Journal article
The Structural Location of DNA Lesions in Nucleosome Core Particles Determines Accessibility by Base Excision Repair Enzymes
The Journal of biological chemistry, Vol.288(19), pp.13863-13875
05/10/2013
Handle:
https://hdl.handle.net/2376/106322
PMCID: PMC3650422
PMID: 23543741
Abstract
Background:
Base excision repair is hindered by nucleosomes.
Results:
Outwardly oriented uracils near the nucleosome center are efficiently cleaved; however, polymerase β is strongly inhibited at these sites.
Conclusion:
The histone octamer presents different levels of constraints on BER, dependent on the structural requirements for enzyme activity.
Significance:
Chromatin remodeling is necessary to prevent accumulation of aborted intermediates in nucleosomes.
Packaging of DNA into chromatin affects accessibility of DNA regulatory factors involved in transcription, replication, and repair. Evidence suggests that even in the nucleosome core particle (NCP), accessibility to damaged DNA is hindered by the presence of the histone octamer. Base excision repair is the major pathway in mammalian cells responsible for correcting a large number of chemically modified bases. We have measured the repair of site-specific uracil and single nucleotide gaps along the surface of the NCP. Our results indicate that removal of DNA lesions is greatly dependent on their rotational and translational positioning in NCPs. Significantly, the rate of uracil removal with outwardly oriented DNA backbones is 2–10-fold higher than those with inwardly oriented backbones. In general, uracils with inwardly oriented backbones farther away from the dyad center of the NCP are more accessible than those near the dyad. The translational positioning of outwardly oriented gaps is the key factor driving gap filling activity. An outwardly oriented gap near the DNA ends exhibits a 3-fold increase in gap filling activity as compared with one near the dyad with the same rotational orientation. Near the dyad, uracil DNA glycosylase/APE1 removes an outwardly oriented uracil efficiently; however, polymerase β activity is significantly inhibited at this site. These data suggest that the hindrance presented by the location of a DNA lesion is dependent on the structural requirements for enzyme catalysis. Therefore, remodeling at DNA damage sites in NCPs is critical for preventing accumulation of aborted intermediates and ensuring completion of base excision repair.
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Details
- Title
- The Structural Location of DNA Lesions in Nucleosome Core Particles Determines Accessibility by Base Excision Repair Enzymes
- Creators
- Yesenia Rodriguez - From theMichael J Smerdon - Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520
- Publication Details
- The Journal of biological chemistry, Vol.288(19), pp.13863-13875
- Academic Unit
- Molecular Biosciences, School of
- Publisher
- American Society for Biochemistry and Molecular Biology; 9650 Rockville Pike, Bethesda, MD 20814, U.S.A
- Grant note
- ES004106 / National Institutes of Health
- Identifiers
- 99900546625101842
- Language
- English
- Resource Type
- Journal article