Pol II Preferentially Regulates Ribosomal Protein Expression by Trapping Disassociated Subunits [RNA-seq]

Pol II has been recognized as a passively regulated holoenzyme. However, whether Pol II plays specific regulatory roles remain unclear. Here, fractions containing disassociated RPB3 (dRPB3) were identified by size exclusion chromatography in various cells. Through a unique strategy, Specific Degradation of Disassociated Subunits (SDDS), we showed that dRPB3 functions as a regulatory component of Pol II to enable the preferential control of 3’ end processing of ribosomal protein genes. Machine learning analysis of large-scale genomic features revealed that the little elongation complex helps to determine the functional specificity of dRPB3. Mechanistically, dRPB3 facilitates CBC-PCF11 axis activity to increase the efficiency of 3’ end processing. Furthermore, the coordination between RPB3 and ribosomal proteins was widespread in diverse tissues and cancer cells. These findings suggest that Pol II gains specific regulatory functions by trapping disassociated subunits. We performed ChAR-seq, TT-seq, RNA-seq, and ChIP-seq to investigate the roles of various specialized subunits in transcription and post-transcriptional regulation. The V6.5 mouse ES (mES) cell line was used for all the high-throughput analyses. Degron mES cells were pretreated with 1 μg/ml Doxycycline for 12h to induce TIR1 expression, and treated with or without 500 μM IAA for different hours; refer to individual Series. For TT-seq, ChAR-seq, and RNA-seq, the Drosophila S2 cells were used as the spike-in cells, and for ChIP-seq, the HEK293T cells were used as the spike-in cells. This dataset includes the RNA-seq data.