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Single nucleotide-level mapping of DNA double-strand breaks in human HEK293T cells
Constitutional biological processes involve the generation of DNA double-strand breaks (DSBs). The production of such breaks and their subsequent resolution are also highly relevant to neurodegenerative diseases and cancer, in which extensive DNA fragmentation has been described Stephens et al. (201...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5133665/ https://www.ncbi.nlm.nih.gov/pubmed/27942458 http://dx.doi.org/10.1016/j.gdata.2016.11.007 |
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author | Pope, Bernard J. Mahmood, Khalid Jung, Chol-hee Georgeson, Peter Park, Daniel J. |
author_facet | Pope, Bernard J. Mahmood, Khalid Jung, Chol-hee Georgeson, Peter Park, Daniel J. |
author_sort | Pope, Bernard J. |
collection | PubMed |
description | Constitutional biological processes involve the generation of DNA double-strand breaks (DSBs). The production of such breaks and their subsequent resolution are also highly relevant to neurodegenerative diseases and cancer, in which extensive DNA fragmentation has been described Stephens et al. (2011), Blondet et al. (2001). Tchurikov et al. Tchurikov et al. (2011, 2013) have reported previously that frequent sites of DSBs occur in chromosomal domains involved in the co-ordinated expression of genes. This group report that hot spots of DSBs in human HEK293T cells often coincide with H3K4me3 marks, associated with active transcription Kravatsky et al. (2015) and that frequent sites of DNA double-strand breakage are likely to be relevant to cancer genomics Tchurikov et al. (2013, 2016) . Recently, they applied a RAFT (rapid amplification of forum termini) protocol that selects for blunt-ended DSB sites and mapped these to the human genome within defined co-ordinate ‘windows’. In this paper, we re-analyse public RAFT data to derive sites of DSBs at the single-nucleotide level across the built genome for human HEK293T cells (https://figshare.com/s/35220b2b79eaaaf64ed8). This refined mapping, combined with accessory ENCODE data tracks and ribosomal DNA-related sequence annotations, will likely be of value for the design of clinically relevant targeted assays such as those for cancer susceptibility, diagnosis, treatment-matching and prognostication. |
format | Online Article Text |
id | pubmed-5133665 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-51336652016-12-09 Single nucleotide-level mapping of DNA double-strand breaks in human HEK293T cells Pope, Bernard J. Mahmood, Khalid Jung, Chol-hee Georgeson, Peter Park, Daniel J. Genom Data Data in Brief Article Constitutional biological processes involve the generation of DNA double-strand breaks (DSBs). The production of such breaks and their subsequent resolution are also highly relevant to neurodegenerative diseases and cancer, in which extensive DNA fragmentation has been described Stephens et al. (2011), Blondet et al. (2001). Tchurikov et al. Tchurikov et al. (2011, 2013) have reported previously that frequent sites of DSBs occur in chromosomal domains involved in the co-ordinated expression of genes. This group report that hot spots of DSBs in human HEK293T cells often coincide with H3K4me3 marks, associated with active transcription Kravatsky et al. (2015) and that frequent sites of DNA double-strand breakage are likely to be relevant to cancer genomics Tchurikov et al. (2013, 2016) . Recently, they applied a RAFT (rapid amplification of forum termini) protocol that selects for blunt-ended DSB sites and mapped these to the human genome within defined co-ordinate ‘windows’. In this paper, we re-analyse public RAFT data to derive sites of DSBs at the single-nucleotide level across the built genome for human HEK293T cells (https://figshare.com/s/35220b2b79eaaaf64ed8). This refined mapping, combined with accessory ENCODE data tracks and ribosomal DNA-related sequence annotations, will likely be of value for the design of clinically relevant targeted assays such as those for cancer susceptibility, diagnosis, treatment-matching and prognostication. Elsevier 2016-11-11 /pmc/articles/PMC5133665/ /pubmed/27942458 http://dx.doi.org/10.1016/j.gdata.2016.11.007 Text en © 2016 The Authors http://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 | Data in Brief Article Pope, Bernard J. Mahmood, Khalid Jung, Chol-hee Georgeson, Peter Park, Daniel J. Single nucleotide-level mapping of DNA double-strand breaks in human HEK293T cells |
title | Single nucleotide-level mapping of DNA double-strand breaks in human HEK293T cells |
title_full | Single nucleotide-level mapping of DNA double-strand breaks in human HEK293T cells |
title_fullStr | Single nucleotide-level mapping of DNA double-strand breaks in human HEK293T cells |
title_full_unstemmed | Single nucleotide-level mapping of DNA double-strand breaks in human HEK293T cells |
title_short | Single nucleotide-level mapping of DNA double-strand breaks in human HEK293T cells |
title_sort | single nucleotide-level mapping of dna double-strand breaks in human hek293t cells |
topic | Data in Brief Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5133665/ https://www.ncbi.nlm.nih.gov/pubmed/27942458 http://dx.doi.org/10.1016/j.gdata.2016.11.007 |
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