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Next-generation sequencing reveals two populations of damage-induced small RNAs at endogenous DNA double-strand breaks
Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Stockholm University, Science for Life Laboratory (SciLifeLab).ORCID iD: 0000-0001-6577-4363
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Number of Authors: 52018 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 46, no 22, p. 11869-11882Article in journal (Refereed) Published
Abstract [en]

Recent studies suggest that transcription takes place at DNA double-strand breaks (DSBs), that transcripts at DSBs are processed by Drosha and Dicer into damage-induced small RNAs (diRNAs), and that diRNAs are required for DNA repair. However, diRNAs have been mostly detected in reporter constructs or repetitive sequences, and their existence at endogenous loci has been questioned by recent reports. Using the homing endonuclease I-PpoI, we have investigated diRNA production in genetically unperturbed human and mouse cells. I-PpoI is an ideal tool to clarify the requirements for diRNA production because it induces DSBs in different types of loci: the repetitive 28S locus, unique genes and intergenic loci. We show by extensive sequencing that the rDNA locus produces substantial levels of diRNAs, whereas unique genic and intergenic loci do not. Further characterization of diRNAs emerging from the 28S locus reveals the existence of two diRNA subtypes. Surprisingly, Drosha and its partner DGCR8 are dispensable for diRNA production and only one diRNAs subtype depends on Dicer processing. Furthermore, we provide evidence that diRNAs are incorporated into Argonaute. Our findings provide direct evidence for diRNA production at endogenous loci in mammalian cells and give insights into RNA processing at DSBs.

Place, publisher, year, edition, pages
2018. Vol. 46, no 22, p. 11869-11882
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Biochemistry and Molecular Biology
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URN: urn:nbn:se:su:diva-166853DOI: 10.1093/nar/gky1107ISI: 000456714000022PubMedID: 30418607OAI: oai:DiVA.org:su-166853DiVA, id: diva2:1294333
Available from: 2019-03-07 Created: 2019-03-07 Last updated: 2019-03-07Bibliographically approved

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Bonath, FranziskaDomingo-Prim, JuditTarbier, MarcelFriedländer, Marc R.Visa, Neus
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