Fine resolution mapping of double-strand break sites for human ribosomal DNA units

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• 作者：Bernard J. Pope^a ; Khalid Mahmood^a ; Chol-hee Jung^a ; Daniel J. Park^a ; ^b ; ^{djp@unimelb.edu.au}
• 关键词：Double-strand breaks ; Fragile sites ; rDNA ; Forum domains ; HEK293T
• 刊名：Genomics Data
• 出版年：2016
• 出版时间：December 2016
• 年：2016
• 卷：10
• 期：Complete
• 页码：19-21
• 全文大小：440 K
• 卷排序：10

文摘

DNA breakage arises during a variety of biological processes, including transcription, replication and genome rearrangements. In the context of disease, extensive fragmentation of DNA has been described in cancer cells and during early stages of neurodegeneration (Stephens et al., 2011 Stephens et al. (2011) [5]; Blondet et al., 2001 Blondet et al. (2001) [1]). Stults et al. (2009) Stults et al. (2009) [6] reported that human rDNA gene clusters are hotspots for recombination and that rDNA restructuring is among the most common chromosomal alterations in adult solid tumours. As such, analysis of rDNA regions is likely to have significant prognostic and predictive value, clinically. Tchurikov et al. (2015a, 2016) Tchurikov et al. (2015a, 2016) [7] and [9] have made major advances in this direction, reporting that sites of human genome double-strand breaks (DSBs) occur frequently at sites in rDNA that are tightly linked with active transcription - the authors used a RAFT (rapid amplification of forum termini) protocol that selects for blunt-ended sites. They reported the relative frequency of these rDNA DSBs within defined co-ordinate ‘windows’ of varying size and made these data (as well as the relevant ‘raw’ sequencing information) available to the public (Tchurikov et al., 2015b). Assay designs targeting rDNA DSB hotspots will benefit greatly from the publication of break sites at greater resolution. Here, we re-analyse public RAFT data and make available rDNA DSB co-ordinates to the single-nucleotide level.