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From single-molecule to genome-wide mapping of DNA lesions: repair-assisted damage detection sequencing
Mapping DNA damage and its repair has immense potential in understanding environmental exposures, their genotoxicity, and their impact on human health. Monitoring changes in genomic stability also aids in the diagnosis of numerous DNA-related diseases, such as cancer, and assists in monitoring their...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8651515/ https://www.ncbi.nlm.nih.gov/pubmed/34939047 http://dx.doi.org/10.1016/j.bpr.2021.100017 |
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author | Gilat, Noa Fridman, Dena Sharim, Hila Margalit, Sapir Gassman, Natalie R. Michaeli, Yael Ebenstein, Yuval |
author_facet | Gilat, Noa Fridman, Dena Sharim, Hila Margalit, Sapir Gassman, Natalie R. Michaeli, Yael Ebenstein, Yuval |
author_sort | Gilat, Noa |
collection | PubMed |
description | Mapping DNA damage and its repair has immense potential in understanding environmental exposures, their genotoxicity, and their impact on human health. Monitoring changes in genomic stability also aids in the diagnosis of numerous DNA-related diseases, such as cancer, and assists in monitoring their progression and prognosis. Developments in recent years have enabled unprecedented sensitivity in quantifying the global DNA damage dose in cells via fluorescence-based analysis down to the single-molecule level. However, genome-wide maps of DNA damage distribution are challenging to produce. Here, we describe the localization of DNA damage and repair loci by repair-assisted damage detection sequencing (RADD-seq). Based on the enrichment of damage lesions coupled with a pull-down assay and followed by next-generation sequencing, this method is easy to perform and can produce compelling results with minimal coverage. RADD-seq enables the localization of both DNA damage and repair sites for a wide range of single-strand damage types. Using this technique, we created a genome-wide map of the oxidation DNA damage lesion 8-oxo-7,8-dihydroguanine before and after repair. Oxidation lesions were heterogeneously distributed along the human genome, with less damage occurring in tight chromatin regions. Furthermore, we showed repair is prioritized for highly expressed, essential genes and in open chromatin regions. RADD-seq sheds light on cellular repair mechanisms and is capable of identifying genomic hotspots prone to mutation. |
format | Online Article Text |
id | pubmed-8651515 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-86515152021-12-20 From single-molecule to genome-wide mapping of DNA lesions: repair-assisted damage detection sequencing Gilat, Noa Fridman, Dena Sharim, Hila Margalit, Sapir Gassman, Natalie R. Michaeli, Yael Ebenstein, Yuval Biophys Rep (N Y) Article Mapping DNA damage and its repair has immense potential in understanding environmental exposures, their genotoxicity, and their impact on human health. Monitoring changes in genomic stability also aids in the diagnosis of numerous DNA-related diseases, such as cancer, and assists in monitoring their progression and prognosis. Developments in recent years have enabled unprecedented sensitivity in quantifying the global DNA damage dose in cells via fluorescence-based analysis down to the single-molecule level. However, genome-wide maps of DNA damage distribution are challenging to produce. Here, we describe the localization of DNA damage and repair loci by repair-assisted damage detection sequencing (RADD-seq). Based on the enrichment of damage lesions coupled with a pull-down assay and followed by next-generation sequencing, this method is easy to perform and can produce compelling results with minimal coverage. RADD-seq enables the localization of both DNA damage and repair sites for a wide range of single-strand damage types. Using this technique, we created a genome-wide map of the oxidation DNA damage lesion 8-oxo-7,8-dihydroguanine before and after repair. Oxidation lesions were heterogeneously distributed along the human genome, with less damage occurring in tight chromatin regions. Furthermore, we showed repair is prioritized for highly expressed, essential genes and in open chromatin regions. RADD-seq sheds light on cellular repair mechanisms and is capable of identifying genomic hotspots prone to mutation. Elsevier 2021-09-03 /pmc/articles/PMC8651515/ /pubmed/34939047 http://dx.doi.org/10.1016/j.bpr.2021.100017 Text en © 2021 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Article Gilat, Noa Fridman, Dena Sharim, Hila Margalit, Sapir Gassman, Natalie R. Michaeli, Yael Ebenstein, Yuval From single-molecule to genome-wide mapping of DNA lesions: repair-assisted damage detection sequencing |
title | From single-molecule to genome-wide mapping of DNA lesions: repair-assisted damage detection sequencing |
title_full | From single-molecule to genome-wide mapping of DNA lesions: repair-assisted damage detection sequencing |
title_fullStr | From single-molecule to genome-wide mapping of DNA lesions: repair-assisted damage detection sequencing |
title_full_unstemmed | From single-molecule to genome-wide mapping of DNA lesions: repair-assisted damage detection sequencing |
title_short | From single-molecule to genome-wide mapping of DNA lesions: repair-assisted damage detection sequencing |
title_sort | from single-molecule to genome-wide mapping of dna lesions: repair-assisted damage detection sequencing |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8651515/ https://www.ncbi.nlm.nih.gov/pubmed/34939047 http://dx.doi.org/10.1016/j.bpr.2021.100017 |
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