Fig 3. Transcriptomic analysis of TMEM216-depleted cells.

The heatmaps were generated by the “heatmaps.2” R function using the log2 normalized gene expression levels in the different conditions. The color keys are presented at the top left corner of each heatmap and show a color variation from dark blue to dark red according to the gene expression level. (A–B) Each line represents the expression level variation for one down-regulated gene (A) or up-regulated gene (B) when TMEM216 is depleted. The differential expression level of the genes between control biological replicates (first three columns) and TMEM216^RNAi biological replicates (fourth and fifth column) is highlighted by the color variation. It is remarkable that these genes are not affected in IFT57-depleted cells (last four columns corresponding to the 4 biological replicates). (C–D) Comparison of the expression of genes differentially expressed (repressed [C] or up-regulated [D]) during the reciliation process [59] (called ciliary genes) with their expression in TMEM216^RNAi and control cells. In C, the vast majority of the ciliary repressed genes are also repressed when TMEM216 is depleted. Likewise, the ciliary up-regulated genes are up-regulated in TMEM216^RNAi. IFT57, intraflagellar transport 57; RNAi, RNA interference; TMEM216, Transmembrane protein 216.