Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig

Abstract Background DNA methylation and demethylation at CpG islands is one of the main regulatory factors that allow cells to respond to different stimuli. These regulatory mechanisms help in developing tissue without affecting the genomic composition or undergoing selection. Liver and backfat play...

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Autores principales:	Devender Arora, Jong-Eun Park, Dajeong Lim, Bong-Hwan Choi, In-Cheol Cho, Krishnamoorthy Srikanth, Jaebum Kim, Woncheoul Park
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	CpG DMR DEGs Differentiation Methylation Motif Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/5959e287a85b473688c831a460253057
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spelling	oai:doaj.org-article:5959e287a85b473688c831a4602530572021-11-14T12:26:51ZComparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig10.1186/s12864-021-08123-x1471-2164https://doaj.org/article/5959e287a85b473688c831a4602530572021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08123-xhttps://doaj.org/toc/1471-2164Abstract Background DNA methylation and demethylation at CpG islands is one of the main regulatory factors that allow cells to respond to different stimuli. These regulatory mechanisms help in developing tissue without affecting the genomic composition or undergoing selection. Liver and backfat play important roles in regulating lipid metabolism and control various pathways involved in reproductive performance, meat quality, and immunity. Genes inside these tissue store a plethora of information and an understanding of these genes is required to enhance tissue characteristics in the future generation. Results A total of 16 CpG islands were identified, and they were involved in differentially methylation regions (DMRs) as well as differentially expressed genes (DEGs) of liver and backfat tissue samples. The genes C7orf50, ACTB and MLC1 in backfat and TNNT3, SIX2, SDK1, CLSTN3, LTBP4, CFAP74, SLC22A23, FOXC1, GMDS, GSC, GATA4, SEMA5A and HOXA5 in the liver, were categorized as differentially-methylated. Subsequently, Motif analysis for DMRs was performed to understand the role of the methylated motif for tissue-specific differentiation. Gene ontology studies revealed association with collagen fibril organization, the Bone Morphogenetic Proteins (BMP) signaling pathway in backfat and cholesterol biosynthesis, bile acid and bile salt transport, and immunity-related pathways in methylated genes expressed in the liver. Conclusions In this study, to understand the role of genes in the differentiation process, we have performed whole-genome bisulfite sequencing (WGBS) and RNA-seq analysis of Nanchukmacdon pigs. Methylation and motif analysis reveals the critical role of CpG islands and transcriptional factors binding site (TFBS) in guiding the differential patterns. Our findings could help in understanding how methylation of certain genes plays an important role and can be used as biomarkers to study tissue specific characteristics.Devender AroraJong-Eun ParkDajeong LimBong-Hwan ChoiIn-Cheol ChoKrishnamoorthy SrikanthJaebum KimWoncheoul ParkBMCarticleCpGDMRDEGsDifferentiationMethylationMotifBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	CpG DMR DEGs Differentiation Methylation Motif Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	CpG DMR DEGs Differentiation Methylation Motif Biotechnology TP248.13-248.65 Genetics QH426-470 Devender Arora Jong-Eun Park Dajeong Lim Bong-Hwan Choi In-Cheol Cho Krishnamoorthy Srikanth Jaebum Kim Woncheoul Park Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig
description	Abstract Background DNA methylation and demethylation at CpG islands is one of the main regulatory factors that allow cells to respond to different stimuli. These regulatory mechanisms help in developing tissue without affecting the genomic composition or undergoing selection. Liver and backfat play important roles in regulating lipid metabolism and control various pathways involved in reproductive performance, meat quality, and immunity. Genes inside these tissue store a plethora of information and an understanding of these genes is required to enhance tissue characteristics in the future generation. Results A total of 16 CpG islands were identified, and they were involved in differentially methylation regions (DMRs) as well as differentially expressed genes (DEGs) of liver and backfat tissue samples. The genes C7orf50, ACTB and MLC1 in backfat and TNNT3, SIX2, SDK1, CLSTN3, LTBP4, CFAP74, SLC22A23, FOXC1, GMDS, GSC, GATA4, SEMA5A and HOXA5 in the liver, were categorized as differentially-methylated. Subsequently, Motif analysis for DMRs was performed to understand the role of the methylated motif for tissue-specific differentiation. Gene ontology studies revealed association with collagen fibril organization, the Bone Morphogenetic Proteins (BMP) signaling pathway in backfat and cholesterol biosynthesis, bile acid and bile salt transport, and immunity-related pathways in methylated genes expressed in the liver. Conclusions In this study, to understand the role of genes in the differentiation process, we have performed whole-genome bisulfite sequencing (WGBS) and RNA-seq analysis of Nanchukmacdon pigs. Methylation and motif analysis reveals the critical role of CpG islands and transcriptional factors binding site (TFBS) in guiding the differential patterns. Our findings could help in understanding how methylation of certain genes plays an important role and can be used as biomarkers to study tissue specific characteristics.
format	article
author	Devender Arora Jong-Eun Park Dajeong Lim Bong-Hwan Choi In-Cheol Cho Krishnamoorthy Srikanth Jaebum Kim Woncheoul Park
author_facet	Devender Arora Jong-Eun Park Dajeong Lim Bong-Hwan Choi In-Cheol Cho Krishnamoorthy Srikanth Jaebum Kim Woncheoul Park
author_sort	Devender Arora
title	Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig
title_short	Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig
title_full	Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig
title_fullStr	Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig
title_full_unstemmed	Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig
title_sort	comparative methylation and rna-seq expression analysis in cpg context to identify genes involved in backfat vs. liver diversification in nanchukmacdon pig
publisher	BMC
publishDate	2021
url	https://doaj.org/article/5959e287a85b473688c831a460253057
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Comparative methylation and RNA-seq expression analysis in CpG context to identify genes involved in Backfat vs. Liver diversification in Nanchukmacdon Pig

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