ChemBio Spotlight #7
Paper: Nucleotide Excision Repair is Impaired by Binding of Transcription Factors to DNA. http://www.nature.com/nature/journal/v532/n7598/full/nature17661.html
Somatic mutations in DNA have a variety of causes including exposure to mutagens, such as ultraviolet (UV) radiation, or errors in DNA replication. These mutations can give rise to diseases such as cancer, so it is important that the cell is able to identify and repair this damaged DNA. Nucleotide excision repair (NER) is one such DNA repair mechanism. NER plays an important role in repairing DNA damage caused by UV radiation. Mutations caused by UV radiation are a cause of melanomas (skin cancer). The authors were interested in studying areas of DNA where higher rates of mutation occur.
In the cell, DNA is wrapped around proteins called histones to form nucleosomes (see above image). The authors hypothesized that the bound or unbound state of the DNA might play a role in the frequency of mutations on particular sections of DNA. There was a link between transcription factor binding sites (TFBS) and areas that had more frequent mutations. This led the authors to believe that the binding of these transcription factors to DNA was preventing the NER mechanism from accessing these stretches of DNA.
The authors first analyzed the genomes of multiple melanomas to determine the amount of mutations at TFBS. They discovered that the rate of mutation was significantly higher in DNA regions where transcription factors were actively binding. Active TFBS occur at DNase I hypersensitive sites (DHS) where the DNA is not bound as a nucleosome. It had previously been accepted that NER was more effective at these DHS sites due to the accessibility of the DNA, an idea brought into question by this paper. The combination of unbound DNA and the active binding of transcription factors to that DNA was correlated to a significantly higher mutation rates. This result was replicated across the genome of both cancerous and healthy cells.
The authors then verified that these areas of increased mutation only occur in DHS where transcription factors are binding, not in DHS where nothing is bound to the DNA. This supported the idea that DNA-bound proteins are preventing the components of NER from accessing and repairing mutated DNA. To test this further, the authors induced mutations. XR-seq was used to cut out the mutated regions which were then examined. There was a definite decrease in repair in the TFBS. The results of this paper strongly support the idea that the binding of transcription factors is a hindrance to NER. The unrepaired mutations have been linked to melanomas and certain types of tobacco-related lung cancer.