Fig. 2: Experimental determination of the U2 and U4 snRNA structures.

a Secondary structure of U2 snRNA probed by SHAPE-MaP inside cells (in vivo), after isolation of cellular RNA (ex vivo) and transcribed in vitro (in vitro). Nucleotides reacting with the SHAPE reagent, indicated by red and yellow circles, were mapped onto the mature snRNA structure from U2 snRNP (based on ref. ⁴⁴; in vivo) or used as constraints to model RNA structure (ex vivo and in vitro). b Comparison of the SHAPE reagent reactivity collected either in vivo or ex vivo for the U2 snRNA. Near Sm site Structure (NSS) predicted by in silico modeling (see Fig. 1) is marked by beige lines, the Sm site by a red line. Analysis of statistically significant reactivity differences between ex vivo and in vivo-determined SHAPE reactivities was performed using the DeltaSHAPE automated analysis tool and default settings. Shaded regions indicate regions in which SHAPE reactivities are significantly different between the two experiments (standard score ≥1). c Secondary structure of in vitro synthesized U4 pre-snRNA probed by SHAPE-MaP. Nucleotide reactivities with the SHAPE reagent, marked by red and yellow circles, were used to predict the presented structure.