ArticleBMC genomics2020
Differential network analysis of bovine muscle reveals changes in gene coexpression patterns in response to changes in maternal nutrition.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 19 citations in OpenAlex.
- Emerging opportunities for DNA methylation biomarkers in cattle improvement.The Journal of reproduction and development · 2026Review
- Maternal Overnutrition in Beef Cattle: Effects on Fetal Programming, Metabolic Health, and Postnatal Outcomes.Biology · 2025Review
- Impact of dietary supplementation of beef cows with rumen-protected methionine during the periconceptional period on prenatal growth and performance to weaning.Journal of animal science · 2025Article
- EnrichKit: a multi-omics tool for livestock research.Frontiers in genetics · 2025Article
- Fine construction of gene coexpression network analysis using GTOM and RECODE detected a critical module of neuroblastoma stages 4 and 4S.Hereditas · 2024Article
- Fetal programming effect of rumen-protected methionine on primiparous Angus × Simmental offspring's performance and skeletal muscle gene expression.Journal of animal science · 2024Article
- Maternal diet induces persistent DNA methylation changes in the muscle of beef calves.Scientific reports · 2023Article
- One-carbon metabolite supplementation to heifers for the first 14 d of the estrous cycle alters the plasma and hepatic one-carbon metabolite pool and methionine-folate cycle enzyme transcript abundance in a dose-dependent manner.Journal of animal science · 2023Article
- Identification of eQTLs and differential gene expression associated with fetal programming in beef cattle.Journal of applied genetics · 2022Article
- Timing of maternal supplementation of dried distillers grains during late gestation influences postnatal growth, immunocompetence, and carcass characteristics of Bos indicus-influenced beef calves.Journal of animal science · 2022Article
- Benchmarking DNA methylation analysis of 14 alignment algorithms for whole genome bisulfite sequencing in mammals.Computational and structural biotechnology journal · 2022Article
- Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle.BMC genomics · 2021Article
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Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCoexpression network analysis is a powerful tool to reveal transcriptional regulatory mechanisms, identify transcription factors, and discover gene functions. It can also be used to investigate changes in coexpression patterns in response to environmental insults or changes in experimental conditions. Maternal nutrition is considered a major intrauterine regulator of fetal developmental programming. The objective of this study was to investigate structural changes in gene coexpression networks in the muscle of bull beef calves gestated under diets with or without methionine supplementation. Both muscle transcriptome and methylome were evaluated using next generation sequencing.
resultsMaternal methionine supplementation significantly perturbed coexpression patterns in the offspring's muscle. Indeed, we found that neither the connection strength nor the connectivity pattern of six modules (subnetworks) detected in the control diet were preserved in the methionine-rich diet. Functional characterization revealed that some of the unpreserved modules are implicated in myogenesis, adipogenesis, fibrogenesis, canonical Wnt/β-catenin pathway, ribosome structure, rRNA binding and processing, mitochondrial activities, ATP synthesis and NAD(P) H oxidoreductases, among other functions. The bisulfite sequencing analysis showed that nearly 2% of all evaluated cytosines were differentially methylated between maternal diets. Interestingly, there were significant differences in the levels of gene body DNA methylation between preserved and unpreserved modules.
conclusionsOverall, our findings provide evidence that maternal nutrition can significantly alter gene coexpression patterns in the offspring, and some of these perturbations are mediated by changes in DNA methylation.
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