In addition, it has been recently shown that hundreds of proteins involved in other cellular processes including cell cycle control, stress response, DNA damage response and repair, senescence and telomerase function and aging also accumulate in the nucleolus. Moreover, the nucleolus is also the target of several viruses as a key site for their replicative process. We found that the genes functionally associated with the nucleolus and downregulated in HIV-1 infected cells encode for proteins mainly involved in regulation of the different steps of ribosome biogenesis, thus leading to the hypothesis that this process could be impaired during viral infection. These results were recapitulated in primary T CD4+. In addition, by Northern Blot analysis of the total RNA isolated from the mock- and HIV-1-infected Jurkat cells, we were able to show an alteration of the normal pre-rRNA processing pathway in the infected cell samples. In particular, we observed a dramatic decrease in the 30S transcript in the infected samples when compared to controls. Altogether, our study sheds new light into the intricate relationship between the host cell machinery and the infecting virus. Globally, we found that gene expression profiles are largely impacted by viral infection: infected cells clearly separate from mock-infected cells in hierarchical clustering and principal component analysis. As expected, technical replicates show very similar expression profiles, while biological replicates display slightly larger differences. Variance-ranked clustering by expression is very robust, with infected cells separating from mock-infected cells regardless the number of genes considered, from 50 genes to 1,000 genes.We detected Vorinostat clinical trial significant change in expression levels for 10% of the 18,382 expressed genes in our samples. When comparing the samples sequenced for this study to those belonging to the CHDT dataset, we found that the overall expression profiles differed. This is not unexpected, due to the difference in cell types, viral strains, infection strength, experimental design and sequencing technology used. In spite of these differences, however, the statistically significant changes between mock and infected cells observed in the two studies display a remarkable agreement, with almost half of the genes differentially expressed in our samples being also significantly deregulated in the CHDT dataset at 24 hr post-infection. This observation supports the biological relevance of the results obtained, for which changes in expression are related to viral infection and not affected by experimental variables. To confirm this hypothesis we assessed whether the pre-rRNA maturation process, one of the steps of the ribosome biogenesis, is affected by viral infection. To this aim, a Northern Blot analysis of total RNA isolated from the mock and infected Jurkat cells was performed using specific probes for the Internal Transcribed Spacer 1 rRNA sequences and for GAPDH mRNA as loading control. We found a substantial reduction in the accumulation of the 30S pre-rRNA in infected samples compared to controls.