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Mammalian genome : official journal of the International Mammalian Genome Society2024; doi: 10.1007/s00335-024-10057-0

In search of epigenetic hallmarks of different tissues: an integrative omics study of horse liver, lung, and heart.

Abstract: DNA methylation and microRNA (miRNA) expression are epigenetic mechanisms essential for regulating tissue-specific gene expression and metabolic processes. However, high-resolution transcriptome, methylome, or miRNAome data is only available for a few model organisms and selected tissues. Up to date, only a few studies have reported on gene expression, DNA methylation, or miRNA expression in adult equine tissues at the genome-wide level. In the present study, we used RNA-Seq, miRNA-seq, and reduced representation bisulfite sequencing (RRBS) data from the heart, lung, and liver tissues of healthy cold-blooded horses to identify differentially expressed genes (DEGs), differentially expressed miRNA (DE miRNA) and differentially methylated sites (DMSs) between three types of horse tissues. Additionally, based on integrative omics analysis, we described the observed interactions of epigenetic mechanisms with tissue-specific gene expression alterations. The obtained data allowed identification from 4067 to 6143 DMSs, 9733 to 11,263 mRNAs, and 155 to 185 microRNAs, differentially expressed between various tissues. We pointed out specific genes whose expression level displayed a negative correlation with the level of CpG methylation and miRNA expression and revealed biological processes that they enrich. Furthermore, we confirmed and validated the accuracy of the Next-Generation Sequencing (NGS) results with bisulfite sequencing PCR (BSP) and quantitative PCR (qPCR). This comprehensive analysis forms a strong foundation for exploring the epigenetic mechanisms involved in tissue differentiation, especially the growth and development of the equine heart, lungs, and liver.
© 2024. The Author(s).
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Publication Date: 2024-08-14 PubMed ID: 39143382PubMed Central: 4373242DOI: 10.1007/s00335-024-10057-0Google Scholar: Lookup
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  • Journal Article

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 explores the epigenetic differences between various horse tissues – heart, lung, and liver. The scientists used advanced techniques to detect variations in gene expression, DNA methylation, and microRNA expression, aiming to shed light on the significant processes involved in tissue differentiation, growth, and development.

Study Objectives and Methods

  • The researchers aimed to locate differentially expressed genes (DEGs), microRNAs (DE miRNA), and differentially methylated sites (DMSs) across heart, lung, and liver tissues of healthy horses.
  • To do this, they used methods like RNA Sequencing (RNA-Seq), microRNA sequencing (miRNA-seq), and Reduced Representation Bisulfite Sequencing (RRBS). These methods helped measure gene expression, microRNA expression, and DNA methylation respectfully.
  • The team also used integrative omics analysis, a comprehensive method that includes genomics, transcriptomics, proteomics, and metabolomics to better observe the complex interactions within the biological system of a horse’s body.

Results and Further Validation

  • The research revealed numerous DMSs, mRNAs, and microRNAs that were differently processed in each type of tissue. These findings suggest that different tissues have unique epigenetic landscapes affecting genes’ expression, hence their function.
  • They observed specific genes whose levels of expression negatively correlated with the level of CpG methylation and miRNA expression. In simpler terms, the more a gene was methylated or targeted by a specific miRNA, the less expressed (active) it was, and vice versa.
  • Biological processes enriched by these genes were identified, revealing crucial processes that each tissue relies on for its specific role.
  • Lastly, to confirm the accuracy of their findings, the team corroborated their results with bisulfite sequencing PCR (BSP) and quantitative PCR (qPCR) validating the Next-Generation Sequencing (NGS) results.

Significance of the Study

  • This research provides a robust platform for understanding the epigenetic contributions to tissue differentiation, a critical process involved in the growth and development of different organs.
  • The results also guide researchers towards beneficial genes and the processes they are involved in, emphasizing their importance in the general function of each tissue type.

Cite This Article

APA
Semik-Gurgul E, Pawlina-Tyszko K, Gurgul A, Szmatoła T, Rybińska J, Ząbek T. (2024). In search of epigenetic hallmarks of different tissues: an integrative omics study of horse liver, lung, and heart. Mamm Genome. https://doi.org/10.1007/s00335-024-10057-0

Publication

Mammalian genome : official journal of the International Mammalian Genome Society
ISSN: 1432-1777
NlmUniqueID: 9100916
Country: United States
Language: English

Researcher Affiliations

Semik-Gurgul, Ewelina
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland. ewelina.semik@iz.edu.pl.
Pawlina-Tyszko, Klaudia
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland.
Gurgul, Artur
  • Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Redzina 1c, Krakow, 30-248, Poland.
Szmatoła, Tomasz
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland.
  • Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Redzina 1c, Krakow, 30-248, Poland.
Rybińska, Justyna
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland.
Ząbek, Tomasz
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1 St, Balice, 32-083, Poland.

Grant Funding

  • 504-180-821 / National Research Institute of Animal Production, Poland

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Citations

This article has been cited 2 times.
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  2. Luo M, Zhao J, Merilä J, Barrett RDH, Guo B, Hu J. The interplay between epigenomic and transcriptomic variation during ecotype divergence in stickleback. BMC Biol 2025 Mar 5;23(1):70.
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