Fig. 3

Transcriptomic mapping of C/D snoRNA chimeras calls novel, high-confidence interactions in mESCs. A Stacked bars indicate the fraction of C/D snoRNA chimeric reads mapping to distinct classes of possible target RNAs from FBL and NOP56 chimeric eCLIP. B Number of high-confidence snoRNA-target interactions identified by chimeric eCLIP according to interaction status and target class. C Browser tracks of snoRNA chimeric reads mapped to pre-rRNA or snRNA as captured by FBL and NOP56 chimeric eCLIP from mESC. Significant peaks at (black) known or (pink) novel sites. (Right) Base pair complementarity of novel interactions. RiboMeth-seq (RMS) score is shown for the 5th nucleotide from the D/D′ box when high methylation is observed. D (Left) Percent complementarity of base pairing in snoRNA-target interactions for significant peaks at known or novel sites and (right) fraction of interactions associated with D or D′ antisense elements. E Consensus sequence of the D or D′ box predicted to guide the known or novel snoRNA-target interactions. F RMS score at rRNA or snRNA target sites for known versus novel interactions. The 5th nucleotide is the expected position for methylation. (RMS scores are average of 2 biological replicates). G (Left) Snord89 expression following treatment with non-targeting (control) or Snord89-targeting ASO and (right) RMS scores at methylated nucleotides in U2 snRNA. * indicates P < 0.05, two-tailed unpaired Welch’s t-test. N = 2 replicates per condition. H (Left) Snord101 expression following treatment with non-targeting (control) or Snord101-tageting ASO and (right) RMS scores at methylated nucleotides in 28S rRNA. * indicates P < 0.05, two-tailed unpaired Welch’s t-test. N = 2 replicates per condition