Dataset Information

Characterisation of the methylation pattern in the intragenic CpG island of the IGF2 gene in Bos taurus indicus cumulus cells during in vitro maturation.

ABSTRACT: PURPOSE: The aim of this study was to characterise the methylation pattern in a CpG island of the IGF2 gene in cumulus cells from 1-3 mm and ???8.0 mm follicles and to evaluate the effects of in vitro maturation on this pattern. METHODS: Genomic DNA was treatment with sodium bisulphite. Nested PCR using bisulphite-treated DNA was performed, and DNA methylation patterns have been characterised. RESULTS: There were no differences in the methylation pattern among groups (P?>?0.05). Cells of pre-IVM and post-IVM from small follicles showed methylation levels of 78.17?±?14.11 % and 82.93±5.86 %, respectively, and those from large follicles showed methylation levels of 81.81?±?10.40 % and 79.64?±?13.04 %, respectively. Evaluating only the effect of in vitro maturation, cells of pre-IVM and post-IVM COCs showed methylation levels of 80.17?±?12.01 % and 81.19?±?10.15 %. CONCLUSIONS: In conclusion, the methylation levels of the cumulus cells of all groups were higher than that expected from the imprinted pattern of somatic cells. As the cumulus cells from the pre-IVM follicles were not subjected to any in vitro manipulation, the hypermethylated pattern that was observed may be the actual physiological methylation pattern for this particular locus in these cells. Due the importance of DNA methylation in oogenesis, and to be a non-invasive method for determining oocyte quality, the identification of new epigenetic markers in cumulus cells has great potential to be used to support reproductive biotechniques in humans and other mammals.

SUBMITTER: Franco MM

PROVIDER: S-EPMC3909130 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

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Characterisation of the methylation pattern in the intragenic CpG island of the IGF2 gene in Bos taurus indicus cumulus cells during in vitro maturation.

Franco Maurício Machaim MM Fagundes Nádia Simarro NS Michalczechen-Lacerda Valquíria Alice VA Caixeta Ester Siqueira ES de Castro Rodrigues Fernanda F Machado Grazieli Marinheiro GM Ferreira Allice Rodrigues AR Dode Margot Alves Nunes MA

Journal of assisted reproduction and genetics 20131031 1

<h4>Purpose</h4>The aim of this study was to characterise the methylation pattern in a CpG island of the IGF2 gene in cumulus cells from 1-3 mm and ≥ 8.0 mm follicles and to evaluate the effects of in vitro maturation on this pattern.<h4>Methods</h4>Genomic DNA was treatment with sodium bisulphite. Nested PCR using bisulphite-treated DNA was performed, and DNA methylation patterns have been characterised.<h4>Results</h4>There were no differences in the methylation pattern among groups (P > 0.05 ...[more]

PMID: 24174298

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Project description:BackgroundReference genomes are essential in the analysis of genomic data. As the cost of sequencing decreases, multiple reference genomes are being produced within species to alleviate problems such as low mapping accuracy and reference allele bias in variant calling that can be associated with the alignment of divergent samples to a single reference individual. The latest reference sequence adopted by the scientific community for the analysis of cattle data is ARS_UCD1.2, built from the DNA of a Hereford cow (Bos taurus taurus-B. taurus). A complementary genome assembly, UOA_Brahman_1, was recently built to represent the other cattle subspecies (Bos taurus indicus-B. indicus) from a Brahman cow haplotype to further support analysis of B. indicus data. In this study, we aligned the sequence data of 15 B. taurus and B. indicus breeds to each of these references.ResultsThe alignment of B. taurus individuals against UOA_Brahman_1 detected up to five million more single-nucleotide variants (SNVs) compared to that against ARS_UCD1.2. Similarly, the alignment of B. indicus individuals against ARS_UCD1.2 resulted in one and a half million more SNVs than that against UOA_Brahman_1. The number of SNVs with nearly fixed alternative alleles also increased in the alignments with cross-subspecies. Interestingly, the alignment of B. taurus cattle against UOA_Brahman_1 revealed regions with a smaller than expected number of counts of SNVs with nearly fixed alternative alleles. Since B. taurus introgression represents on average 10% of the genome of Brahman cattle, we suggest that these regions comprise taurine DNA as opposed to indicine DNA in the UOA_Brahman_1 reference genome. Principal component and admixture analyses using genotypes inferred from this region support these taurine-introgressed loci. Overall, the flagged taurine segments represent 13.7% of the UOA_Brahman_1 assembly. The genes located within these segments were previously reported to be under positive selection in Brahman cattle, and include functional candidate genes implicated in feed efficiency, development and immunity.ConclusionsWe report a list of taurine segments that are in the UOA_Brahman_1 assembly, which will be useful for the interpretation of interesting genomic features (e.g., signatures of selection, runs of homozygosity, increased mutation rate, etc.) that could appear in future re-sequencing analysis of indicine cattle.

Project description:Proteins are the major constituents of muscle and are key molecules regulating the metabolic changes during conversion of muscle to meat. Brazil is one of the largest exporters of beef and most Brazilian cattle are composed by zebu (Nellore) genotype. Bos indicus beef is generally leaner and tougher than Bos taurus such as Angus. The aim of this study was to compare the muscle proteomic and phosphoproteomic profile of Angus and Nellore. Seven animals of each breed previously subjected the same growth management were confined for 84 days. Proteins were extracted from Longissimus lumborum samples collected immediately after slaughter and separated by two-dimensional electrophoresis. Pro-Q Diamond stain was used in phosphoproteomics. Proteins identification was performed using matrix assisted laser desorption/ionization time-of-flight mass spectrometry. Tropomyosin alpha-1 chain, troponin-T, myosin light chain-1 fragment, cytoplasmic malate dehydrogenase, alpha-enolase and 78 kDa glucose-regulated protein were more abundant in Nellore, while myosin light chain 3, prohibitin, mitochondrial stress-70 protein and heat shock 70 kDa protein 6 were more abundant in Angus (P<0.05). Nellore had higher phosphorylation of myosin regulatory light chain-2, alpha actin-1, triosephosphate isomerase and 14-3-3 protein epsilon. However, Angus had greater phosphorylation of phosphoglucomutase-1 and troponin-T (P<0.05). Therefore, proteins involved in contraction and muscle organization, myofilaments expressed in fast or slow-twitch fibers and heat shock proteins localized in mitochondria or sarcoplasmic reticulum and involved in cell flux of calcium and apoptosis might be associated with differences in beef quality between Angus and Nellore. Furthermore, prohibitin appears to be a potential biomarker of intramuscular fat in cattle. Additionally, differences in phosphorylation of myofilaments and glycolytic enzymes could be involved with differences in muscle contraction force, susceptibility to calpain, apoptosis and postmortem glycolysis, which might also be related to differences in beef quality among Angus and Nellore.

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Dataset Information

Characterisation of the methylation pattern in the intragenic CpG island of the IGF2 gene in Bos taurus indicus cumulus cells during in vitro maturation.

Publications

Characterisation of the methylation pattern in the intragenic CpG island of the IGF2 gene in Bos taurus indicus cumulus cells during in vitro maturation.

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