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

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


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Binding Sites
  • Cell Line, Tumor
  • Epithelial-Mesenchymal Transition
  • Female
  • Gene Expression Regulation, Neoplastic
  • Gene Regulatory Networks
  • Humans
  • MicroRNAs
  • Prognosis
  • RNA Interference
  • RNA, Messenger / genetics*
  • Sequence Analysis, RNA
  • Transcription, Genetic
  • Triple Negative Breast Neoplasms / diagnosis
  • Triple Negative Breast Neoplasms / metabolism*


  • MIRN522 microRNA, human
  • MicroRNAs
  • RNA, Messenger