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. 2018 Mar 1;8:3850. doi: 10.1038/s41598-018-21806-y

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© The Author(s) 2018

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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DNA:RNA hybrids occur at the break site: (A) DRIP-qPCR analysis of DNA:RNA hybrid structure at TetR-IRES-NeoR gene in undamaged cells or after DSB induction. Primers targeting the APOE gene are used as a positive control for R loop formation, and primers specific to an intergenic region are used as a negative control. The values, corresponding to the signal following S9.6 IP of isolated DNA (dark grey bar) or of in vitro RNaseH-treated DNA (clear grey bar), are represented as fold increase normalised to the APOE positive control (Undamaged, n = 7 (from Fig. 4(F)); I-SceI, n = 7; I-SceI + RNaseH1, n = 3; I-SceI + siSETX, n = 4). (B) Model of DSB-induced large deletion dependent on a DNA:RNA hybrid associated with transcription from the DSB: Generally a DSB occurring in close proximity to a gene is efficiently repaired, either by HR or NHEJ, and the transcription program is not affected over the long term (left side). Alternatively (right side), transcription and DNA:RNA hybrid generation displaces the 5′ DNA strand. Senataxin is shown reversing this, promoting correct repair. ERCC1/XPF is required to cleave the displaced 3′ DNA strands.