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Multi-tissue transcriptomic characterization of endogenous retrovirus-derived transcripts in Capra hircus
Ming-Di Li1,2, Hu-Rong Li1, Shao-Hui Ye1
1Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China.
Frontiers in Genetics
|April 3, 2025
Summary
Transposable elements (TEs) comprise nearly half of the goat genome. This study reveals endogenous retroviruses (ERVs) are highly active in goat embryos and respond to viral infections, impacting nearby gene expression.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Transposable elements (TEs) are repetitive DNA sequences constituting a significant portion of mammalian genomes.
- While often silenced, certain TEs, particularly endogenous retroviruses (ERVs), can be expressed under specific physiological conditions.
- The expression patterns of TEs in less-studied species like goats (Capra hircus) were previously unclear.
Purpose of the Study:
- To comprehensively analyze the genomic and transcriptomic characteristics of TEs and ERVs in goats.
- To investigate the expression patterns of TEs and ERVs across various goat tissues and conditions.
- To explore the co-expression of ERVs with neighboring genes to understand regulatory mechanisms.
Main Methods:
- Systematic annotation of TE distribution across goat genome classes, families, and subfamilies.
- Analysis of TE-derived transcript expression in multiple tissues at subfamily and location levels.
- Differential expression analysis of ERV-derived reads under physiological (embryo development) and pathological (virus infection) conditions.
- Exploration of co-expression between ERV reads and proximal genes.
Main Results:
- Approximately 800 TE subfamilies were identified, accounting for 49.1% of the goat genome.
- TE-derived reads represented 10% of the transcriptome, with relatively consistent abundance across tissues.
- ERV expression varied among tissues, showing high activity in 16-cell embryos and in response to RNA virus infection in lung, spleen, caecum, and immune cells.
- Specific ERVK elements (CapAeg_1.233) showed dysregulation during endometrium development and infection, co-expressing with proximal genes like OAS1 and TMPRSS2.
Conclusions:
- Generated comprehensive ERV transcriptomes for goat tissues.
- Identified specific ERVs activated during distinct physiological and pathological states in goats.
- Demonstrated the influence of proximal gene expression on nearby ERV activity.
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