Fig. 1

Many snoRNAs show an interaction with their host gene transcripts. A General methodology shared between PARIS, LIGR-Seq, and SPLASH. The blue and pink lines represent two interacting RNA molecules. B Pipeline for de novo analysis of PARIS, LIGR-Seq, and SPLASH. Starting with over half a billion raw reads and keeping only chimeric reads involving snoRNAs left close to 305,000 reads which after merging overlapping reads, resulted in 6110 distinct interactions. Filtering of short interactions (≤ 8 bp) and interactions involving intergenic regions left 5140 interactions involving snoRNAs. Interactions composed of the snoRNA and its host gene (HG) transcripts were extracted (lighter blue; 215 interactions), and from those, 140 were identified between the snoRNA and a protein-coding HG. C, D Distribution of the position of the snoRNA target (i.e., interacting region) in the HG. E Comparison of functional classification of HGs between snoRNAs that interact with their host transcript (HT) vs the others. **p < 0.01. F SnoRNAs interacting with their HG are encoded in genes with complex regulation producing large numbers of transcripts. Density plot of the total number of transcripts for each protein-coding gene according to Ensembl annotation (v101). All distributions were significantly different from each other according to the Mann–Whitney U test, p-values 1.0e − 26 and 1.6e − 05 for hosts non-interacting with their snoRNA (red) vs non-host (green) and interacting snoRNA hosts (blue) vs non-interacting snoRNA hosts (red), respectively