Ribosomal RNA (rRNA) gene (rDNA) transcription by RNA Polymerase I (Pol-I) occurs in the nucleolus, the site of ribosome biogenesis, and determines proliferation and cell growth in all organisms. There are ~400 copies of rDNA genes per diploid genome, but remarkably less than 50% are typically transcribed in normal cells. However, it is well documented that elevated Pol-I transcription is a common feature in malignancy, and that Pol-I inhibition prolongs the overall survival of lymphoma-bearing mice. In addition to rRNA production, it has been proposed that epigenetic state of rDNA may affect the transcriptional activity of interacting genomic regions and thus plays a role in regulating global gene expression. To take full advantage of targeting Pol-I transcription as a cancer therapy, a detailed understanding of rDNA chromatin structure, the transcription factors involved, and how they change during malignant transformation is crucial.
This study utilised a mouse model of spontaneous B-cell lymphoma (Eμ-Myc) to characterise the epigenetic and transcriptional changes in malignancy. Chromatin Immunoprecipitation Sequencing (ChIP-seq) followed by novel bioinformatics approaches revealed that the transition from wildtype to pre-malignant to malignant B cells is associated with marked changes in rDNA chromatin. This includes increased binding of Pol-I, upstream binding factor (UBF) and active histone marks, and depletion of linker histone H1 and repressive histone marks at regulatory and coding regions. Integration of genome-wide ChIP-seq and RNA-seq data demonstrated that epigenetic alterations during malignancy correlated with the observed transcriptional changes, notably a significant upregulation of Pol-II dependent genes related to translation and biosynthesis. We are currently evaluating how rDNA epigenetic state may affect the global transcriptional activity via interacting genomic regions, and the potential rDNA copy number variability in malignancy. These findings will provide further insight into the role of rDNA chromatin in malignant transformation and its potential as a therapeutic target.