Selective microRNA uridylation by Zcchc6 (TUT7) and Zcchc11 (TUT4)

Nucleic Acids Res. 2014 Oct;42(18):11777-91. doi: 10.1093/nar/gku805. Epub 2014 Sep 15.

Abstract

Recent small RNA sequencing data has uncovered 3' end modification of mature microRNAs (miRNAs). This non-templated nucleotide addition can impact miRNA gene regulatory networks through the control of miRNA stability or by interfering with the repression of target mRNAs. The miRNA modifying enzymes responsible for this regulation remain largely uncharacterized. Here we describe the ability for two related terminal uridyl transferases (TUTases), Zcchc6 (TUT7) and Zcchc11 (TUT4), to 3' mono-uridylate a specific subset of miRNAs involved in cell differentiation and Homeobox (Hox) gene control. Zcchc6/11 selectively uridylates these miRNAs in vitro, and we biochemically define a bipartite sequence motif that is necessary and sufficient to confer Zcchc6/11 catalyzed uridylation. Depletion of these TUTases in cultured cells causes the selective loss of 3' mono-uridylation of many of the same miRNAs. Upon TUTase-dependent loss of uridylation, we observe a concomitant increase in non-templated 3' mono-adenylation. Furthermore, TUTase inhibition in Zebrafish embryos causes developmental defects and aberrant Hox expression. Our results uncover the molecular basis for selective miRNA mono-uridylation by Zcchc6/11, highlight the precise control of different 3' miRNA modifications in cells and have implications for miRNA and Hox gene regulation during development.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism*
  • Gene Expression Regulation, Developmental
  • Genes, Homeobox
  • Humans
  • MicroRNAs / chemistry
  • MicroRNAs / metabolism*
  • Nucleotide Motifs
  • RNA Nucleotidyltransferases / antagonists & inhibitors
  • RNA Nucleotidyltransferases / genetics
  • RNA Nucleotidyltransferases / metabolism*
  • Uridine / metabolism*
  • Zebrafish / genetics

Substances

  • DNA-Binding Proteins
  • MicroRNAs
  • TUT4 protein, human
  • RNA Nucleotidyltransferases
  • TUT7 protein, human
  • Uridine

Associated data

  • GEO/GSE52575