# Regulation of DNA Excision Repair in Chromatin

> **NIH NIH R01** · WASHINGTON STATE UNIVERSITY · 2024 · $336,218

## Abstract

ABSTRACT
Efficient repair of DNA base lesions, such as UV-induced cyclobutane pyrimidine dimers (CPDs) or DNA
alkylation damage, is critical to maintain genome stability and prevent mutations that can lead to cancer.
Repair of these abundant classes of DNA lesions is the responsibility of the nucleotide excision repair (NER)
and base excision repair (BER) pathways. The importance of efficient excision repair is highlighted by the
severe phenotypes of patients with Xeroderma pigmentosum (XP), which have inherited defects in NER genes,
and the cancer predisposition of individuals with variants in key BER genes. While the basic mechanisms by
which the NER and BER pathways repair DNA base lesions are well understood, how these excision repair
pathways efficiently recognize and repair DNA lesions resident in eukaryotic chromatin is unclear. To address
this question, we have developed a new high-throughput sequencing method known as MNase-CPD-seq,
which provides an unprecedented snapshot of the dynamics of damaged nucleosomes in UV-irradiated cells.
Our preliminary MNase-CPD-seq data indicate that damaged nucleosomes rapidly alter their rotational setting
to move CPDs to more accessible Minor-Out rotational settings, and at later repair time points, alter
translational positioning to expand linker regions between nucleosomes. These preliminary data form the basis
of Aim I, where we will use MNase-CPD-seq to characterize the role of damage recognition factors, such as
XPC or UV-DDB, and histone modifications in promoting repositioning of damaged nucleosomes in yeast and
human cells and in vitro. In parallel, we also plan to develop related methods to map nucleosome dynamics
associated with other classes of DNA lesions (i.e., UV-induced 6-4 photoproducts and N-methylpurine (NMP)
lesions). In Aim II, we will test the hypothesis that ACR complexes in yeast and human cells are required for
efficient repair of UV damage in chromatin by repositioning damaged nucleosomes during repair. We will also
investigate how ACR mutants affect UV mutagenesis in UV-exposed yeast cells and human skin cancers.
Finally, in the previous award we identified novel roles for histone PTMs in regulating distinct NER and BER
pathways in chromatin. Aim III will build on the studies by characterizing the mechanisms by which histone
acetylation regulates NER and BER in yeast chromatin, and the role of histone H3 K36 methylation by Set2 in
yeast and SETD2 in human cells in regulating canonical and cryptic transcription coupled-nucleotide excision
repair (TC-NER). Since ACR subunits (e.g., ARID2) and SETD2 are frequently mutated in human cancers,
including melanoma, these studies have important implications to mechanisms of carcinogenesis and
chemotherapeutic resistance in cancer.

## Key facts

- **NIH application ID:** 10883199
- **Project number:** 2R01ES028698-06
- **Recipient organization:** WASHINGTON STATE UNIVERSITY
- **Principal Investigator:** John J Wyrick
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $336,218
- **Award type:** 2
- **Project period:** 2018-08-01 → 2029-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10883199

## Citation

> US National Institutes of Health, RePORTER application 10883199, Regulation of DNA Excision Repair in Chromatin (2R01ES028698-06). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10883199. Licensed CC0.

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