Screen for Small Molecule Inhibitors of ATP Dependent Chromatin Remodeling

描述（由申请人提供）：尽管人类基因组编码约30种不同的ATP依赖性染色质重塑复合物，但其机制在很大程度上是未知的。在某种程度上，这是由于缺乏快速作用的小分子抑制剂，可以允许精确的时间分析所需的机制研究。基于Brg和Brm ATP酶的这些复合物（BAF或mSWI/SNF复合物）的一个家族是必需的，并且在某些情况下足以诱导多能状态。BAF复合物亚基也是肿瘤抑制因子，在某些人类恶性肿瘤中发生杂合性丢失。最后，它们已被证明是外显性衰老所必需的，并且它们的缺失增加了人成纤维细胞的增殖寿命。蛋白质组学分析表明，BAF复合物的多样性功能是来自编码亚基的基因家族的复合物组合组装的结果。对ES细胞中BAF复合物占据率的全基因组分析表明，它们最常见的是从远处抑制其靶基因，这表明了一种意想不到的作用机制。 为了理解SWI/SNF样BAF复合物用于促进多能性和抑制肿瘤的不明确机制，该项目旨在使用敲入ESC报告细胞系鉴定一组全面的快速作用的小分子抑制剂。该细胞系含有插入Bmi 1基因座的荧光素酶，并在BAF复合物的ATP酶亚基基因缺失后迅速活化。2 MDa复合物含有13个亚基，预期表面积为50万至250万E2。复合物的超大表面被假设为进行一系列连续的反应，这些反应可以用小分子进行排序和探测。 一旦确定，我们将使用在复合物亚基中具有无效突变的已建立的胚胎干细胞系来定义小分子抑制剂的结合位点。因为抑制剂也可以阻止调控机制冲击BAF复合物，我们将其定义后的复杂的翻译后修饰的影响进行表征。每种抑制剂在抑制Polycomb基因和激活重要的多能性靶标如Fgf 4和Bmp 4中的作用时间将有助于进一步确定每种快速作用抑制剂的功能水平。具体而言，它们的作用将在高阶染色质结构、长程相互作用、染色质可及性、核小体定位和转录因子占有率上确定。这种全面和系统的调查应导致更深入地了解这种染色质重塑复合物的作用，它在多能性，人类肿瘤抑制和细胞衰老中起着至关重要的作用。此外，这种有价值的小分子探针工具箱对于其他研究染色质调控的研究人员来说也是无价的。 公共卫生相关性：我们打算找到抑制蛋白质复合物活性的小分子，该蛋白质复合物控制DNA包装到细胞核中。这种蛋白质复合物在人类胚胎干细胞和人类肿瘤抑制中起着关键作用。这种复合物的抑制剂可以改善干细胞疗法和新的癌症治疗方法。

DESCRIPTION (provided by applicant): Although the human genome encodes about 30 different ATP-dependent chromatin remodeling complexes, their mechanism[s] are largely unknown. In part, this is due to the lack of rapidly acting small molecule inhibitors that could permit precise temporal analysis needed for mechanistic studies. One family of these complexes based on the Brg and Brm ATPases (BAF or mSWI/SNF complexes) are both necessary and in some contexts sufficient to induce the pluripotent state. BAF complex subunits are also tumor suppressors and undergo loss of heterozygosity in certain human malignancies. Finally, they have been shown to be necessary for explicative senescence and their deletion increases the proliferative life of human fibroblasts. Proteomic analysis indicates that the diverse functions of BAF complexes are the result of combinatorial assembly of the complexes from gene families encoding the subunits. Genome wide analysis of the occupancy of BAF complexes in ES cells has revealed that they most commonly suppress their target genes from a distance, suggesting an unanticipated mechanism of action. To understand the poorly defined mechanisms used by SWI/SNF-like BAF complexes to promote pluripotency and suppress tumors, this project aims to identify a comprehensive set of rapidly acting small- molecule inhibitors using a knock-in ESC reporter line. This line contains luciferase inserted into the Bmi1 locus and undergoes rapid activation upon genetic deletion of the ATPase subunit of the BAF complex. The 2 MDa complex contains 13 subunits and has an expected surface area of 0.5 to 2.5 million E2. The extraordinarily large surface of the complex is hypothesized to carry out a sequential series of reactions that can be ordered and probed with small molecules. Once identified, we will define the binding sites of the small molecule inhibitors using established embryonic stem cell lines with null mutations in subunits of the complex. Because the inhibitors could also block regulatory mechanisms impinging upon BAF complexes, we will characterize their effect upon defined post-translational modifications of the complex. The time-of-action of each of the inhibitors in both the repression of Polycomb genes and the activation of important pluripotency targets such as Fgf4 and Bmp4 will help to further define the level of function of each of the rapidly acting inhibitors. Specifically, their effects will be determined on higher-order chromatin structures, long-range interactions, chromatin accessibility, nucleosome positioning, and transcription factor occupancy. This comprehensive and systematic investigation should lead to deeper understanding of the actions of this chromatin-remodeling complex, which plays an essential role in pluripotency, human tumor suppression and cellular senescence. In addition, this valuable toolbox of small molecule probes will be invaluable for other researchers studying chromatin regulation. PUBLIC HEALTH RELEVANCE: We intend to find small molecules that inhibit the activities of a complex of proteins that control the packaging of DNA into the nucleus of a cell. This protein complex plays a critical role in human embryonic stem cells and human tumor suppression. Inhibitors of this complex could lead to improved stem cell therapies and new cancer treatments.