Fig. 7

HIV-1 alternative splicing program in primary T cells at the early times of infection. Usage of SD (a) and SA (b) sites during a time course of infection of CD4+ T cells from donor 4 was based on the number of reads harbouring these particular SS involved in a splice junction and normalized with DESeq2 included in the Eoulsan’s pipeline. Usage of SD (c) and SA (d) sites was then expressed as % of the total number of viral annotated reads at each time point. Splice tree representations of HIV-1 alternative splicing regulation at 12 (e) and 24 (f) hpi were drawn on Cytoscape as in Fig. 5 based on ONT quantification of SS usage and spliced isoform levels at each time point. Only transcripts that were found at least 5 times in a sample and produced by usage of major SS were considered. Size of nodes is function of relative SS usage and size of triangles is function of transcript level as indicated by the scale. As D1 is present in all spliced isoforms, value of D1 was set at 100%. Non-coding exons (NCE) 2 and 3 are indicated