FIGURE 2.

A, Z-score for single-stranded RNA preference and target A/U content. Previous studies have suggested that HuR binds hairpin loops (13), which the preference for ssRNA supports. B, the histogram shows the occurrence density of the sequence logo (inset), which is built from the top 1% of heptamers enriched at 3′-UTR iCLIP sites. This enrichment suggests that HuR may be preferentially binding uracil-rich sequences, rather than AU-rich sequences in general (see supplemental Fig. 2 for further details). Shown also is cross-species conservation of A/U nucleotides (percentages of non-matching nucleotides to human A/U, which are also A/U or a gap) and cross-species indel rate at 3′-UTR iCLIP sites. Previous studies have suggested that HuR binds hairpin loops (13); our observation of an increased indel rate across species indicates that the size and exact primary sequence of this loop may be highly variable.