Nucleosome architecture in aging and nuclear receptor activation in the liver

描述（由申请人提供）：我的长期目标是成为一名独立的多学科研究者，应用实验和计算方法研究代谢功能障碍背后的年龄依赖性染色质变化。我正在努力争取在一个领先的研究机构获得终身教职，这样我就可以把我的时间用于基础研究和培养学生和研究员在我的实验室。在博士工作期间，我利用功能基因组学方法研究肝脏的转录调控网络，发现翼螺旋转录因子Foxa2在胆汁酸代谢中起重要作用。在完成我的博士学位后，我决定追随科学，由于我享受创造性和财务自由，我能够从事我在Kaestner博士的实验室开发的项目。作为Kaestner实验室的博士后，我在一个小鼠模型中发现了一种新的年龄性肥胖表型，其中基因缺失只发生在肝脏中，强调了肝脏在发育中所起的重要作用

DESCRIPTION (provided by applicant): My long-term goal is to become an independent multidisciplinary investigator, applying both experimental and computational approaches to age-dependent chromatin changes underlying metabolic dysfunction. I am working towards obtaining a tenure-track faculty position at a leading research institution, so that I can devote m time to basic research and training of students and fellows in my laboratory. During the course of my doctoral work, I utilized functional genomic approaches to investigate transcriptional regulatory networks in the liver and discovered that winged-helix transcription factor Foxa2 plays an important role in bile acid metabolism. After completing my doctoral degree I decided to follow the science and, due to creative and financial freedom I enjoyed, was able to pursue projects that I developed in Dr. Kaestner's laboratory. As a postdoctoral fellow in the Kaestner lab, I discovered a novel age-onset obesity phenotype in a mouse model where genetic deletion occurs only in the liver, underscoring the importance of the role the liver plays in development of obesity. Loss of Foxa2 in the liver of older mice results in a premature aging phenotype, as Foxa2-deficient mice exhibit reduced food intake, decreased energy expenditure, and triglyceride accumulation. Foxa2 antagonizes mTOR signaling, leading to activation of LXR� and increased lipogenesis. This finding piqued my interest in age-dependent metabolic changes. In order to become a productive multidisciplinary researcher, it is essential to know both how to perform experiments properly to generate the data and how to analyze the data appropriately. I came to Regev lab at the Broad Institute to complement my experimental background and build upon my computational skills with training in analysis of large data sets and modeling of genomic data. I am currently analyzing the data from MNase-seq and RNA-seq experiments I performed in livers isolated from mice of different ages (Aim 1). We are expecting to finish the analysis and submit the paper in the fall. Dr. Regev has supported my decision to continue metabolic research in her laboratory. While my primary mentor Dr. Regev is a computational biologist with extensive experience in epigenetic regulation, genomics methods and computational analysis, I am co-advised by a multidisciplinary committee that includes Dr. Waxman, an expert in transcriptional and epigenetic networks that govern hepatic gene expression, Dr. Timchenko, an expert in the field of aging liver and age-associated chromatin changes, Dr. Moore, a leader in the field of nuclear receptors and lipid metabolism, and Dr. Rosen, a clinician with experience in epigenetics and human obesity. With their guidance, I will build a foundation necessary to pursue the relationship between age-dependent chromatin changes and metabolic dysfunction as an independent investigator. Epigenetic changes act as crucial mediators of age-dependent impairments in the liver and other tissues, suggesting a common mechanism could be responsible. I hypothesize that nucleosome architecture changes with aging are a key part of this mechanism in the aging liver. To test this hypothesis, I will examine genome-wide nucleosome positioning and occupancy in livers isolated from mice of three different ages in Aim 1. Next, I will examine changes in histone modifications with age in Aim 2. Integrating nucleosome occupancy, chromatin state, and gene expression at different ages should converge on regulators and a molecular mechanism for age-associated dysfunction. The unbiased search for regulators of age-dependent metabolic phenotypes will be complemented by a candidate approach. Current ChIP-Seq data for nuclear receptors have challenged the classical model of nuclear-receptor-dependent gene regulation. However, the genome-wide location analysis shows that LXR� binding in the liver is largely ligand-dependent and that the agonist enables LXR� to occupy less accessible sites. These observations led me to hypothesize that chromatin architecture plays a larger role in nuclear receptor binding and metabolic gene regulation than previously appreciated. Since uncontrolled hepatic lipogenesis, regulated by LXR�, can contribute to development of age-dependent obesity and DAF-12, LXR homolog in C.elegans, mediates responses to environmental conditions during aging, it is crucial to understand the complete mechanism of activation and the contribution of low and high affinity LXR� binding sites to gene regulation (Aim 3), which can be extrapolated to other nuclear receptors and their metabolic targets. In this application, I hypothesize that chromatin architecture changes with aging and plays a larger role in nuclear receptor binding and metabolic gene regulation than previously appreciated and propose a series of experiments and analyses to test these ideas. The ultimate goal is to determine how epigenetic changes lead to changes in transcription factor binding modulating gene regulation responsible for age-dependent metabolic phenotypes. The object of this unbiased search, which is complemented by a candidate approach, is to find candidate regulators that can be manipulated to treat age-dependent metabolic dysfunction. Integrating the training in epigenetics and analysis of large-scale genomic data, supported by this K01 award, with my background in metabolic research, aging, transcriptional regulation, and gene regulatory networks makes me uniquely qualified to pursue the relationship between age-dependent chromatin changes and metabolic dysregulation.