High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors
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 (T...
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2022-03-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/73943 |
| _version_ | 1797998336937033728 |
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| author | Mingrui Duan Smitha Sivapragasam Jacob S Antony Jenna Ulibarri John M Hinz Gregory MK Poon John J Wyrick Peng Mao |
| author_facet | Mingrui Duan Smitha Sivapragasam Jacob S Antony Jenna Ulibarri John M Hinz Gregory MK Poon John J Wyrick Peng Mao |
| author_sort | Mingrui Duan |
| collection | DOAJ |
| description | 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 show that alkylation damage formation was mainly suppressed at the binding sites of yeast TFs ARS binding factor 1 (Abf1) and rDNA enhancer binding protein 1 (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 ultraviolet (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. |
| first_indexed | 2024-04-11T10:47:03Z |
| format | Article |
| id | doaj.art-bea7f5af29e0459caf975a8a096437e0 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-11T10:47:03Z |
| publishDate | 2022-03-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-bea7f5af29e0459caf975a8a096437e02022-12-22T04:29:01ZengeLife Sciences Publications LtdeLife2050-084X2022-03-011110.7554/eLife.73943High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factorsMingrui Duan0https://orcid.org/0000-0002-2352-1840Smitha Sivapragasam1https://orcid.org/0000-0002-5599-9988Jacob S Antony2https://orcid.org/0000-0002-1481-9768Jenna Ulibarri3John M Hinz4Gregory MK Poon5John J Wyrick6Peng Mao7https://orcid.org/0000-0003-2068-1344Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, United StatesSchool of Molecular Biosciences, Washington State University, Pullman, United StatesSchool of Molecular Biosciences, Washington State University, Pullman, United StatesDepartment of Internal Medicine, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, United StatesSchool of Molecular Biosciences, Washington State University, Pullman, United StatesDepartment of Chemistry, Georgia State University, Atlanta, United StatesSchool of Molecular Biosciences, Washington State University, Pullman, United States; Center for Reproductive Biology, Washington State University, Pullman, United StatesDepartment of Internal Medicine, University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, United StatesDNA 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 show that alkylation damage formation was mainly suppressed at the binding sites of yeast TFs ARS binding factor 1 (Abf1) and rDNA enhancer binding protein 1 (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 ultraviolet (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.https://elifesciences.org/articles/73943BERNERMMSchromatinmutagenesis |
| spellingShingle | Mingrui Duan Smitha Sivapragasam Jacob S Antony Jenna Ulibarri John M Hinz Gregory MK Poon John J Wyrick Peng Mao High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors eLife BER NER MMS chromatin mutagenesis |
| title | High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors |
| title_full | High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors |
| title_fullStr | High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors |
| title_full_unstemmed | High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors |
| title_short | High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors |
| title_sort | high resolution mapping demonstrates inhibition of dna excision repair by transcription factors |
| topic | BER NER MMS chromatin mutagenesis |
| url | https://elifesciences.org/articles/73943 |
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