Isolation and sequencing of AGO-bound RNAs reveals characteristics of mammalian stem-loop processing in vivo

Ian M. Silverman; Sager J. Gosai; Nicholas Vrettos; Shawn W. Foley; Nathan D. Berkowitz; Zissimos Mourelatos; Brian D. Gregory

It is well established that pre-miRNA trimming and non-templated tailing (uridylation) is a mechanism of regulation (17, 18, 20) . However, most studies have investigated individual miRNAs or used targeted approaches to examine a predetermined subset of miRNAs. Using our novel datasets, we examined the end concordance of sequenced pre-miRNA-seq ( Figs. 2A and S2D ) and miRNAseq reads (Figs. 2B and S2E), relative to high confidence human and mouse miRBase miRNA ends. We found that the majority (>90%) of 5' read ends of pre-miRNAs coincided with annotated 5' ends of 5p miRNAs for both human and mouse ( Figs. 2A and S2D) . In contrast 3' read ends of pre-miRNAs were highly variable, with only 40% and 20% of reads ending precisely at the annotated 3' end of 3p miRNAs in human and mouse cells, respectively ( Figs. 2A and S2D) .