Unpaired nucleotides on the stem of microRNA precursor are important for precise cleavage by Dicer-like 1 in Arabidopsis

Rikako Hirata, Tomoya Makabe, Kei ichiro Mishiba, Nozomu Koizumi, Samir M. Hamdan, Yuji Iwata*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


Dicer-like 1 (DCL1) is a core component of the plant microRNA (miRNA) biogenesis machinery. MiRNA is transcribed as a precursor RNA, termed primary miRNA (pri-miRNA), which is cleaved by DCL1 in two steps to generate miRNA/miRNA* duplex. Pri-miRNA is a single-stranded RNA that forms a hairpin structure with a number of unpaired bases, hereafter called mismatches, on its stem. In the present study, by using purified recombinant Arabidopsis DCL1, we presented evidence that mismatches on the stem of pri-miRNA are important for precise DCL1 cleavage. We showed that a mismatch at the loop-distal side of the end of miRNA/miRNA* duplex is important for efficient cleavage of pri-miRNA in vitro, as previously suggested in planta. On the contrary, mismatches distant from the miRNA/miRNA* duplex region are important for determining the cleavage position by DCL1. The purified DCL1 proteins cleaved mutant pri-miRNA variants without such mismatches at a position at which wild-type pri-miRNA variants are not usually cleaved, resulting in an increased accumulation of small RNA different from miRNA. Therefore, our results suggest that, in addition to the distance from the ssRNA-dsRNA junction, mismatches on the stem of pri-miRNA function as a determinant for precise processing of pri-miRNA by DCL1 in plants.

Original languageEnglish (US)
Pages (from-to)280-292
Number of pages13
JournalGenes to Cells
Issue number4
StatePublished - Apr 2022


  • Arabidopsis thaliana
  • Dicer
  • microRNA
  • microRNA biogenesis
  • RNA secondary structure

ASJC Scopus subject areas

  • Genetics
  • Cell Biology


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