1. The Landscape of Genomic Imprinting at the Porcine SGCE/PEG10 Locus from Methylome and Transcriptome of Parthenogenetic Embryos
- Author
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In-Cheol Cho, In-Sul Hwang, Mi-Ryung Park, Jinsoo Ahn, Seongsoo Hwang, and Kichoon Lee
- Subjects
embryo ,Locus (genetics) ,Chromosome 9 ,QH426-470 ,Biology ,peg10 ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,SGCE ,Genetics ,rna sequencing ,Imprinting (psychology) ,Molecular Biology ,Genetics (clinical) ,030304 developmental biology ,0303 health sciences ,parthenogenetic ,porcine ,genomic imprinting ,differentially methylated region ,Differentially methylated regions ,DNA methylation ,sgce ,Genomic imprinting ,030217 neurology & neurosurgery ,whole-genome bisulfite sequencing - Abstract
In mammals, imprinted genes often exist in the form of clusters in specific chromosome regions. However, in pigs, genomic imprinting of a relatively few genes and clusters has been identified, and genes within or adjacent to putative imprinted clusters need to be investigated including those at the SGCE/PEG10 locus. The objective of this study was to, using porcine parthenogenetic embryos, investigate imprinting status of genes within the genomic region spans between the COL1A2 and ASB4 genes in chromosome 9. Whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) were conducted with normal and parthenogenetic embryos, and methylome and transcriptome were analyzed. As a result, differentially methylated regions (DMRs) between the embryos were identified, and parental allele-specific expressions of the SGCE and PEG10 genes were verified. The pig imprinted interval was limited between SGCE and PEG10, since both the COL1A2 and CASD1 genes at the centromere-proximal region and the genes between PPP1R9A and ASB4 toward the telomere were non-imprinted and biallelically expressed. Consequently, our combining analyses of methylome, transcriptome, and informative polymorphisms revealed the boundary of imprinting cluster at the SGCE/PEG10 locus in pig chromosome 9 and consolidated the landscape of genomic imprinting in pigs.
- Published
- 2020
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