Fig. 7: FOREST identifies translational regulatory elements by profiling the binding properties of the EIF3 complex.

a An enriched sequence motif determined by MEME analysis of the population with the top 5% of cellular EIF3-complex binding intensities. b Two RNA structures derived from the 5′UTR of TCF25. c A dual-luciferase reporter assay using the designed 5′UTR of the identified candidates. A reporter mRNA encoding Nanoluc Luciferase was transfected into 293FT cells with Firefly Luciferase mRNA as the internal control. The CU-tracts of the RNA structures were redesigned as follows: mutants (MT) were designed by converting CU to GA sequences, and deletants (Del) were designed by deleting CU sequences. d Schematic of each 5′UTR of the reporter mRNAs. Reporter mRNAs contained the analyzed RNA structures with their whole 5′UTR sequences. The analyzed structures, the CU-tracts, and the converted GA-tracts are represented as turquoise, blue, and black regions, respectively. e Representative CU-rich RNA structures. According to the Z-scores, the DNAJC18-derived structure and the DDX21-derived structure have a high and medium affinity for the EIF3 complex, respectively. f Translational activity analysis. The intensities were normalized to those of each wild type. Error bars indicate means ± s.e.m. The experiments were performed with three biological replicates, each with two technical replicates. The p values were determined by two-tailed Dunnett’s test. ***p < 0.001, **p < 0.01, *p < 0.05. n.d. indicates no significant difference. Each “◇” indicates a data point. Source data are provided as a Source Data file.