Viral miRNA adaptor differentially recruits miRNAs to target mRNAs through alternative base-pairing

All identified interactions involve sequences located between the 5’ end and the binding site for Sm proteins in HSUR2 (Figure 2C). Surprisingly, conserved sequences (Cazalla et al., 2010) in the 3’ terminal loop of HSUR2 are not found to participate in base-pairing with target mRNAs. Even though HSUR2 binds to target sequences with a significantly lower Gibbs free energy difference (ΔG) when compared to random sequences of similar length (Figure 2D), HSUR2 does not utilize a dedicated single sequence to do so (Figure 2C and Supplementary file 2). Thorough sequence analysis of 171 HSUR2 binding sites (see Materials and methods), with lengths ranging from 11 to 66 nts (Figure 2—figure supplement 1B and Supplementary file 2), failed to identify a sequence motif shared by most targets. HSUR2 sequences involved in interactions with target mRNAs differ in length (Figure 2—figure supplement 1B) and identity for each target (Figure 1C,D and Figure 1—figure supplement 2C; see also Supplementary file 2). Even in cases in which HSUR2 utilizes a similar subregion to base-pair with two different targets, the arrangement of base pairs always differs between the two interactions (Figure 1—figure supplement 2A–C). Altogether, these findings suggest that unlike other classes of small ncRNAs that participate in RNA-based regulatory systems (Gorski et al., 2017), HSUR2 does not feature a subregion or seed sequence that binds to target mRNAs, but instead uses different sequences to interact with different RNA partners, a characteristic shared with other Sm-class ncRNAs (Cotten et al., 1988; Nilsen, 1994; Roca and Krainer, 2009; Staley and Guthrie, 1998).