Splicing stimulates antisense transcription by RNA polymerase II at DNA double-strand breaks in Drosophila cells

DNA double-strand breaks are among the most toxic lesions that can occur in a genome and their faithful repair is thus of great importance. Recent findings have uncovered a role for local transcription that initiates at the break and forms a non-coding transcript, called damage-induced long non-coding RNA or dilncRNA, which helps to coordinate the DNA transactions necessary for repair. We provide nascent RNA sequencing-based evidence that dilncRNA transcription by RNA polymerase II is more efficient if the DNA break occurs in an intron-containing gene in Drosophila. The spliceosome thus stimulates recruitment of RNA polymerase to the break, rather than the annealing of sense and antisense RNA. In contrast, RNA polymerase III nascent RNA libraries did not contain reads corresponding to the cleaved loci. Furthermore, selective inhibition of RNA polymerase III did not reduce the yield of damage-induced siRNAs (derived from the dilncRNA in Drosophila) and the damage-induced siRNA density was unchanged downstream of a T8 sequence, which terminates RNA polymerase III transcription. We thus found no evidence for a participation of RNA polymerase III in dilncRNA transcription and damage-induced siRNA generation in flies.