Nuclear Architecture, NcRNAs and Epigenetics in Transcriptional Regulation by ER

ER 转录调控中的核结构、NcRNA 和表观遗传学

• 批准号: 8281291
• 负责人: Chunru Lin
• 金额: $ 9万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-08-15 至 2013-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8281291
• 关键词: Address; Affect; Antibodies; Architecture; Award; Binding; Biological Assay; Breast Cancer Cell; Cell Line; ChIP-seq; Chromatin; Complex; Cytoplasmic Granules; Data; Databases; Development; Disease; Environment; Epigenetic Process; Epithelial Cells; Estradiol; Estrogen Receptor alpha; Estrogen Receptors; Estrogens; Event; Excision; Female; Functional RNA; Gene Activation; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Gene Targeting; Genes; Genetic Transcription; Goals; Growth; Histone Code; Histones; Homeostasis; In Vitro; Ligands; Location; Mammary gland; Mediating; Metabolic; Metabolism; Methylation; Modification; Molecular; Nuclear; Peptides; Play; Polycomb; Positioning Attribute; Process; Proteins; RNA; Reader; Reading; Regulation; Repression; Research Personnel; Role; Signal Transduction; Small Interfering RNA; Small RNA; Structure; Tail; Testing; Therapeutic; Time; Transcript; Transcriptional Regulation; base; blood glucose regulation; cofactor; demethylation; digital; drug development; genome-wide; glucose metabolism; in vivo; innovation; insight; malignant breast neoplasm; mammary gland development; novel; novel strategies; preference; programs; promoter; protein function; reproductive function; response; transcription factor

DESCRIPTION (provided by applicant): Estradiol, which acts through the Estrogen Receptor alpha (ER¿), is essential for the development and homeostasis of female reproductive function, exerting critical control of many transcriptional programs, including these regulatory proliferatio, and metabolism. The molecular mechanism used by ER¿ to mediate coactivator/corepressor exchanges in gene activation has been reasonably well elucidated. ER¿, chromatin modifiers and dynamic positioning of particular loci are all essential for establishing precise transcriptionl regulation and achieving the correct patterns of gene expression. However, it is not clear how these factors are spatially regulated in distinct subnuclear structures and how this regulation may contribute to gene regulation. ) Our recent findings demonstrated a signal-induced relocation of the transcription units from a transcriptional repressive compartment to a permissive environment. I hypothesize that non-coding RNAs (ncRNAs) TUG1 and NEAT2 control ER¿ target genes to relocate from the transcriptional repressive Polycomb bodies (PcGs) to the gene activation milieu of the interchromatin granules, by selectively interacting with methylated and unmethylated Polycomb 2 protein (Pc2) present on ER¿ target gene promoters. To address this long-term goal, I propose to investigate the hypothesis from three specific aims: 1) to define non- histone methylation/demethylation events and ncRNAs as a novel molecular strategy responsible for genome- wide ER¿ transcriptional programs; 2) to determine the potential role of two ncRNAs, TUG1 and NEAT2, located in PcGs and interchromatin granules, respectively, in controlling relocation of ER¿ target genes between these two subnuclear structures, depending on the status of Pc2 methylation in response to estrogen; 3) to investigate the potential allosteric role of ncRNA in modulating the ability of "readers" of the histone code, such as Pc2, to recognize histone tail modifications. To achieve these aims, I propose to define the genome-wide location of methylated vs. unmethylated Pc2 by ChIP-Seq analysis using specific antibodies and the functional roles of Pc2 or other active "readers" and ncRNAs in controlling the ER¿ transcriptome by a combination of GRO-Seq, RNA-Seq analysis and siRNA knockdown strategies. I will also investigate the potential relocalization of ER¿-regulated genes from PcG bodies to interchromatin granules upon E2 stimulation and the underlying mechanisms, by which the binding of TUG1 or NEAT2 ncRNAs directs the preference of Pc2 recognition of histone tail modification. Taken together, the proposed study evaluates a new concept that ER¿ target gene loci relocate between functionally distinct nuclear architectural structures and the roles of several novel modulators that play a critical role in ER¿ target gene regulation. These findings will provide innovative targets for drugs development for a number of intriguing therapeutic implications. Based on the extensive preliminary data, I am confident of accomplishing these aims in the period of the award and emerging as an Independent Investigator. PUBLIC HEALTH RELEVANCE: It has been well established that estrogen plays important roles in promoting mammary gland development, regulating transcription and metabolism, and many pathological conditions. While much is understood about actions of Estrogen Receptor, additional unexplored molecular strategies appear to contribute to the critical aspect of estrogen function. The proposed studies in this application dissect the control of estrogen receptor target gene expression from an innovative view that incorporates three-dimensional context of nuclear architecture, epigenetic modifications and novel non-coding RNAs, which will uncover new approaches to treat estrogen-related disease using small RNAs to target ncRNA transcripts.

描述（由申请人提供）：雌激素通过雌激素受体α（ER？）发挥作用，对女性生殖功能的发育和稳态至关重要，对许多转录程序（包括这些调节性增殖和代谢）发挥关键控制作用。在基因激活中，ER <$介导辅激活子/辅阻遏子交换的分子机制已经得到了合理的阐明。呃，染色质修饰剂和特定基因座的动态定位对于建立精确的转录调控和获得正确的基因表达模式都是必不可少的。然而，目前尚不清楚这些因素是如何在不同的亚核结构的空间调控，以及如何这种调节可能有助于基因调控。我们最近的发现证明了信号诱导的转录单位从转录抑制区室到允许环境的重新定位。我假设非编码RNA（ncRNA）TUG 1和NEAT 2通过选择性地与ER <$靶基因启动子上的甲基化和未甲基化的Polycomb 2蛋白（Pc 2）相互作用，控制ER <$靶基因从转录抑制性Polycomb小体（PcGs）重新定位到染色质间颗粒的基因激活环境。为了实现这一长期目标，我建议从三个具体目标来研究这一假说：1）将非组蛋白甲基化/去甲基化事件和ncRNA定义为负责全基因组ER <$转录程序的新分子策略; 2）确定分别位于PcGs和染色质间颗粒的两个ncRNA TUG 1和NEAT 2在控制ER <$重新定位中的潜在作用。这两个亚核结构之间的靶基因，这取决于响应雌激素的Pc 2甲基化的状态; 3）研究ncRNA在调节组蛋白密码子的“阅读器”（如Pc 2）识别组蛋白尾部修饰的能力中的潜在变构作用。为了实现这些目标，我建议使用特异性抗体通过ChIP-Seq分析来定义甲基化与未甲基化的Pc 2的全基因组位置，以及Pc 2或其他活性“阅读器”和ncRNA在控制ER？转录组中的功能作用，通过GRO-Seq，RNA-Seq分析和siRNA敲低策略的组合。我还将研究E2刺激后ER？调节基因从PcG体到染色质间颗粒的潜在重新定位以及潜在机制，通过这些机制，TUG 1或NEAT 2 ncRNA的结合指导Pc 2识别组蛋白尾部修饰的偏好。总之，这项研究评估了一个新的概念，即ER <$靶基因位点在功能不同的核结构结构之间重新定位，以及在ER <$靶基因调控中发挥关键作用的几种新型调节剂的作用。这些发现将为药物开发提供创新靶点，以实现许多有趣的治疗意义。基于广泛的初步数据，我有信心在获奖期间实现这些目标，并成为一名独立调查员。 公共卫生关系：雌激素在促进乳腺发育、调节转录和代谢以及多种病理状态中发挥重要作用。虽然对雌激素受体的作用了解很多，但其他未探索的分子策略似乎有助于雌激素功能的关键方面。本申请中提出的研究从一个创新的角度剖析了雌激素受体靶基因表达的控制，该观点结合了核结构、表观遗传修饰和新型非编码RNA的三维背景，这将揭示使用小RNA靶向ncRNA转录物治疗雌激素相关疾病的新方法。

项目成果

The Genomic Landscape and Pharmacogenomic Interactions of Clock Genes in Cancer Chronotherapy.

• DOI: 10.1016/j.cels.2018.01.013
• 发表时间: 2018-03-28
• 期刊: Cell systems
• 影响因子: 9.3
• 作者: Ye Y;Xiang Y;Ozguc FM;Kim Y;Liu CJ;Park PK;Hu Q;Diao L;Lou Y;Lin C;Guo AY;Zhou B;Wang L;Chen Z;Takahashi JS;Mills GB;Yoo SH;Han L
• 通讯作者: Han L