Revealing masked specificities of human Nuclear Receptors

项目概要/摘要 人核受体（NR）家族在重要的细胞功能中发挥重要作用， 新陈代谢和生理学。由于NR突变或 在相关的DNA调控位点，已被牵连在已牵连在几种疾病 包括青光眼、白内障、视网膜疾病、哮喘、炎症、自身免疫和发育 失调、激素失衡、肥胖、癌症和糖尿病。人类的核反应堆是最有效的 药物靶点和数十亿美元的药物的焦点。对NR基因的全面认识 体内靶向，特别是当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， 药物开发和部署的方法。最先进的方法不足以充分表征 NR的DNA同源位点，因为它们通常作为合作的同型或异型寡聚体与 其他TF此外，NR的位置偏好以非明显的方式受到某些自然条件的调节。 配体和相关的合成药物。最先进的方法也往往忽略了中低 密切相关的转录因子的序列特异性差异，这反过来又是至关重要的了解重要的 NR之间生物学功能的差异。该项目的第一个目标是开发创新的 计算方法来阐明NR的复杂结合特性，并确定重要的 密切相关的NR的结合特征的差异。分析将利用最近收集的实验数据， 来自所有全长的DNA相互作用组的高通量测序的同源位点鉴定（CSI）数据 在全细胞提取物的情况下的功能性人NR。我们还建议严格评估 广泛的生理小分子配体以及NR-DNA上的处方治疗剂/药物 相互作用体通过计算确定的序列偏好将通过使用 生物化学、生物物理学和细胞生物学测定。因此，我们将结合计算和实验 验证以破译NR如何靶向基因组并表现出它们的生物学作用。此外，努力将 通过定义当前治疗方法在以下背景下指导NR的影响，实现精确医学 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.