Fig. 3

The interaction between SNORD2 and its host transcript is predicted to mask the branch point. A SNORD2 is encoded in the 3rd intron of the EIF4A2 gene, which serves as a host gene for a total of 5 snoRNAs. SnoRNAs are shown in orange, exons in steel blue, and the SNORD2 interacting region in cyan and introns are displayed as lines. B Both PARIS and LIGR-seq methodologies detect interactions between SNORD2 and its host intron. Zoom in from panel A representing exons 3 and 4 of EIF4A2 as well as the intervening intron containing SNORD2. Chimeric reads detected in PARIS and LIGR-seq datasets are represented above the gene diagram. The interaction position between SNORD2 and its intron as predicted by IntaRNA (shown in C) is indicated on the diagram. C IntaRNA duplex prediction between SNORD2 and Intron 3 (minimal free energy − 5.76 kcal/mol). D SNORD2 forms a stable structure with the downstream part of intron 3. SNORD2 and SNORD2-intron were folded using the LinearPartition tool. The highly paired region (pink and violet) was also predicted by IntaRNA (see panels B and C). The branch point (BP) for the intron as predicted by the branchpointer R package is located in the middle of this strong interaction. IR: interaction region. E The target region of SNORD2 in intron 3 of EIF4A2 is highly conserved. PhastCons score (100 vertebrates) was used to represent the conservation of the EIF4A2 gene region from exon 3 to intron 4 (salmon overlay). The target region is represented in cyan