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bioRxiv · 10.1101/294488

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

Silverman, I. M.·Gosai, S. J.·Vrettos, N.·Foley, S. W.·Berkowitz, N. D.·Mourelatos, Z.·Gregory, B. D.
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Abstract

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.

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Silverman, I. M., Gosai, S. J., Vrettos, N., Foley, S. W., Berkowitz, N. D., Mourelatos, Z., Gregory, B. D.. 2018-04-06. Isolation and sequencing of AGO-bound RNAs reveals characteristics of mammalian stem-loop processing in vivo. https://doi.org/10.1101/294488

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