Gene Regulation from Long-Distance Chromosomal Interactions in Yeast

酵母中长距离染色体相互作用的基因调控

• 批准号: 9923700
• 负责人: Lu Bai
• 金额: $ 30.52万
• 依托单位: PENNSYLVANIA STATE UNIVERSITY, THE
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-05-06 至 2022-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9923700
• 关键词: 3-Dimensional; Affect; Alleles; Area; Bioinformatics; Biological Assay; Case Study; Cell Communication; Cell Proliferation; Cells; Characteristics; Chromatin; Chromosome Structures; Chromosomes; Computational Biology; Data; Development; Diploid Cells; Diploidy; Disease; Drosophila genus; Enhancers; Eukaryota; Galactose; Galectin 1; Gene Expression; Gene Expression Profiling; Gene Expression Regulation; Genes; Genetic; Genetic Transcription; Genome; Goals; Growth; Haploidy; Health; Human; Knowledge; Lead; Length; Libraries; Light; Locus Control Region; Mammalian Cell; Measurement; Mediating; Methods; Modeling; Noise; Nuclear; Nucleic Acid Regulatory Sequences; Organism; Pattern; Physiological; Play; Polyploid Cells; Positioning Attribute; Regulation; Regulator Genes; Regulatory Element; Reporter; Reporter Genes; Reporting; Research; Role; Saccharomycetales; Study models; Survival Rate; Techniques; Testing; Time; Training; Work; Yeasts; base; beta Globin; chromosome conformation capture; density; design; experimental study; genomic locus; high throughput screening; in vivo; insight; live cell imaging; novel; programs; promoter; public health relevance; yeast genetics; yeast genome

 DESCRIPTION (provided by applicant): Rigorously controlled gene expression is essential for cellular proliferation and differentiation. In recent years, more and more evidence show that the 3D organization of the genome is important for regulation of gene activity. Chromosome Conformation Capture (3C) technique and its derivatives (4C, Hi-C, etc.) have revealed extensive intra- and inter-chromosomal interactions in various eukaryotic species. Some of these interactions, such as the enhancer-promoter looping at the beta-globin Locus Control Region, play an essential role in gene regulation. Another type of long-distance interaction, homologous pairing, can also affect gene expression in somatic diploid cells. Both long-distance chromosomal interactions and homologous pairing were observed in budding yeast during vegetative growth. However, the functional significance of these interactions are not understood. The goal of this proposal is to identify and mechanistically dissect long-distance interactions tha regulate gene expression in budding yeast. We will assay gene expression in single live cells to probe the regulatory effect on the average level, cell-to-cell variability (noise), and dynamics of gene expression. In Aim 1, we focus on gene regulatory effect by interactions between homologous alleles. Our preliminary data have provided strong evidence that a reporter gene can make contacts with its allelic copy and influence its activity. We plan to fully characterize this phenomenon and elucidate the underlying mechanism. In addition, we will pioneer a method to manipulate long-distance chromosomal interactions and probe the corresponding effect on gene regulation. In Aim 2, we will study gene regulation by non-homologous long-distance chromosomal interactions. We designed a novel yeast library containing dual reporters to screen for long-distance interactions that lead to change in gene expression. Altered reporter expression (both the average level and noise) was found in a fraction of the library strains, potentially caused by chromosomal looping / clustering. We propose further characterization of the gene regulation in these strains and an in-depth analysis of the regulatory mechanism. Completion of these studies will provide key insights into the regulatory function of long-distance interactions and establish budding yeast as an important model for studying long-distance gene regulation. These works may also generate proof-of-principle concepts for designing similar experiments in multi-cellular eukaryote.

 描述（由申请人提供）：严格控制的基因表达对细胞增殖和分化至关重要。近年来，越来越多的证据表明，基因组的三维结构对于基因活性的调控是重要的。染色体构象捕获（3C）技术及其衍生物（4C、Hi-C等）已经揭示了各种真核生物中广泛的染色体内和染色体间的相互作用。其中一些相互作用，如在β-珠蛋白基因座控制区的增强子-启动子环，在基因调控中发挥重要作用。另一种类型的远距离相互作用，同源配对，也可以影响体细胞二倍体细胞中的基因表达。在芽殖酵母的营养生长过程中，染色体长距离相互作用和同源配对都被观察到。然而，这些相互作用的功能意义尚不清楚。这个建议的目的是确定和机械解剖长距离的相互作用，调节基因表达芽殖酵母。我们将在单个活细胞中测定基因表达，以探测对平均水平、细胞间变异性（噪音）和基因表达动力学的调节作用。 基因表达。目的一是研究同源等位基因间相互作用对基因表达的调控作用。我们的初步数据提供了强有力的证据，报告基因可以使其等位基因拷贝的联系，并影响其活动。我们计划充分描述这种现象，并阐明其内在机制。此外，我们将开创一种方法来操纵长距离染色体相互作用，并探测对基因调控的相应影响。在目标2中，我们将研究非同源长距离染色体相互作用的基因调控。我们设计了一个新的酵母文库，包含双报告筛选长距离相互作用，导致基因表达的变化。在一部分文库菌株中发现了改变的报告基因表达（平均水平和噪声），这可能是由染色体成环/成簇引起的。我们建议进一步表征这些菌株中的基因调控，并深入分析调控机制。这些研究的完成将提供关键的见解，调节功能的长距离 建立了芽殖酵母作为研究远距离基因调控的重要模型。这些工作也可能产生原理验证的概念，设计类似的实验，在多细胞真核生物。