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Ahn J, Wu H, Lee J, Hwang IS, Yu D, Ahn JS, Lee JW, Hwang S, Lee K. Identification of a Novel Imprinted Transcript in the Porcine GNAS Complex Locus Using Methylome and Transcriptome of Parthenogenetic Fetuses. Genes (Basel) 2020; 11:genes11010096. [PMID: 31947640 PMCID: PMC7017182 DOI: 10.3390/genes11010096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 12/27/2022] Open
Abstract
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.
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Affiliation(s)
- Jinsoo Ahn
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA; (J.A.); (H.W.); (J.L.); (D.Y.)
| | - Huiguang Wu
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA; (J.A.); (H.W.); (J.L.); (D.Y.)
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Joonbum Lee
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA; (J.A.); (H.W.); (J.L.); (D.Y.)
| | - In-Sul Hwang
- Animal Biotechnology Division, National Institute of Animal Science, RDA, Jeonbuk 55365, Korea;
| | - Debing Yu
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA; (J.A.); (H.W.); (J.L.); (D.Y.)
- Department of Animal Breeding & Genetics, College of Animal Science & Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jin-Seop Ahn
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (J.-S.A.)
| | - Jeong-Woong Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (J.-S.A.)
| | - Seongsoo Hwang
- Animal Biotechnology Division, National Institute of Animal Science, RDA, Jeonbuk 55365, Korea;
- Correspondence: (S.H.); (K.L.)
| | - Kichoon Lee
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA; (J.A.); (H.W.); (J.L.); (D.Y.)
- Correspondence: (S.H.); (K.L.)
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