Identification of factors involved in target RNA-directed microRNA degradation

Nucleic Acids Res. 2016 Apr 7;44(6):2873-87. doi: 10.1093/nar/gkw040. Epub 2016 Jan 24.


The mechanism by which micro (mi)RNAs control their target gene expression is now well understood. It is however less clear how the level of miRNAs themselves is regulated. Under specific conditions, abundant and highly complementary target RNA can trigger miRNA degradation by a mechanism involving nucleotide addition and exonucleolytic degradation. One such mechanism has been previously observed to occur naturally during viral infection. To date, the molecular details of this phenomenon are not known. We report here that both the degree of complementarity and the ratio of miRNA/target abundance are crucial for the efficient decay of the small RNA. Using a proteomic approach based on the transfection of biotinylated antimiRNA oligonucleotides, we set to identify the factors involved in target-mediated miRNA degradation. Among the retrieved proteins, we identified members of the RNA-induced silencing complex, but also RNA modifying and degradation enzymes. We further validate and characterize the importance of one of these, the Perlman Syndrome 3'-5' exonuclease DIS3L2. We show that this protein interacts with Argonaute 2 and functionally validate its role in target-directed miRNA degradation both by artificial targets and in the context of mouse cytomegalovirus infection.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Argonaute Proteins / genetics
  • Argonaute Proteins / metabolism
  • Base Sequence
  • Biotinylation
  • Cell Line, Tumor
  • Cytomegalovirus / genetics
  • Cytomegalovirus Infections / genetics
  • Cytomegalovirus Infections / virology
  • Exoribonucleases / genetics*
  • Exoribonucleases / metabolism
  • Gene Expression Regulation
  • HEK293 Cells
  • HeLa Cells
  • Hepatocytes / cytology
  • Hepatocytes / metabolism
  • Humans
  • Mice
  • MicroRNAs / antagonists & inhibitors
  • MicroRNAs / genetics*
  • MicroRNAs / metabolism
  • Molecular Sequence Data
  • Nucleotidyltransferases / genetics*
  • Nucleotidyltransferases / metabolism
  • Oligonucleotides, Antisense / genetics
  • Oligonucleotides, Antisense / metabolism
  • Polynucleotide Adenylyltransferase
  • RNA Stability*
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • mRNA Cleavage and Polyadenylation Factors / genetics
  • mRNA Cleavage and Polyadenylation Factors / metabolism


  • AGO2 protein, human
  • Argonaute Proteins
  • MicroRNAs
  • Oligonucleotides, Antisense
  • RNA, Messenger
  • mRNA Cleavage and Polyadenylation Factors
  • Nucleotidyltransferases
  • TUT1 protein, human
  • Polynucleotide Adenylyltransferase
  • TENT2 protein, human
  • DIS3L2 protein, human
  • Dis3l2 protein, mouse
  • Exoribonucleases