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Nucleosomes determine their own patch size in base excision repair

Base excision repair (BER) processes non-helix distorting lesions (e.g., uracils and gaps) and is composed of two subpathways that differ in the number of nucleotides (nts) incorporated during the DNA synthesis step: short patch (SP) repair incorporates 1 nt and long patch (LP) repair incorporates 2...

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Autores principales: Meas, Rithy, Smerdon, Michael J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4893620/
https://www.ncbi.nlm.nih.gov/pubmed/27265863
http://dx.doi.org/10.1038/srep27122
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author Meas, Rithy
Smerdon, Michael J.
author_facet Meas, Rithy
Smerdon, Michael J.
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description Base excision repair (BER) processes non-helix distorting lesions (e.g., uracils and gaps) and is composed of two subpathways that differ in the number of nucleotides (nts) incorporated during the DNA synthesis step: short patch (SP) repair incorporates 1 nt and long patch (LP) repair incorporates 2–12 nts. This choice for either LP or SP repair has not been analyzed in the context of nucleosomes. Initial studies with uracil located in nucleosome core DNA showed a distinct DNA polymerase extension profile in cell-free extracts that specifically limits extension to 1 nt, suggesting a preference for SP BER. Therefore, we developed an assay to differentiate long and short repair patches in ‘designed’ nucleosomes containing a single-nucleotide gap at specific locations relative to the dyad center. Using cell-free extracts or purified enzymes, we found that DNA lesions in the nucleosome core are preferentially repaired by DNA polymerase β and there is a significant reduction in BER polymerase extension beyond 1 nt, creating a striking bias for incorporation of short patches into nucleosomal DNA. These results show that nucleosomes control the patch size used by BER.
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spelling pubmed-48936202016-06-10 Nucleosomes determine their own patch size in base excision repair Meas, Rithy Smerdon, Michael J. Sci Rep Article Base excision repair (BER) processes non-helix distorting lesions (e.g., uracils and gaps) and is composed of two subpathways that differ in the number of nucleotides (nts) incorporated during the DNA synthesis step: short patch (SP) repair incorporates 1 nt and long patch (LP) repair incorporates 2–12 nts. This choice for either LP or SP repair has not been analyzed in the context of nucleosomes. Initial studies with uracil located in nucleosome core DNA showed a distinct DNA polymerase extension profile in cell-free extracts that specifically limits extension to 1 nt, suggesting a preference for SP BER. Therefore, we developed an assay to differentiate long and short repair patches in ‘designed’ nucleosomes containing a single-nucleotide gap at specific locations relative to the dyad center. Using cell-free extracts or purified enzymes, we found that DNA lesions in the nucleosome core are preferentially repaired by DNA polymerase β and there is a significant reduction in BER polymerase extension beyond 1 nt, creating a striking bias for incorporation of short patches into nucleosomal DNA. These results show that nucleosomes control the patch size used by BER. Nature Publishing Group 2016-06-06 /pmc/articles/PMC4893620/ /pubmed/27265863 http://dx.doi.org/10.1038/srep27122 Text en Copyright © 2016, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Meas, Rithy
Smerdon, Michael J.
Nucleosomes determine their own patch size in base excision repair
title Nucleosomes determine their own patch size in base excision repair
title_full Nucleosomes determine their own patch size in base excision repair
title_fullStr Nucleosomes determine their own patch size in base excision repair
title_full_unstemmed Nucleosomes determine their own patch size in base excision repair
title_short Nucleosomes determine their own patch size in base excision repair
title_sort nucleosomes determine their own patch size in base excision repair
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4893620/
https://www.ncbi.nlm.nih.gov/pubmed/27265863
http://dx.doi.org/10.1038/srep27122
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