Differential network analysis of bovine muscle reveals changes in gene coexpression patterns in response to changes in maternal nutrition

BMC Genomics

Rocío Amorín¹  Francisco Peñagaricano²  Lihe Liu²  Phillip A. Lancaster³  Nicolás DiLorenzo⁴  Philipe Moriel⁵ 

[1] Department of Animal Sciences, University of Florida, 32611, Gainesville, FL, USA;Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Drive, 53706, Madison, WI, USA;Department of Animal Sciences, University of Florida, 32611, Gainesville, FL, USA;Department of Clinical Sciences, Kansas State University, 66506, Manhattan, KS, USA;North Florida Research and Education Center, University of Florida, 32351, Marianna, FL, USA;Range Cattle Research and Education Center, University of Florida, 33865, Ona, FL, USA;

关键词: Correlation network;    Fetal programming;    Maternal diet;    Muscle transcriptome;   

DOI  :  10.1186/s12864-020-07068-x

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY