Homodimerization of HYL1 ensures the correct selection of cleavage sites in primary miRNA

Nucleic Acids Res. 2014 Oct 29;42(19):12224-36. doi: 10.1093/nar/gku907. Epub 2014 Oct 7.


MicroRNA (miRNA) plays an important role in the control of gene expression. HYPONASTIC LEAVES1 (HYL1) is a double-stranded RNA-binding protein that forms a complex with DICER-LIKE1 (DCL1) and SERRATE (SE) to process primary miRNA (pri-miRNA) into mature miRNA. Although HYL1 has been shown to partner with DCL1 to enhance miRNA accuracy, the mechanism by which HYL1 selects the DCL1-targeted cleavage sites in pri-miRNA has remained unknown. By mutagenesis of HYL1 and analysis of in vivo pri-miRNA processing, we investigated the role of HYL1 in pri-miRNA cleavage. HYL1 forms homodimers in which the residues Gly147 and Leu165 in the dsRBD2 domain are shown to be critical. Disruption of HYL1 homodimerization causes incorrect cleavage at sites in pri-miRNA without interrupting the interaction of HYL1 with DCL1 and accumulation of pri-miRNAs in HYL1/pri-miRNA complexes, leading to a reduction in the efficiency and accuracy of miRNAs that results in strong mutant phenotypes of the plants. HYL1 homodimers may function as a molecular anchor for DCL1 to cleave at a distance from the ssRNA-dsRNA junction in pri-miRNA. These results suggest that HYL1 ensures the correct selection of pri-miRNA cleavage sites through homodimerization and thus contributes to gene silencing and plant development.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics
  • Arabidopsis / growth & development
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / chemistry*
  • Arabidopsis Proteins / metabolism
  • Calcium-Binding Proteins / metabolism
  • Cell Cycle Proteins / metabolism
  • Dimerization
  • Gene Silencing
  • Glycine / chemistry
  • Intercellular Signaling Peptides and Proteins / metabolism
  • Leucine / chemistry
  • Membrane Proteins / metabolism
  • MicroRNAs / metabolism*
  • Protein Multimerization
  • Protein Structure, Tertiary
  • RNA Cleavage
  • RNA Processing, Post-Transcriptional*
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / metabolism
  • Ribonuclease III / metabolism
  • Serrate-Jagged Proteins


  • Arabidopsis Proteins
  • Calcium-Binding Proteins
  • Cell Cycle Proteins
  • HYL1 protein, Arabidopsis
  • Intercellular Signaling Peptides and Proteins
  • Membrane Proteins
  • MicroRNAs
  • RNA-Binding Proteins
  • SE protein, Arabidopsis
  • Serrate-Jagged Proteins
  • DCL1 protein, Arabidopsis
  • Ribonuclease III
  • Leucine
  • Glycine