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

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. 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 3 technical replicates (different plates, but treated on the same day) with auxin for 8 hours, DMSO for 8 hours, or 6 hour of ActD (5 µg/mL), we generated total RNA-seq for each set of samples. We performed diffrential expression analysis for coding and non-coding transcripts with this data.