Targeted knockdown of the PAF49 component of the PAF53/PAF49 heterodimer causes the degradation of PAF53.

There are significant differences in the components of the ribosomal DNA transcription apparatuses of yeast and mammals. Moreover, the patterns of regulation between mammals and yeast are also different. To overcome, deficits in our understanding of mammalian rDNA transcription, we have developed a system to introduce an inducible degron into the endogenous genes of mammalian cells. This allows us to combine a knock out the endogenous gene product and replace it with mutant proteins in order to study their function in ribosomal DNA transcription. Using this system, we show that the knockout of PAF49, the mammalian ortholog of yeast A34, results in the relatively rapid degradation of PAF53, the ortholog of yeast A49. Interestingly, the steady-state levels of the core subunits of RNA polymerase I are unaffected.