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

Almost nothing is known about the relationship between pre-miRNA and mature miRNA abundance. In order to assess this, we first grouped miRNAs into their families and merged the mapped reads (Table S4) . This was necessary to avoid artifacts, given that multiple distinct precursors give rise to identical, or nearly identical mature miRNAs. We further refined our analysis by only focusing on high confidence miRNAs, which left us with 158 human and 159 mouse miRNAs with reads mapping from pre-miRNA-seq and/or miRNA-seq libraries (Table S5) . We analyzed the correlation between pre-miRNAs and mature miRNA levels expressed from these families (Figs. 4A-B) . We found a positive but modest correlation between pre-miRNA and mature miRNA expression in both humans (Spearman correlation R = 0.53, p-value < 6.635e -08 ) and mouse (Spearman correlation R = 0.52, p-value < 2.047e -07 ). We also assessed the relationship between smRNA-seq and pre-miRNA-seq in HEK293T cells (Fig. S3A ). We found a strikingly similar correlation to that of miRNA-seq (Spearman correlation; R = 0.53, p-value < 4.331e -08 ), which is explained by the high correlation of smRNA-seq to miRNA-seq (Spearman correlation; R = 0.90, pvalue < 2.2e -16 ) (Fig. S3B) . Together, these results reveal that in general pre- The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/294488 doi: bioRxiv preprint