{ "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.", "abstract_shown": true, "affiliations": [ "Department of Science of Biological Production, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan", "Ritsumeikan-Global Innovation Research Organization, Ritsumeikan University, Kusatsu, Shiga, Japan", "Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan", "Database Center for Life Science (DBCLS), Joint Support-Center for Data Science Research, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka, Japan", "Laboratory of Bio-DX, Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan", "Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima City, Hiroshima, Japan", "Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan", "Cooperative Major in Advanced Health Science, Graduate School of Bio-Applications and System Engineering, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan" ], "article_type": "Research Article", "arxiv": null, "author_total": 11, "authors": [ { "affs": [ 0 ], "name": "Mayuko Harada" }, { "affs": [ 1 ], "name": "Midori Tabara" }, { "affs": [ 2 ], "name": "Kazunori Kuriyama" }, { "affs": [ 3 ], "name": "Katsuhiko Ito" }, { "affs": [ 4 ], "name": "Hidemasa Bono" }, { "affs": [ 5 ], "name": "Takuma Sakamoto" }, { "affs": [ 6 ], "name": "Miho Nakano" }, { "affs": [ 7 ], "name": "Toshiyuki Fukuhara" }, { "name": "Atsushi Toyoda" }, { "name": "Asao Fujiyama" }, { "name": "Hiroko Tabunoki" } ], "bibtex": "https://research.draconitic.com/paper/c1zebpxt6xyzq.bib", "cited_by": 0, "doi": "10.1371/journal.pone.0346656", "fulltext_url": null, "id": "c1zebpxt6xyzq", "issns": [ "1932-6203" ], "landing_url": "https://doi.org/10.1371/journal.pone.0346656", "language": null, "licence": "CC-BY-4.0", "licence_label": "CC BY 4.0", "licence_source": "journal", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "1306|MicroRNA in disease regulation" ], [ "plos", "/Biology and life sciences/Biochemistry/Nucleic acids/RNA/Messenger RNA" ], [ "plos", "/Biology and life sciences/Biochemistry/Nucleic acids/RNA/Non-coding RNA/Natural antisense transcripts/MicroRNAs" ], [ "plos", "/Biology and life sciences/Biochemistry/Nucleic acids/RNA/RNA structure" ], [ "plos", "/Biology and life sciences/Developmental biology/Life cycles/Larvae" ], [ "plos", "/Biology and life sciences/Genetics/Gene expression" ], [ "plos", "/Biology and life sciences/Genetics/Gene expression/Gene regulation/MicroRNAs" ], [ "plos", "/Biology and life sciences/Molecular biology/Macromolecular structure analysis/RNA structure" ], [ "plos", "/Biology and life sciences/Molecular biology/Molecular biology techniques/Artificial gene amplification and extension/Polymerase chain reaction" ], [ "plos", "/Biology and life sciences/Molecular biology/Molecular biology techniques/Sequencing techniques/Nucleotide sequencing" ], [ "plos", "/Biology and life sciences/Organisms/Eukaryota/Animals/Invertebrates/Arthropoda/Insects/Silkworms" ], [ "plos", "/Biology and life sciences/Zoology/Animals/Invertebrates/Arthropoda/Insects/Silkworms" ], [ "plos", "/Biology and life sciences/Zoology/Entomology/Insects/Silkworms" ], [ "plos", "/Research and analysis methods/Molecular biology techniques/Artificial gene amplification and extension/Polymerase chain reaction" ], [ "plos", "/Research and analysis methods/Molecular biology techniques/Sequencing techniques/Nucleotide sequencing" ] ], "openalex": "W7220711754", "pdf_url": "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0346656&type=printable", "pmcid": null, "pmid": null, "published": "2026-10-06", "publisher": "Public Library of Science", "ris": "https://research.draconitic.com/paper/c1zebpxt6xyzq.ris", "sources": [ { "first_seen": "2026-10-30T12:17:30Z", "native_id": "10.1371/journal.pone.0346656", "source": "plos", "url": "https://doi.org/10.1371/journal.pone.0346656" } ], "subjects": [ { "field": "biochemistry", "origin": "plos:gene expression", "subfield": "molecular-biology" } ], "title": "Identification of an atypical microRNA with sequence variation in the silkworm Bombyx mori", "title_text": "Identification of an atypical microRNA with sequence variation in the silkworm Bombyx mori", "type": "peer-reviewed", "updated_at": "2026-10-30T12:17:30Z", "url": "https://research.draconitic.com/paper/c1zebpxt6xyzq", "venue": "PLOS One", "versions": [] }