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Open AccessArticle

Identification of a Novel Imprinted Transcript in the Porcine GNAS Complex Locus Using Methylome and Transcriptome of Parthenogenetic Fetuses

1
Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA
2
College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
3
Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
4
Animal Biotechnology Division, National Institute of Animal Science, RDA, Jeonbuk 55365, Korea
5
Department of Animal Breeding & Genetics, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China
6
Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2020, 11(1), 96; https://doi.org/10.3390/genes11010096
Received: 9 December 2019 / Revised: 10 January 2020 / Accepted: 13 January 2020 / Published: 14 January 2020
(This article belongs to the Section Animal Genetics and Genomics)
Genomic imprinting in domestic animals contributes to the variance of performance traits. However, research remains to be done on large-scale detection of epigenetic landscape of porcine imprinted loci including the GNAS complex locus. The purpose of this study was to generate porcine parthenogenetic fetuses and comprehensively identify imprinting patterns of the GNAS locus in transcript levels. To this end, both normally fertilized and bimaternal (uniparental) parthenogenetic porcine fetuses were generated, and whole genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) were performed to construct methylome and transcriptome, respectively. Differentially methylated regions (DMRs) between the fetuses were identified through methylome analysis, and parental-origin-specific expression patterns of transcripts were examined with transcriptome. As a result, three major DMRs were identified: paternally methylated Nesp DMR, maternally methylated Nespas-Gnasxl DMR, and maternally methylated Exon1B–Exon1A DMR. Parental-origin-specific expressions of those five DMR-affected transcripts were found, including a novel imprinted transcript, Exon1B, in pigs. In conclusion, using parthenotes, parental-origin-specific imprinting patterns in the porcine GNAS locus was comprehensively identified, and our approach paves the way for the discovery of novel imprinted genes and loci in a genomic context across species. View Full-Text
Keywords: genomic imprinting; GNAS; porcine; parthenogenetic; fetus; whole genome bisulfite sequencing; RNA-sequencing; differentially methylated region; parthenote genomic imprinting; GNAS; porcine; parthenogenetic; fetus; whole genome bisulfite sequencing; RNA-sequencing; differentially methylated region; parthenote
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MDPI and ACS Style

Ahn, J.; Wu, H.; Lee, J.; Hwang, I.-S.; Yu, D.; Ahn, J.-S.; Lee, J.-W.; Hwang, S.; Lee, K. Identification of a Novel Imprinted Transcript in the Porcine GNAS Complex Locus Using Methylome and Transcriptome of Parthenogenetic Fetuses. Genes 2020, 11, 96. https://doi.org/10.3390/genes11010096

AMA Style

Ahn J, Wu H, Lee J, Hwang I-S, Yu D, Ahn J-S, Lee J-W, Hwang S, Lee K. Identification of a Novel Imprinted Transcript in the Porcine GNAS Complex Locus Using Methylome and Transcriptome of Parthenogenetic Fetuses. Genes. 2020; 11(1):96. https://doi.org/10.3390/genes11010096

Chicago/Turabian Style

Ahn, Jinsoo; Wu, Huiguang; Lee, Joonbum; Hwang, In-Sul; Yu, Debing; Ahn, Jin-Seop; Lee, Jeong-Woong; Hwang, Seongsoo; Lee, Kichoon. 2020. "Identification of a Novel Imprinted Transcript in the Porcine GNAS Complex Locus Using Methylome and Transcriptome of Parthenogenetic Fetuses" Genes 11, no. 1: 96. https://doi.org/10.3390/genes11010096

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