Quantitative Proteomics Analysis Reveals Novel Targets of miR-21 in Zebrafish Embryos

Sci Rep. 2017 Jun 22;7(1):4022. doi: 10.1038/s41598-017-04166-x.


MicroRNAs (miRNAs) are noncoding RNAs which control gene expression by the suppression of translation or the degradation of mRNAs. Dre-miR-21 (miR-21) has been reported to impact cardiac valvulogenesis in zebrafish embryos. However, the target genes of miR-21 are still largely unknown. Here a tandem isobaric mass tag (TMT)-based quantitative proteomic strategy was employed to identify the global profile of miR-21-regulated proteins. A total of 251 proteins were dysregulated after miR-21 knockdown, suggesting that they may be regulated by miR-21. Bioinformatics analysis indicated that these differentially expressed proteins (DEPs) participate in various biological processes, suggesting that miR-21 may be involved in diverse cellular pathways. Sixteen DEPs were also predicted to be miR-21 targets by at least two algorithms, and several candidate target genes were selected for further luciferase reporter analysis. The results showed that genes encoding tropomyosin 1 (tpm1) and poly(rC) binding protein 2 (pcbp2) are direct miR-21 targets. Taken together, our results not only reveal a large number of novel miR-21 regulated proteins that possess pleiotropic functions, but also provide novel insights into the molecular mechanisms of miR-21 regulation of zebrafish cardiac valvulogenesis and embryonic development.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Computational Biology / methods
  • Embryo, Nonmammalian
  • Embryonic Development / genetics*
  • Female
  • Gene Expression Regulation, Developmental*
  • Gene Knockdown Techniques
  • Male
  • MicroRNAs*
  • Proteomics* / methods
  • RNA Interference
  • RNA, Messenger / genetics
  • Reproducibility of Results
  • Zebrafish / embryology
  • Zebrafish / genetics*
  • Zebrafish / metabolism*


  • MIRN21 microRNA, zebrafish
  • MicroRNAs
  • RNA, Messenger