Fig. 4: In vivo mapping of HEK293 5′ UTR RNA structure ensembles.
a, Heat map depicting the enrichment of reads at the 5′ end of transcripts in 5′UTR-MaP experiments, as compared to standard DMS-MaPseq25. TES, transcription end site. b, Known structure of SL1 in the 5′ UTR of the ODC1 mRNA, as captured by 5′UTR-MaP57. c, Pie chart depicting the percentages of bases in the 5′ UTRome of HEK293 cultured under standard conditions, populating one, two or three or more conformations. Only bases populating the same number of conformations in both replicate experiments were considered. d, Distribution of median bulk (ensemble average) in vivo DMS reactivities in 1 versus 2+ regions. e, Distribution of Gini indices calculated on bulk (ensemble average) in vivo DMS reactivities in 1 versus 2+ regions. f, Pie chart depicting the percentages of bases in the 5′ UTRome of HEK293 upon ATP depletion, populating one, two or three or more conformations. Only bases populating the same number of conformations in both replicate experiments were considered. g, Pie chart depicting the percentages of bases in the 5′ UTRome of HEK293, for transcripts expressed under both standard and ATP-depleted conditions, for which the ensemble heterogeneity increases (red), decreases (blue) or remains unchanged (gray) upon ATP depletion. h, Distribution of translation efficiencies for genes whose 5′ UTRs encompass regions always populating 1 or 2+ conformations under standard or ATP-depleted conditions. NS< not significant. i, Distribution of densities of NTG triplets within regions populating 1 or 2+ conformations under standard or ATP-depleted conditions. For all box plots, boxes span the 25th to the 75th percentile. The center represents the median. Outliers (values below the 25th percentile − 1.5× the IQR or above the 75th percentile + 1.5× the IQR) are not shown. P values were calculated using a two-sided Wilcoxon rank-sum test.
