Figure 6.

PKM2 directly binds and regulates translation of target mRNAs that are commonly translated at the ER.

A, PKM1/2 is endogenously tagged seamlessly with a C-terminal tandem FLAG-HA tag. Schematic of PKM2-FAST iCLIP experimental flow.

B, Percentage of the total iCLIP reads for various RNA classes. Positions of PKM2 crosslinks on the mature rRNA region is shown. ‘Others’ refer to U1, U2, U6 and other snoRNAs. Diagram for the A-site finger is taken from Comparative RNA Web (http://www.rna.ccbb.utexas.edu). Canonical base pairs are depicted with (-), GU wobble base pairs with (.). The nucleotide corresponding to the highest peak in the mature rRNA region, signifying the PKM2 crosslinking site on the A-site finger, is highlighted with yellow.

C, Overview of ribosome profiling workflow for control and PKM knockdown experiments.

D, Scatter plot showing the correlation between PKM2 iCLIP enrichment and translational efficiency change upon PKM depletion. Spearman coefficient (ρ) is presented.

E, Cumulative distributions of translational efficiency change upon PKM-depletion. PKM2 iCLIP targets are divided into four groups according to the degree of their iCLIP enrichment. Strong binders have lower translational efficiency in PKM-depleted cells relative to weak binders (P-value < 2.2 ×10–16 between top 5% and bottom 50% iCLIP targets, Mann-Whitney U test). See Table S5.

F, GO analysis for cellular compartment and biological process for PKM2 iCLIP targets. Adjusted P-values (Benjamini–Hochberg) are shown.