Epigenetic regulation and functional characterization of microRNA-142 in mesenchymal cells

PLoS One. 2013 Nov 13;8(11):e79231. doi: 10.1371/journal.pone.0079231. eCollection 2013.

Abstract

The transcripts encoded by the microRNA mir-142 gene are highly active in hematopoietic cells, but expressed at low levels in many other cell types. Treatment with the demethylating agent 5-Aza-2'-deoxycytidine increased both the 1,636 nucleotide primary transcript and mature miR-142-5p/3p in mesenchymal cells, indicating that mir-142 is epigenetically repressed by DNA methylation. The transcription start site was determined to be located 1,205 base pairs upstream of the precursor sequence within a highly conserved CpG island. In addition, a second CpG island overlapped with the precursor. A TATA-box, several promoter-proximal elements and enrichment of conserved transcription factor binding sites within the first 100 base pairs upstream of the transcription start site, suggests that this region represents the core/proximal mir-142 promoter. Moreover, both CpG islands were heavily methylated in mesenchymal cells, having low levels of miR-142-5p/3p, and unmethylated in hematopoietic cells where both miRNAs were abundantly expressed. We show that treatment with 5-Aza-2'-deoxycytidine significantly reduced the DNA methylation of the upstream CpG island, which led to increased expression, and that in vitro DNA methylation of the upstream region of the mir-142 precursor repressed its transcriptional activity. When overexpressed, miR-142-5p/3p reduced proliferation of cells with epigenetic silencing of endogenous mir-142. This finding is interesting as miR-142-5p/3p have been reported to be deregulated in tumors of mesenchymal origin. We provide the first experimental evidence that transcription of mir-142 is directly repressed by DNA methylation. In addition, we discovered that the antisense strand of mir-142 might act as a precursor for functional mature antisense miRNAs. Thus, our study expands the current knowledge about the regulation of mir-142 and function of miR-142-5p/3p, and adds novel insight into the rapidly increasing field of microRNA regulation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Azacitidine / analogs & derivatives
  • Azacitidine / pharmacology
  • Base Pairing
  • Base Sequence
  • Cell Line, Tumor
  • Cell Movement / genetics
  • Cell Proliferation
  • CpG Islands
  • DNA Methylation
  • Decitabine
  • Epigenesis, Genetic* / drug effects
  • Gene Expression Profiling
  • Gene Expression Regulation* / drug effects
  • Gene Silencing
  • Humans
  • MicroRNAs / chemistry
  • MicroRNAs / genetics*
  • Molecular Sequence Data
  • Osteosarcoma / genetics
  • Osteosarcoma / metabolism
  • Promoter Regions, Genetic
  • RNA Precursors / genetics
  • RNA, Antisense / genetics
  • Transcription, Genetic
  • Tumor Stem Cell Assay

Substances

  • MIRN142 microRNA, human
  • MicroRNAs
  • RNA Precursors
  • RNA, Antisense
  • Decitabine
  • Azacitidine

Grants and funding

The study was supported by the Norwegian Cancer Society and the Norwegian Stem Cell Centre (funded by the Research Council of Norway). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.