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

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Two enzymes, Zcchc6 and Zcchc11, add uridines to microRNAs (miRNAs), impacting gene regulation. Their depletion affects miRNA modification, leading to developmental issues in zebrafish and altered Homeobox gene expression.

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Area of Science:

  • Molecular Biology
  • Developmental Biology
  • RNA Biology

Background:

  • MicroRNAs (miRNAs) are key regulators of gene expression.
  • Post-transcriptional modifications, including 3' end nucleotide additions, affect miRNA function.
  • The enzymes responsible for specific miRNA 3' end modifications are largely unknown.

Purpose of the Study:

  • To identify the enzymes responsible for 3' end mono-uridylation of specific microRNAs.
  • To elucidate the mechanism and regulatory role of miRNA uridylation.
  • To investigate the impact of miRNA uridylation on gene regulation and development.

Main Methods:

  • Small RNA sequencing to identify modified miRNAs.
  • In vitro biochemical assays using purified terminal uridyl transferases (TUTases).
  • Cellular depletion of TUTases (Zcchc6/TUT7 and Zcchc11/TUT4) and subsequent miRNA analysis.
  • Zebrafish embryo experiments with TUTase inhibition.

Main Results:

  • Zcchc6 (TUT7) and Zcchc11 (TUT4) were identified as the primary enzymes catalyzing 3' mono-uridylation of specific miRNAs involved in cell differentiation and Homeobox (Hox) gene control.
  • A bipartite sequence motif was biochemically defined as necessary and sufficient for Zcchc6/11-mediated uridylation.
  • Depletion of Zcchc6/11 in cells led to a selective loss of miRNA uridylation and a compensatory increase in miRNA adenylation.
  • Inhibition of TUTases in zebrafish embryos resulted in developmental defects and aberrant Hox gene expression.

Conclusions:

  • Zcchc6 and Zcchc11 are key regulators of miRNA 3' end uridylation, controlling the stability and function of specific miRNA subsets.
  • This study reveals the molecular basis for selective miRNA uridylation and its role in precise control of miRNA modifications.
  • MiRNA uridylation by Zcchc6/11 has significant implications for gene regulatory networks, particularly in the context of development and Homeobox gene regulation.