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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2017-03-01
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| Series: | Genomics Data |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2213596016301428 |
| _version_ | 1819203256530763776 |
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| author | Bernard J. Pope Khalid Mahmood Chol-hee Jung Peter Georgeson Daniel J. Park |
| author_facet | Bernard J. Pope Khalid Mahmood Chol-hee Jung Peter Georgeson Daniel J. Park |
| author_sort | Bernard J. Pope |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-23T04:17:02Z |
| format | Article |
| id | doaj.art-7d0546e9b9c445478db978ffc75e372d |
| institution | Directory Open Access Journal |
| issn | 2213-5960 |
| language | English |
| last_indexed | 2024-12-23T04:17:02Z |
| publishDate | 2017-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Genomics Data |
| spelling | doaj.art-7d0546e9b9c445478db978ffc75e372d2022-12-21T18:00:22ZengElsevierGenomics Data2213-59602017-03-0111C434510.1016/j.gdata.2016.11.007Single nucleotide-level mapping of DNA double-strand breaks in human HEK293T cellsBernard J. Pope0Khalid Mahmood1Chol-hee Jung2Peter Georgeson3Daniel J. Park4Victorian Life Sciences Computation Initiative, The University of Melbourne, AustraliaVictorian Life Sciences Computation Initiative, The University of Melbourne, AustraliaVictorian Life Sciences Computation Initiative, The University of Melbourne, AustraliaVictorian Life Sciences Computation Initiative, The University of Melbourne, AustraliaVictorian Life Sciences Computation Initiative, The University of Melbourne, AustraliaConstitutional 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.http://www.sciencedirect.com/science/article/pii/S2213596016301428Double-strand breaksFragile sitesHuman genomeForum domainsHEK293T |
| spellingShingle | Bernard J. Pope Khalid Mahmood Chol-hee Jung Peter Georgeson Daniel J. Park Single nucleotide-level mapping of DNA double-strand breaks in human HEK293T cells Genomics Data Double-strand breaks Fragile sites Human genome Forum domains HEK293T |
| 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 | Double-strand breaks Fragile sites Human genome Forum domains HEK293T |
| url | http://www.sciencedirect.com/science/article/pii/S2213596016301428 |
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