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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...dCPD sequencing (dCPD-seq) and use it to map dCPDs across the of repair-deficient yeast cells in order to characterize the impact of DNA sequence, genomic context, and chromatin organization on CPD deamination.ResultsTo develop a method to map the deamination of cytosine-containing CPDs, we...
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Research: Nucleosome remodeling at origins of global genome–nucleotide excision repair occurs at the boundaries of higher-order chromatin structure
- Patrick van Eijk,
- Shuvro Prokash Nandi,
- Shirong Yu,
- Mark Bennett,
- Matthew Leadbitter,
- Yumin Teng,
- and Simon H. Reed
Genome Res. January 2019 29: 74-84; Published in Advance December 14, 2018, doi:10.1101/gr.237198.118
...is excised from the as an oligonucleotide of ∼30 nucleotides (nt) in length by one of two subpathways: transcription-coupled NER (TC-NER) and global NER (GG-NER). The two pathways differ in the way in which DNA repair is initiated. In TC-NER, this is achieved following the recognition of damage-stalled RNA...
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Research: Distinct roles for RSC and SWI/SNF chromatin remodelers in genomic excision repair
- Kaitlynne A. Bohm,
- Amelia J. Hodges,
- Wioletta Czaja,
- Kathiresan Selvam,
- Michael J. Smerdon,
- Peng Mao,
- and John J. Wyrick
Genome Res. June 2021 31: 1047-1059; Published in Advance May 17, 2021, doi:10.1101/gr.274373.120
...damage residing in transcribed DNA (Hanawalt and Spivak 2008; Lans et al. 2019). In contrast, the global-genomic nucleotide excision repair (GG-NER) pathway uses a damage sensor consisting of Rad4 and Rad23 in yeast, in conjunction with accessory proteins such as the Rad7–Rad16 complex, to recognize DNA...
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Research: Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency
- Benjamin Morledge-Hampton,
- Kathiresan Selvam,
- Manish Chauhan,
- Alan G. Goodman,
- and John J. Wyrick
Genome Res. February 2025 35: 257-267; Published in Advance January 6, 2025, doi:10.1101/gr.279605.124
...that is important for removing bulky, helix-distorting DNA lesions, such as ultraviolet (UV)-induced cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs) (Schärer 2013). Global genomic NER (GG-NER) is an NER subpathway that removes lesions throughout the (Sugasawa et al. 2001; Gillet and Schärer 2006...
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Research: Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer
- Myrthe Jager,
- Francis Blokzijl,
- Ewart Kuijk,
- Johanna Bertl,
- Maria Vougioukalaki,
- Roel Janssen,
- Nicolle Besselink,
- Sander Boymans,
- Joep de Ligt,
- Jakob Skou Pedersen,
- Jan Hoeijmakers,
- Joris Pothof,
- Ruben van Boxtel,
- and Edwin Cuppen
Genome Res. July 2019 29: 1067-1077; Published in Advance June 20, 2019, doi:10.1101/gr.246223.118
...Institute, 3584 CT Utrecht, The Netherlands Corresponding author: ecuppen@umcutrecht.nlAbstractNucleotide excision repair (NER) is one of the main DNA repair pathways that protect cells against genomic damage. Disruption of this pathway can contribute to the development of cancer and accelerate aging...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...genes; however, its function, or absence thereof, is highly debated. The different outputs that mC can have raise questions as to how it is interpreted—or read—differently in these sequence and genomic contexts. To screen for potential mC-binding proteins, we performed an unbiased DNA affinity pull...
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Method: High resolution mapping of modified DNA nucleobases using excision repair enzymes
- D. Suzi Bryan,
- Monica Ransom,
- Biniam Adane,
- Kerri York,
- and Jay R. Hesselberth
Genome Res. September 2014 24: 1534-1542; Published in Advance July 11, 2014, doi:10.1101/gr.174052.114
...et al. 2013). The Excision-seqmethodwill be useful in generating high resolution global maps of DNA modification that can be integrated with surveys of DNA sequence polymorphisms (The 1000 Genomes Project Consortium 2012) and functional chromatin states (The ENCODE Project Consortium 2012) to provide...
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Research: Asymmetric repair of UV damage in nucleosomes imposes a DNA strand polarity on somatic mutations in skin cancer
- Peng Mao,
- Michael J. Smerdon,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2020 30: 12-21; Published in Advance December 23, 2019, doi:10.1101/gr.253146.119
...rate of skin cancers, including squamous cell carcinomas (SCC) and melanomas (DiGiovanna and Kraemer 2012). The primary NER pathway, known as global genomic-NER (GG-NER), initiates when the XPC protein (and its cofactors, such as UV-DDB) recognize a bulky, helix-distorting DNA lesion (Scharer 2013...
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Research: Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity
- Peng Mao,
- Alexander J. Brown,
- Ewa P. Malc,
- Piotr A. Mieczkowski,
- Michael J. Smerdon,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. October 2017 27: 1674-1684; Published in Advance September 14, 2017, doi:10.1101/gr.225771.117
...2015; Rodriguez et al. 2015). Moreover, nucleosomes in vivo are marked by different histone post-translational modifications, which could potentially alter repair efficiency (Rodriguez et al. 2016). Our understanding of how chromatin and other genomic features influence the formation and repair of DNA...
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Research: Developmental timing of programmed DNA elimination in Paramecium tetraurelia recapitulates germline transposon evolutionary dynamics
- Coralie Zangarelli,
- Olivier Arnaiz,
- Mickaël Bourge,
- Kevin Gorrichon,
- Yan Jaszczyszyn,
- Nathalie Mathy,
- Loïc Escoriza,
- Mireille Bétermier,
- and Vinciane Régnier
Genome Res. November/December 2022 32: 2028-2042; Published in Advance November 23, 2022, doi:10.1101/gr.277027.122
...development. Whereas TE elimination is generally imprecise, excision of approximately 45,000 TE-derived internal eliminated sequences (IESs) is precise, allowing for functional gene assembly. Programmed DNA elimination is concomitant with amplification. It is guided by noncoding RNAs and repressive chromatin...

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