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Frontiers in genetics2022; 13; 944933; doi: 10.3389/fgene.2022.944933

Analysis of ancient and modern horse genomes reveals the critical impact of lncRNA-mediated epigenetic regulation on horse domestication.

Abstract: The domestication of horses has played critical roles in human civilizations. The excavation of ancient horse DNA provides crucial data for studying horse domestication. Studies of horse domestication can shed light on the general mechanisms of animal domestication. We wish to explore the gene transcription regulation by long noncoding RNAs (lncRNAs) that influence horse domestication. First, we assembled the ancient DNA sequences of multiple horses at different times and the genomes of horses, donkeys, and Przewalski horses. Second, we extracted sequences of lncRNA genes shared in ancient horses and sequences of lncRNA genes and the promoter regions of domestication-critical genes shared in modern horses, modern donkeys, and Przewalski horses to form two sample groups. Third, we used the LongTarget program to predict potential regulatory interactions between these lncRNAs and these domestication-critical genes and analyzed the differences between the regulation in ancient/modern horses and between horses/donkeys/Przewalski horses. Fourth, we performed functional enrichment analyses of genes that exhibit differences in epigenetic regulation. First, genes associated with neural crest development and domestication syndrome are important targets of lncRNAs. Second, compared with undomesticated Przewalski horses, more lncRNAs participate in the epigenetic regulation in modern horses and donkeys, suggesting that domestication is linked to more epigenetic regulatory changes. Third, lncRNAs' potential target genes in modern horses are mainly involved in two functional areas: 1) the nervous system, behavior, and cognition, and 2) muscle, body size, cardiac function, and metabolism. Domestication is linked to substantial epigenetic regulatory changes. Genes associated with neural crest development and domestication syndrome underwent noticeable lncRNA-mediated epigenetic regulation changes during horse domestication.
Copyright © 2022 Xu, Yang, Jiao and Zhu.
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Publication Date: 2022-10-05 PubMed ID: 36276948PubMed Central: PMC9579347DOI: 10.3389/fgene.2022.944933Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research investigates the genetic factors behind horse domestication, specifically the role of long noncoding RNAs (lncRNAs) in regulating gene transcription. The study analyzed ancient and modern horse genomes and identified significant changes in lncRNA-mediated epigenetic regulation that relate to domestication.

Methodology

  • The researchers began their investigation by gathering ancient horse DNA from various periods in history as well as modern genomes of horses, donkeys, and Przewalski horses (a wild relative of domestic horses).
  • They then singled out shared lncRNA genes in the ancient horse genomes and the shared lncRNA genes, along with promoter regions of genes critical for domestication, in the modern genomes.
  • With these gene samples, the team used a software program called LongTarget to predict potential regulatory associations between these lncRNAs and the crucial domestication genes. They then analyzed the regulatory differences in ancient versus modern horses, and between domesticated and undomesticated horse species.
  • Lastly, the researchers performed a functional enrichment analysis of those genes that showed alterations in their epigenetic, or lncRNA-mediated, regulation.

Findings

  • The analysis revealed that genes associated with neural crest development and what’s known as domestication syndrome are crucial targets of lncRNAs. This suggests a strong link between lncRNA-mediated epigenetic regulation and the domestication process.
  • It was found that more lncRNAs participate in this epigenetic regulation in modern, domesticated horses and donkeys compared with the Przewalski horses. This indicates that the domestication process affected a greater epigenetic regulatory change in these species.
  • The lncRNAs’ target genes in modern domesticated horses were mainly involved in two key functional areas: the nervous system (including behavior and cognition) and physical attributes (like muscle development, body size, cardiac function, and metabolism).

Conclusion

The researchers concluded that horse domestication is connected to considerable change in epigenetic regulation, mediated by lncRNAs. Genes associated with neural crest development and domestication syndrome specifically, showed significant lncRNA-mediated epigenetic regulatory changes during the process of horse domestication.

Cite This Article

APA
Xu B, Yang G, Jiao B, Zhu H. (2022). Analysis of ancient and modern horse genomes reveals the critical impact of lncRNA-mediated epigenetic regulation on horse domestication. Front Genet, 13, 944933. https://doi.org/10.3389/fgene.2022.944933

Publication

Frontiers in genetics
ISSN: 1664-8021
NlmUniqueID: 101560621
Country: Switzerland
Language: English
Volume: 13
Pages: 944933
PII: 944933

Researcher Affiliations

Xu, Baoyan
  • Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
  • Medical Engineering Department, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China.
Yang, Guixian
  • Zhujiang Hospital, Southern Medical University, Guangzhou, China.
Jiao, Baowei
  • State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming, China.
Zhu, Hao
  • Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.

Conflict of Interest Statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

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Citations

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