Ribosomal RNAs – the structural and catalytic components of ribosomes – are encoded by multiple copies of head-to-tail tandemly arrayed ribosomal RNA genes (rDNA) separated by an intergenic spacer (IGS). The rDNA is a recombination hotspot, and as a consequence of this and its repetitive nature, is one of the most unstable regions of the genome. Interestingly, several types of solid tumours have chromosomal rearrangements involving the rDNA. In addition, a number of non-coding RNAs (ncRNAs) are transcribed from the IGS region of rDNA, and our preliminary data indicates that their transcription is increased during malignant progression in the Eu-Myc mouse lymphoma model. However, the role of rDNA recombination and non-coding transcription in tumorigenesis is yet to be investigated.
Here we performed hybridisation capture RNA-sequencing to determine the full profile of long ncRNAs transcribed from the rDNA IGS in Eu-Myc cells. From this, we identified a number of ncRNAs located across the IGS. We are also developing a chromatin immunoprecipitation-based assay (ChIP-qPCR) to measure rDNA recombination in mammalian cells, based on assumption that recombination factors (such as Rad50, Rad54 and RBBP8) are recruited to DNA in proportion to the level of recombination. We have shown that recombination factors are detectable at rDNA by ChIP-qPCR and, in conditions where the recombination rate is expected to differ, their levels vary consistently. Identification of the ncRNAs transcribed from the rDNA and development of a tool to measure rDNA recombination will provide a platform for determining whether altered recombination and non-coding transcription in the rDNA play roles in malignancy.