Fig. 2

Characteristics of snoRNAs interacting with their host introns support functional regulatory relationships. A SnoRNAs interacting with their HG are in close proximity to alternative splicing events. Cumulative percentage plots of the distance to the closest alternative splicing event for both snoRNAs interacting with their host intron (blue) and all other snoRNAs (red) are shown. A Mann–Whitney U test showed a significant difference between the two distributions, p = 1.2e − 5. B Intronic interaction regions between snoRNAs and host introns display unexpected levels of conservation. Bar chart showing the proportion of snoRNA-intronic interaction regions with high conservation compared to negative regions located at same distance from snoRNAs not interacting with their host transcript (HT). The mean conservation of the target regions was calculated using PhastCons on 100 vertebrates. **p < 0.01. C Minimum free energy (mfe) predicted by IntaRNA is significantly lower (Kolmogorov–Smirnov test, p = 0.038) for snoRNAs and target regions than snoRNA and matched negative regions. D TGIRT-Seq read coverage was observed from the 3′ end of SNORA12 to the intron interacting region, located in the CWF19L gene. Reads detected in two LIGR-seq datasets are shown as colored rectangles with their corresponding support (i.e., number of reads observed). Such an extension was observed for a total of 18 snoRNAs (Additional file 2: Table S1). E Upset plot displaying the features supporting a functional relationship for each of the 102 detected interactions between snoRNAs and their own intron in a protein-coding host gene. To be positive in one category, the interaction was required to pass the following thresholds: P/L/S support > 3 detected chimeric reads, stable structure required a minimal energy of the interaction duplex < 0 kcal/mol, average conservation score > 0.2, proximity to ASE required a splicing distance of closest alternative event < 150 nt and extension ratio > 2