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DNA methylation profiles (RRBS) of the muscle of pigs distinct in metabolic types and genetic background

ABSTRACT: DNA methylation profiles (RRBS) of the muscle of pigs distinct in metabolic types and genetic background

PROVIDER: PRJEB29380 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2856960.fastq.gz	Fastqsanger.gz
	ERR2856970.fastq.gz	Fastqsanger.gz
	ERR2856980.fastq.gz	Fastqsanger.gz
	ERR2856961.fastq.gz	Fastqsanger.gz
	ERR2856971.fastq.gz	Fastqsanger.gz

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DNA methylation profiles (RRBS) of the muscle of pigs distinct in metabolic types and genetic background

Project description:DNA methylation is an epigenetic mechanism that plays roles in gene regulation and expression. This study aims to profile DNA methylation at genome-wide scale and single base resolution using reduced representation bisulfite sequencing (RRBS) of the muscle of pigs differing in muscle metabolism and genetic background. Pietrain homozygous- positive (PiPP) and negative (PiNN) for the ryanodine receptor mutation and malignant hyperthermia-susceptible (MHS), Duroc and F2 crossbred Duroc-Pietrain homozygous-negative (DuPi) pigs were investigated to identify differentially methylated CpG sites/ regions and to integrate the results with gene expression data.

2024-12-01 | E-MTAB-7338 | biostudies-arrayexpress

Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs.

Project description:BackgroundEpigenetic variation may result from selection for complex traits related to metabolic processes or appear in the course of adaptation to mediate responses to exogenous stressors. Moreover epigenetic marks, in particular the DNA methylation state, of specific loci are driven by genetic variation. In this sense, polymorphism with major gene effects on metabolic and cell signaling processes, like the variation of the ryanodine receptors in skeletal muscle, may affect DNA methylation.MethodsDNA-Methylation profiles were generated applying Reduced Representation Bisulfite Sequencing (RRBS) on 17 Musculus longissimus dorsi samples. We examined DNA methylation in skeletal muscle of pig breeds differing in metabolic type, Duroc and Pietrain. We also included F2 crosses of these breeds to get a first clue to DNA methylation sites that may contribute to breed differences. Moreover, we compared DNA methylation in muscle tissue of Pietrain pigs differing in genotypes at the gene encoding the Ca2+ release channel (RYR1) that largely affects muscle physiology.ResultsMore than 2000 differently methylated sites were found between breeds including changes in methylation profiles of METRNL, IDH3B, COMMD6, and SLC22A18, genes involved in lipid metabolism. Depending on RYR1 genotype there were 1060 differently methylated sites including some functionally related genes, such as CABP2 and EHD, which play a role in buffering free cytosolic Ca2+ or interact with the Na+/Ca2+ exchanger.ConclusionsThe change in the level of methylation between the breeds is probably the result of the long-term selection process for quantitative traits involving an infinite number of genes, or it may be the result of a major gene mutation that plays an important role in muscle metabolism and triggers extensive compensatory processes.

| S-EPMC6567458 | biostudies-literature

Effects of dietary fat types on growth performance, pork quality, and gene expression in growing-finishing pigs

Project description:This study was performed to determine the effects of dietary fat sources, i.e., beef tallow, soybean oil, olive oil and coconut oil (each 3% in feed), on the growth performance, meat quality and gene expression in growing-finishing pigs. The results of this study indicate that the type of dietary fat affects fatty acid composition and insulin signaling-related gene expression in the longissimus dorsi muscle of pigs. Effects of dietary fat types on meat quantity, meat quality and gene expression in pig.

2012-05-22 | E-GEOD-38146 | biostudies-arrayexpress

Transcriptional profiling during fetal skeletal muscle development of Piau and Yorkshire-Landrace crossbred pigs

Project description:The aim of this study was to identify differentially expressed genes and pathways in longissimus dorsi (LD) of pigs at 40 and 70 d of gestation (stages encompassing the transition from primary to secondary fiber formation) in U.S. commercial crossbred pigs (Yorkshire x Landrace) and Brazilian native Piau pigs. We confirmed the expression patterns for a subset of genes by qRT-PCR. Pathway analysis revealed functionally related genes, and indicated commonalities and differences between the breed types and developmental ages evaluated. Results from qRT-PCR analysis confirmed the expression patterns observed on the array for most of the genes tested (85%). This study reveals transcriptional profiles in LD at 40 and 70 d gestation for commercial and Piau pigs, which helps elucidate phenotypic differences between these breed types.

2010-04-22 | GSE21412 | GEO

DNA methylation profiling (RRBS) of differentiating porcine synovial mesenchymal stem cells (PSMSCs) during the course of osteogenic induction

Project description:This study aims to investigate DNA methylation of differentiating synovial mesenchymal stem cells (psMSCs) isolated from German Landrace (DL) and Angeln Saddleback (AS) pigs previously characterized and described (Siengdee et al 2020, Frontiers in Cell and Developmental Biology). The 3rd passage of psMSCs were induced to differentiate in osteogenic differentiation media. DNA methylation profiles by Reduced Representation Bisulfite Sequencing (RRBS) of the differentiating cells were compared with the undifferentiated control cells at day 1, 7, 14 and 21 post-osteogenic induction to identify differentially methylated CpGs during the course of differentiation and between pig breeds (DL vs AS).

2024-12-01 | E-MTAB-9913 | biostudies-arrayexpress

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Effects of dietary fat types on growth performance, pork quality, and gene expression in growing-finishing pigs

2012-05-23 | GSE38146 | GEO

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Project description:Lactobacillus acidophilus strain:Pigs | isolate:Pigs Genome sequencing

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Porcine placenta, Erhualian pigs and Large White pigs, gestation day 75 and 90

Project description:From gestation day 75 to gestation day 90, an important stage for the placental and fetal development, the fetuses grow rapidly and need adequate nutrition. The Meishan pigs and the Large White pigs employ different ways in supplying the enough nutrients and oxygen to the fetus. The Meishan pigs increased the vascular density and the Large White pigs have the second increase in the surface of placenta. To understand the molecular basis related to late gestation placenta development in Chinese indigenous and Western breeds with different placental efficiency, samples were collected and used to hybridized. The results offered new data on understanding the molecular basis of placenta efficiency, and indicated that Erhualian pigs had the more efficient than the Large White pigs.

2009-06-20 | GSE11853 | GEO

Genome-wide DNA methylation analysis using next generation sequencing to reveal candidate genes responsible for boar taint in pigs

Project description:Boar taint (BT) is an offensive flavor observed in non-castrated male pigs that reduces the carcass price. Surgical castration effectively avoids the taint but is associated with animal welfare concerns. The functional annotation of farm animal genomes (FAANG) for understanding the biology of complex traits and diseases can be used in the selection of breeding animals to achieve favorable phenotypic outcomes. The characterization of pig epigenomes/methylation changes between animals with high and low BT and genome-wide epigenetic markers that can predict BT are lacking. Reduced representation bisulfite sequencing (RRBS) of DNA methylation patterns based on next generation sequencing (NGS) is an efficient technology to identify candidate epigenetic biomarkers associated with BT. Three different BT levels were analyzed using RRBS data to calculate the methylation levels of cytosine. The co-analysis of differentially methylated cytosines (DMCs) identified by this study and differentially expressed (DE) genes identified by previous study found 32 significant co-located genes. The joint analysis of GO terms and pathways revealed that methylation and gene expression of seven candidate genes were associated with BT; in particular, FASN plays a key role in fatty acid biosynthesis, and PEMT might be involved in estrogen regulation and the development of BT. This study is the first to report the genome-wide DNA methylation profiles of BT in pigs using NGS and summarize candidate genes associated with epigenetic markers of BT, which could contribute to the understanding of functional biology of BT traits and selective breeding of pigs against BT based on epigenetic biomarkers.

2019-10-01 | GSE129385 | GEO

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