UBF and Pol I ChIP-seq
Integrative genomic analysis of human ribosomal DNA
UBF and RPA116 (a subunit of RNA polymerase I) are critical regulators of rRNA transcription.  We mapped their distribution on chromatin at high resolution using ChIP-seq.  We confirmed the previously described distributions of UBF and RPA116 at rDNA.  In addition, we found that UBF was associated with many sites on non-rDNA chromatin, suggesting a role for this factor in regulating nucleoplasmic transcription.
The transcription of rRNA is critical to life. Despite its importance, rDNA is not included in current genome assemblies, and consequently, genomic analyses to date have excluded rDNA.  Here, we show that short sequence reads can be aligned to a genome assembly containing a single rDNA repeat.  Integrated analysis of ChIP-seq, DNase-seq, MNase-seq, and RNA-seq data reveals several novel findings.  First, the coding region of active rDNA is contained within nucleosome-depleted open chromatin that is highly transcriptionally active.  Second, histone modifications are located not only at the rDNA promoter but also at novel sites within the intergenic spacer.  Third, the distributions of active modifications are more similar within and between different cell types than repressive modifications.  Fourth, we show that UBF, a positive regulator of rRNA transcription, binds to sites throughout the genome.  Lastly, we show that the insulator binding protein CTCF associates with the spacer promoter of rDNA, suggesting that transcriptional insulation plays a role in regulating the transcription of rRNA.  Taken together, these analyses confirm and expand the results of previous ChIP studies of rDNA and provide novel avenues for exploration of chromatin-mediated regulation of rDNA.