While no difference in loading of the RNA samples was observed by using a GAPDH specific probe. Transcriptome sequencing by RNA-Seq produces a highly multidimensional type of data, allowing studies on simultaneously different aspects of gene expression, transcription and mRNA processing at a genome-wide scale. In this study, we focused on ribosome biogenesis, a process that we showed may be largely Vemurafenib altered during viral infection. Ribosome biogenesis is a highly regulated multistep process that starts with pre-rRNA transcription within the nucleolus and ends with the formation of functional ribosomes in the cytoplasm. Viral interactions with the nucleolus, sometimes disrupting nucleolar function, have been documented before for several viruses. Upon infection, many viral and/or cellular proteins transit through the nucleoli of the cells, and numerous host nucleolar proteins are redistributed to other cellular compartments. In this regard, in the early stages of infection, Newcastle disease virus matrix protein accumulates in the nucleolus of the host cells by binding the B23 nucleolar phosphoprotein and this interaction facilitate NDV replication. Upon infection with herpes simplex type 1, profound alterations of nucleolar morphology of the host cell occur. Nucleolin, B23 and UBF proteins leave the nucleolus to accumulate into the viral DNA replication centres. In addition, ribosomal protein L9 interacts with the mouse mammary tumor virus Gag protein in the nucleolus of the cells and knockdown of the endogenous L9 cause an impairment of virus production. These results lead to the hypothesis that efficient MMTV particle assembly is dependent upon the interaction of Gag and L9 in the nucleoli of infected cells. Recently, the use of proteomic analysis of cells either infected with different viruses or stably expressing specific viral proteins allowed to identify changes in nucleolar composition that are of functional relevance to the infection. In general, the role of viral perturbation of protein localization is not completely elucidated, but it has been shown to affect different steps of viral replication and various cellular processes, such as transcription, post-transcriptional processing and cell cycle control. Concerning HIV-1, it was previously reported that the viral regulatory proteins Tat and Rev are both mainly localized in the nucleolus. We have demonstrated that nucleolar localization of Tat and Rev, as well as the trafficking of some viral transcripts through this sub-cellular compartment, is critical for viral replication. Furthermore, it has been recently demonstrated that a subpopulation of Gag polyprotein of HIV-1 traffic trough the nucleolus during viral replication suggesting that in this nuclear compartment could contribute to HIV-1 RNA assembly and packaging. In addition, a quantitative proteomic analysis of the nucleolar composition of Jurkat cells stably expressing the HIV-1 Tat protein has shown that the expression of this viral protein causes changes in abundance of specific host nucleolar proteins which may reflect a viral strategy to facilitate viral production.