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Genetic and epigenetic markers in the METTL21C gene associated with umbilical hernia in pigs

cris.virtual.author-orcid0000-0002-1806-0891
cris.virtual.author-orcid0000-0001-9465-3851
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cris.virtualsource.author-orcida96d2343-ee65-450d-8ce2-355a51255d10
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dc.abstract.enBackground: Hernias, particularly umbilical hernias (UH), are prevalent anatomical anomalies in swine, leading to significant welfare issues and economic losses. Besides environmental factors also genetic components contribute to the development of UHs, though the exact mechanisms remain unclear. This study employed a multiple approaches integrating RNA-seq, DNA methylation analysis, Sanger sequencing, droplet digital PCR and western blot analysis to investigate the genetic and epigenetic underpinnings of UH in pigs. Muscle tissue from affected and control pigs was examined to identify differentially expressed genes (DEGs) and associated pathways. Results: We found 59 significant DEGs, including SIM1, PITX1, HOXA7, METTL21C, PVALB, ALX1, EYA2, and TBX1. Interestingly, RNA-seq analysis of METTL21C revealed its significant upregulation in UH-affected pigs. This was corroborated by epigenetic analysis, which identified hypomethylation at four CpG sites in the METTL21C within potential regulatory region, aligning with increased mRNA levels. Furthermore, Sanger sequencing uncovered an SNP (rs330073569) in the METTL21C regulatory region, which was significantly associated with UH condition. This SNP can potentially alter transcription factor binding leading to enhanced METTL21C transcription, and putatively contributing to the gene’s increased expression in UH pigs. Conclusions: This study highlights potential genetic and epigenetic factors in UH etiology. The most significant result suggests that METTL21C plays an important role in the development of UH. This finding makes this gene a promising candidate for further research aimed at better characterizing umbilical hernia in pigs and at potentially eliminating undesirable variants from the gene pool.
dc.affiliationWydział Medycyny Weterynaryjnej i Nauk o Zwierzętach
dc.affiliation.instituteKatedra Genetyki i Podstaw Hodowli Zwierząt​​
dc.contributor.authorWozniak, Jakub
dc.contributor.authorSzabelska-Beręsewicz, Alicja
dc.contributor.authorZyprych-Walczak, Joanna Grażyna
dc.contributor.authorNiemyjski, Rafal
dc.contributor.authorDudek, Klaudia
dc.contributor.authorStachowiak, Monika
dc.contributor.authorNowacka-Woszuk, Joanna
dc.date.access2025-12-12
dc.date.accessioned2025-12-12T09:00:07Z
dc.date.available2025-12-12T09:00:07Z
dc.date.copyright2025-12-11
dc.date.issued2025
dc.description.abstract<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Background</jats:title> <jats:p>Hernias, particularly umbilical hernias (UH), are prevalent anatomical anomalies in swine, leading to significant welfare issues and economic losses. Besides environmental factors also genetic components contribute to the development of UHs, though the exact mechanisms remain unclear. This study employed a multiple approaches integrating RNA-seq, DNA methylation analysis, Sanger sequencing, droplet digital PCR and western blot analysis to investigate the genetic and epigenetic underpinnings of UH in pigs. Muscle tissue from affected and control pigs was examined to identify differentially expressed genes (DEGs) and associated pathways.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p> We found 59 significant DEGs, including <jats:italic>SIM1</jats:italic> , <jats:italic>PITX1</jats:italic> , <jats:italic>HOXA7</jats:italic> , <jats:italic>METTL21C</jats:italic> , <jats:italic>PVALB</jats:italic> , <jats:italic>ALX1</jats:italic> , <jats:italic>EYA2</jats:italic> , and <jats:italic>TBX1</jats:italic> . Interestingly, RNA-seq analysis of <jats:italic>METTL21C</jats:italic> revealed its significant upregulation in UH-affected pigs. This was corroborated by epigenetic analysis, which identified hypomethylation at four CpG sites in the <jats:italic>METTL21C</jats:italic> within potential regulatory region, aligning with increased mRNA levels. Furthermore, Sanger sequencing uncovered an SNP (rs330073569) in the <jats:italic>METTL21C</jats:italic> regulatory region, which was significantly associated with UH condition. This SNP can potentially alter transcription factor binding leading to enhanced <jats:italic>METTL21C</jats:italic> transcription, and putatively contributing to the gene’s increased expression in UH pigs. </jats:p> </jats:sec> <jats:sec> <jats:title>Conclusions</jats:title> <jats:p> This study highlights potential genetic and epigenetic factors in UH etiology. The most significant result suggests that <jats:italic>METTL21C</jats:italic> plays an important role in the development of UH. This finding makes this gene a promising candidate for further research aimed at better characterizing umbilical hernia in pigs and at potentially eliminating undesirable variants from the gene pool. </jats:p> </jats:sec>
dc.description.accesstimeat_publication
dc.description.bibliographyil., bibliogr.
dc.description.financepublication_act
dc.description.financecost14270,46
dc.description.if3,7
dc.description.number1
dc.description.points140
dc.description.versionfinal_published
dc.description.volume26
dc.identifier.doi10.1186/s12864-025-12315-0
dc.identifier.issn1471-2164
dc.identifier.urihttps://sciencerep.up.poznan.pl/handle/item/6375
dc.identifier.weblinkhttps://link.springer.com/article/10.1186/s12864-025-12315-0
dc.languageen
dc.relation.ispartofBMC Genomics
dc.relation.pagesart. 1096
dc.rightsCC-BY
dc.sciencecloudnosend
dc.share.typeOPEN_JOURNAL
dc.subject.enRNA-seq
dc.subject.enHernia
dc.subject.enGene expression
dc.subject.enDNA methylation
dc.subject.enSNP
dc.subject.enCNV
dc.titleGenetic and epigenetic markers in the METTL21C gene associated with umbilical hernia in pigs
dc.typeJournalArticle
dspace.entity.typePublication
oaire.citation.issue1
oaire.citation.volume26