Comparison of differentially occupied mRNA regions to RNA secondary structure predictions, presence of RNA binding motifs and changes in mRNA half-lives. (A, B) Average positional accessibility around the top 300 positions with significantly increased (A) or decreased (B) T-C transitions in MCF7 versus HEK293. Accessibility reflects the probability of each nucleotide to be unpaired as computed by the LocalFold algorithm  averaged over all 300 regions. Accessibility of real positions is indicated in red/blue while results obtained from random regions are indicated in grey. Light grey areas around random accessibilities reflect one standard deviation. We smoothed the data by using a window of ±2 nucleotides. (C, D) RNA binding proteins associated with the 20 most significantly enriched RNAcompete position weight matrices (PWMs)  found in a ±25 nucleotide region around positions with increased (C) and decreased (D) T-C transitions. CisBP-RNA database IDs of each PWM are indicated in brackets. The significance level of each PWM is represented by a -log10 transformation of the respective P-value on the left, while the ratio between top differentially occupied and random positions is given in log2-scale on the right. Additional files 6 and 7 contain the full list of significant PWMs. (E) Empirical cumulative density distribution of log2 fold changes in mRNA half-lives between MCF7 and HEK293 cells. The top 300 genes with decreased occupancy are shown in blue while the top 300 genes with increased occupancy are shown in red. Both groups are shifted to longer half-lives in MCF7 relative to the distribution of all other genes (black). We determined the significance levels of both shifts with a one-sided t-test yielding P-values of 0.000898 and 0.00644 for targets harboring positions of increased and decreased occupancy, respectively.