Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms

Nucleic Acids Res. 2009 Oct;37(18):5969-80. doi: 10.1093/nar/gkp638. Epub 2009 Aug 10.

Abstract

Recent miRNA transfection experiments show strong evidence that miRNAs influence not only their target but also non-target genes; the precise mechanism of the extended regulatory effects of miRNAs remains to be elucidated. A hypothetical two-layer regulatory network in which transcription factors (TFs) function as important mediators of miRNA-initiated regulatory effects was envisioned, and a comprehensive strategy was developed to map such miRNA-centered regulatory cascades. Given gene expression profiles after miRNA-perturbation, along with putative miRNA-gene and TF-gene regulatory relationships, highly likely degraded targets were fetched by a non-parametric statistical test; miRNA-regulated TFs and their downstream targets were mined out through linear regression modeling. When applied to 53 expression datasets, this strategy discovered combinatorial regulatory networks centered around 19 miRNAs. A tumor-related regulatory network was diagrammed as an example, with the important tumor-related regulators TP53 and MYC playing hub connector roles. A web server is provided for query and analysis of all reported data in this article. Our results reinforce the growing awareness that non-coding RNAs may play key roles in the transcription regulatory network. Our strategy could be applied to reveal conditional regulatory pathways in many more cellular contexts.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Gene Expression Regulation, Neoplastic
  • Gene Regulatory Networks*
  • Humans
  • Linear Models
  • MicroRNAs / metabolism*
  • RNA Interference*
  • Transcription Factors / metabolism*

Substances

  • MicroRNAs
  • Transcription Factors