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. 2014 Aug 21;8(4):1225-39.
doi: 10.1016/j.celrep.2014.07.023. Epub 2014 Aug 14.

Sequencing of captive target transcripts identifies the network of regulated genes and functions of primate-specific miR-522

Shen Mynn Tan  1 , Rory Kirchner  2 , Jingmin Jin  3 , Oliver Hofmann  2 , Larry McReynolds  3 , Winston Hide  4 , Judy Lieberman  5
Affiliations
Free article

Sequencing of captive target transcripts identifies the network of regulated genes and functions of primate-specific miR-522

Shen Mynn Tan et al. Cell Rep. .
Free article

Abstract

Identifying microRNA (miRNA)-regulated genes is key to understanding miRNA function. However, many miRNA recognition elements (MREs) do not follow canonical "seed" base-pairing rules, making identification of bona fide targets challenging. Here, we apply an unbiased sequencing-based systems approach to characterize miR-522, a member of the oncogenic primate-specific chromosome 19 miRNA cluster, highly expressed in poorly differentiated cancers. To identify miRNA targets, we sequenced full-length transcripts captured by a biotinylated miRNA mimic. Within these targets, mostly noncanonical MREs were identified by sequencing RNase-resistant fragments. miR-522 overexpression reduced mRNA, protein levels, and luciferase activity of >70% of a random list of candidate target genes and MREs. Bioinformatic analysis suggested that miR-522 regulates cell proliferation, detachment, migration, and epithelial-mesenchymal transition. miR-522 induces G1 cell-cycle arrest and causes cells to detach without anoikis, become invasive, and express mesenchymal genes. Thus, our method provides a simple but effective technique for identifying miRNA-regulated genes and biological function.

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