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

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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. © 2014 The Authors.

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Tan, S. M., Kirchner, R., Jin, J., Hofmann, O., McReynolds, L., Hide, W., & Lieberman, J. (2014). Sequencing of captive target transcripts identifies the network of regulated genes and functions of rimate-specific miR-522. Cell Reports, 8(4), 1225–1239. https://doi.org/10.1016/j.celrep.2014.07.023

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