Fig. 5

diffBUM-HMM detects a larger number of differentially modified nucleotides in the ex vivo Xist lncRNA data compared to deltaSHAPE and dStruct. A The differential reactivities of two deltaSHAPE replicate experiments [23] compared to the diffBUM-HMM posterior probabilities and dStruct outputs, which show the SHAPE reactivities of the regions it calls DRRs. The Xist RNA transcript was binned into 500 nucleotides regions and the differential reactivities for each bin is plotted. Regions with negative reactivities or posterior probability values are more reactive in vivo. Only those nucleotides that according to the deltaSHAPE analyses had sufficient coverage are plotted. The normalized diffBUM-HMM posteriors and dStruct panels indicate those nucleotides that were called differentially modified after normalizing the mutation rates in treated and untreated samples based on the denatured data (denoted as “den norm” in D). B Overview of the RNA-binding sites detected in the Xist transcript, as shown in [23]. C Overview of the number of DRNs that overlap with RNA-binding protein (RBP) binding sites in Xist in the in vivo and ex vivo data. Total DRNs indicates the total number of DRNs identified by diffBUM-HMM and deltaSHAPE in the datasets. “Den norm” indicates the data where we normalized the mutation frequencies of treated and control samples based on the denatured RNA data. D Enrichment of DRNs in RBP binding sites in Xist obtained from the CLIPdb database. Statistical significance for enrichment was determined using a hypergeometric test. Color legend indicates significance level, with binding sites for RBPs that are not statistically significant colored in gray