Identification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylation

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dc.contributor.authorMaldonado, Mariângela B.C. [UNESP]
dc.contributor.authorDe Rezende Neto, Nelson B.
dc.contributor.authorNagamatsu, Sheila T.
dc.contributor.authorCarazzolle, Marcelo F.
dc.contributor.authorHoff, Jesse L.
dc.contributor.authorWhitacre, Lynsey K.
dc.contributor.authorSchnabel, Robert D.
dc.contributor.authorBehura, Susanta K.
dc.contributor.authorMcKay, Stephanie D.
dc.contributor.authorTaylor, Jeremy F.
dc.contributor.authorLopes, Flavia L. [UNESP]
dc.contributor.institutionUniversidade Estadual Paulista (Unesp)
dc.contributor.institutionABC Federal University
dc.contributor.institutionUniversidade Estadual de Campinas (UNICAMP)
dc.contributor.institutionBrazilian Center for Research in Energy and Materials (CNPEM)
dc.contributor.institutionUniversity of Missouri
dc.contributor.institutionUniversity of Vermont
dc.date.accessioned2019-10-06T15:56:23Z
dc.date.available2019-10-06T15:56:23Z
dc.date.issued2019-01-01
dc.description.abstractMethylation patterns established and maintained at CpG sites may be altered by single nucleotide polymorphisms (SNPs) within these sites and may affect the regulation of nearby genes. Our aims were to: 1) identify and generate a database of SNPs potentially subject to epigenetic control by DNA methylation via their involvement in creating, removing or displacing CpG sites (meSNPs), and; 2) investigate the association of these meSNPs with CpG islands (CGIs), and with methylation profiles of DNA extracted from tissues from cattle with divergent feed efficiencies detected using MIRA-Seq. Using the variant annotation for 56,969,697 SNPs identified in Run5 of the 1000 Bull Genomes Project and the UMD3.1.1 bovine reference genome sequence assembly, we identified and classified 12,836,763 meSNPs according to the nature of variation created at CpGs. The majority of the meSNPs were located in intergenic regions (68%) or introns (26.3%). We found an enrichment (p<0.01) of meSNPs located in CGIs relative to the genome as a whole, and also in differentially methylated sequences in tissues from animals divergent for feed efficiency. Seven meSNPs, located in differentially methylated regions, were fixed for methylation site creating (MSC) or destroying (MSD) alleles in the differentially methylated genomic sequences of animals differing in feed efficiency. These meSNPs may be mechanistically responsible for creating or deleting methylation targets responsible for the differential expression of genes underlying differences in feed efficiency. Our methyl SNP database (dbmeSNP) is useful for identifying potentially functional epigenetic polymorphisms underlying variation in bovine phenotypes.en
dc.description.affiliationSchool of Veterinary Medicine Universidade Estadual Paulista (UNESP), Rua Clóvis Pestana, 793-Jd. Dona Amélia
dc.description.affiliationNatural and Human Sciences Center ABC Federal University
dc.description.affiliationGenomics and Expression Laboratory University of Campinas
dc.description.affiliationBrazilian Bioethanol Science and Technology Laboratory (CTBE) Brazilian Center for Research in Energy and Materials (CNPEM)
dc.description.affiliationNational Center for High Performance Computing (CENAPAD-SP) University of Campinas
dc.description.affiliationDivision of Animal Sciences University of Missouri
dc.description.affiliationInformatics Institute University of Missouri
dc.description.affiliationDepartment of Animal and Veterinary Sciences University of Vermont
dc.description.affiliationUnespSchool of Veterinary Medicine Universidade Estadual Paulista (UNESP), Rua Clóvis Pestana, 793-Jd. Dona Amélia
dc.identifierhttp://dx.doi.org/10.1371/journal.pone.0222329
dc.identifier.citationPLoS ONE, v. 14, n. 9, 2019.
dc.identifier.doi10.1371/journal.pone.0222329
dc.identifier.issn1932-6203
dc.identifier.scopus2-s2.0-85072146112
dc.identifier.urihttp://hdl.handle.net/11449/188072
dc.language.isoeng
dc.relation.ispartofPLoS ONE
dc.rights.accessRightsAcesso aberto
dc.sourceScopus
dc.titleIdentification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylationen
dc.typeArtigo

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