RT Journal Article SR Electronic T1 Isolation and sequencing of AGO-bound RNAs reveals characteristics of mammalian stem-loop processing in vivo JF bioRxiv FD Cold Spring Harbor Laboratory SP 294488 DO 10.1101/294488 A1 Ian M. Silverman A1 Sager J. Gosai A1 Nicholas Vrettos A1 Shawn W. Foley A1 Nathan D. Berkowitz A1 Zissimos Mourelatos A1 Brian D. Gregory YR 2018 UL http://biorxiv.org/content/early/2018/04/06/294488.abstract AB MicroRNA precursors (pre-miRNAs) are short hairpin RNAs that are rapidly processed into mature microRNAs (miRNAs) in the cytoplasm. Due to their low abundance in cells, sequencing-based studies of pre-miRNAs have been limited. We successfully enriched for and deep sequenced pre-miRNAs in human cells by capturing these RNAs during their interaction with Argonaute (AGO) proteins. Using this approach, we detected > 350 pre-miRNAs in human cells and > 250 pre-miRNAs in a reanalysis of a similar study in mouse cells. We uncovered widespread trimming and non-templated additions to the 3’ ends of pre- and mature miRNAs. Additionally, we created an index for microRNA precursor processing efficiency. This analysis revealed a subset of pre-miRNAs that produce low levels of mature miRNAs despite abundant precursors, including an annotated miRNA in the 5’ UTR of the DiGeorge syndrome critical region 8 mRNA transcript. This led us to search for AGO-associated stem-loops originating from other mRNA species, which identified hundreds of putative pre-miRNAs derived from human and mouse mRNAs. In summary, we provide a wealth of information on mammalian pre-miRNAs, and identify novel microRNA and microRNA-like elements localized in mRNAs.