Revealing Masked Specificities of Human Nuclear Receptors

项目摘要/摘要 人类核受体(NR)家族在重要的细胞功能中发挥重要作用，如发育、 新陈代谢和生理学。它们的DNA结合特异性的中断，原因是NR或 在相关的DNA调控位点中，已经被牵连到了几种疾病中 包括青光眼、白内障、视网膜疾病、哮喘、炎症、自身免疫和发育 疾病、荷尔蒙失衡、肥胖、癌症和糖尿病。人类的自然资源是最有效的 药物目标和数十亿美元制药的焦点。对NR基因的全面认识 体内靶向，尤指与不同的生理配体以及广泛处方的药物结合时 对不同的个体和不同的细胞类型有不同的影响，将导致高度知情的 药物开发和部署的方法。最先进的方法不足以完全表征 NRS的DNA同源位点，因为它们经常以合作的同型或异型寡聚体的形式与 其他的TF。此外，NRS的选址偏好是由某些自然因素以不明显的方式调整的 配体和相关的合成药物。最先进的方法也经常忽略中到低层的 密切相关的转录因子的序列特异性差异，这反过来对理解至关重要的 不同NRs之间生物学功能的差异。这个项目的第一个目标是开发创新的 用计算方法阐明NRs的复杂结合特性并识别关键的 亲缘关系密切的NRs结合谱的差异。分析将利用最近收集的实验数据 来自所有全长DNA相互作用的高通量测序的同源位点识别(CSI)数据 全细胞萃取物背景下的功能性人类NRS。我们还建议严格评估影响 一系列生理性小分子配体以及处方疗法/药物对NR-DNA的影响 互动。通过计算确定的序列首选项将通过使用 生化、生物物理和细胞生物学检测。因此，我们将把计算和实验结合起来 验证以破译NRS如何以基因组为靶标并显示其生物学作用。此外，这些努力将 通过定义当前疗法在指导NRS方面的影响来实现精准医学 个体基因组。

PROJECT SUMMARY/ABSTRACT Human Nuclear Receptor (NR) family play significant roles in critical cellular functions such as development, metabolism, and physiology. Disruptions in their DNA binding specificities, due to either mutation in the NR or in the associated DNA regulatory sites, have been implicated in has been implicated in several diseases including glaucoma, cataract, retinal diseases, asthma, inflammation, autoimmune and developmental disorders, hormonal imbalances, obesity, cancers and diabetes. Human NRs are some of the most effective drug targets and the focus of multi-billion dollar pharmaceuticals. A comprehensive understanding of NR gene targeting in vivo, especially when bound to different physiological ligands as well as widely prescribed drugs that have different impact in different individuals and different cell types, will result in a highly informed approach to drug development and deployment. State-of-the-art methods are inadequate to fully characterize the DNA cognate sites of NRs because they often bind as cooperative homotypic or heterotypic oligomers with other TFs. Additionally, the site preferences of NRs are modulated in non-obvious ways by certain natural ligands and related synthetic drugs. The state-of-the-art methods also often ignore the medium-to-low sequence specificity differences of closely related TFs, which in turn are crucial to understanding the vital differences in the biological functions among the NRs. This project’s first aim is to develop innovative computational approaches to elucidate the complex binding characteristics of NRs and to identify the vital differences in binding profiles of closely related NRs. The analysis will utilize recently collected experimental cognate site identification (CSI) data from high throughput sequencing of DNA-interactomes of all full-length functional human NRs in the context of whole cell extracts. We also propose to rigorously evaluate the impact of a wide-range of physiological small molecule ligands as well as prescribed therapeutics/drugs on NR-DNA interactomes. The computationally determined sequence preferences will be experimentally tested using biochemical, biophysical and cell biological assays. Thus we will integrate computation and experimental validation to decipher how NRs target the genome and manifest their biological roles. Moreover, the efforts will enable precision-medicine by defining the impact of current therapeutics in guiding NRs in the context of individual genomes.