Biological physics of protein clustering in epigenetic memory and transcriptional control

点击翻译按钮获取中文摘要

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.