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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
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PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...
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RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
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Updated: Sep 11, 2025

mirMachine: A One-Stop Shop for Plant miRNA Annotation
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Key RNA elements influencing DCL1 cleavage in plant microRNA biogenesis.

Thi Nhu-Y Le1, Trung Duc Nguyen1, Yu Yu2

  • 1Division of Life Science, Hong Kong University of Science & Technology, Hong Kong, China.

Nature Plants
|August 13, 2025
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Summary

Researchers identified a key RNA motif, the GHR motif, that guides the plant enzyme DICER-LIKE 1 (DCL1) in processing microRNAs. This discovery clarifies how DCL1 ensures precise gene regulation in plants.

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Area of Science:

  • Plant molecular biology
  • RNA biology
  • Gene regulation

Background:

  • DICER-LIKE 1 (DCL1) is a plant enzyme crucial for microRNA (miRNA) biogenesis.
  • DCL1 processes precursor miRNAs into mature miRNAs, essential for post-transcriptional gene silencing.
  • The specific RNA elements dictating DCL1's cleavage site selection were previously unknown.

Purpose of the Study:

  • To identify and characterize the RNA elements that guide DCL1 cleavage site selection.
  • To elucidate the molecular mechanisms underlying DCL1's specificity in miRNA processing.
  • To investigate the role of identified RNA elements in plant gene regulation.

Main Methods:

  • High-throughput sequencing analysis of Arabidopsis thaliana DCL1 cleavage patterns.
  • Analysis of over 46,000 short hairpin RNA sequences.
  • Comparative analysis with human DICER cleavage patterns.

Main Results:

  • DCL1 cleavage preferences are determined by specific RNA secondary structures and sequence motifs.
  • A novel RNA element, the GHR motif, was identified as pivotal for DCL1 cleavage site selection.
  • The GHR motif influences cleavage independently of DCL1's dsRNA-binding and helicase domains, primarily via the RNase IIIDa domain.
  • The GHR motif is conserved across plant species and essential for precise miRNA precursor cleavage.
  • Evidence suggests the GHR motif's role in the biogenesis of non-canonical 22-nt miRNAs.

Conclusions:

  • The GHR motif is a critical determinant of DCL1 specificity in miRNA processing.
  • This finding enhances understanding of DCL1's function in plant gene regulatory networks.
  • The GHR motif's role extends to non-canonical miRNA biogenesis, broadening its functional significance.