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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...

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Autores principales: Gilat, Noa, Fridman, Dena, Sharim, Hila, Margalit, Sapir, Gassman, Natalie R., Michaeli, Yael, Ebenstein, Yuval
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2021
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.
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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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