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Peer-reviewedCC BY 4.0PLOS One

Identification of an atypical microRNA with sequence variation in the silkworm Bombyx mori

  • Mayuko Harada1
  • Midori Tabara2
  • Kazunori Kuriyama3
  • Katsuhiko Ito4
  • Hidemasa Bono5
  • Takuma Sakamoto6
  • Miho Nakano7
  • Toshiyuki Fukuhara8
  • Atsushi Toyoda
  • Asao Fujiyama
  • Hiroko Tabunoki
8 affiliations
  1. 1Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
  2. 2Ritsumeikan-Global Innovation Research Organization, Ritsumeikan University, Kusatsu, Shiga, Japan
  3. 3Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
  4. 4Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka, Japan
  5. 5Laboratory of Bio-DX, Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan
  6. 6Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan
  7. 7Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
  8. 8Cooperative Major in Advanced Health Science, Graduate School of Bio-Applications and System Engineering, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
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Abstract

MicroRNAs (miRNAs) play essential roles in posttranscriptional regulation of gene expression. During miRNA biosynthesis, miRNA precursors are cleaved by Dicer at their loop structure to generate mature miRNAs. However, the functional consequences of sequence alterations in the loop region remain poorly understood. The silkworm Bombyx mori is a lepidopteran insect with many genetic strains. In a B. mori strain exhibiting translucent larval skin, we unexpectedly identified a mutant form of miR-3260 in which part of the predicted loop structure was deleted. Here, we aimed to analyze the function of wild-type miR-3260 and the impact of this loop structure mutation in B. mori. First, we predicted potential binding partners for wild-type miR-3260 using the RNAhybrid tool and identified eight candidates, including two juvenile hormone (JH)-related genes. Expression analysis revealed high miR-3260 expression in the corpora allata. Furthermore, treatment of BmN cells with JH led to upregulated miR-3260 expression, suggesting a relationship between miR-3260 and JH signaling. Although miR-3260 mimics and inhibitors altered the expression of two JH-related candidate genes, the observed changes were not consistent with the predicted regulatory effects of miR-3260, and no observable larval phenotype was detected. Additionally, analysis of Dicer processing showed that neither the wild-type nor mutant miR-3260 precursor underwent Dicer-mediated cleavage. Although miR-3260 responds to JH, its function as a conventional miRNA was not supported. These findings suggest that miR-3260 may act as a JH-responsive non-coding RNA or represent a novel atypical RNA distinct from canonical miRNAs.

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Cite

BibTeXRIS
BibTeX
@article{harada2026identification,
  title = {{Identification of an atypical microRNA with sequence variation in the silkworm Bombyx mori}},
  author = {Mayuko Harada and Midori Tabara and Kazunori Kuriyama and Katsuhiko Ito and Hidemasa Bono and Takuma Sakamoto and Miho Nakano and Toshiyuki Fukuhara and Atsushi Toyoda and Asao Fujiyama and Hiroko Tabunoki},
  journal = {PLOS One},
  year = {2026},
  month = oct,
  doi = {10.1371/journal.pone.0346656},
  url = {https://doi.org/10.1371/journal.pone.0346656},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Identification of an atypical microRNA with sequence variation in the silkworm Bombyx mori
AU  - Mayuko Harada
AU  - Midori Tabara
AU  - Kazunori Kuriyama
AU  - Katsuhiko Ito
AU  - Hidemasa Bono
AU  - Takuma Sakamoto
AU  - Miho Nakano
AU  - Toshiyuki Fukuhara
AU  - Atsushi Toyoda
AU  - Asao Fujiyama
AU  - Hiroko Tabunoki
PY  - 2026
DA  - 2026/10/06
JO  - PLOS One
DO  - 10.1371/journal.pone.0346656
UR  - https://doi.org/10.1371/journal.pone.0346656
AB  - MicroRNAs (miRNAs) play essential roles in posttranscriptional regulation of gene expression. During miRNA biosynthesis, miRNA precursors are cleaved by Dicer at their loop structure to generate mature miRNAs. However, the functional consequences of sequence alterations in the loop region remain poorly understood. The silkworm Bombyx mori is a lepidopteran insect with many genetic strains. In a B. mori strain exhibiting translucent larval skin, we unexpectedly identified a mutant form of miR-3260 in which part of the predicted loop structure was deleted. Here, we aimed to analyze the function of wild-type miR-3260 and the impact of this loop structure mutation in B. mori. First, we predicted potential binding partners for wild-type miR-3260 using the RNAhybrid tool and identified eight candidates, including two juvenile hormone (JH)-related genes. Expression analysis revealed high miR-3260 expression in the corpora allata. Furthermore, treatment of BmN cells with JH led to upregulated miR-3260 expression, suggesting a relationship between miR-3260 and JH signaling. Although miR-3260 mimics and inhibitors altered the expression of two JH-related candidate genes, the observed changes were not consistent with the predicted regulatory effects of miR-3260, and no observable larval phenotype was detected. Additionally, analysis of Dicer processing showed that neither the wild-type nor mutant miR-3260 precursor underwent Dicer-mediated cleavage. Although miR-3260 responds to JH, its function as a conventional miRNA was not supported. These findings suggest that miR-3260 may act as a JH-responsive non-coding RNA or represent a novel atypical RNA distinct from canonical miRNAs.
SN  - 1932-6203
ER  -