的多重RNA标记系统并用其刻画了单细胞内合成基因线路的动态信号传递规律，为解析基因线路动力学如何影响细胞异质性提供了新工具；揭示了酵母细胞通过调控同源转录因子的脉冲相位差来响应刺激，为理解转录因子动力学的机制和功能提供了全新角度；发现了转录因子与共激活因子的协同相分离现象并解析了其如何影响转录爆发动力学，为深入理解基因表达的动态调控机制及细胞间基因表达异质性机制提供了全新角度。