2. Academic Validation
  3. A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis

A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis

  • Mol Cell. 2017 Apr 20;66(2):270-284.e13. doi: 10.1016/j.molcel.2017.03.014.
Thomas Treiber 1,  Nora Treiber 1,  Uwe Plessmann 2,  Simone Harlander 1,  Julia-Lisa Daiß 1,  Norbert Eichner 1,  Gerhard Lehmann 1,  Kevin Schall 1,  Henning Urlaub 2,  Gunter Meister 3
Affiliations

Affiliations

  • 1 Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany.
  • 2 Bioanalytical Mass Spectrometry Group, Max-Planck-Institute of Biophysical Chemistry, 37077 Göttingen, Germany.
  • 3 Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany. Electronic address: [email protected].
PMID: 28431233 DOI: 10.1016/j.molcel.2017.03.014
Abstract

During MicroRNA (miRNA) biogenesis, two endonucleolytic reactions convert stem-loop-structured precursors into mature miRNAs. These processing steps can be posttranscriptionally regulated by RNA-binding proteins (RBPs). Here, we have used a proteomics-based pull-down approach to map and characterize the interactome of a multitude of pre-miRNAs. We identify ∼180 RBPs that interact specifically with distinct pre-miRNAs. For functional validation, we combined RNAi and CRISPR/Cas-mediated knockout experiments to analyze RBP-dependent changes in miRNA levels. Indeed, a large number of the investigated candidates, including splicing factors and other mRNA processing proteins, have effects on miRNA processing. As an example, we show that TRIM71/LIN41 is a potent regulator of miR-29a processing and its inactivation directly affects miR-29a targets. We provide an extended database of RBPs that interact with pre-miRNAs in extracts of different cell types, highlighting a widespread layer of co- and posttranscriptional regulation of miRNA biogenesis.

Keywords

LIN28; RNA binding proteins; RNA processing; RNA pull-down; TRIM71; ZC3H10; ZC3H7; microRNA-guided gene silencing; regulation of microRNA biogenesis; siRNA pool.

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