A damaged genome’s transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks

Fabio Iannelli (), Alessandro Galbiati, Ilaria Capozzo, Quan Nguyen, Brian Magnuson, Flavia Michelini, Giuseppina D’Alessandro, Matteo Cabrini, Marco Roncador, Sofia Francia, Nicola Crosetto, Mats Ljungman, Piero Carninci and Fabrizio d’Adda di Fagagna ()
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Fabio Iannelli: IFOM, The FIRC Institute of Molecular Oncology
Alessandro Galbiati: IFOM, The FIRC Institute of Molecular Oncology
Ilaria Capozzo: IGM (Istituto di Genetica Molecolare)-CNR (Consiglio Nazionale delle Ricerche)
Quan Nguyen: RIKEN Center for Life Science Technologies
Brian Magnuson: University of Michigan
Flavia Michelini: IFOM, The FIRC Institute of Molecular Oncology
Giuseppina D’Alessandro: IFOM, The FIRC Institute of Molecular Oncology
Matteo Cabrini: IGM (Istituto di Genetica Molecolare)-CNR (Consiglio Nazionale delle Ricerche)
Marco Roncador: IGM (Istituto di Genetica Molecolare)-CNR (Consiglio Nazionale delle Ricerche)
Sofia Francia: IFOM, The FIRC Institute of Molecular Oncology
Nicola Crosetto: Science for Life Laboratory, Karolinska Institutet
Mats Ljungman: University of Michigan
Piero Carninci: RIKEN Center for Life Science Technologies
Fabrizio d’Adda di Fagagna: IFOM, The FIRC Institute of Molecular Oncology

Nature Communications, 2017, vol. 8, issue 1, 1-12

Abstract: Abstract Of the many types of DNA damage, DNA double-strand breaks (DSBs) are probably the most deleterious. Mounting evidence points to an intricate relationship between DSBs and transcription. A cell system in which the impact on transcription can be investigated at precisely mapped genomic DSBs is essential to study this relationship. Here in a human cell line, we map genome-wide and at high resolution the DSBs induced by a restriction enzyme, and we characterize their impact on gene expression by four independent approaches by monitoring steady-state RNA levels, rates of RNA synthesis, transcription initiation and RNA polymerase II elongation. We consistently observe transcriptional repression in proximity to DSBs. Downregulation of transcription depends on ATM kinase activity and on the distance from the DSB. Our study couples for the first time, to the best of our knowledge, high-resolution mapping of DSBs with multilayered transcriptomics to dissect the events shaping gene expression after DSB induction at multiple endogenous sites.

Date: 2017
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DOI: 10.1038/ncomms15656

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