Gene Expression is Co-regulated by Non-nucleolar RNA Polymerase I [Hi-C]

Due to its role in mRNA synthesis, many studies of the relationship between transcription and chromatin organization have focused on the regulation of RNA polymerase II (Pol-II) function by supranucleosomal structure and vice-versa. In contrast, there is little work on the function of RNA polymerase I (Pol-I) in non-nucleolar chromatin. Prior work has shown that Pol-I engages with components of Pol-II on rDNA, but it's role in global transcription and chromatin structure beyond the nucleolus has largely been ignored. By pairing auxin-inducible degron technology with nanoscopic imaging, RNA-Seq, and Hi-C, we found that Pol-I and Pol-II co-regulate conformationally defined chromatin domains and mRNA synthesis. Mechanistically, Pol-I maintains the positioning of intronic and intergenic chromatin within domains for the proper expression of exon elements. Consequently, Pol-I loss disrupts genome connectivity, in situ chromatin domains, and the expression of mRNA, genome-wide. Overall design: To investigate the structure-function relationship between Pol-I and Pol-II transcription and genome organization, we took advantage of two auxin inducible degron lines targeting either POLR1A or POLR2A. After treating 2 technical replicates (different plates, but treated on the same day) with auxin for 6 hours, DMSO for 6 hours, or 1 hour of ActD (5 µg/mL), we generated Hi-C for each set of samples using the Qiagen Epitect Hi-C Kit (Qiagen, #59971). We processed each replicate using the Juicer pipeline and generated .hic files for each replicate. Replicates were merged to maximize resolution