Physiological Model of Gene Regulation in Drosophila

果蝇基因调控的生理模型

• 批准号: 10205184
• 负责人: John B. Reinitz
• 金额: $ 65.92万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-01-01 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10205184
• 关键词: Alleles; Architecture; Atlases; Bacteria; Basic Science; Behavior; Binding; Binding Sites; Biological Assay; Biology; Chironomus Genus; Chromatin; Chromatin Loop; Chromosomes; Code; Codon Nucleotides; Complex; Congenital Abnormality; Coupling; DNA; DNA Sequence; Data; Development; Dissection; Distant; Drosophila genus; Drosophila melanogaster; Embryo; Enhancers; Frequencies; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genetic Code; Genetic Structures; Genetic Transcription; Genome; Goals; Homologous Gene; Human; Individual; Investigation; Learning; Location; Malignant Neoplasms; Mammals; Medical; Modeling; Modernization; Monitor; Mutation; Organism; Output; Pattern; Positioning Attribute; Process; Proteins; RNA; RNA chemical synthesis; Resolution; Role; Series; Site; Specific qualifier value; Structure; System; Techniques; Testing; Time; Transcript; Transcription Initiation; Transcriptional Regulation; Variant; Work; cell fate specification; design and construction; developmental disease; experimental study; flexibility; genomic locus; in vivo; physiologic model; programs; promoter; support tools; transcription factor; translational medicine

Abstract/Project Summary The goal of this proposal is to discover and interpret the code by which cis-regulatory DNA controls gene expression. This regulatory DNA controls the specification of cell fates with exquisite precision in multicellular organisms, including humans, and its dysregulation underlies both developmental diseases and cancer. The manner in which this control is coded into the genome remains poorly understood. Moreover, the recent discovery that metazoan genes are transcribed in random bursts raises the problem of understanding how this random process is controlled to give rise to the highly precise distribution of mature transcripts observed. Both of these problems constitute a roadblock to further progress in basic science and translational medicine, and we propose to remove them by the work proposed here. The key supporting tool is an established model of transcriptional control that takes DNA sequence and the concentrations of transcription factors as inputs and gives RNA synthesis rate as output. This model is not limited to enhancers, but can also treat an entire genetic locus. We previously used this model to understand how conservation of enhancer function across phylogeneti- cally distant species occurred in the absence of conservation of DNA sequence. We found that the conserved entities were small clusters of binding sites in which the exact positions of binding sites and the identity of bound transcription factors can vary, but only within certain limits. These clusters, which we call “soft codons,” may have a role as essential as the structural genetic code. To test this, we propose to Aim 1: (a) Discover and model soft codons in the entire eve locus of D. melanogaster, D. virilis, and D. erecta in their native context, and selected enhancers from distant dipterans in the genuses Megaselia, Clogmia, and Chironomus expressed in D. melanogaster. The random bursts of transcription observed in vivo are also under the control of transcription factors. We propose to extend our transcription model to treat control of these bursts by a program of parallel experimen- tation and modeling. All experiments will be conducted in the context of a native intact locus, in which we will analyze the effects of a series of carefully selected perturbations. Specifically, we propose to Aim 2: Perform an in vivo regulatory dissection of the Drosophila eve locus in which we will monitor bursting in (a) The whole locus; (b) A series of key stripe two enhancer constructs designed to vary strength and variability of transcription; (c) Rearrangements of enhancers within the whole locus; and (d) Pure transvective constructs in which all interactions between the enhancer and basal promoter are in trans. We will use the resulting data, together with our preexisting quantitative atlas of gene expression at cellular resolution to Aim 3: Construct a new stochastic model of transcriptional control by coupling our current model of transcription to a simple model of stochastic transcription initiation.

摘要/项目摘要 这项提议的目标是发现和解释顺式调控dna控制基因的密码。 表情。这种受调控的dna在多细胞中精确地控制着细胞命运的特殊fi阳离子。 包括人类在内的生物体及其失调是导致发育疾病和癌症的基础。这个 这种控制被编码到基因组中的方式仍然知之甚少。而且，最近的 后生动物基因以随机爆发的方式转录的发现引发了理解如何 这个随机过程受到控制，以产生观察到的成熟转录本的高度精确的分布。 这两个问题都构成了基础科学和转化医学进一步发展的障碍， 我们建议通过这里提出的工作来消除它们。关键的支持工具是已建立的模型 以DNA序列和转录因子浓度为输入的转录控制 并给出了RNA合成率作为输出。这种模式不仅限于增强剂，还可以治疗整个 遗传基因。 我们以前使用这个模型来理解增强子的保守性如何在系统发育过程中发挥作用。 在DNA序列缺乏保守性的情况下，出现了远缘种。我们发现，保守的 实体是结合位点的小簇，其中结合位点的确切位置和 结合的转录因子可以变化，但只能在一定的范围内。这些簇，我们称之为“软密码子”， 可能具有与结构遗传密码一样重要的作用。为了测试这一点，我们建议目标1：(A)发现 并在黑腹隐翅虫、维氏隐翅虫和直纹夜蛾的整个夏娃轨迹中模拟软密码子 本地背景，以及从远距离的双翅目昆虫中选择的增强子。 和摇蚊在黑腹盘藻中的表达。 体内观察到的随机转录爆发也受转录因子的控制。我们 建议扩展我们的转录模型，通过一个平行实验程序来处理这些突发事件的控制。 注塑和造型。所有的实验都将在一个天然完整的轨道上进行，在这个轨道中，我们将 分析一系列精心挑选的扰动的影响。特别是fi，我们建议目标2：执行 对果蝇夏娃基因的体内调控解剖，我们将在其中监测突入(A) 整个轨迹；(B)一系列关键的条纹两个增强器构造，旨在改变强度和 转录的可变性；(C)整个基因座内增强子的重排；和(D)纯的 其中增强子和基本启动子之间的所有相互作用都在 互换。我们将使用结果数据，以及我们先前存在的基因表达定量图谱 细胞分辨目标3：通过耦合构建一个新的随机转录调控模型 我们目前的转录模型是一个简单的随机转录启动模型。