Since its discovery a little over a decade ago, the PAQosome (also known as R2TP/PFDL) has emerged as a critical organizer in the biogenesis of several protein complexes and networks such as protein assemblies involved in transcription, mRNA maturation, translation and nutrient-sensitive signalling pathways. Unsurprisingly, evidence is mounting that this chaperone complex may be involved in tumorigenesis, consistent with a role in regulating proliferation. We present here our most recent results that led to the identification of new client protein complexes and novel post-translational modification (PTM)-based modes of regulation of the PAQosome. Similar to what has recently been reported for axonemal dynein complexes involved in cilium motility; we now identify cytoplasmic dynein complexes that are responsible for cargo transport along microtubules as new clients of the PAQosome. We have also identified a phosphorylation-dependent association of the PAQosome subunit RPAP3 with preribosome complexes. Additionally, we report for the first time the identification of a small ORF-encoded PAQosome subunit, along with a possible role in the regulation of downstream gene, asparagine synthetase (ASNS) whose expression is linked to neurological disorders and response to asparaginase, a chemotherapeutic drug used in the treatment of acute lymphoblastic leukemia (ALL). These results define novel aspects of PAQosome function and regulation, some being associated with human diseases.