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

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 parthenogeneti...

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Autores principales: Ahn, Jinsoo, Wu, Huiguang, Lee, Joonbum, Hwang, In-Sul, Yu, Debing, Ahn, Jin-Seop, Lee, Jeong-Woong, Hwang, Seongsoo, Lee, Kichoon
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017182/
https://www.ncbi.nlm.nih.gov/pubmed/31947640
http://dx.doi.org/10.3390/genes11010096
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author Ahn, Jinsoo
Wu, Huiguang
Lee, Joonbum
Hwang, In-Sul
Yu, Debing
Ahn, Jin-Seop
Lee, Jeong-Woong
Hwang, Seongsoo
Lee, Kichoon
author_facet Ahn, Jinsoo
Wu, Huiguang
Lee, Joonbum
Hwang, In-Sul
Yu, Debing
Ahn, Jin-Seop
Lee, Jeong-Woong
Hwang, Seongsoo
Lee, Kichoon
author_sort Ahn, Jinsoo
collection PubMed
description 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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spelling pubmed-70171822020-02-28 Identification of a Novel Imprinted Transcript in the Porcine GNAS Complex Locus Using Methylome and Transcriptome of Parthenogenetic Fetuses Ahn, Jinsoo Wu, Huiguang Lee, Joonbum Hwang, In-Sul Yu, Debing Ahn, Jin-Seop Lee, Jeong-Woong Hwang, Seongsoo Lee, Kichoon Genes (Basel) Article 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. MDPI 2020-01-14 /pmc/articles/PMC7017182/ /pubmed/31947640 http://dx.doi.org/10.3390/genes11010096 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ahn, Jinsoo
Wu, Huiguang
Lee, Joonbum
Hwang, In-Sul
Yu, Debing
Ahn, Jin-Seop
Lee, Jeong-Woong
Hwang, Seongsoo
Lee, Kichoon
Identification of a Novel Imprinted Transcript in the Porcine GNAS Complex Locus Using Methylome and Transcriptome of Parthenogenetic Fetuses
title Identification of a Novel Imprinted Transcript in the Porcine GNAS Complex Locus Using Methylome and Transcriptome of Parthenogenetic Fetuses
title_full Identification of a Novel Imprinted Transcript in the Porcine GNAS Complex Locus Using Methylome and Transcriptome of Parthenogenetic Fetuses
title_fullStr Identification of a Novel Imprinted Transcript in the Porcine GNAS Complex Locus Using Methylome and Transcriptome of Parthenogenetic Fetuses
title_full_unstemmed Identification of a Novel Imprinted Transcript in the Porcine GNAS Complex Locus Using Methylome and Transcriptome of Parthenogenetic Fetuses
title_short Identification of a Novel Imprinted Transcript in the Porcine GNAS Complex Locus Using Methylome and Transcriptome of Parthenogenetic Fetuses
title_sort identification of a novel imprinted transcript in the porcine gnas complex locus using methylome and transcriptome of parthenogenetic fetuses
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017182/
https://www.ncbi.nlm.nih.gov/pubmed/31947640
http://dx.doi.org/10.3390/genes11010096
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