Biological physics of protein clustering in epigenetic memory and transcriptional control

表观遗传记忆和转录控制中蛋白质聚类的生物物理学

• 批准号: EP/T00214X/1
• 负责人: Caroline Dean
• 金额: $ 91.56万
• 依托单位: John Innes Centre
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2019
• 资助国家: 英国
• 起止时间: 2019 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=EP%2FT00214X%2F1
• 关键词: Biological; physics; protein; clustering; epigenetic

In recent years it has become clear that many proteins act collectively inside single cells by teaming-up in large numbers into dense molecular clusters. However, how these clusters form and what biological function they perform often remains a mystery. In this proposal, we aim to unlock these mysteries by investigating two types of clustering at a single target, a gene called FLOWERING LOCUS C in the plant Arabidopsis. The first type of clustering is caused by proteins gathering together in an ordered way, such that close association of a critical number of proteins will then stimulate further feedback to recruit more proteins into the cluster. This phenomenon is called oligomerization. Our preliminary evidence indicates that this type of clustering occurs at FLC and has a critical function in establishing a memory of how active the gene is. Specifically, the presence of this cluster of proteins attached to the FLC DNA can cause transcription to be switched off, a state that is then inherited through DNA replication, cell division and through many subsequent cell cycles. Such memory is vitally important in controlling how cells behave and is sometimes called epigenetic memory.The second type of protein clustering has a different physical origin: many proteins undergo what is called liquid-liquid phase separation, where they will spontaneously separate themselves from the surrounding medium and form a self-assembling compartment. This process is analogous to the spontaneous separation of oil in water into droplets. Our preliminary evidence demonstrates that this type of clustering is also present at FLC, though at a different time period in plant development to the oligomeric clustering. We believe that these phase-separated clusters are also critical regulators of gene expression. In this project, we aim to mechanistically understand the formation and biological function of both types of cluster. To do this will require a wide diversity of techniques and expertise from both biology and physics. Physics thinking is specifically needed because the mechanisms by which the clusters are believed to form, oligomerization and phase separation, are intrinsic physics phenomena. We will use molecular biology and genetics to perturb the components of the clusters and examine their effects on gene expression. We will use advanced single-molecule imaging techniques to observe the clusters, measure their dynamics and count the number of molecules involved. Finally, we will develop detailed theoretical physics models of the two types of clusters incorporating the results from the experiments. These experiments and models may potentially reveal how new kinds of biological physics have been exploited by biology to provide the exquisite control needed for transcriptional regulation and memory.

近年来，许多蛋白质通过大量聚集成密集的分子簇，在单个细胞内共同发挥作用已经变得很清楚。然而，这些星系团是如何形成的，它们执行什么生物功能往往仍然是一个谜。在这项提议中，我们的目标是通过研究在一个单一目标上的两种类型的聚集来解开这些谜团，在植物拟南芥中，一个被称为开花基因C的基因。第一种类型的聚集是由蛋白质以有序的方式聚集在一起引起的，这样，关键数量的蛋白质的紧密结合将刺激进一步的反馈，以将更多的蛋白质招募到集群中。这种现象被称为齐聚反应。我们的初步证据表明，这种类型的聚集发生在FLC，并在建立对基因活性的记忆方面具有关键功能。具体地说，FLC DNA上附着的这一簇蛋白质的存在可能导致转录关闭，这种状态随后通过DNA复制、细胞分裂和许多后续的细胞周期而继承。这种记忆在控制细胞行为方面至关重要，有时被称为表观遗传记忆。第二种类型的蛋白质聚集有不同的物理来源：许多蛋白质经历所谓的液-液分离，在这种分离中，它们会自发地将自己与周围的介质分开，形成一个自组装的隔间。这一过程类似于将水中的油自发分离成液滴。我们的初步证据表明，这种类型的聚集也存在于FLC，尽管在植物发育的不同时期与寡聚体聚集不同。我们认为，这些相分离的簇也是基因表达的关键调节因子。在这个项目中，我们的目标是从机械上理解这两种类型星系团的形成和生物功能。要做到这一点，需要生物学和物理学的广泛多样的技术和专业知识。特别需要物理思维，因为人们认为团簇形成的机制--齐聚和相分离--是内在的物理现象。我们将使用分子生物学和遗传学来扰乱簇的成分，并检查它们对基因表达的影响。我们将使用先进的单分子成像技术来观察星团，测量它们的动力学，并计算涉及的分子数量。最后，我们将结合实验结果建立这两类团簇的详细理论物理模型。这些实验和模型可能会潜在地揭示生物学如何利用新的生物物理学来提供转录调控和记忆所需的精细控制。

项目成果

Cold-induced Arabidopsis FRIGIDA nuclear condensates for FLC repression.

• DOI: 10.1038/s41586-021-04062-5
• 发表时间: 2021-11
• 期刊: Nature
• 影响因子: 64.8
• 作者: Zhu P;Lister C;Dean C
• 通讯作者: Dean C

Hybrid protein assembly-histone modification mechanism for PRC2-based epigenetic switching and memory.

• DOI: 10.7554/elife.66454
• 发表时间: 2021-09-02
• 期刊: eLife
• 影响因子: 7.7
• 作者: Lövkvist C;Mikulski P;Reeck S;Hartley M;Dean C;Howard M
• 通讯作者: Howard M

VAL1 acts as an assembly platform co-ordinating co-transcriptional repression and chromatin regulation at Arabidopsis FLC.

• DOI: 10.1038/s41467-022-32897-7
• 发表时间: 2022-09-21
• 期刊: Nature communications
• 影响因子: 16.6

Head-to-tail polymerization by VEL proteins underpins cold-induced Polycomb silencing in flowering control.

• DOI: 10.1016/j.celrep.2022.111607
• 发表时间: 2022-11-08
• 期刊: Cell reports
• 影响因子: 8.8
• 作者: Fiedler M;Franco-Echevarría E;Schulten A;Nielsen M;Rutherford TJ;Yeates A;Ahsan B;Dean C;Bienz M
• 通讯作者: Bienz M

Publisher Correction: Temperature-dependent growth contributes to long-term cold sensing.

出版商更正：温度依赖性生长有助于长期冷感。

• DOI: 10.1038/s41586-020-2694-x
• 发表时间: 2020
• 期刊: Nature
• 影响因子: 64.8
• 作者: Zhao Y