Supplementary Figure 6: Differences between in vivo and in vitro RNA structures are not uniformly distributed along transcripts.

a, Cumulative distributions of global 5’-UTR (837), CDS (1,122) and 3’-UTR (1,051) accessibilities in vivo and in vitro from the transcriptome of 2 hpf embryos. Only transcripts with a minimum of 85% coverage of As and Cs and with at least 10 reads in average per As and Cs for both in vivo and in vitro DMS-seq experiments are shown. P-values were computed using two-sided Wilcoxon signed-rank tests. b, Distribution of differentially structured windows along the transcripts of 2 hpf embryos, comparing in vivo and in vitro conditions. Windows with increased structure in vivo are depicted in orange, whereas those with decreased structure in vivo are shown in turquoise. Each transcript region (5’-UTR, CDS, 3’-UTR) has been normalized by its length, as well as by total number of windows analyzed in each region. Transcripts have been binned into quintiles based on their translation efficiency, which has been determined using ribosome profiling data