Fig. 1: Transcriptional and translational changes in HIV-1 infected cells.

A Schematic representation of the procedure to monitor transcript abundance and translation in HIV-1 infected cells (Created in BioRender. Ricci, E. (2022) BioRender.com/k47z556). Briefly, SupT1 cells were infected or not (Mock) with HIV-1 (NL4.3 strain) at MOI 5. At 0, 1, 12, 24 and 36 hours post infection (hpi), cells were lysed to recover the cytoplasmic fraction and prepare ribosome profiling and RNA-seq libraries subjected to high-throughput sequencing on the Illumina Hiseq platform (n = 4 independent experiments). Total cell lysates were recovered for mass spectrometry analysis (n = 4 independent experiments). B Scatter-plot of the fold-change (log2) in cytoplasmic RNA-seq and Ribo-Seq of the Mock-infected and HIV-1 infected cells at each time point of infection. Orange dots (“Transcript-level only”) corresponds to genes exclusively regulated at the transcript abundance level. Blue dots (“Translation only”) correspond to genes which display differences in ribosome occupancy while transcript abundance remains unchanged. Green dots (“Translationally regulated”) correspond to genes with significant changes in transcript abundance and significantly further changes, in the same direction, in ribosome occupancy upon infection. Red dots (“Translationally buffered”) correspond to transcripts displaying significant changes in transcript abundance but for which there is compensation at the translational level to maintain unchanged ribosome occupancy levels upon infection. C Gene ontology analysis of differentially expressed genes at each time point.