Intron Lariat RNA Inhibits MicroRNA Biogenesis by Sequestering the Dicing Complex in Arabidopsis

PLoS Genet. 2016 Nov 21;12(11):e1006422. doi: 10.1371/journal.pgen.1006422. eCollection 2016 Nov.

Abstract

Lariat RNAs formed as by-products of splicing are quickly degraded by the RNA debranching enzyme 1 (DBR1), leading to their turnover. Null dbr1 mutants in both animals and plants are embryo lethal, but the mechanism underlying the lethality remains unclear. Here we characterized a weak mutant allele of DBR1 in Arabidopsis, dbr1-2, and showed that a global increase in lariat RNAs was unexpectedly accompanied by a genome-wide reduction in miRNA accumulation. The dbr1-2 mutation had no effects on expression of miRNA biogenesis genes or primary miRNAs (pri-miRNAs), but the association of pri-miRNAs with the DCL1/HYL1 dicing complex was impaired. Lariat RNAs were associated with the DCL1/HYL1 dicing complex in vivo and competitively inhibited the binding of HYL1 with pri-miRNA. Consistent with the impacts of lariat RNAs on miRNA biogenesis, over-expression of lariat RNAs reduced miRNA accumulation. Lariat RNAs localized in nuclear bodies, and partially co-localize with HYL1, and both DCL1 and HYL1 were mis-localized in dbr1-2. Together with our findings that nearly four hundred lariat RNAs exist in wild type plants and that these lariat RNAs also associate with the DCL1/HYL1 dicing complex in vivo, we thus propose that lariat RNAs, as decoys, inhibit miRNA processing, suggesting a hitherto unknown layer of regulation in miRNA biogenesis.

MeSH terms

  • Alleles
  • Arabidopsis / genetics
  • Arabidopsis Proteins / genetics*
  • Arabidopsis Proteins / metabolism
  • Cell Cycle Proteins / genetics*
  • Cell Cycle Proteins / metabolism
  • Gene Expression Regulation, Plant
  • Introns / genetics
  • MicroRNAs / biosynthesis*
  • MicroRNAs / genetics
  • Mutant Proteins / genetics
  • RNA Nucleotidyltransferases / genetics*
  • RNA Nucleotidyltransferases / metabolism
  • RNA Processing, Post-Transcriptional / genetics
  • RNA Splicing / genetics
  • RNA-Binding Proteins / genetics*
  • RNA-Binding Proteins / metabolism
  • Ribonuclease III / genetics*
  • Ribonuclease III / metabolism

Substances

  • Arabidopsis Proteins
  • Cell Cycle Proteins
  • HYL1 protein, Arabidopsis
  • MicroRNAs
  • Mutant Proteins
  • RNA-Binding Proteins
  • DBR1 protein, Arabidopsis
  • RNA Nucleotidyltransferases
  • DCL1 protein, Arabidopsis
  • Ribonuclease III

Grants and funding

The authors received no specific funding for this work.