miR-634 is a Pol III-dependent intronic microRNA regulating alternative-polyadenylated isoforms of its host gene PRKCA

Biochim Biophys Acta Gen Subj. 2017 May;1861(5 Pt A):1046-1056. doi: 10.1016/j.bbagen.2017.02.016. Epub 2017 Feb 14.


Background: The protein kinase C alpha (PRKCA) gene, coding for a Th17-cell-selective kinase, shows a complex splicing pattern, with at least 2 stable alternative transcripts characterized by an alternative upstream polyadenylation site. Polymorphisms in this gene were associated with several conditions, including multiple sclerosis, asthma, schizophrenia, and cancer. The presence of a microRNA (miRNA), i.e. miR-634, within intron 15 of the PRKCA gene, suggests the intriguing possibility that this miRNA might play a role in the susceptibility to these pathologies.

Methods: Here, we characterized miR-634 expression profile and searched for its putative targets using a combination of RT-PCR and gene reporter assays.

Results: The quantitative analysis of PRKCA and miR-634 transcripts in a panel of human tissues and cell lines revealed discordant expression profiles, suggesting the presence of an independent miR-634 promoter and/or a possible direct role of miR-634 in modulating PRKCA expression. Functional studies demonstrated the existence of a miRNA-specific promoter, which was shown to be Pol-III-dependent. Furthermore, transfection experiments showed that miR-634 is able to target its host gene by specifically down-regulating the shorter alternative-polyadenylated isoforms.

Conclusions: MiR-634 is a Pol III-dependent intronic miRNA, which could target its host gene through a "first-order" negative feedback.

General significance: MiR-634 is one of the few characterized examples of Pol-III-dependent intronic miRNAs. Its independent transcription from the host gene suggests caution in using expression profiles of host genes as proxies for the expression of the corresponding intronic miRNAs.

Keywords: Multiple sclerosis; PRKCA; Promoter; Target gene; miR-634.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line
  • Cell Line, Tumor
  • Down-Regulation / genetics
  • Gene Expression Regulation / genetics
  • Genes, Reporter / genetics
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Introns / genetics*
  • MicroRNAs / genetics*
  • Polyadenylation / genetics*
  • Promoter Regions, Genetic / genetics
  • Protein Isoforms / genetics*
  • Protein Kinase C-alpha / genetics*
  • RNA Polymerase III / genetics
  • RNA Polymerase III / metabolism*
  • Transcription, Genetic / genetics
  • Transcriptome / genetics


  • MIRN-634 microRNA, human
  • MicroRNAs
  • Protein Isoforms
  • PRKCA protein, human
  • Protein Kinase C-alpha
  • RNA Polymerase III