Genomic analysis of ribosomal DNA and its application to the investigation of disease pathogenesis

The synthesis of rRNA is critical to all growing organisms, accounting for well over half of all cellular transcription. Highlighting its central function in cellular life, dysregulation of rRNA biogenesis and subsequent ribosome assembly has been implicated in human genetic diseases and cancer. While the transcription of rRNA is highly regulated at the chromatin level, it has not been analyzed by genomic methods due to the exclusion of rDNA from current genome assemblies. This work describes a novel method of analysis that enables the alignment of high-throughput sequencing data to a single copy of rDNA in the context of the full human genome. Integrated analysis of genomic datasets reveals that the coding region of rDNA is contained within nucleosomepoor open chromatin with high transcriptional activity. We find that histone modifications are enriched not only at the rDNA promoter but also at novel sites within the noncoding intergenic spacer. The distribution of active modifications is more similar within and between cell types than that of repressive modifications. Using ChIP-seq, we show that the nucleolar protein UBF is bound to sites throughout the genome and may play a role in regulating the transcription of nucleoplasmic genes. Lastly, the insulator-binding protein CTCF is bound to a