In search of epigenetic hallmarks of different tissues: an integrative omics study of horse liver, lung, and heart.
Horse
Methylome
Tissue
Transcriptome
miRNAome
Journal
Mammalian genome : official journal of the International Mammalian Genome Society
ISSN: 1432-1777
Titre abrégé: Mamm Genome
Pays: United States
ID NLM: 9100916
Informations de publication
Date de publication:
14 Aug 2024
14 Aug 2024
Historique:
received:
17
05
2024
accepted:
01
08
2024
medline:
15
8
2024
pubmed:
15
8
2024
entrez:
14
8
2024
Statut:
aheadofprint
Résumé
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.
Identifiants
pubmed: 39143382
doi: 10.1007/s00335-024-10057-0
pii: 10.1007/s00335-024-10057-0
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : National Research Institute of Animal Production, Poland
ID : 504-180-821
Informations de copyright
© 2024. The Author(s).
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