Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle

Abstract

BackgroundThe amount of intramuscular fat can influence the sensory characteristics and nutritional value of beef, thus the selection of animals with adequate fat deposition is important to the consumer. There is growing knowledge about the genes and pathways that control the biological processes involved in fat deposition in muscle. MicroRNAs (miRNAs) belong to a well-conserved class of non-coding small RNAs that modulate gene expression across a range of biological functions in animal development and physiology. The aim of this study was to identify differentially expressed (DE) miRNAs, regulatory candidate genes and co-expression networks related to intramuscular fat (IMF) deposition. To achieve this, we used mRNA and miRNA expression data from the Longissimus dorsi muscle of 30 Nelore steers with high (H) and low (L) genomic estimated breeding values (GEBV) for IMF deposition.ResultsDifferential miRNA expression analysis between animals with extreme GEBV values for IMF identified six DE miRNAs (FDR 10%). Functional annotation of the target genes for these microRNAs indicated that the PPARs signaling pathway is involved with IMF deposition. Candidate regulatory genes such as SDHAF4, FBXO17, ALDOA and PKM were identified by partial correlation with information theory (PCIT), phenotypic impact factor (PIF) and regulatory impact factor (RIF) co-expression approaches from integrated miRNA-mRNA expression data. Two DE miRNAs (FDR 10%), bta-miR-143 and bta-miR-146b, which were upregulated in the Low IMF group, were correlated with regulatory candidate genes, which were functionally enriched for fatty acid oxidation GO terms. Co-expression patterns obtained by weighted correlation network analysis (WGCNA), which showed possible interaction and regulation between mRNAs and miRNAs, identified several modules related to immune system function, protein metabolism, energy metabolism and glucose catabolism according to in silico analysis performed herein.ConclusionIn this study, several genes and miRNAs were identified as candidate regulators of IMF by analyzing DE miRNAs using two different miRNA-mRNA co-expression network methods. This study contributes to the understanding of potential regulatory mechanisms of gene signaling networks involved in fat deposition processes measured in muscle. Glucose metabolism and inflammation processes were the main pathways found in silico to influence intramuscular fat deposition in beef cattle in the integrative mRNA-miRNA co-expression analysis.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4514-3) contains supplementary material, which is available to authorized users.

Identification and characterization of circRNAs in the deposition of intramuscular fat in Aohan fine-wool sheep

“…The Wnt signaling pathway is related to bovine longissimus dorsi muscle IMF content [41], and is a negative regulator of adipogenesis [42]. According to relevant research reports, glycolipid catabolic process (GO: 19377), calcium ion homeostasis (GO: 55074), lipid metabolic process (GO: 6629), and others are enrichment GO terms signi cantly related to IMF characteristics [43]. The KEGG is a set of databases and related software used to extract genomic information [44].…”

Integrative Network Analysis of Predicted miRNA-Targets Regulating Expression of Immune Response Genes in Bovine Coronavirus Infection

“…It creates a visual representation of these interactions. In order to tie the identified miRNAs, target genes and pathways in to a critical network and infer significant biological process/mechanism for gene regulation, Cytoscape version 3.7.2 was utilized to create a network that incorporated the miRNAs, their target genes, and the pathways that the target genes are associated with as described (Oliveira et al, 2018;Lucas et al, 2020).…”

“…They were searched under "Bos taurus" and "biological process." The results were sorted by the p-Values and FDR as described (Oliveira et al, 2018).…”

Identificação de sequências >i<motifs>/i< e elementos regulatórios em ATAC-Seq >i<peaks>/i< associados à expressão gênica e à deposição de gordura intramuscular em bovinos da raça Nelore

“…A GIM, também conhecida como marmoreio, é ocasionada pelo acúmulo de fosfolipídios e triglicerídeos no interior das células musculares ou entre as fibras do músculo 64 . A deposição de GIM não é influenciada por fatores isolados, mas por um conjunto de características tais como sexo, idade, nutrição e genética do animal 65,66 .…”

“…A gordura intramuscular (GIM), por sua vez, afeta o valor nutricional e interfere na maciez, na palatabilidade e em outras características sensoriais que favorecem a satisfação do consumidor, a competitividade comercial brasileira e a economia nacional 70,71 . A deposição de GIM é considerada um fenótipo poligênico visto que é influenciada por diversos fatores genéticos que se associam e se comunicam entre si 65,[72][73][74] . Em vista disso, é importante elucidar os mecanismos genéticos que regulam a deposição de GIM no músculo esquelético.…”