Statistical physics models for the regulation of the structure of chromatin

我的研究项目应用计算物理学的方法来解决物理约束如何导致细胞中复杂的空间组织的问题。它的重点是通过与实验生物学家的密切合作，开发数据驱动的模型。细胞生物学中一个重要的物理过程是将DNA包装到小体积的细胞中。DNA被精心排列；它的结构影响许多细胞的功能。我有两项研究努力及时地解决了关于这一过程的未解之谜。***我们与图卢兹法国科学研究中心的染色质生物学家Olivier Cuvier合作，致力于开发一种预测机制模型，用于研究细胞中DNA的结构如何调节可读出的遗传信息。在真核细胞中，DNA被包装成一种称为染色质的结构。由于与DNA结合的蛋白质之间的相互作用，它是一个高度环化的结构。环的适当形成决定了基因是否开启。通过分析居维叶实验室的数据，我的团队发现了一个复杂的蛋白质相互作用网络，即调节DNA环和基因表达的绝缘体。利用最近开发的实验技术，居维叶实验室将绘制出基因组的哪些部分在物理上是相互接触的，以及绝缘体网络的突变如何改变地图。我的团队将把这些数据与统计物理模型相匹配，以确定具体的接触能量，从而开发基于聚合物的模型，研究绝缘体如何调节染色质结构。随着对基因循环机制过程的更好理解，我们希望能够预测基因何时何地表达。***我们的第二个努力集中在揭示自然界用来在最小的细胞（即细菌）内组织其分子部分的简单物理机制。我们已经证明，基因组DNA聚合物的熵可以驱动蛋白质聚集到极点的定位。在一些细菌中，极性定位的蛋白质与分离复制DNA的机制相互作用并提供帮助。这种分离机制也是动态的，最近的体外测量已经对其机制有了一些了解。然而，这两个相互作用的系统是如何在重要的复制过程中对细胞进行稳健的模式化的，目前还不清楚。通过对耦合系统进行建模，我们希望能够揭示这些生物分子机器的设计原理。***刚才描述的研究项目将为学员提供多样化的技能。过去的学员从学术界到工业研究机构都从事计算生物学的职业。在加拿大不断发展的生物技术领域，这类研究人员需求量很大

My research program applies methods of computational physics to address the question of how physical constraints lead to complex spatial organization in a cell. It is focused on developing data driven models that draw from strong collaborations with experimental biologists. An important physical process in cell biology is the packaging of DNA into the small volume of the cell. DNA is meticulously arranged; the structure of which affects a host of cellular functions. I have two research efforts that address timely unanswered questions about this process.*** In collaboration with Olivier Cuvier, a chromatin biologist at CNRS Toulouse, we are working on the development of a predictive mechanistic model for how the structuring of DNA in a cell regulates the genetic information that can get read out. In eukaryotic cells, DNA is packaged into a structure known as chromatin. It is a highly looped structure due to interactions between proteins that are bound to the DNA. The appropriate formation of loops determines whether a gene gets turned on or not. Analyzing data from the Cuvier lab, my group was able to uncover a complex network of interactions between proteins known as insulators which regulate DNA looping and gene expression. Using recently developed experimental techniques, the Cuvier lab will map out which parts of the genome are physically in contact, and how mutations to the insulator network can alter the map. My group will fit this data to a statistical physics model to determine the specific contact energies, leading to the development of a polymer based model for how insulators regulate chromatin structure. With a better understanding of the mechanistic processes involved in looping, we hope to be able to make predictions about when and where a gene will be expressed.*** Our second effort is focused on uncovering simple physical mechanisms that Nature uses to organize its molecular parts within the tiniest of cells, namely bacteria. We have shown that the entropy of the polymer of genomic DNA can drive localization of protein aggregates to the poles. In some bacteria, polar localized proteins interact with and aid the machinery that segregates replicating DNA. This segregation machinery is also dynamically patterned and recent in vitro measurements have given some insight into its mechanism. However, how the both interacting systems pattern the cell robustly during the important process of replication is not well understood. By modeling the coupled system, our hope is to be able to uncover the design principles of these biomolecular machines.*** The program of research just described will provide trainees with a diverse skill set. Past trainees have pursued careers in computational biology from academia to the industrial research setting. Such researchers are in high demand in Canada's growing biotech sector.**