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Cell–cell contact globally activates microRNA biogenesis

  1. Hun-Way Hwanga,
  2. Erik A. Wentzelb and
  3. Joshua T. Mendella,b,c,d,1
  1. aProgram in Human Genetics and Molecular Biology,
  2. bMcKusick–Nathans Institute of Genetic Medicine,
  3. cDepartment of Pediatrics, and
  4. dDepartment of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205

  1. Edited by Phillip A. Sharp, Massachusetts Institute of Technology, Cambridge, MA, and approved March 5, 2009 (received for review November 13, 2008)

Abstract

MicroRNAs (miRNAs) are 18- to 24-nt RNA molecules that regulate messenger RNAs (mRNAs). Posttranscriptional mechanisms regulate miRNA abundance during development as well as in cancer cells where miRNAs frequently exhibit dysregulated expression. The molecular mechanisms that govern the global efficiency of miRNA biogenesis in these settings remain incompletely understood, and experimental systems for the biochemical dissection of these pathways are currently lacking. Here, we demonstrate that miRNAs are subject to dynamic posttranscriptional regulation in widely used cell culture systems. As diverse mammalian and Drosophila cell lines are grown to increasing density, miRNA biogenesis is globally activated, leading to elevated mature miRNA levels and stronger repression of target constructs. This broad increase in miRNA abundance is associated with enhanced processing of miRNAs by Drosha and more efficient formation of RNA-induced silencing complexes. These findings uncover a critical parameter necessary for accurate analysis of miRNAs in cell culture settings, establish a tractable system for the study of regulated miRNA biogenesis, and may provide insight into mechanisms that influence miRNA expression in physiologic and pathophysiologic states.

Footnotes

  • 1To whom correspondence should be addressed at:
    733 North Broadway, BRB 471, Baltimore, MD 21205.
    E-mail: jmendell{at}jhmi.edu

  • Author contributions: H.-W.H. and J.T.M. designed research; H.-W.H., E.A.W., and J.T.M. performed research; H.-W.H. and J.T.M. analyzed data; and H.-W.H. and J.T.M. wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission.

  • This article contains supporting information online at www.pnas.org/cgi/content/full/0811523106/DCSupplemental.

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