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. 2021 Nov 15;12:6604. doi: 10.1038/s41467-021-26923-3

Fig. 4. The RNA helicase eIF4A1 promotes free scanning of the PIC.

Fig. 4

a Evaluation of global translation by Ribo-seq in MEF cells with or without eIF4A1 knockdown. Ribosome densities on individual transcripts were normalized to the number of mitochondrial reads and plotted as cumulative fractions. b Translation efficiency of Fluc mRNA reporters with ultra-short 5ʹ UTR in MEF cells with or without eIF4A1 knockdown. Fluc activities in the absence of eIF4A1 were normalized to the control. Error bars: mean ± SEM; n = 3 biological replicates. Two-tailed t-test, * p < 0.05; *** p < 0.001. c. Translation efficiency of Fluc mRNA reporters containing 3 AUG codons near the 5ʹ end in MEF cells with or without eIF4A1 knockdown. Fluc activities in the absence of eIF4A1 were normalized to the control. Error bars: mean ± SEM; n = 3 biological replicates. Two-tailed t-test, * p < 0.05; *** p < 0.001; **** p < 0.0001. d Comparison of read length distribution in cells with or without eIF4A1 knockdown. Reads mapped to TSS, 5ʹ UTR, or start codons are plotted separately. e Aggregation plots of 5ʹ end (green) and 3’ end (red) of reads on mRNAs aligned to TSS using eIF3-seq data sets obtained from cells with or without eIF4A1 knockdown. f Aggregation plots of 5ʹ end (green) and 3ʹ end (red) of reads on mRNAs aligned to start codons using eIF3-seq data sets obtained from cells with or without eIF4A1 knockdown. Highlighted squares indicate upstream footprints (3’ end of reads) and downstream footprints (5ʹ end of reads). Source data are provided as a Source Data file.