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

Jinsoo Ahn,Huiguang Wu,Kichoon Lee,Seongsoo Hwang,Joonbum Lee,Jeong-Woong Lee,In-Sul Hwang,Debing Yu,Jin-Seop Ahn

doi:10.3390/genes11010096

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.

Highlights

Genomic imprinting in mammals occurs in a subset of genes, often in clusters, and results in epigenetic regulation of monoallelical gene expression in a parental-origin-specific manner [1].Imprinting has been extensively studied in mice and humans to understand epigenetic architectureGenes 2020, 11, 96; doi:10.3390/genes11010096 www.mdpi.com/journal/genesGenes 2020, 11, 96 of complex diseases and traits [2,3,4,5,6,7]
Previous approaches of identifying imprinted genes in animals based on single nucleotide polymorphisms (SNPs) or sequence deletions/insertions might face efficiency limitation when there is a lack of informative variations
Our results revealed the full-scale imprinting status of the GNAS locus, including the discovery of a novel imprinted transcript, and confirmed the appropriateness of the strategy to identifying imprinting patterns using whole genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-Seq) of parthenogenetic fetuses

Summary

Introduction

Genomic imprinting in mammals occurs in a subset of genes, often in clusters, and results in epigenetic regulation of monoallelical gene expression in a parental-origin-specific manner [1].Imprinting has been extensively studied in mice and humans to understand epigenetic architectureGenes 2020, 11, 96; doi:10.3390/genes11010096 www.mdpi.com/journal/genesGenes 2020, 11, 96 of complex diseases and traits [2,3,4,5,6,7]. Studies on domestic animals have further reported the contribution of genomic imprinting to the variance in performance traits [8,9]. Previous approaches of identifying imprinted genes in animals based on single nucleotide polymorphisms (SNPs) or sequence deletions/insertions might face efficiency limitation when there is a lack of informative variations. To overcome this issue, the generation of uniparental fetuses followed by genome-wide detection of epigenetic landscape may be a definitive approach to pursue, especially for complex loci such as the locus of GNAS. Comprehensive expression patterns of multiple groups of transcripts on the porcine GNAS locus remain to be elucidated

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Conclusion