Fig. 2: CHIKV reshapes the translational landscape at the ER but not the cytosol.

a Composition of RNA-seq and Ribo-seq libraries from the cytosol and ER compartments in non-infected and CHIKV-infected cells. Displayed are the percentages of total cellular and viral counts (for NSP - non-structural, and SP - structural proteins) after converting raw counts to counts per million (CPM) and averaging the CPM per condition across all samples passing QC. Colors indicate cellular mRNAs (blue), viral genomic RNA encoding non-structural proteins (red) and viral SG RNA encoding structural proteins (green). The percentage of viral NSP RNA-seq counts from the ER compartment in CHIKV-infected cells was too low (0.57%) to be visualized in the figure. b Normalized ribosome footprints of cellular mRNAs (n = 12220 mRNAs) and viral RNAs (n = 2) in both translation compartments in non-infected and CHIKV-infected cells. Normalized ribosome footprints were calculated for each gene (dots) by dividing the mean RPF CPM by mean mRNA CPM and subsequent log₁₀ transformation. Colors as in (a). Upper and lower limits of the box correspond to the 1st and 3rd quartile score distribution with whiskers extending to 1.5 times the range from top/bottom of the box. The line represents the median. c and d Analyses of RNA-seq and RPF libraries comparing CHIKV-infected and non-infected cells in the (c) cytosolic and (d) ER fractions. Each dot represents one gene, with a red dot highlighting KIAA1456 (which will be discussed in the next sections). Colors indicate no significant changes (grey), significantly increased translation rate (blue), significantly decreased translation rate (green). HEK293T cells were infected at a MOI of 4 and samples collected at twelve hours post-infection. Three independent replicates were carried for each condition.