Global transcriptome analysis identifies differentially expressed genes related to lipid metabolism in Wagyu and Holstein cattle

Adipose deposits influence the quality of ruminant carcasses, and in suckling lambs, internal types of adipose deposits represent a notable proportion of total fat. The aim of this study was to perform a comparative analysis of the perirenal fat transcriptomes of suckling lambs from two breeds with different growth and carcass characteristics. The perirenal fat tissue from 14 suckling lambs (Assaf, n = 8; Churra, n = 6) was used for the RNA-seq analysis. The functional enrichment analysis of the 670 highly expressed genes (>150 fragments per kilobase of exon per million fragments mapped) in the perirenal fat transcriptome of both breeds revealed that the majority of these genes were involved in energy processes. The expression of the UCP1 gene, a classical biomarker of brown fat, and the presence of multilocular adipocytes in the two breeds supported the presence of brown fat at the transition stage towards white fat tissue. The differential expression analysis performed identified 373 differentially expressed genes (DEGs) between the two compared breeds. Brown/white fat gene biomarkers were not included in the list of DEGs. In Assaf lambs, DEGs were enriched in Gene Ontology (GO) biological processes related to fatty-acid oxidation, whereas in Churra lambs, the majority of the significantly enriched GO terms were related to cholesterol synthesis, which suggests that upregulated DEGs in Assaf lambs are implicated in fat burning, whereas the Churra upregulated DEGs are linked to fat accumulation. These results can help to increase knowledge of the genes controlling early fat deposition in ruminants and shed light on fundamental aspects of adipose tissue growth.

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“…Moreover, they play a role in the regulation of adipocyte differentiation and lipid metabolism (Huang et al . ,b; Muret et al . ).…”

Section: Discussionmentioning

confidence: 99%

Early adipose deposits in sheep: comparative analysis of the perirenal fat transcriptome of Assaf and Churra suckling lambs

et al. 2018

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“…The precise understanding of the cascade of these molecular events and the way to regulate them will be crucial for efficiently treating obesity. PPAR signaling pathway is a key pathway closely associated with metabolism of fatty acid and sterols, and adipogenic differentiation [21,55,56]. Lim et al used qRT-PCR to analyze the genes associated with PPAR signaling pathway in the longissimus dorsi muscle of Hanwoo cattle [57].…”

Section: Pigsmentioning

confidence: 99%

“…LncRNAs, nonprotein coding transcripts longer than 200 nucleotides, have important regulatory functions in adipogenesis and lipid metabolism. With the development of high throughput sequencing technology, RNA-seq has been widely applied in the identification and functional analysis of lncRNAs and mRNAs of adipose tissues in pig [7,13,16,17], chicken [18], sheep [19,20] and cattle [21]. Ramayo et al [22] identified 270 and 186 lncRNAs in the liver tissues of female pigs with high and low intramuscular fatty acid contents, respectively.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis of mRNAs and lncRNAs of Intramuscular Fat Related to Lipid Metabolism in Two Pig Breeds

Huang

Zhang

et al. 2018

Cell Physiol Biochem

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Background/Aims: Long non-coding RNAs (lncRNAs) can regulate adipogenesis and lipid accumulation. Intramuscular fat deposition appears to vary in different pig breeds, and the regulation mechanism has not yet been fully elucidated at molecular level. Moreover, little is known about the function and profile of lncRNAs in intramuscular fat deposition and metabolism in pig. The aim of this study was thus to explore the regulatory functions of lncRNAs in intramuscular fat deposition. Methods: In this study, Laiwu (LW) pig and Large White (LY) pig with significant difference in fat deposition were selected for use. RNA-seq technology and bioinformatics methods were used to comparatively analyze the gene expression profiles of intramuscular fat between LW and LY pigs to identify key mRNAs and lncRNAs associated with lipid metabolism and adipogenesis. Real-time fluorescence-based quantitative PCR was applied to verify the expression level of the differentially expressed mRNAs and lncRNAs. Results: A total of 513 mRNAs and 55 lncRNAs were differentially expressed between two pig breeds. By co-expression network construction as well as cis- and trans-regulated target gene analysis, 31 key lncRNAs were identified. Gene Ontology and KEGG pathway analyses revealed that differentially expressed genes and lncRNAs were mainly involved in the biological processes and pathways related to adipogenesis and lipid metabolism. Conclusion: XLOC_046142, XLOC_004398 and XLOC_015408 may target MAPKAPK2, NR1D2 and AKR1C4, respectively, and play critical regulatory roles in intramuscular adipogenesis and lipid accumulation in pig. XLOC_064871 and XLOC_011001 may play a role in lipid metabolism-related disease via regulating TRIB3 and BRCA1. This study provides a valuable resource for lncRNA study and improves our understanding of the biological roles of lipid metabolism- related genes and molecular mechanism of intramuscular fat metabolism and deposition.

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“…Recently, there has been an increase in the utilization of Next Generation Sequencing (NGS) to examine the transcriptome for the identification of differential expression as well as for the opportunity to discover novel transcripts, including new alternative isoforms and miRNAs [14][15][16][17][18][19][20][21][22][23][24][25][26]. Therefore, in the present study, a comparison of the miRNA profiles of the adipose tissue of the Laiwu pig and Large White pig was performed using RNA-seq.…”

Section: Introductionmentioning

confidence: 99%

WITHDRAWN: An integrated analysis of microRNAs involved in fat deposition in different pig breeds

Zhang¹,

Huang²,

Guo³

et al. 2017

Oncotarget

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The domestic pig, an important species in the animal production industry, is also a model system for studying fat deposition and fat-associated diseases in humans. In order to investigate the genetic relationships of the miRNAs that may regulate fat deposition, we performed a genome-wide analysis of miRNAs derived from subcutaneous adipose tissue of Laiwu and Large White pig using RNA-seq. A total of 26,486,906 reads were obtained. Further analysis indicated that 39 known miRNAs and 56 novel miRNAs had significantly differential expression between the two breeds of pigs. Gene Ontology and KEGG pathway analysis revealed that the predicted targets of these differentially expressed miRNAs were involved in several fat-associated pathways, such as the PPAR, MAPK and Wnt signaling pathways. In addition, we found that three miRNAs, ssc-miR-133a-3p, ssc-miR-486 and ssc-miR-1, had an impact on the development of porcine subcutaneous fat through the PPAR signaling pathway. This study provides clues to understand the potential mechanisms of adipogenesis and fat deposition between two different pig breeds. Furthermore, these results may also contribute to the research involving human obesity.

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Global transcriptome analysis identifies differentially expressed genes related to lipid metabolism in Wagyu and Holstein cattle

Cited by 70 publications

References 74 publications

Early adipose deposits in sheep: comparative analysis of the perirenal fat transcriptome of Assaf and Churra suckling lambs

Early adipose deposits in sheep: comparative analysis of the perirenal fat transcriptome of Assaf and Churra suckling lambs

Genome-Wide Analysis of mRNAs and lncRNAs of Intramuscular Fat Related to Lipid Metabolism in Two Pig Breeds

WITHDRAWN: An integrated analysis of microRNAs involved in fat deposition in different pig breeds

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