Different structural states in oligonucleosomes are required for early versus late steps of base excision repair

Shima Nakanishi; Rajendra Prasad; Samuel H Wilson; Michael Smerdon

doi:10.1093/nar/gkm436

Back

Different structural states in oligonucleosomes are required for early versus late steps of base excision repair

Journal article

Open access

Peer reviewed

Different structural states in oligonucleosomes are required for early versus late steps of base excision repair

Shima Nakanishi, Rajendra Prasad, Samuel H Wilson and Michael Smerdon

Nucleic acids research, Vol.35(13), pp.4313-4321

2007

DOI: https://doi.org/10.1093/nar/gkm436

Handle:

https://hdl.handle.net/2376/104004

PMCID: PMC1934998

PMID: 17576692

Files and links (1)

url

https://doi.org/10.1093/nar/gkm436View

Published (Version of record) Open

Abstract

Uracil-DNA Glycosidase - metabolism

Nucleosomes - chemistry

Humans

Adenosine Triphosphatases - metabolism

Chromatin Assembly and Disassembly

Nucleosomes - metabolism

Base Pair Mismatch

DNA-Binding Proteins - metabolism

Transcription Factors - metabolism

DNA-(Apurinic or Apyrimidinic Site) Lyase - metabolism

DNA Repair

Saccharomyces cerevisiae Proteins

Uracil - metabolism

DNA Polymerase beta - metabolism

Nucleic Acid Conformation

Chromatin in eukaryotic cells is folded into higher order structures of folded nucleosome filaments, and DNA damage occurs at all levels of this structural hierarchy. However, little is known about the impact of higher order folding on DNA repair enzymes. We examined the catalytic activities of purified human base excision repair (BER) enzymes on uracil-containing oligonucleosome arrays, which are folded primarily into 30 nm structures when incubated in repair reaction buffers. The catalytic activities of uracil DNA glycosylase (UDG) and apyrimidinic/apurinic endonuclease (APE) digest G:U mismatches to completion in the folded oligonucleosomes without requiring significant disruption. In contrast, DNA polymerase beta (Pol beta) synthesis is inhibited in a major fraction ( approximately 80%) of the oligonucleosome array, suggesting that single strand nicks in linker DNA are far more accessible to Pol beta in highly folded oligonucleosomes. Importantly, this barrier in folded oligonucleosomes is removed by purified chromatin remodeling complexes. Both ISW1 and ISW2 from yeast significantly enhance Pol beta accessibility to the refractory nicked sites in oligonucleosomes. These results indicate that the initial steps of BER (UDG and APE) act efficiently on highly folded oligonucleosome arrays, and chromatin remodeling may be required for the latter steps of BER in intact chromatin.

Metrics

7 Record Views

Details

Title: Different structural states in oligonucleosomes are required for early versus late steps of base excision repair
Creators: Shima Nakanishi - Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, WA 99164-4660, USA
Rajendra Prasad
Samuel H Wilson
Michael Smerdon
Publication Details: Nucleic acids research, Vol.35(13), pp.4313-4321
Academic Unit: Molecular Biosciences, School of
Publisher: England
Grant note: Intramural NIH HHS R37 ES002614 / NIEHS NIH HHS R01 ES002614 / NIEHS NIH HHS ES02614 / NIEHS NIH HHS
Identifiers: 99900546652901842
Language: English
Resource Type: Journal article