High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors
- University of New Mexico, United States
- Washington State University, United States
- Georgia State University, United States
Abstract
DNA base damage arises frequently in living cells and needs to be removed by base excision repair (BER) to prevent mutagenesis and genome instability. Both the formation and repair of base damage occur in chromatin and are conceivably affected by DNA-binding proteins such as transcription factors (TFs). However, to what extent TF binding affects base damage distribution and BER in cells is unclear. Here, we used a genome-wide damage mapping method, N-methylpurine-sequencing (NMP-seq), and characterized alkylation damage distribution and BER at TF binding sites in yeast cells treated with the alkylating agent methyl methanesulfonate (MMS). Our data shows that alkylation damage formation was mainly suppressed at the binding sites of yeast TFs Abf1 and Reb1, but individual hotspots with elevated damage levels were also found. Additionally, Abf1 and Reb1 binding strongly inhibits BER in vivo and in vitro, causing slow repair both within the core motif and its adjacent DNA. Repair of UV damage by nucleotide excision repair (NER) was also inhibited by TF binding. Interestingly, TF binding inhibits a larger DNA region for NER relative to BER. The observed effects are caused by the TF-DNA interaction, because damage formation and BER can be restored by depletion of Abf1 or Reb1 protein from the nucleus. Thus, our data reveal that TF binding significantly modulates alkylation base damage formation and inhibits repair by the BER pathway. The interplay between base damage formation and BER may play an important role in affecting mutation frequency in gene regulatory regions.
Data availability
New DNA sequencing data has been deposited to GEO under accession code GSE183622. All data generated or analyzed are included in the manuscript and supplemental file. Source data files containing the numerical data for Figure 1 and Figure 2 are uploaded. Source codes used for sequencing reads mapping to identify alkylation lesions and repair analysis at yeast Abf1 and Reb1 binding sites are also uploaded.
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Analysis of alkylation damage formation and base excision repair at yeast transcription factor binding sitesNCBI Gene Expression Omnibus, GSE183622.
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CPD-seq mapping of transcription-coupled DNA repair in yeastNCBI Gene Expression Omnibus, GSE145911.
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Genome-wide Maps of Alkylation Damage, Repair, and Mutagenesis in Yeast Reveal Mechanisms of Mutational HeterogeneityNCBI Gene Expression Omnibus, GSE98031.
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A high-resolution protein architecture of the budding yeast genomeNCBI Gene Expression Omnibus, GSE147927.
Article and author information
Author details
Smitha Sivapragasam
Funding
National Institute of Environmental Health Sciences (R21ES029302)
- John J Wyrick
- Peng Mao
National Institute of Environmental Health Sciences (R01ES032814)
- John J Wyrick
National Institute of Environmental Health Sciences (R01ES028698)
- John J Wyrick
National Science Foundation (MCB 2028902)
- Gregory MK Poon
National Institute of General Medical Sciences (P20GM130422)
- Peng Mao
National Cancer Institute (P30CA118100)
- Mingrui Duan
- Peng Mao
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, Duan et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors
eLife 11:e73943.
https://doi.org/10.7554/eLife.73943
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