Fig. 7

Differentially reactive nucleotides detected by diffBUM-HMM are preferentially localized in single-stranded regions and at the base of stems. A A secondary structure for a region in the Xist lncRNA containing CELF1, TARDBP, and HuR binding sites. The red dots indicate the nucleotides called modified only in the ex vivo data by diffBUM-HMM, while the violet lines indicate binding sites for RNA-binding proteins that were identified by CLIP/RIP (left). Also shown is the same secondary structure with the deltaSHAPE results from the two replicates individually (right). Those nucleotides called differentially modified in replicates 1 and 2 are colored red and cyan, respectively. B The same as in A but now for the FUS interaction domain of Xist