RNA-Seq Analysis Reveals the Potential Molecular Mechanisms of Puerarin on Intramuscular Fat Deposition in Heat-Stressed Beef Cattle

Chen, Huan; Peng, Tao; Shang, Hanle; Shang, XiangLong; Zhao, Xianghui; Qu, Mingren; Song, Xiaozhen

doi:10.3389/fnut.2022.817557

Cited by 12 publications

(9 citation statements)

References 60 publications

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“…Numerous studies have evidenced that gene expression analysis is a great strategy to identify positional and functional candidate genes associated with an organism’s response to heat stress [ 45 ]. Furthermore, the development of RNA-Seq technology has greatly improved the accuracy and comprehensiveness of gene expression analyses and accelerated the progress of heat stress-related research [ 84 , 85 ]. In the current study, RNA-Seq analysis was performed on three tissues (blood, liver, and adrenal glands) and four treatment groups (CT, H30, H60, and H120) and was not only able to identify the known mRNA isoforms annotated to known genes but also detected some novel transcripts associated with non-annotated genes.…”

Section: Resultsmentioning

confidence: 99%

Identification of Novel mRNA Isoforms Associated with Acute Heat Stress Response Using RNA Sequencing Data in Sprague Dawley Rats

Dou

Sammad

Cánovas

et al. 2022

Biology

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The molecular mechanisms underlying heat stress tolerance in animals to high temperatures remain unclear. This study identified the differentially expressed mRNA isoforms which narrowed down the most reliable DEG markers and molecular pathways that underlie the mechanisms of thermoregulation. This experiment was performed on Sprague Dawley rats housed at 22 °C (control group; CT), and three acute heat-stressed groups housed at 42 °C for 30 min (H30), 60 min (H60), and 120 min (H120). Earlier, we demonstrated that acute heat stress increased the rectal temperature of rats, caused abnormal changes in the blood biochemical parameters, as well as induced dramatic changes in the expression levels of genes through epigenetics and post-transcriptional regulation. Transcriptomic analysis using RNA-Sequencing (RNA-Seq) data obtained previously from blood (CT and H120), liver (CT, H30, H60, and H120), and adrenal glands (CT, H30, H60, and H120) was performed. The differentially expressed mRNA isoforms (DEIs) were identified and annotated by the CLC Genomics Workbench. Biological process and metabolic pathway analyses were performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. A total of 225, 5764, and 4988 DEIs in the blood, liver, and adrenal glands were observed. Furthermore, the number of novel differentially expressed transcript lengths with annotated genes and novel differentially expressed transcript with non-annotated genes were 136 and 8 in blood, 3549 and 120 in the liver, as well as 3078 and 220 in adrenal glands, respectively. About 35 genes were involved in the heat stress response, out of which, Dnaja1, LOC680121, Chordc1, AABR07011951.1, Hsp90aa1, Hspa1b, Cdkn1a, Hmox1, Bag3, and Dnaja4 were commonly identified in the liver and adrenal glands, suggesting that these genes may regulate heat stress response through interactions between the liver and adrenal glands. In conclusion, this study would enhance our understanding of the complex underlying mechanisms of acute heat stress, and the identified mRNA isoforms and genes can be used as potential candidates for thermotolerance selection in mammals.

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Section: Resultsmentioning

confidence: 99%

Identification of Novel mRNA Isoforms Associated with Acute Heat Stress Response Using RNA Sequencing Data in Sprague Dawley Rats

Dou

Sammad

Cánovas

et al. 2022

Biology

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“…Studies indicate that the PPAR signaling pathway is important for the regulation of cell differentiation, energy balance, and lipid metabolism [ 49 , 50 ]. During lipogenesis, activation of this pathway upregulates the expression of FABP , FASN , and SCD [ 51 , 52 ].…”

Section: Discussionmentioning

confidence: 99%

Effect of Cow-Calf Supplementation on Gene Expression, Processes, and Pathways Related to Adipogenesis and Lipogenesis in Longissimus thoracis Muscle of F1 Angus × Nellore Cattle at Weaning

et al. 2023

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The aim of this study was to identify differentially expressed genes, biological processes, and metabolic pathways related to adipogenesis and lipogenesis in calves receiving different diets during the cow-calf phase. Forty-eight uncastrated F1 Angus × Nellore males were randomly assigned to two treatments from thirty days of age to weaning: no creep feeding (G1) or creep feeding (G2). The creep feed offered contained ground corn (44.8%), soybean meal (40.4%), and mineral core (14.8%), with 22% crude protein and 65% total digestible nutrients in dry matter. After weaning, the animals were feedlot finished for 180 days and fed a single diet containing 12.6% forage and 87.4% corn-based concentrate. Longissimus thoracis muscle samples were collected by biopsy at weaning for transcriptome analysis and at slaughter for the measurement of intramuscular fat content (IMF) and marbling score (MS). Animals of G2 had 17.2% and 14.0% higher IMF and MS, respectively (p < 0.05). We identified 947 differentially expressed genes (log2 fold change 0.5, FDR 5%); of these, 504 were upregulated and 443 were downregulated in G2. Part of the genes upregulated in G2 were related to PPAR signaling (PPARA, SLC27A1, FABP3, and DBI), unsaturated fatty acid synthesis (FADS1, FADS2, SCD, and SCD5), and fatty acid metabolism (FASN, FADS1, FADS2, SCD, and SCD5). Regarding biological processes, the genes upregulated in G2 were related to cholesterol biosynthesis (EBP, CYP51A1, DHCR24, and LSS), unsaturated fatty acid biosynthesis (FADS2, SCD, SCD5, and FADS1), and insulin sensitivity (INSIG1 and LPIN2). Cow-calf supplementation G2 positively affected energy metabolism and lipid biosynthesis, and thus favored the deposition of marbling fat during the postweaning period, which was shown here in an unprecedented way, by analyzing the transcriptome, genes, pathways, and enriched processes due to the use of creep feeding.

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“…Researchers can make use of RNA‐seq to profile variations in gene expression at various embryonic stages or under diverse dietary conditions. Several researchers used RNA‐seq to examine the gene expression profile in beef cattle subcutaneous adipose tissue and identify significant transcription factors and pathways connected to fat formation (Chen et al., 2022; Khan et al., 2020; Li, Yang, Lu, et al., 2022; Salleh et al., 2017; Sheng et al., 2014; Song et al., 2019; Waerp et al., 2018; Wang, Liang, et al., 2022; Yun et al., 2018).…”

Section: Functional Genomics Methodsmentioning

confidence: 99%

A review of the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle

Abebe,

Wang,

et al. 2023

J Animal Breeding Genetics

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In the past few decades, genomic selection and other refined strategies have been used to increase the growth rate and lean meat production of beef cattle. Nevertheless, the fast growth rates of cattle breeds are often accompanied by a reduction in intramuscular fat (IMF) deposition, impairing meat quality. Transcription factors play vital roles in regulating adipogenesis and lipogenesis in beef cattle. Meanwhile, understanding the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle has gained significant attention to increase IMF deposition and meat quality. Therefore, the aim of this paper was to provide a comprehensive summary and valuable insight into the complex role of transcription factors in adipogenesis and lipogenesis in beef cattle. This review summarizes the contemporary studies in transcription factors in adipogenesis and lipogenesis, genome‐wide analysis of transcription factors, epigenetic regulation of transcription factors, nutritional regulation of transcription factors, metabolic signalling pathways, functional genomics methods, transcriptomic profiling of adipose tissues, transcription factors and meat quality and comparative genomics with other livestock species. In conclusion, transcription factors play a crucial role in promoting adipocyte development and fatty acid biosynthesis in beef cattle. They control adipose tissue formation and metabolism, thereby improving meat quality and maintaining metabolic balance. Understanding the processes by which these transcription factors regulate adipose tissue deposition and lipid metabolism will simplify the development of marbling or IMF composition in beef cattle.

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RNA-Seq Analysis Reveals the Potential Molecular Mechanisms of Puerarin on Intramuscular Fat Deposition in Heat-Stressed Beef Cattle

Cited by 12 publications

References 60 publications

Identification of Novel mRNA Isoforms Associated with Acute Heat Stress Response Using RNA Sequencing Data in Sprague Dawley Rats

Identification of Novel mRNA Isoforms Associated with Acute Heat Stress Response Using RNA Sequencing Data in Sprague Dawley Rats

Effect of Cow-Calf Supplementation on Gene Expression, Processes, and Pathways Related to Adipogenesis and Lipogenesis in Longissimus thoracis Muscle of F1 Angus × Nellore Cattle at Weaning

A review of the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle

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