Effects of the RNA Exosome on damage induced small RNAs in the 28S ribosomal locus

The repair of DNA double strand breaks (DSBs) has recently been shown to depend not only on protein function but also on RNA. In particular, the processing of a long damage-induced RNA into small damage induced RNAs (diRNAs) has been a focus of interest. Given that the RNA exosome has been shown in Drosophila and human cells to participate in DSB repair, we investigated whether the catalytic components EXOSC10 and DIS3 have a function in diRNA biogenesis in human cells. Overall design: EXOSC10 or DIS3 was depleted in Hela cells and the cells subsequently transfected with a plasmid coding for the homing endonuclease I-PpoI that induces a double strand break in the 28S rDNA. After transfection the small RNA fraction was sequenced using standard Illumina sequencing and analyzed for reads mapping to the 28S rDNA.