Stage-specific RNA regulomes of Trichophyton mentagrophytes: mRNA-lncRNA-miRNA interplay in spore-hypha transition

Wudian Xiao; Zhaodan Wu; Jia Zhang; Jun Wan; Ruihuan Zhang; Xinyi Xiang; Yang Yu; Lu Fu; Kui Yang; Yang Chen; Ziyao Xiao; Ziyu Wang; Lvqin He; Jingcan You; Chunxiang Zhang

doi:10.3897/imafungus.16.166433

Research Article

IMA Fungus 16: e166433
https://doi.org/10.3897/imafungus.16.166433 (05 Nov 2025)

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Article title
Abstract
Key words
Introduction
Materials and methods
- Fungal culture and sample collection
- Germination analysis of T. mentagrophytes spores
- mRNA-lncRNA isolation, ribosomal RNA-depleted strand-specific library construction, and sequencing
- miRNA isolation, library construction, and sequencing
- Analysis of differentially expressed mRNA
- Identification and analysis of lncRNAs
- miRNA identification and analysis
- Enrichment analysis
- Orthology-inferred Protein-Protein interaction (PPI)
- Construction and analysis of candidate lncRNA – miRNA – mRNA network (ceRNA)
- qRT-PCR validation
- Statistical analyses
- Abbreviations
Results
- Germination of T. mentagrophytes spores
- Overview of RNA-sequencing
- Analysis of mRNAs
  - Identification and characterization of mRNAs
  - Functional enrichment analysis of mRNAs
  - Gene set enrichment analysis of mRNAs
  - Protein-protein interaction network analysis of mRNAs
- Analysis of lncRNAs
  - Identification and characterization of lncRNAs
  - Identification and analysis of differentially expressed lncRNAs
  - Functional enrichment analysis of antisense lncRNAs
  - Functional enrichment analysis of cis-lncRNAs
  - Functional enrichment analysis of trans-lncRNAs
- Analysis of miRNAs
  - Identification and characterization of miRNAs
  - Identification and analysis of differentially expressed miRNAs
  - Functional enrichment analysis of miRNAs
- Analysis of ceRNAs
  - Construction of a candidate ceRNA network
  - Exploratory enrichment analysis of ceRNAs
- qRT-PCR verification of the RNA-Seq results
Discussion
- Germination dynamics and transcriptional reprogramming
- LncRNAs orchestrate developmental transitions through multilayered regulation
  - Cis-regulatory mechanisms and their functions
  - Trans-regulatory networks and their functions
- miRNA-guided post-transcriptional control
- Integrated ceRNA networks coordinate development
- Biological significance of key pathways and molecular targets
  - Dynamic reprogramming of amino acid metabolism
  - Coordination of cell cycle and morphogenesis
- Limitations and future perspectives
Conclusion
Acknowledgements
Additional information
- Conflict of interest
- Ethical statement
- Use of AI
- Adherence to national and international regulations
- Funding
- Author contributions
- Author ORCIDs
- Data availability
References
Supplementary materials

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