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

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.