EMD-43601

Composite map
Single-particle
3.6 Å
EMD-43601 Deposition: 02/02/2024
Map released: 30/10/2024
Last modified: 15/01/2025
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-43601

OGG1 bound to a nucleosome containing 8oxoG at SHL4 (composite map)

EMD-43601

Composite map
Single-particle
3.6 Å
EMD-43601 Deposition: 02/02/2024
Map released: 30/10/2024
Last modified: 15/01/2025
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Homo sapiens, synthetic construct
Sample: OGG1 bound to a nucleosome containing 8oxoG at SHL4 (composite map)
Fitted models: 8vwv (Avg. Q-score: 0.359)

Deposition Authors: Weaver TM , Ling JA , Freudenthal BD
Contributing factors to the oxidation-induced mutational landscape in human cells.
Cordero C , Mehta KPM , Weaver TM , Ling JA , Freudenthal BD , Cortez D , Roberts SA
(2024) Nat Commun , 15 , 10722 - 10722
PUBMED: 39715760
DOI: doi:10.1038/s41467-024-55497-z
ISSN: 2041-1723
Abstract:
8-oxoguanine (8-oxoG) is a common oxidative DNA lesion that causes G > T substitutions. Determinants of local and regional differences in 8-oxoG-induced mutability across genomes are currently unknown. Here, we show DNA oxidation induces G > T substitutions and insertion/deletion (INDEL) mutations in human cells and cancers. Potassium bromate (KBrO3)-induced 8-oxoGs occur with similar sequence preferences as their derived substitutions, indicating that the reactivity of specific oxidants dictates mutation sequence specificity. While 8-oxoG occurs uniformly across chromatin, 8-oxoG-induced mutations are elevated in compact genomic regions, within nucleosomes, and at inward facing guanines within strongly positioned nucleosomes. Cryo-electron microscopy structures of OGG1-nucleosome complexes indicate that these effects originate from OGG1's ability to flip outward positioned 8-oxoG lesions into the catalytic pocket while inward facing lesions are occluded by the histone octamer. Mutation spectra from human cells with DNA repair deficiencies reveals contributions of a DNA repair network limiting 8-oxoG mutagenesis, where OGG1- and MUTYH-mediated base excision repair is supplemented by the replication-associated factors Pol η and HMCES. Transcriptional asymmetry of KBrO3-induced mutations in OGG1- and Pol η-deficient cells also demonstrates transcription-coupled repair can prevent 8-oxoG-induced mutation. Thus, oxidant chemistry, chromatin structures, and DNA repair processes combine to dictate the oxidative mutational landscape in human genomes.