Collaborative Research: NSF/MCB-BSF: The effect of transcription factor binding on UV lesion accumulation

合作研究：NSF/MCB-BSF：转录因子结合对紫外线损伤积累的影响

• 批准号: 2324614
• 负责人: Raluca Gordan
• 金额: $ 69.97万
• 依托单位: Duke University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-15 至 2026-08-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2324614&HistoricalAwards=false
• 关键词: Collaborative; Research; NSF; MCB; BSF

The DNA sequence of the human genome varies among people. However, these variations or mutations are not evenly dispersed throughout the genome. Variation is highest where regulatory proteins bind to DNA, a process that is poorly understood despite the fact that these changes can significantly impact human biology. This project will determine whether genomic variation is increased because protein binding makes DNA more susceptible to damage, and subsequently mutations, or because proteins block repair of damaged DNA leading to mutations. Assessing these possibilities requires development of innovative methods. This project will not only answer the question of whether proteins make DNA more susceptible to damage or harder to repair, but the newly developed methods will be a major leap forward in quantitative measurement of DNA damage. To ensure the broader impact of the newly developed methods, investigators will reach out to the next generations of scientists in two ways. A workshop entitled “What is Damaging My DNA” will be offered to high school students to engage the younger generation. In addition, an intensive summer workshop entitled “Computational Thinking for Academic Professionals” will be offered to academic scientists who need training handling larger datasets, such as those in this project.Transcription factor (TF) proteins bind to specific DNA sequences across the genome to regulate gene expression. Surprisingly, recent genomic studies indicate that TF binding sites are characterized by increased DNA damage and are highly enriched for somatic mutations, suggesting that TF‐DNA binding is mutagenic. This project hypothesizes that that TFs induce unique patterns of lesion accumulation within binding sites, which are dictated by the ability of TFs to enhance lesion formation and to occlude access to the nucleotide excision repair machinery. UV light will be used as a source of DNA damage to develop high‐throughput in vitro techniques and quantitative models for: the affinity of TFs from different families for lesion-containing DNA and ability to compete with repair proteins; and the modulation of DNA damage formation by TF binding. These models will be used to predict genome‐wide DNA damage and repair in human cells and to develop cell‐based assays of damage and repair in genomic contexts. Successful completion of this work will link increases in mutation rates in TF binding sites to the molecular mechanisms by which TFs increase UV damage frequency in the human genome.This collaborative US/Israel project is supported by the US National Science Foundation, with joint funding from Molecular and Cellular Biosciences and the Established Program to Stimulate Competitive Research (EPSCoR), and the Israeli Binational Science Foundation.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.

人类基因组的 DNA 序列因人而异，但这些变异或突变并不是均匀分布在整个基因组中，调节蛋白与 DNA 结合的地方变异最高，尽管这些变化会显着影响这一过程，但人们对这一过程知之甚少。该项目将确定基因组变异是否增加是因为蛋白质结合使 DNA 更容易受到损伤和随后的突变，或者是因为蛋白质阻止了受损 DNA 的修复而导致突变。评估这些可能性需要开发创新方法。不仅回答蛋白质是否使DNA更丰富的问题损伤或难以修复，但新开发的方法将是定量易感 DNA 损伤测量的重大飞跃，为了确保新开发的方法产生更广泛的影响，研究人员将通过两种方式接触下一代科学家。将为高中生举办题为“什么正在损害我的 DNA”的研讨会，以吸引年轻一代的参与。此外，还将为需要处理更大规模问题的学术科学家举办题为“学术专业人员的计算思维”的强化夏季研讨会。数据集，例如本项目中的数据集。转录令人惊讶的是，TF 蛋白与基因组中的特定 DNA 序列结合来调节基因表达，最近的基因组研究表明 TF 结合位点的特点是 DNA 损伤增加，并且体细胞突变高度富集，这表明 TF-DNA 结合具有诱变性。该项目开创性地认为，转录因子在结合位点内诱导独特的损伤积累模式，这是由转录因子增强损伤形成和阻断核苷酸切除修复机制的能力决定的，紫外光将被用作核苷酸切除修复机制的来源。 DNA 损伤，开发高通量体外技术和定量模型：来自不同家族的 TF 对含有病变的 DNA 的亲和力以及与修复蛋白竞争的能力；以及通过 TF 结合调节 DNA 损伤形成。 ‐人类细胞中广泛的 DNA 损伤和修复，并开发基于细胞的基因组损伤和修复检测方法。这项工作的成功完成将把 TF 结合位点突变率的增加与 TF 增加紫外线损伤频率的分子机制联系起来。在这个美国/以色列合作项目得到了美国国家科学基金会的支持，并得到了分子和细胞生物科学和刺激竞争性研究既定计划 (EPSCoR) 以及以色列两国科学基金会的联合资助。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。