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Literature DB >> 30170831

Initiating base excision repair in chromatin.

Erin E Kennedy¹, Paul J Caffrey², Sarah Delaney³.

Abstract

The base excision repair (BER) pathway removes modified nucleobases that can be deleterious to an organism. BER is initiated by a glycosylase, which finds and removes these modified nucleobases. Most of the characterization of glycosylase activity has been conducted in the context of DNA oligomer substrates. However, DNA within eukaryotic organisms exists in a packaged environment with the basic unit of organization being the nucleosome core particle (NCP). The NCP is a complex substrate for repair in which a variety of factors can influence glycosylase activity. In this Review, we focus on the geometric positioning of modified nucleobases in an NCP and the consequences on glycosylase activity and initiating BER.

Entities: CellLine Chemical Disease Gene Species

Keywords: Base excision repair; Chromatin; DNA damage; DNA repair; Glycosylase; Nucleosome

Mesh：

Substances：

Year: 2018 PMID： 30170831 PMCID： PMC6340775 DOI： 10.1016/j.dnarep.2018.08.011

Source DB: PubMed Journal: DNA Repair (Amst) ISSN： 1568-7856

67 in total

Review 1. A mechanistic perspective on the chemistry of DNA repair glycosylases.

Authors: James T Stivers; Yu Lin Jiang
Journal: Chem Rev Date: 2003-07 Impact factor: 60.622

2. Acetylation of histone H3 at the nucleosome dyad alters DNA-histone binding.

Authors: Mridula Manohar; Alex M Mooney; Justin A North; Robin J Nakkula; Jonathan W Picking; Annick Edon; Richard Fishel; Michael G Poirier; Jennifer J Ottesen
Journal: J Biol Chem Date: 2009-06-11 Impact factor: 5.157

3. Characterization of nucleosome core particles containing histone proteins made in bacteria.

Authors: K Luger; T J Rechsteiner; A J Flaus; M M Waye; T J Richmond
Journal: J Mol Biol Date: 1997-09-26 Impact factor: 5.469

4. Crystal structure of the nucleosome core particle at 2.8 A resolution.

Authors: K Luger; A W Mäder; R K Richmond; D F Sargent; T J Richmond
Journal: Nature Date: 1997-09-18 Impact factor: 49.962

5. Human cells contain a factor that facilitates the DNA glycosylase-mediated excision of oxidized bases from occluded sites in nucleosomes.

Authors: R L Maher; C G Marsden; A M Averill; S S Wallace; J B Sweasy; D S Pederson
Journal: DNA Repair (Amst) Date: 2017-07-05

6. Dynamics of nucleosome assembly and effects of DNA methylation.

Authors: Ju Yeon Lee; Jaehyoun Lee; Hongjun Yue; Tae-Hee Lee
Journal: J Biol Chem Date: 2014-12-29 Impact factor: 5.157

7. Single-Molecule Observation Reveals Spontaneous Protein Dynamics in the Nucleosome.

Authors: Jongseong Kim; Sijie Wei; Jaehyoun Lee; Hongjun Yue; Tae-Hee Lee
Journal: J Phys Chem B Date: 2016-08-16 Impact factor: 2.991

8. Mapping nucleosome position at single base-pair resolution by using site-directed hydroxyl radicals.

Authors: A Flaus; K Luger; S Tan; T J Richmond
Journal: Proc Natl Acad Sci U S A Date: 1996-02-20 Impact factor: 11.205

9. Human OGG1 activity in nucleosomes is facilitated by transient unwrapping of DNA and is influenced by the local histone environment.

Authors: Katharina Bilotti; Erin E Kennedy; Chuxuan Li; Sarah Delaney
Journal: DNA Repair (Amst) Date: 2017-09-01

10. The mechanics behind DNA sequence-dependent properties of the nucleosome.

Authors: Eugene Y D Chua; Dileep Vasudevan; Gabriela E Davey; Bin Wu; Curt A Davey
Journal: Nucleic Acids Res Date: 2012-03-26 Impact factor: 16.971

8 in total

1. Rotational and translational positions determine the structural and dynamic impact of a single ribonucleotide incorporated in the nucleosome.

Authors: Iwen Fu; Duncan J Smith; Suse Broyde
Journal: DNA Repair (Amst) Date: 2018-11-29

Initiating base excision repair in chromatin.

Review 1. A mechanistic perspective on the chemistry of DNA repair glycosylases.

2. Acetylation of histone H3 at the nucleosome dyad alters DNA-histone binding.

3. Characterization of nucleosome core particles containing histone proteins made in bacteria.

4. Crystal structure of the nucleosome core particle at 2.8 A resolution.

5. Human cells contain a factor that facilitates the DNA glycosylase-mediated excision of oxidized bases from occluded sites in nucleosomes.

6. Dynamics of nucleosome assembly and effects of DNA methylation.

7. Single-Molecule Observation Reveals Spontaneous Protein Dynamics in the Nucleosome.

8. Mapping nucleosome position at single base-pair resolution by using site-directed hydroxyl radicals.

9. Human OGG1 activity in nucleosomes is facilitated by transient unwrapping of DNA and is influenced by the local histone environment.

10. The mechanics behind DNA sequence-dependent properties of the nucleosome.

1. Rotational and translational positions determine the structural and dynamic impact of a single ribonucleotide incorporated in the nucleosome.

2. Global Repair Profile of Human Alkyladenine DNA Glycosylase on Nucleosomes Reveals DNA Packaging Effects.

3. DNA-Protein Cross-Linking Sequencing for Genome-Wide Mapping of Thymidine Glycol.

Review 4. Obstacles and opportunities for base excision repair in chromatin.

Review 5. Expanding molecular roles of UV-DDB: Shining light on genome stability and cancer.

6. Recognition of 1,N ²-ethenoguanine by alkyladenine DNA glycosylase is restricted by a conserved active-site residue.

7. HECTD1 promotes base excision repair in nucleosomes through chromatin remodelling.

8. VRK1 Depletion Facilitates the Synthetic Lethality of Temozolomide and Olaparib in Glioblastoma Cells.