Impact of enhancer sequence and interacting factors on estrogen receptor-mediated

增强子序列和相互作用因素对雌激素受体介导的影响

• 批准号: 8513388
• 负责人: Jason Gertz
• 金额: $ 9.51万
• 依托单位: HUDSON-ALPHA INSTITUTE FOR BIOTECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-07-18 至 2013-10-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8513388
• 关键词: Address; Adverse effects; Affect; Award; Base Sequence; Behavior; Binding; Binding Sites; Biological Assay; Breast Cancer Cell; Breast Cancer Treatment; Cancer cell line; Cell Line; Cells; ChIP-seq; Chromatin; Collaborations; Communication; Communities; DNA Sequence; Data; Deoxyribonuclease I; Deoxyribonucleases; Disease; Dissection; Distal; Endometrial; Endometrial Carcinoma; Engineering; Enhancers; Environmental Estrogen; Estrogen Receptors; Estrogens; Event; Exhibits; Faculty; Fibrinogen; Gene Expression; Gene Expression Regulation; Gene Targeting; Genes; Genetic; Genome; Genomics; Goals; Health; Human; Human Cell Line; Human body; Hypersensitivity; Individual; Instruction; Knock-out; Knowledge; Learning; Light; Location; Maps; Measurement; Mediating; Mentors; Mentorship; Methods; Modeling; Molecular; Mutation; Nuclear Receptors; Osteoporosis; Outcome; Pathway interactions; Phase; Physiological; Physiology; Play; Positron-Emission Tomography; Postdoctoral Fellow; Property; Reading; Receptor Cell; Regulation; Regulator Genes; Reporter Genes; Research; Research Personnel; Research Proposals; Role; Signal Transduction; Specificity; Study models; System; Techniques; Testing; Tissue Engineering; Tissues; Training; Work; Writing; base; career; cell type; driving force; experience; functional genomics; gene discovery; genome sequencing; genome-wide; graduate student; insight; malignant breast neoplasm; meetings; member; receptor binding; response; skills; symposium; transcription factor; transcriptome sequencing

DESCRIPTION (provided by applicant): My long-term research goal is to read the gene regulation instructions written in our genome sequence. I would like to be able to predict gene expression levels in a given cell type from genome sequence alone and understand how the gene regulation instructions are differentially interpreted in diverse cell types. The ability to decipher the relationship between genome sequence and gene expression would have a wide reaching impact on human health. For example, very precise control of gene expression could be achieved through engineered regulatory sequences and gene regulatory mutations could be identified and easily interpreted in disease and then potentially fixed. Before achieving this loft goal, insights from directed studies in important biomedical systems must be gained. To dissect cell type-specific differences in gene regulation and how genome sequence mediates these changes, the proposed research focuses on gene regulation in response to estrogens. Estrogen signaling provides a good model for studying gene expression responses that are specific to different cell types. Estrogens produce diverse effects in a number of tissues; however, the molecular basis underlying physiological outcomes remains poorly understood. In previous work, I identified two human cell lines that exhibit very dissimilar responses to estrogen treatment, including disparity in the genes whose expression is affected and the locations of estrogen receptor binding. Through the use of multiple functional genomics assays, I hope to shed light on the mechanisms and therefore DNA sequences that underlie these cell type- specific responses. I will approach cell type-specific estrogen signaling from two angles: 1) Identify factors that interact with estrogen receptor to drive estrogen signaling in a cell type-specific manner; 2) Dissect DNA sequence constraints on cell type-specific estrogen receptor-bound enhancers. To study interacting factors I will create a list of candidate factors through analysis of DNase hypersensitivity and DNA sequence motifs. I will then test these candidates for co-occurrence with ChIP-seq and determine necessity and sufficiency by making knock out and stable over-expression cell lines. In order to dissect sequence constraints on cell type-specific estrogen responsive enhancers, I will first find active estrogen receptor bound enhancers and the genes they target using ChIA-PET, a method that analyses long-range chromatin interactions on a genome scale. I will then develop a technique to study the behavior of cell type-specific enhancer sequences in isolation that takes advantage of high-throughput sequencing. The combination of these approaches should give a robust picture of the events that dictate cell type-specificity and how genome sequence encodes cell type dependent gene regulation. The short term goals of this research proposal set me on a path towards achieving my long-term career goals of becoming a tenure-track faculty member studying gene regulation in relation to genome sequence. During the transitional award I will learn new functional genomics techniques and analysis methods, including DNase hypersensitivity mapping and ChIA-PET. I will also become an active member of the nuclear receptor community through the attendance of large conferences and individual meetings. In addition to the scientific training that I will receive during this award, I plan to learn the managerial and communication skills necessary to becoming a successful mentor. I will gain experience managing a technician, contributing to the mentorship of a graduate student and participating in collaborations with other labs. These skills, along with scientific training, should prepare me for the transition from postdoctoral fellow to independent investigator.

描述（申请人提供）：我的长期研究目标是阅读写在我们基因组序列中的基因调控指令。我希望能够单独从基因组序列预测给定细胞类型中的基因表达水平，并了解基因调控指令如何在不同细胞类型中进行差异解释。破译基因组序列和基因表达之间关系的能力将对人类健康产生广泛影响。例如，可以通过工程化的调控序列实现对基因表达的非常精确的控制，并且可以在疾病中识别和容易地解释基因调控突变，然后潜在地固定。在实现这一目标之前，必须从重要的生物医学系统的定向研究中获得见解。为了剖析基因调控中细胞类型特异性的差异以及基因组序列如何介导这些变化，拟议的研究重点是对雌激素的基因调控。雌激素信号提供了一个很好的模型，用于研究基因表达反应，是特定于不同的细胞类型。雌激素在许多组织中产生不同的作用;然而，生理结果的分子基础仍然知之甚少。在以前的工作中，我发现了两种对雌激素治疗表现出非常不同反应的人类细胞系，包括表达受影响的基因和雌激素受体结合位置的差异。通过使用多种功能基因组学分析，我希望阐明这些细胞类型特异性反应的机制和DNA序列。我将从两个角度探讨细胞类型特异性雌激素信号传导：1）识别与雌激素受体相互作用的因子，以细胞类型特异性的方式驱动雌激素信号传导; 2）解剖细胞类型特异性雌激素受体结合增强子的DNA序列约束。为了研究相互作用的因素，我将通过分析DNA酶超敏性和DNA序列基序来创建一个候选因素列表。然后，我将测试这些候选人与ChIP-seq的共现，并通过建立敲除和稳定的过表达细胞系来确定必要性和充分性。为了剖析细胞类型特异性雌激素反应增强子的序列限制，我将首先使用ChIA-PET找到活性雌激素受体结合增强子及其靶向基因，ChIA-PET是一种在基因组规模上分析长距离染色质相互作用的方法。然后，我将开发一种技术来研究细胞类型特异性增强子序列的行为，该技术利用高通量测序。这些方法的组合应该给出一个强大的图片的事件，决定细胞类型特异性和基因组序列如何编码细胞类型依赖性基因调控。这项研究计划的短期目标使我走上了实现我的长期职业目标的道路，成为一名终身教职员工，研究基因组序列相关的基因调控。在过渡奖期间，我将学习新的功能基因组学技术和分析方法，包括DNase超敏反应图谱和ChIA-PET。我还将通过参加大型会议和个人会议成为核受体界的积极成员。除了在获奖期间接受的科学培训外，我还计划学习成为一名成功导师所需的管理和沟通技巧。我将获得管理技术人员的经验，为研究生的指导做出贡献，并参与与其他实验室的合作。这些技能，沿着科学的训练，应该让我从 从博士后到独立调查员

项目成果

Distinct properties of cell-type-specific and shared transcription factor binding sites.

• DOI: 10.1016/j.molcel.2013.08.037
• 发表时间: 2013-10-10
• 期刊: MOLECULAR CELL
• 影响因子: 16
• 作者: Gertz, Jason;Savic, Daniel;Varley, Katherine E.;Partridge, E. Christopher;Safi, Alexias;Jain, Preti;Cooper, Gregory M.;Reddy, Timothy E.;Crawford, Gregory E.;Myers, Richard M.
• 通讯作者: Myers, Richard M.