Nucleosomal Proofreading of Activator-Promoter Recognition

激活子-启动子识别的核小体校对

• 批准号: 2111763
• 负责人: Hinrich Boeger
• 金额: $ 110万
• 依托单位: University of California-Santa Cruz
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-06-15 至 2025-05-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2111763&HistoricalAwards=false
• 关键词: Nucleosomal; Proofreading; Activator; Promoter; Recognition

This research program investigates the role of random molecular behavior in regulating gene expression by "transcriptional activators", molecules that control the activity of genes by binding to specific regulatory sequences in DNA. The project introduces students from diverse backgrounds to a fundamental theoretical problem at the interface between molecular genetics and statistical physics as well as advanced experimental tools to address this problem. Pedagogically, the program aims to integrate mathematical, physical, and quantitative reasoning into the biology curriculum for undergraduate and graduate students and provide research opportunities to high school students to increase participation in STEM fields.The specificity of transcriptional regulation – which genes are transcribed in response to a particular signal – is thought to rest entirely with the specificity of activator-gene recognition. Yet, for many eukaryotic activators the energetic differences between correct and incorrect sequence binding are remarkably small – too small to explain observed regulatory specificities. The specificity problem may be solved by "kinetic proofreading", i.e., insertion of a free energy-transducing delay step between activator-promoter binding and transcription. The mechanism enhances specificity not by increasing the energetic difference between correct and incorrect associations but by exploiting the same difference twice, before the delay step and afterward, when free energy dissipation favors complex dissociation over formation and return of the suspended delay mechanism to its repressive state. A prime candidate among possible delay mechanisms for activator proofreading is ATP-dependent chromatin remodeling, which relieves genes from nucleosomal repression in an activator-dependent manner. Logical implications of this proposition, including the prediction that perturbation of chromatin remodeling affects the ability of activators to distinguish between correct and incorrect genes, will be tested by employing a combination of live-cell multifocus fluorescence microscopy, single molecule-fluorescence in situ hybridization, nanopore sequencing, and reverse genetics in yeast. The outcomes will provide new insights on how near deterministic behavior of biological systems emerges from the random behavior of their molecular components.This project is jointly funded by the Genetic Mechanisms program of the Molecular and Cellular Biosciences Division in the Biological Sciences Directorate and the Mathematical Biology program of the Mathematical Sciences Division in the Mathematical and Physical Sciences Directorate.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

该研究项目调查了随机分子行为在通过“转录激活因子”调节基因表达中的作用，转录激活因子是通过与DNA中的特定调控序列结合来控制基因活性的分子。该项目向来自不同背景的学生介绍了分子遗传学和统计物理学之间接口的基本理论问题，以及解决这一问题的先进实验工具。在教学上，该计划旨在将数学，物理和定量推理融入本科生和研究生的生物课程，并为高中生提供研究机会，以增加STEM领域的参与。转录调控的特异性-基因转录响应特定信号-被认为完全取决于激活基因识别的特异性。然而，对于许多真核生物激活剂，正确和不正确的序列结合之间的能量差异非常小-小到无法解释观察到的调节特异性。特异性问题可以通过“动力学校正”来解决，即，在激活子-启动子结合和转录之间插入自由能转导延迟步骤。该机制不是通过增加正确和不正确的关联之间的能量差异来增强特异性，而是通过利用相同的差异两次，在延迟步骤之前和之后，当自由能耗散有利于复合物解离而不是形成和返回暂停延迟机制到其抑制状态时。激活剂校正的可能延迟机制中的一个主要候选者是ATP依赖性染色质重塑，其以激活剂依赖的方式解除基因的核小体抑制。这一命题的逻辑含义，包括染色质重塑的扰动影响激活剂区分正确和不正确的基因的能力的预测，将通过采用活细胞多焦点荧光显微镜，单分子荧光原位杂交，纳米孔测序和酵母反向遗传学的组合进行测试。该研究成果将为生物系统的确定性行为如何从其分子组成的随机行为中出现提供新的见解。该项目由生物科学理事会分子和细胞生物科学部的遗传机制计划和数学和物理科学理事会数学科学部的数学生物学计划共同资助。该奖项反映了NSF的法定基金会的使命是履行其使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评价，被认为值得支持。

项目成果

Kinetic Proofreading

动力学校对

• DOI: 10.1146/annurev-biochem-040320-103630
• 发表时间: 2022
• 期刊: Annual Review of Biochemistry
• 影响因子: 16.6
• 作者: Boeger, Hinrich

The energetics of activator–promoter recognition

激活子-启动子识别的能量学

• DOI: 10.1016/j.coisb.2022.100434
• 发表时间: 2022
• 期刊: Current Opinion in Systems Biology
• 影响因子: 3.7
• 作者: Boeger, Hinrich