Surveying the repair of ancient DNA from bones via high-throughput sequencing
DNA damage in the form of abasic sites, chemically altered nucleotides, and strand fragmentation is the foremost limitation in obtaining genetic information from many ancient samples. Upon cell death, DNA continues to endure various chemical attacks such as hydrolysis and oxidation, but repair pathw...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2015-07-01
|
| Series: | BioTechniques |
| Subjects: | |
| Online Access: | https://www.future-science.com/doi/10.2144/000114307 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850153056338968576 |
|---|---|
| author | Nathalie Mouttham Jennifer Klunk Melanie Kuch Ron Fourney Hendrik Poinar |
| author_facet | Nathalie Mouttham Jennifer Klunk Melanie Kuch Ron Fourney Hendrik Poinar |
| author_sort | Nathalie Mouttham |
| collection | DOAJ |
| description | DNA damage in the form of abasic sites, chemically altered nucleotides, and strand fragmentation is the foremost limitation in obtaining genetic information from many ancient samples. Upon cell death, DNA continues to endure various chemical attacks such as hydrolysis and oxidation, but repair pathways found in vivo no longer operate. By incubating degraded DNA with specific enzyme combinations adopted from these pathways, it is possible to reverse some of the post-mortem nucleic acid damage prior to downstream analyses such as library preparation, targeted enrichment, and high-throughput sequencing. Here, we evaluate the performance of two available repair protocols on previously characterized DNA extracts from four mammoths. Both methods use endonucleases and glycosylases along with a DNA polymerase-ligase combination. PreCR Repair Mix increases the number of molecules converted to sequencing libraries, leading to an increase in endogenous content and a decrease in cytosine-to-thymine transitions due to cytosine deamination. However, the effects of Nelson Repair Mix on repair of DNA damage remain inconclusive. |
| format | Article |
| id | doaj-art-5f480bc9723642f2b3df0b62437f2197 |
| institution | OA Journals |
| issn | 0736-6205 1940-9818 |
| language | English |
| publishDate | 2015-07-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | BioTechniques |
| spelling | doaj-art-5f480bc9723642f2b3df0b62437f21972025-08-20T02:25:50ZengTaylor & Francis GroupBioTechniques0736-62051940-98182015-07-01591192510.2144/000114307Surveying the repair of ancient DNA from bones via high-throughput sequencingNathalie Mouttham0Jennifer Klunk1Melanie Kuch2Ron Fourney3Hendrik Poinar41McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada1McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada1McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada3Science and Strategic Partnerships, Forensic Science and Identification Services, Royal Canadian Mounted Police, Ottawa, ON, Canada1McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, CanadaDNA damage in the form of abasic sites, chemically altered nucleotides, and strand fragmentation is the foremost limitation in obtaining genetic information from many ancient samples. Upon cell death, DNA continues to endure various chemical attacks such as hydrolysis and oxidation, but repair pathways found in vivo no longer operate. By incubating degraded DNA with specific enzyme combinations adopted from these pathways, it is possible to reverse some of the post-mortem nucleic acid damage prior to downstream analyses such as library preparation, targeted enrichment, and high-throughput sequencing. Here, we evaluate the performance of two available repair protocols on previously characterized DNA extracts from four mammoths. Both methods use endonucleases and glycosylases along with a DNA polymerase-ligase combination. PreCR Repair Mix increases the number of molecules converted to sequencing libraries, leading to an increase in endogenous content and a decrease in cytosine-to-thymine transitions due to cytosine deamination. However, the effects of Nelson Repair Mix on repair of DNA damage remain inconclusive.https://www.future-science.com/doi/10.2144/000114307ancient DNADNA damageDNA repairhigh-throughput sequencing |
| spellingShingle | Nathalie Mouttham Jennifer Klunk Melanie Kuch Ron Fourney Hendrik Poinar Surveying the repair of ancient DNA from bones via high-throughput sequencing BioTechniques ancient DNA DNA damage DNA repair high-throughput sequencing |
| title | Surveying the repair of ancient DNA from bones via high-throughput sequencing |
| title_full | Surveying the repair of ancient DNA from bones via high-throughput sequencing |
| title_fullStr | Surveying the repair of ancient DNA from bones via high-throughput sequencing |
| title_full_unstemmed | Surveying the repair of ancient DNA from bones via high-throughput sequencing |
| title_short | Surveying the repair of ancient DNA from bones via high-throughput sequencing |
| title_sort | surveying the repair of ancient dna from bones via high throughput sequencing |
| topic | ancient DNA DNA damage DNA repair high-throughput sequencing |
| url | https://www.future-science.com/doi/10.2144/000114307 |
| work_keys_str_mv | AT nathaliemouttham surveyingtherepairofancientdnafrombonesviahighthroughputsequencing AT jenniferklunk surveyingtherepairofancientdnafrombonesviahighthroughputsequencing AT melaniekuch surveyingtherepairofancientdnafrombonesviahighthroughputsequencing AT ronfourney surveyingtherepairofancientdnafrombonesviahighthroughputsequencing AT hendrikpoinar surveyingtherepairofancientdnafrombonesviahighthroughputsequencing |