It is not clear how spontaneous DNA double-strand breaks (DSBs) form and are processed in normal cells, and whether they predispose to cancer-associated translocations. We show that DSBs in normal mammary cells form upon release of paused RNA polymerase II (Pol II) at promoters, 5′ splice sites and active enhancers, and are processed by end-joining in the absence of a canonical DNA-damage response. Logistic and causal-association models showed that Pol II pausing at long genes is the main predictor and determinant of DSBs. Damaged introns with paused Pol II-pS5, TOP2B and XRCC4 are enriched in translocation breakpoints, and map at topologically associating domain boundary-flanking regions showing high interaction frequencies with distal loci. Thus, in unperturbed growth conditions, release of paused Pol II at specific loci and chromatin territories favors DSB formation, leading to chromosomal translocations.
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We thank R. Mirzazadeh for initial training on the BLISS method; I. Pallavicini and T. Kallas for technical assistance with cell culture; L. Rotta and T. Capra of the Sequencing Facility at the IEO Genomic Unit; E. Colombo for helpful discussions; and P. Dalton and S. Averaimo for critical review of the manuscript. F.P. was supported by a fellowship from Fondazione Umberto Veronesi (grant no. FUV 2018). N.C. acknowledges support from the Karolinska Institutet, the Swedish Research Council (grant no. 521-2014-2866), the Swedish Cancer Research Foundation (grant no. CAN 2015/585) and the Ragnar Söderberg Foundation. M.F. acknowledges support from Italian Ministry of Health grant no. RF-2011-02347946. This study was supported by European Research Council advanced grant no. 341131 (to P.G.P.).
The authors declare no competing interests.
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Dellino, G.I., Palluzzi, F., Chiariello, A.M. et al. Release of paused RNA polymerase II at specific loci favors DNA double-strand-break formation and promotes cancer translocations. Nat Genet 51, 1011–1023 (2019). https://doi.org/10.1038/s41588-019-0421-z
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