A noncanonical microRNA derived from the snaR-A noncoding RNA targets a metastasis inhibitor

MicroRNAs (miRNAs) are small noncoding RNAs that function as critical posttranscriptional regulators in various biological processes. While most miRNAs are generated from processing of long primary transcripts via sequential Drosha and Dicer cleavage, some miRNAs that bypass Drosha cleavage can be transcribed as part of another small noncoding RNA. Here, we develop the target-oriented miRNA discovery (TOMiD) bioinformatic analysis method to identify Drosha-independent miRNAs from Argonaute crosslin king and sequencing of lilybrids (Ago-CLASH) data sets. Using this technique, we discovered a novel miRNA derived from a primate specific noncoding RNA, the small NF90 associated RNA A (snaR-A). The miRNA derived from snaR-A (miR-snaR) arises independently of Drosha processing but requires Exportin-5 and Dicer for biogenesis. We identify that miR-snaR is concurrently up-regulated with the full snaR-A transcript in cancer cells. Functionally, miR-snaR associates with Ago proteins and targets NME1, a key metastasis inhibitor, contributing to snaRA's role in promoting cancer cell migration. Our findings suggest a functional link between a novel miRNA and its precursor noncoding RNA.

Automated summary

Researchers developed a target-oriented miRNA discovery (TOMiD) bioinformatic analysis method to identify Drosha-independent miRNAs from Argonaute crosslinking and sequencing of lilybrids (Ago-CLASH) datasets. They discovered a novel miRNA derived from a primate specific noncoding RNA, the small NF90 associated RNA A (snaR-A), which arises independently of Drosha processing but requires Exportin-5 and Dicer for biogenesis. The miRNA, miR-snaR, is concurrently up-regulated with the full snaR-A transcript in cancer cells, associates with Ago proteins, and targets NME1, contributing to cancer cell migration.