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Updated: Jul 19, 2025
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Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
Published on: June 15, 2016
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Transposable Elements-Derived MicroRNA Expression Patterns in TCGA Dataset for 10 Species.
Chan-Mi Lee1, Sang Woo Jin2, Byunghyun Jang3
1Department of Otorhinolaryngology-Head and Neck Surgery, Korea University Guro Hospital, Seoul, South Korea.
Evolutionary Bioinformatics Online
|August 17, 2023
Summary
Transposable element-derived microRNAs (miRNAs) show evolutionary patterns linked to cancer. Conserved miRNAs like miR-130a and species-specific ones like miR-625 offer insights into carcinoma diagnosis and prognosis.
Area of Science:
- Evolutionary biology
- Genomics
- Cancer research
Background:
- MicroRNAs (miRNAs) are crucial non-coding RNA regulators in disease pathogenesis.
- Understanding the evolutionary context of disease-related miRNAs, particularly those derived from transposable elements (TEs), can enhance diagnostic and prognostic capabilities.
- TE-derived miRNAs represent a potentially valuable area for exploring disease mechanisms.
Purpose of the Study:
- To investigate the evolutionary patterns of transposable element-derived microRNAs (TE-miRNAs) in relation to various carcinomas.
- To identify differentially expressed miRNAs (DEMs) associated with cancer status, stage, and survival.
- To explore cross-species gene-miRNA interactions for evolutionarily conserved and species-specific TE-miRNAs.
Main Methods:
- Comparative analysis of 34 miRNAs across 33 carcinomas from The Cancer Genome Atlas (TCGA).
- Statistical comparison (t-test) to identify differentially expressed miRNAs (DEMs) based on cancer status, stage, and survival.
- Cross-species (10 species) analysis of gene-miRNA interactions using the TargetScan database and Gene Ontology (GO) enrichment.
Main Results:
- At least one miRNA was significantly differentially expressed (P < .05, |fold change| >.05) in 18 out of 33 carcinomas.
- A total of 128 DEMs involving 9 miRNAs were identified, with conserved miR-130a found in all 10 species and human-specific miR-151a identified.
- Evolutionarily conserved miR-130a was linked to renal and thyroid cancers; human and rhesus monkey-specific miR-625 was associated with various carcinomas.
Conclusions:
- TE-derived miRNAs exhibit evolutionary conservation patterns that are relevant to carcinoma development and progression.
- Specific miRNAs, such as the conserved miR-130a and species-specific miR-625, demonstrate potential as biomarkers for certain cancers.
- Evolutionary analysis of TE-miRNAs provides valuable insights into cancer biology and may aid in developing novel diagnostic and prognostic strategies.
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