Ribosomal gene (rDNA) transcription is important for determining proliferation rate and cell fate in all organisms. RNA Polymerase I (PolI) is responsible for the transcription of the rDNA which occurs in the nucleolus, also the site of ribosome biogenesis. Remarkably, despite rDNA transcription being limiting for growth, over 50% of the ribosomal genes are transcriptionally silent at any one time. It is well documented that elevated PolI transcription is a common feature in malignancy, and that PolI inhibition prolongs the overall survival of lymphoma-bearing mice. To take full advantage of targeting PolI transcription as a cancer therapy and understand the role of rDNA chromatin in malignancy, a detailed understanding of the chromatin structure, the transcription factors involved, and how they change during the stages of malignant transformation is crucial.
In order to assess epigenetic changes across the genome and at the rDNA repeats, and whether elevated PolI transcription facilitates malignant transformation, we will use the transgenic Eμ-Myc mouse model of B-cell lymphoma. Our preliminary results show that transition from wild-type to pre-malignancy and malignancy is associated with marked changes in rDNA chromatin. Further Chromatin Immunoprecipitation (ChIP)-seq (and/or cut and run) and RNA-seq followed by systematic approaches of bioinformatic analysis will allow us to comprehensively study chromatin features, including changes in the abundance of chromatin modifying and transcription factors, heterochromatic and euchromatic histone marks that may affect rDNA transcription during malignant transformation.
In summary, we will evaluate the role of rDNA chromatin and PolI transcription in malignant transformation, using ChIP-seq and RNA-seq data to determine how gene expression alterations relate to chromatin changes at the rDNA repeats and genome-wide.