Increasing evidence suggests that the ubiqutin/proteasome system is directly involved in the regulation of transcription. The human proteasome-associated protein, PAAF1 regulates proteasome assemble and is required for recruitment of 19S-like complex to the HIV-1 promoter by Tat that stimulates transcriptional elongation (Lassot et al., 2007).

Here, we show that PAAF1 is required to couple transcriptional elongation to nucleosome reassembly. Ablation of PAAF1 using siRNA in HeLa cells containing a stably integrated HIV-1 promoter increases HIV-1 transcription. However, the transcripts are largely defective and not result in protein synthesis. ChIP analysis revealed a paucity of core histones as well as an aberrant accumulation of RNA polymerase II particularly at the promoter-proximal region of the LTR in PAAF1 knock-down cells.

We also found that the protein level of the histone chaperone, hSpt6, is decreased post-transcriptionally in PAAF1 knockdown cells. Knockdown of Spt6, like that of PAAF1, showed histone depletion and increased HIV-1 transcription. Furthermore, the phenotype of PAAF1 knock-down could be rescued by over-expression of hSpt6 or inhibition of proteasome activity. PAAF1, as well as hSpt6 and RNA polymerase II, localizes to sites of HIV-1 transcription. Together, these findings suggest that PAAF1 is required for transcriptional elongation through chromatin via regulation of hSpt6