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Jaglan K, Dhaka SS, Magotra A, Patil CS, Ghanghas A. Exploring MicroRNA biogenesis, applications and bioinformatics analysis in livestock: A comprehensive review. Reprod Domest Anim 2024; 59:e14529. [PMID: 38268204 DOI: 10.1111/rda.14529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Small non-coding RNAs called microRNAs (miRNAs) control the expression of genes post-transcriptionally. Their correlation with commercial economic traits including milk, meat and egg production, as well as their effective role in animal productivity, fertility, embryo survival and disease resistance, make them significant in livestock research. The miRNAs exhibit distinct spatial and temporal expression patterns, offering insights into their functional roles within cells and tissues. Aberrant miRNA production can disrupt vital cellular processes and genetic networks, contributing to conditions like metabolic disorders and viral diseases. These short RNA molecules are present in extracellular fluids, displaying remarkable stability against RNA degradation enzymes and extreme environmental conditions. miRNAs preservation is facilitated through packaging in lipid vesicles or complex formation with RNA-binding proteins. Numerous studies have illuminated the roles of miRNAs in diverse physiological processes, including embryonic stem cell differentiation, haematopoietic stem cell proliferation and differentiation and the coordinated development of organ systems. The integration of miRNA profiling, next-generation sequencing and bioinformatics analysis paves the way for transformative advancements in livestock research and industry. The present review underscores the applications of miRNAs in livestock, showcasing their potential to improve breeding strategies, diagnose diseases and enhance our understanding of fundamental biological processes.
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Affiliation(s)
- Komal Jaglan
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - S S Dhaka
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Ankit Magotra
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - C S Patil
- Department of Animal Genetics & Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Amandeep Ghanghas
- Department of Livestock Production Management, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
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Yeruva L, Mulakala BK, Rajasundaram D, Gonzalez S, Cabrera-Rubio R, Martínez-Costa C, Collado MC. Human milk miRNAs associate to maternal dietary nutrients, milk microbiota, infant gut microbiota and growth. Clin Nutr 2023; 42:2528-2539. [PMID: 37931372 DOI: 10.1016/j.clnu.2023.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 11/08/2023]
Abstract
BACKGROUND Maternal diet influences the milk composition, yet little information is available on the impact of maternal diet on milk miRNAs expression. Further, the association of human milk miRNAs to maternal diet and milk microbiota is not explored. In addition, the role of milk miRNAs on the infant gut microbiota, infant growth and development has not been investigated. METHODS Milk samples were collected from 60 healthy lactating women at ≤15d post-partum, HTG transcriptome assay was performed to examine milk miRNA profile. Maternal clinical and dietary clusters information were available and infant anthropometric measures were followed up to one year of age. Milk and infant microbiota were analyzed by 16S rRNA gene sequencing and integrative multi-omics data analysis was performed to identify potential association between microRNA, maternal dietary nutrients and microbiota. RESULTS Discriminant analysis revealed that the milk miRNAs were clustered into groups according to the maternal protein source. Interestingly, 31 miRNAs were differentially expressed (P adj < 0.05) between maternal dietary clusters (Cluster 1: enriched in plant protein and fibers and Cluster 2: enriched in animal protein), with 30 miRNAs downregulated in the plant protein group relative to animal protein group. Pathway analysis revealed that the top enriched pathways (P adj < 0.01) were involved in cell growth and proliferation processes. Furthermore, significant features contributing to the clustering were associated with maternal dietary nutrients and milk microbiota (r > 0.70). Further, miR-378 and 320 family miRNAs involved in adipogenesis were positively correlated to the infant BMI-z-scores, weight, and weight for length-z-scores at 6 months of age. CONCLUSIONS Maternal dietary source impacts the milk miRNA expression profile. Further, miRNAs were associated with maternal dietary nutrients, milk microbiota and to the infant gut microbiota and infant growth and development. CLINICAL TRIAL The study is registered in ClinicalTrials.gov. The identification number is NCT03552939.
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Affiliation(s)
- Laxmi Yeruva
- Microbiome and Metabolism Research Unit, USDA-ARS, SEA, Little Rock, AR, USA; Arkansas Children's Nutrition Center, Little Rock, AR, USA.
| | - Bharat Kumar Mulakala
- Microbiome and Metabolism Research Unit, USDA-ARS, SEA, Little Rock, AR, USA; Arkansas Children's Nutrition Center, Little Rock, AR, USA; Texas A&M AgriLife Institute for Advancing Health Through Agriculture, TX, USA
| | | | - Sonia Gonzalez
- Department of Functional Biology, Faculty of Medicine, University of Oviedo, Oviedo, Spain; Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (DIMISA, ISPA), Oviedo, Spain
| | - Raul Cabrera-Rubio
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia, Spain
| | | | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia, Spain.
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3
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Zhang S, Jiang E, Kang Z, Bi Y, Liu H, Xu H, Wang Z, Lei C, Chen H, Lan X. CircRNA Profiling Reveals an Abundant circBDP1 that Regulates Bovine Fat Development by Sponging miR-181b/miR-204 Targeting Sirt1/TRARG1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14312-14328. [PMID: 36269615 DOI: 10.1021/acs.jafc.2c05939] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The proliferation and differentiation of preadipocytes is an important factor determining bovine fat development, which is closely related to the feed conversion ratio, carcass traits, and beef quality. The purpose of this study was to identify the effects of candidate circRNA and miRNA on the proliferation and differentiation of bovine preadipocytes in order to provide basic materials for molecular breeding in cattle. circRNA sequencing was performed on bovine adipocyte samples at different differentiation time points, and a total of 1830 differentially expressed circRNAs were identified. Among them, circBDP1, derived from the bovine BDP1 gene, has potential binding sites for miR-204 (known as a regulator of bovine fat development) and miR-181b, which gives us a hint that circBDP1 may regulate bovine fat development by adsorbing miR-204 and miR-181b. Here, our results revealed that circBDP1 overexpression promoted the proliferation and differentiation of bovine preadipocytes. The miRNA profile of bovine adipocytes at different differentiation time points was also analyzed using the small RNA sequencing method, and a total of 89 differentially expressed miRNAs were identified, including miR-204 and miR-181b. As expected, dual-luciferase reporter results showed that circBDP1 competitively adsorbed miR-181b and miR-204. Overexpression and interference of miR-181b in bovine preadipocytes and 3T3-L1 showed that miR-181b promoted the proliferation and differentiation of preadipocytes. Further results displayed that miR-181b and miR-204 simultaneously targeted the SIRT1 gene, and miR-204 also targeted the 3' UTR region of the TRARG1 gene. In summary, this study found that miR-181b and miR-204 were involved in fat development by targeting SIRT1 and TRARG1. The results of this study will lay a foundation for the research of fat development and beef cattle industry.
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Affiliation(s)
- Sihuan Zhang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
- College of Animal Science and Technology, Anhui Agricultural University, Hefei230036, P.R. China
| | - Enhui Jiang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
| | - Zihong Kang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100193, China
| | - Yi Bi
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
| | - Hongfei Liu
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing100193, China
| | - Han Xu
- School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong510006, China
| | - Zhen Wang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing100193, China
| | - Chuzhao Lei
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
| | - Hong Chen
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
| | - Xianyong Lan
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
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4
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Emerging Roles of Non-Coding RNAs in the Feed Efficiency of Livestock Species. Genes (Basel) 2022; 13:genes13020297. [PMID: 35205343 PMCID: PMC8872339 DOI: 10.3390/genes13020297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 01/27/2023] Open
Abstract
A global population of already more than seven billion people has led to an increased demand for food and water, and especially the demand for meat. Moreover, the cost of feed used in animal production has also increased dramatically, which requires animal breeders to find alternatives to reduce feed consumption. Understanding the biology underlying feed efficiency (FE) allows for a better selection of feed-efficient animals. Non-coding RNAs (ncRNAs), especially micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), play important roles in the regulation of bio-logical processes and disease development. The functions of ncRNAs in the biology of FE have emerged as they participate in the regulation of many genes and pathways related to the major FE indicators, such as residual feed intake and feed conversion ratio. This review provides the state of the art studies related to the ncRNAs associated with FE in livestock species. The contribution of ncRNAs to FE in the liver, muscle, and adipose tissues were summarized. The research gap of the function of ncRNAs in key processes for improved FE, such as the nutrition, heat stress, and gut–brain axis, was examined. Finally, the potential uses of ncRNAs for the improvement of FE were discussed.
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5
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Li D, Wang H, Li Y, Qu C, Zhang Y, Liu H, Zhang X. MicroRNA-378 regulates adipogenic differentiation in bovine intramuscular preadipocytes by targeting CaMKK2. Adipocyte 2021; 10:483-492. [PMID: 34693860 PMCID: PMC8547835 DOI: 10.1080/21623945.2021.1982526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Intramuscular fat, as one of the most important palatability attribute of beef carcase, is the primary determinant of beef quality. The research of adipogenesis mechanism would provide new insight into intramuscular fatty deposition. Here, the role of microRNA-378 was investigated during bovine adipogenic differentiation. It was revealed that miR-378 expression exists variably in bovine major tissue and organs by RT-qPCR. It was predicted that miR-378 targets CaMKK2, as an AMPKα kinase, by DIANA Tools. For better research, primary preadipocytes with stable transfection for up-/down-regulated expression of miR-378 were constructed by lentiviral vectors with GFP gene. The analyses of qPCR showed that PPARγ and adiponectin mRNA levels increased, but C/EBPβ, pref-1 and CaMKK2 mRNA levels decreased during adipogenic differentiation. When miR-378 was overexpressed, preadipocytes proliferation became slower, there are more cellular lipid droplets, and PPARγ and C/EBPβ mRNA levels were higher, but pref-1, adiponectin and CaMKK2 were lower than control groups. Luciferase assay and western blot analysis validated that miR-378 binds the nucleotide sites of the 3′- untranslated region of CaMKK2, which inhibits the mRNA and protein expression of CaMKK2. These findings suggest that miR-378 promotes adipogenic differentiation in bovine intramuscular preadipocytes by targeting CaMKK2 via AMPK signalling pathway.
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Affiliation(s)
- Dongwei Li
- College of Animal Science and Technology, Anhui Agricultural University, Hefei China
- Conservation Biology Research Center, School of Biology and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Heng Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei China
| | - Yongmin Li
- Conservation Biology Research Center, School of Biology and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Changqing Qu
- Anhui Provincial Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine, Fuyang Normal University, Fuyang, China
| | - Yunhai Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei China
| | - Hongyu Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei China
| | - Xiaorong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei China
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6
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Zhang Y, Gong S, Su Y, Yao M, Liu X, Gong Z, Sui H, Luo M. Follicular development in livestock: Influencing factors and underlying mechanisms. Anim Sci J 2021; 92:e13657. [PMID: 34796578 DOI: 10.1111/asj.13657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/23/2021] [Accepted: 10/26/2021] [Indexed: 12/01/2022]
Abstract
Livestock farming development has become increasingly important in recent years. It not only provides us with meat nutrition and pet feeding but also increases the economic value by providing numerous employment opportunities, which improves our life quality. The livestock farming development depends on successful animal reproduction. As a vital process in animal reproduction, folliculogenesis and its influencing factors as well as their underlying mechanisms need to be understood thoroughly. This review is aimed at summarizing the factors such as cellular processes, gene regulation, noncoding RNAs and other endocrine or paracrine regulatory factors that affect follicular development, and their underlying mechanisms of action in livestock in order to provide novel insights for future studies. The above factors were found as significant determinants influencing the follicular development in livestock through various signaling pathways.
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Affiliation(s)
- Yanjun Zhang
- College of Animal Science and Veterinary, Shandong Agricultural University, Tai'an, China.,Jiaxiang County Animal Husbandry and Veterinary Bureau, Jining, China
| | - Shuai Gong
- College of Animal Science and Veterinary, Shandong Agricultural University, Tai'an, China
| | - Yanping Su
- Department of Histology and Embryology, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, China
| | - Minhua Yao
- Department of Histology and Embryology, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, China
| | - Xiaocui Liu
- Department of Histology and Embryology, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, China
| | - Zhaoqing Gong
- Department of Histology and Embryology, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, China
| | - Hongshu Sui
- Department of Histology and Embryology, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, China
| | - Mingjiu Luo
- College of Animal Science and Veterinary, Shandong Agricultural University, Tai'an, China
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7
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Cui X, Zhang S, Zhang Q, Guo X, Wu C, Yao M, Sun D. Comprehensive MicroRNA Expression Profile of the Mammary Gland in Lactating Dairy Cows With Extremely Different Milk Protein and Fat Percentages. Front Genet 2020; 11:548268. [PMID: 33343617 PMCID: PMC7744623 DOI: 10.3389/fgene.2020.548268] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/05/2020] [Indexed: 12/27/2022] Open
Abstract
A total of 31 differentially expressed genes in the mammary glands were identified in our previous study using RNA sequencing (RNA-Seq), for lactating cows with extremely high and low milk protein and fat percentages. To determine the regulation of milk composition traits, we herein investigated the expression profiles of microRNA (miRNA) using small RNA sequencing based on the same samples as in the previous RNA-Seq experiment. A total of 497 known miRNAs (miRBase, release 22.1) and 49 novel miRNAs among the reads were identified. Among these miRNAs, 71 were found differentially expressed between the high and low groups (p < 0.05, q < 0.05). Furthermore, 21 of the differentially expressed genes reported in our previous RNA-Seq study were predicted as target genes for some of the 71 miRNAs. Gene ontology and KEGG pathway analyses showed that these targets were enriched for functions such as metabolism of protein and fat, and development of mammary gland, which indicating the critical role of these miRNAs in regulating the formation of milk protein and fat. With dual luciferase report assay, we further validated the regulatory role of 7 differentially expressed miRNAs through interaction with the specific sequences in 3'UTR of the targets. In conclusion, the current study investigated the complexity of the mammary gland transcriptome in dairy cattle using small RNA-seq. Comprehensive analysis of differential miRNAs expression and the data from previous study RNA-seq provided the opportunity to identify the key candidate genes for milk composition traits.
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Affiliation(s)
- Xiaogang Cui
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Key Lab of Medical Molecular Cell Biology of Shanxi Province, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Shengli Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiangyu Guo
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Changxin Wu
- Key Lab of Medical Molecular Cell Biology of Shanxi Province, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Mingze Yao
- Key Lab of Medical Molecular Cell Biology of Shanxi Province, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Dongxiao Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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8
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Feng S, Ma J, Long K, Zhang J, Qiu W, Li Y, Jin L, Wang X, Jiang A, Liu L, Xiao W, Li X, Tang Q, Li M. Comparative microRNA Transcriptomes in Domestic Goats Reveal Acclimatization to High Altitude. Front Genet 2020; 11:809. [PMID: 32849809 PMCID: PMC7411263 DOI: 10.3389/fgene.2020.00809] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 07/06/2020] [Indexed: 01/30/2023] Open
Abstract
High-altitude acclimatization is a representative example of vertebrates' acclimatization to harsh and extreme environments. Previous studies reported sufficient evidence for a molecular genetic basis of high-altitude acclimatization, and genomic patterns of genetic variation among populations and species have been widely elucidated in recent years. However, understanding of the miRNA role in high-altitude acclimatization have lagged behind, especially in non-model species. To investigate miRNA expression alterations of goats that were induced by high-altitude stress, we performed comparative miRNA transcriptome analysis on six hypoxia-sensitive tissues (heart, kidney, liver, lung, skeletal muscle, and spleen) in two goat populations from distinct altitudes (600 and 3000 m). We obtained the expression value of 1391 mature miRNAs and identified 138 differentially expressed (DE) miRNAs between high and low altitudes. Combined with tissue specificity analysis, we illustrated alterations of expression levels among altitudes and tissues, and found that there were coexisting tissue-specific and -conserved mechanisms for hypoxia acclimatization. Notably, the interplay between DE miRNA and DE target genes strongly indicated post-transcriptional regulation in the hypoxia inducible factor 1, insulin, and p53 signaling pathways, which might play significant roles in high-altitude acclimatization in domestic goats. It's also worth noting that we experimentally confirmed miR-106a-5p to have a negative regulation effect on angiogenesis by directly targeting FLT-1. These results provide insight into the complicated miRNA expression patterns and regulatory mechanisms of high-altitude acclimatization in domestic goats.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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9
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Mir BA, Reyer H, Komolka K, Ponsuksili S, Kühn C, Maak S. Differentially Expressed miRNA-Gene Targets Related to Intramuscular Fat in Musculus Longissimus Dorsi of Charolais × Holstein F 2-Crossbred Bulls. Genes (Basel) 2020; 11:genes11060700. [PMID: 32630492 PMCID: PMC7348786 DOI: 10.3390/genes11060700] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/12/2022] Open
Abstract
Intramuscular fat (IMF) is a meat quality indicator associated with taste and juiciness. IMF deposition, influenced by genetic and non-genetic factors, occurs through a transcriptionally coordinated process of adipogenesis. MicroRNAs (miRNAs) are transcriptional regulators of vital biological processes, including lipid metabolism and adipogenesis. However, in bovines, limited data on miRNA profiling and association with divergent intramuscular fat content, regulated exclusively by genetic parameters, have been reported. Here, a microarray experiment was performed to identify and characterize the miRNA expression pattern in the Musculus longissimus dorsi of F2-cross (Charolais × German Holstein) bulls with high and low IMF. A total of 38 differentially expressed miRNAs (DE miRNAs), including 33 upregulated and 5 downregulated (corrected p-value ≤ 0.05, FC ≥ ±1.2), were reported. Among DE miRNAs, the upregulated miRNAs miR-105a/b, miR-695, miR-1193, miR-1284, miR-1287-5p, miR-3128, miR-3178, miR-3910, miR-4443, miR-4445 and miR-4745, and the downregulated miRNAs miR-877-5p, miR-4487 and miR-4706 were identified as novel fat deposition regulators. DE miRNAs were further analyzed, along with previously identified differentially expressed genes (DEGs) from the same samples and predicted target genes, using multiple bioinformatic approaches, including target prediction tools and co-expression networks, as well as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. We identified DE miRNAs and their gene targets associated with bovine intramuscular adipogenesis, and we provide a basis for further functional investigations.
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Affiliation(s)
- Bilal Ahmad Mir
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, Germany; (K.K.); (S.M.)
- Correspondence: ; Tel.: +49-38208-68885
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, Germany; (H.R.); (S.P.); (C.K.)
| | - Katrin Komolka
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, Germany; (K.K.); (S.M.)
| | - Siriluck Ponsuksili
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, Germany; (H.R.); (S.P.); (C.K.)
| | - Christa Kühn
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, Germany; (H.R.); (S.P.); (C.K.)
| | - Steffen Maak
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), D-18196 Dummerstorf, Germany; (K.K.); (S.M.)
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10
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Xu B, Shen J, Li D, Ning B, Guo L, Bing H, Chen J, Li Y. Overexpression of microRNA-9 inhibits 3T3-L1 cell adipogenesis by targeting PNPLA3 via activation of AMPK. Gene 2020; 730:144260. [DOI: 10.1016/j.gene.2019.144260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022]
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11
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Chen X, Zhao C, Dou M, Sun Y, Yu T, Pang W, Yang G. Deciphering the miRNA transcriptome of Rongchang pig longissimus dorsi at weaning and slaughter time points. J Anim Physiol Anim Nutr (Berl) 2020; 104:954-964. [PMID: 32056287 DOI: 10.1111/jpn.13314] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/26/2019] [Accepted: 12/28/2019] [Indexed: 11/28/2022]
Abstract
MicroRNA (miRNA) is essential for the process of gene posttranscriptional regulation in skeletal muscle of many species, such as mice, cattle and so on. However, a little number of miRNAs have been reported in the muscle development of Chinese native pig breeds. In this study, the longissimus dorsi transcripts of Chinese native Rongchang pig at weaning and slaughter time points were analysed for miRNA-seq. The results showed that 19 novel and 186 known miRNAs involved in the Rongchang pig skeletal muscle development were identified. Based on these findings, we further confirmed that porcine miR-127, miR-299 and miR-432-5p were obviously down-expressed in adult pig (287 days of age), while miR-7134-3p and 664-5p were significantly up-expressed in weaning pig (35 days of age). In other words, these miRNAs could be the potential molecular markers and play vital roles in the muscle development process. Moreover, we found miR-127 could inhibit the proliferation and myogenesis of porcine satellite cells in longissimus dorsi muscle. Our findings will provide deep insight into miRNA function for pork quality research with Chinese indigenous pig breeds.
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Affiliation(s)
- Xiaochang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chen Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Mingle Dou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yunmei Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Taiyong Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Weijun Pang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Gongshe Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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12
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Sun Y, Xia H, Lu X, Xu C, Li M, Chen Z, Yang Z. MicroRNA-141 participates in milk lipid metabolism by targeting SIRT1 in bovine mammary epithelial cells. ANIMAL PRODUCTION SCIENCE 2020. [DOI: 10.1071/an19593] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Context
The regulation of milk lipids is important for the evaluation of dairy cows’ performance. Lipids are produced and secreted by mammary gland under the regulation of steroid hormones, growth factors and microRNAs (miRNAs). MicroRNAs have been verified to be involved in numerous biological processes. Previous studies have shown that miR-141 is expressed at higher levels in dairy cows at peak lactation than in those at early lactation. However, the roles of miR-141 in bovine mammary epithelial cells (BMECs) and the mechanisms how it affects lipid metabolism are as yet unknown.
Aims
The aims of this study were to clarify (i) the molecular mechanisms of miR-141 in milk lipid metabolism, and (ii) how miR-141 affects milk lipid metabolism in BMECs.
Methods
Triglycerides were observed in BMECs using triglyceride analysis after overexpression or inhibition of miR-141; selected potential candidate genes that are targeted by miR-141 using TargetScan. The regulatory relationship among miR-141, SIRT1 gene and lipid metabolism-related genes (SREBF1, FASN and PPARγ) by using the dual luciferase assay, quantitative real-time PCR and western blotting.
Key results
Through overexpression or inhibition of miR-141 expression, we found that miR-141 promoted lipid metabolism in BMECs and an increase in triglycerides was observed in these cells. Further, miR-141 targets the 3′UTR of SIRT1 mRNA, and negative regulates the expression of SIRT1 gene in BMECs. Also, the expression levels of SREBF1, FASN and PPARγ, which are related to milk lipid metabolism, were also altered after overexpression miR-141.
Conclusions
Our results have revealed that miR-141 could promote milk lipid metabolism in BMECs by means of negative regulates SIRT1 gene and positive effects lipid metabolism-related genes (SREBF1, FASN and PPARγ) in BMECs.
Implications
Our research indicates that miR-141 could be considered a marker in cattle breeding to obtain high quality dairy products. It would be useful to study the function of miRNAs in milk lipid metabolism and synthesis. In the long term these findings might be helpful in developing practical means to improve the quality of ruminant milk.
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Chen Y, Zhao Y, Jin W, Li Y, Zhang Y, Ma X, Sun G, Han R, Tian Y, Li H, Kang X, Li G. MicroRNAs and their regulatory networks in Chinese Gushi chicken abdominal adipose tissue during postnatal late development. BMC Genomics 2019; 20:778. [PMID: 31653195 PMCID: PMC6815035 DOI: 10.1186/s12864-019-6094-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 09/10/2019] [Indexed: 12/13/2022] Open
Abstract
Background Abdominal fat is the major adipose tissue in chickens. The growth status of abdominal fat during postnatal late development ultimately affects meat yield and quality in chickens. MicroRNAs (miRNAs) are endogenous small noncoding RNAs that regulate gene expression at the post-transcriptional level. Studies have shown that miRNAs play an important role in the biological processes involved in adipose tissue development. However, few studies have investigated miRNA expression profiles and their interaction networks associated with the postnatal late development of abdominal adipose tissue in chickens. Results We constructed four small RNA libraries from abdominal adipose tissue obtained from Chinese domestic Gushi chickens at 6, 14, 22, and 30 weeks. A total of 507 known miRNAs and 53 novel miRNAs were identified based on the four small RNA libraries. Fifty-one significant differentially expressed (SDE) miRNAs were identified from six combinations by comparative analysis, and the expression patterns of these SDE miRNAs were divided into six subclusters by cluster analysis. Gene ontology enrichment analysis showed that the SDE miRNAs were primarily involved in the regulation of fat cell differentiation, regulation of lipid metabolism, regulation of fatty acid metabolism, and unsaturated fatty acid metabolism in the lipid metabolism- or deposition-related biological process categories. In addition, we constructed differentially expressed miRNA–mRNA interaction networks related to abdominal adipose development. The results showed that miRNA families, such as mir-30, mir-34, mir-199, mir-8, and mir-146, may have key roles in lipid metabolism, adipocyte proliferation and differentiation, and cell junctions during abdominal adipose tissue development in chickens. Conclusions This study determined the dynamic miRNA transcriptome and characterized the miRNA–mRNA interaction networks in Gushi chicken abdominal adipose tissue for the first time. The results expanded the number of known miRNAs in abdominal adipose tissue and provide novel insights and a valuable resource to elucidate post-transcriptional regulation mechanisms during postnatal late development of abdominal adipose tissue in chicken.
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Affiliation(s)
- Yi Chen
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng zhou, Henan Province, 450002, People's Republic of China
| | - Yinli Zhao
- College of Biological Engineering, Henan University of Technology, Zheng zhou, Henan Province, 450001, People's Republic of China
| | - Wenjiao Jin
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng zhou, Henan Province, 450002, People's Republic of China
| | - Yuanfang Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng zhou, Henan Province, 450002, People's Republic of China
| | - Yanhua Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng zhou, Henan Province, 450002, People's Republic of China
| | - Xuejie Ma
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng zhou, Henan Province, 450002, People's Republic of China
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng zhou, Henan Province, 450002, People's Republic of China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng zhou, Henan Province, 450002, People's Republic of China
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng zhou, Henan Province, 450002, People's Republic of China
| | - Hong Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng zhou, Henan Province, 450002, People's Republic of China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng zhou, Henan Province, 450002, People's Republic of China
| | - Guoxi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng zhou, Henan Province, 450002, People's Republic of China.
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14
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de Oliveira PSN, Coutinho LL, Cesar ASM, Diniz WJDS, de Souza MM, Andrade BG, Koltes JE, Mourão GB, Zerlotini A, Reecy JM, Regitano LCA. Co-Expression Networks Reveal Potential Regulatory Roles of miRNAs in Fatty Acid Composition of Nelore Cattle. Front Genet 2019; 10:651. [PMID: 31354792 PMCID: PMC6637853 DOI: 10.3389/fgene.2019.00651] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/19/2019] [Indexed: 12/15/2022] Open
Abstract
Fatty acid (FA) content affects the sensorial and nutritional value of meat and plays a significant role in biological processes such as adipogenesis and immune response. It is well known that, in beef, the main FAs associated with these biological processes are oleic acid (C18:1 cis9, OA) and conjugated linoleic acid (CLA-c9t11), which may have beneficial effects on metabolic diseases such as type 2 diabetes and obesity. Here, we performed differential expression and co-expression analyses, weighted gene co-expression network analysis (WGCNA) and partial correlation with information theory (PCIT), to uncover the complex interactions between miRNAs and mRNAs expressed in skeletal muscle associated with FA content. miRNA and mRNA expression data were obtained from skeletal muscle of Nelore cattle that had extreme genomic breeding values for OA and CLA. Insulin and MAPK signaling pathways were identified by WGCNA as central pathways associated with both of these fatty acids. Co-expression network analysis identified bta-miR-33a/b, bta-miR-100, bta-miR-204, bta-miR-365-5p, bta-miR-660, bta-miR-411a, bta-miR-136, bta-miR-30-5p, bta-miR-146b, bta-let-7a-5p, bta-let-7f, bta-let-7, bta-miR 339, bta-miR-10b, bta-miR 486, and the genes ACTA1 and ALDOA as potential regulators of fatty acid synthesis. This study provides evidence and insights into the molecular mechanisms and potential target genes involved in fatty acid content differences in Nelore beef cattle, revealing new candidate pathways of phenotype modulation that could positively benefit beef production and human consumption.
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Affiliation(s)
| | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - Aline S M Cesar
- Department of Agroindustry, Food and Nutrition, University of São Paulo, Piracicaba, Brazil
| | | | - Marcela M de Souza
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Bruno G Andrade
- Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Carlos, Brazil
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Gerson B Mourão
- Department of Agroindustry, Food and Nutrition, University of São Paulo, Piracicaba, Brazil
| | | | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Luciana C A Regitano
- Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Carlos, Brazil
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15
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Multi-Omics Analysis Reveals Up-Regulation of APR Signaling, LXR/RXR and FXR/RXR Activation Pathways in Holstein Dairy Cows Exposed to High-Altitude Hypoxia. Animals (Basel) 2019; 9:ani9070406. [PMID: 31266191 PMCID: PMC6680605 DOI: 10.3390/ani9070406] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Blood has been widely collected and analyzed for diagnosing and monitoring diseases in human beings and animals. A range of plasma proteins and peptides were set as biomarkers for pathological and physiological status. Previous researchers have explored how humans, pigs, dogs, and horses adapt to hypoxia at high altitudes. Additionally, the mechanism of hypoxia adaptation in human, mice, and shrimp was studied by proteomics. However, information on the adaptation mechanism of Holstein cows introduced to high altitudes is limited. The present study was conducted to the adaptation mechanism of Holstein dairy cows to high-altitude hypoxia by miRNA microarray analysis and the isobaric tags for relative and absolute quantitation (iTRAQ) iTRAQ technology. Based on the obtained results, Holstein dairy cows transported to Nyingchi may adapt to the high-altitude hypoxia through regulation of inflammatory homeostasis by up-regulating the acute phase response (APR) APR and activation of the liver X receptor/retinoid X receptor (LXR/RXR)LXR/RXR and farnesoid X receptor/ retinoid X receptor (FXR/RXR) FXR/RXR pathways. Abstract Changes in the environment such as high-altitude hypoxia (HAH) high-altitude hypoxia can lead to adaptive changes in the blood system of mammals. However, there is limited information about the adaptation of Holstein dairy cows introduced to high-altitude areas. This study used 12 multiparous Holstein dairy cows (600 ± 55 kg, average three years old) exposed to HAH conditions in Nyingchi of Tibet (altitude 3000 m) and HAH-free conditions in Shenyang (altitude 50 m). The miRNA microarray analysis and iTRAQ proteomics approach (accepted as more suitable for accurate and comprehensive prediction of miRNA targets) were applied to explore the differences in the plasma proteomic and miRNA profiles in Holstein dairy cows. A total of 70 differential miRNAs (54 up-regulated, Fold change (FC) FC > 2, and 16 down-regulated, FC < 0.5) and 226 differential proteins (132 up-regulated, FC > 1.2, and 94 down-regulated, FC < 0.8) were found in the HAH-stressed group compared with the HAH-free group. Integrative analysis of proteomic and miRNA profiles demonstrated the biological processes associated with differential proteins were the immune response, complement activation, protein activation, and lipid transport. The integrative analysis of canonical pathways were most prominently associated with the APR signaling (z = 1.604), and LXR/RXR activation (z = 0.365), and FXR/RXR activation (z = 0.446) pathways. The current results indicated that Holstein dairy cows exposed to HAH could adapt to high-altitude hypoxia by up-regulating the APR, activating the LXR/RXR and FXE/RXR pathways.
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16
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De Oliveira PSN, Coutinho LL, Tizioto PC, Cesar ASM, de Oliveira GB, Diniz WJDS, De Lima AO, Reecy JM, Mourão GB, Zerlotini A, Regitano LCA. An integrative transcriptome analysis indicates regulatory mRNA-miRNA networks for residual feed intake in Nelore cattle. Sci Rep 2018; 8:17072. [PMID: 30459456 PMCID: PMC6244318 DOI: 10.1038/s41598-018-35315-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/30/2018] [Indexed: 12/21/2022] Open
Abstract
Residual Feed Intake (RFI) is an economically relevant trait in beef cattle. Among the molecular regulatory mechanisms, microRNAs (miRNAs) are an important dimension in post-transcriptional regulation and have been associated with different biological pathways. Here, we performed differential miRNAs expression and weighted gene co-expression network analyses (WGCNA) to better understand the complex interactions between miRNAs and mRNAs expressed in bovine skeletal muscle and liver. MiRNA and mRNA expression data were obtained from Nelore steers that were genetically divergent for RFI (N = 10 [low RFI or feed efficient]; N = 10 [high RFI or feed inefficient]). Differentially expressed and hub miRNAs such as bta-miR-486, bta-miR-7, bta-miR15a, bta-miR-21, bta-miR 29, bta- miR-30b, bta-miR-106b, bta-miR-199a-3p, bta-miR-204, and bta-miR 296 may have a potential role in variation of RFI. Functional enrichment analysis of differentially expressed (DE) miRNA's target genes and miRNA-mRNA correlated modules revealed that insulin, lipid, immune system, oxidative stress and muscle development signaling pathways might potentially be involved in RFI in this population. Our study identified DE miRNAs, miRNA - mRNA regulatory networks and hub miRNAs related to RFI. These findings suggest a possible role of miRNAs in regulation of RFI, providing new insights into the potential molecular mechanisms that control feed efficiency in Nelore cattle.
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Affiliation(s)
| | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Aline S M Cesar
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Wellison J da S Diniz
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Andressa O De Lima
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil
| | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Gerson B Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
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Li N, Zhang Y, Li HP, Han L, Yan XM, Li HB, Du W, Zhang JS, Yu QL. Differential expression of mRNA-miRNAs related to intramuscular fat content in the longissimus dorsi in Xinjiang brown cattle. PLoS One 2018; 13:e0206757. [PMID: 30412616 PMCID: PMC6226300 DOI: 10.1371/journal.pone.0206757] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/18/2018] [Indexed: 02/07/2023] Open
Abstract
In this study, we examined the role of mRNAs and miRNAs in variations in intramuscular fat content in the longissimus dorsi muscle in Xinjiang brown cattle. Two groups of Xinjiang brown cattle with extremely different intramuscular fat content in the longissimus dorsi were selected for combined of miRNA and mRNA analysis using an RNA-Seq. In total, 296 mRNAs and 362 miRNAs were significantly differentially expressed, including 155 newly predicted miRNAs, 275 significantly upregulated genes, 252 significantly upregulated miRNAs, 21 significantly downregulated genes and 110 significantly downregulated miRNAs. The combined miRNA and mRNA analysis identified 96 differentially expressed miRNAs and 27 differentially expressed mRNAs. In all, 47 upregulated miRNAs had a regulatory effect on 14 differentially downregulated target genes, and 49 downregulated miRNAs had a regulatory effect on 13 upregulated target genes. To verify the sequencing results, 10 differentially expressed genes (DEGs) and 10 differentially expressed miRNAs were selected for qRT-PCR. The qRT-PCR results confirmed the sequencing results. The results of this study shed light on the molecular regulation of bovine adipose tissue, which might help with the development of new strategies for improving meat quality and animal productivity in beef cattle to provide healthier meat products for consumers.
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Affiliation(s)
- Na Li
- Department of Food Science and Engineering, Gansu Agricultural University, Lanzhou, Gansu, China
- Department of Research Livestock, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Yang Zhang
- Department of Research Livestock, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Hai-Peng Li
- Department of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ling Han
- Department of Food Science and Engineering, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xiang-Min Yan
- Department of Research Livestock, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Hong-Bo Li
- Department of Research Livestock, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Wei Du
- Department of Research Livestock, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Jin-Shan Zhang
- Department of Research Livestock, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Qun-Li Yu
- Department of Food Science and Engineering, Gansu Agricultural University, Lanzhou, Gansu, China
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Zhang P, Du J, Wang L, Niu L, Zhao Y, Tang G, Jiang Y, Shuai S, Bai L, Li X, Wang J, Zhang S, Zhu L. MicroRNA-143a-3p modulates preadipocyte proliferation and differentiation by targeting MAPK7. Biomed Pharmacother 2018; 108:531-539. [PMID: 30243086 DOI: 10.1016/j.biopha.2018.09.080] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/10/2018] [Accepted: 09/12/2018] [Indexed: 01/08/2023] Open
Abstract
Adipogenesis plays a key role in increasing fat mass, which is a main characteristic for obesity, and involves preadipocyte proliferation and differentiation. Recently, more and more evidences suggested that microRNAs (miRNAs) is an important member of the regulatory network of adipogenesis. In this study, miR-143a-3p was highly expressed in adipose tissues of obese mice, and was up-regulated at the middle and last stage of 3T3-L1 adipocyte differentiation. Using mouse 3T3-L1 cells line, which is an ideal model in vitro for the study of adipogenesis, we observed that overexpression of miR-143a-3p inhibited the preadipocyte proliferation, and enhanced the preadipocyte differentiation. In contrast, the inhibition of miR-143a-3p expression promoted the preadipocyte proliferation, and inhibited the preadipocyte differentiation. Further analysis suggested that miR-143a-3p mediating preadipocyte differentiation might be involved in fatty acid metabolism. In addition, we found that miR-143-3p and PPARγ, an activator of miR-143a-3p transcription, could regulate each other. Compared with miR-143a-3p, MAPK7 played an opposite role in the proliferation and differentiation of adipocyte. Further analysis indicated that MAPK7 is a target gene of miR-143a-3p in 3T3-L1 cells, and inhibition of MAPK7 recede the effect of miR-143a-3p on preadipocyte proliferation and differentiation. Taken together, these results indicated that as a regulator of PPARγ, miR-143a-3p play an important role in adipogenesis via regulating MAPK7 and fatty acid.
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Affiliation(s)
- Peiwen Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jingjing Du
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Linghui Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lili Niu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ye Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guoqing Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yanzhi Jiang
- College of Life and Biology Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Surong Shuai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lin Bai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xuewi Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jinyong Wang
- Chongqing Academy of Animal Science, Rongchang, 402460, China
| | - Shunhua Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
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Do DN, Dudemaine PL, Fomenky BE, Ibeagha-Awemu EM. Integration of miRNA and mRNA Co-Expression Reveals Potential Regulatory Roles of miRNAs in Developmental and Immunological Processes in Calf Ileum during Early Growth. Cells 2018; 7:E134. [PMID: 30208606 PMCID: PMC6162677 DOI: 10.3390/cells7090134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 01/04/2023] Open
Abstract
This study aimed to investigate the potential regulatory roles of miRNAs in calf ileum developmental transition from the pre- to the post-weaning period. For this purpose, ileum tissues were collected from eight calves at the pre-weaning period and another eight calves at the post-weaning period and miRNA expression characterized by miRNA sequencing, followed by functional analyses. A total of 388 miRNAs, including 81 novel miRNAs, were identified. A total of 220 miRNAs were differentially expressed (DE) between the two periods. The potential functions of DE miRNAs in ileum development were supported by significant enrichment of their target genes in gene ontology terms related to metabolic processes and transcription factor activities or pathways related to metabolism (peroxisomes), vitamin digestion and absorption, lipid and protein metabolism, as well as intracellular signaling. Integration of DE miRNAs and DE mRNAs revealed several DE miRNA-mRNA pairs with crucial roles in ileum development (bta-miR-374a-FBXO18, bta-miR-374a-GTPBP3, bta-miR-374a-GNB2) and immune function (bta-miR-15b-IKBKB). This is the first integrated miRNA-mRNA analysis exploring the potential roles of miRNAs in calf ileum growth and development during early life.
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Affiliation(s)
- Duy N Do
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
- Department of Animal Science, McGill University, Ste-Anne-de-Bellevue, QC H9X 3V9, Canada.
| | - Pier-Luc Dudemaine
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
| | - Bridget E Fomenky
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
- Département de Sciences Animale, Université Laval, Quebec, QC G1V 0A6, Canada.
| | - Eveline M Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada.
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20
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MicroRNA-200b regulates preadipocyte proliferation and differentiation by targeting KLF4. Biomed Pharmacother 2018; 103:1538-1544. [DOI: 10.1016/j.biopha.2018.04.170] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 01/17/2023] Open
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Ioannidis J, Donadeu FX. Comprehensive analysis of blood cells and plasma identifies tissue-specific miRNAs as potential novel circulating biomarkers in cattle. BMC Genomics 2018; 19:243. [PMID: 29636028 PMCID: PMC5894187 DOI: 10.1186/s12864-018-4646-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 04/03/2018] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The potential of circulating miRNAs as biomarkers of tissue function, both in health and disease, has been extensively demonstrated in humans. In addition, circulating miRNA biomarkers offer significant potential towards improving the productivity of livestock species, however, such potential has been hampered by the absence of information on the nature and source of circulating miRNA populations in these species. In addition, many miRNAs originally proposed as robust biomarkers of a particular tissue or disease in humans have been later shown not to be tissue specific and thus to actually have limited biomarker utility. In this study, we comprehensively analysed miRNA profiles in plasma and cell fractions of blood from cattle with the aim to identify tissue-derived miRNAs which may be useful as biomarkers of tissue function in this important food animal species. RESULTS Using small RNA sequencing, we identified 92 miRNAs with significantly higher expression in plasma compared to paired blood cell samples (n = 4 cows). Differences in miRNA levels between plasma and cell fractions were validated for eight out of 10 miRNAs using RT-qPCR (n = 10 cows). Among miRNAs found to be enriched in plasma, we confirmed miR-122 (liver), miR-133a (muscle) and miR-215 (intestine) to be tissue-enriched, as reported for other species. Profiling of additional miRNAs across different tissues identified the human homologue, miR-802, as highly enriched specifically in liver. CONCLUSIONS These results provide novel information on the source of bovine circulating miRNAs and could significantly facilitate the identification of production-relevant tissue biomarkers in livestock. In particular, miR-802, a circulating miRNA not previously identified in cattle, can reportedly regulate insulin sensitivity and lipid metabolism, and thus could potentially provide a specific biomarker of liver function, a key parameter in the context of post-partum negative energy balance in dairy cows.
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Affiliation(s)
- Jason Ioannidis
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, UK
| | - F. Xavier Donadeu
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, UK
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22
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Oliveira GB, Regitano LCA, Cesar ASM, Reecy JM, Degaki KY, Poleti MD, Felício AM, Koltes JE, Coutinho LL. Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle. BMC Genomics 2018; 19:126. [PMID: 29415651 PMCID: PMC5804041 DOI: 10.1186/s12864-018-4514-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 01/31/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The 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. RESULTS Differential 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. CONCLUSION In 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.
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Affiliation(s)
- Gabriella B. Oliveira
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | | | - Aline S. M. Cesar
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | - James M. Reecy
- Department of Animal Science, Iowa State University, Ames, IA 50011 USA
| | - Karina Y. Degaki
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | - Mirele D. Poleti
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | - Andrezza M. Felício
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | - James E. Koltes
- Department of Animal Science, University of Arkansas, Fayetteville, AR 72701 USA
| | - Luiz L. Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
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Paneru BD, Al-Tobasei R, Kenney B, Leeds TD, Salem M. RNA-Seq reveals MicroRNA expression signature and genetic polymorphism associated with growth and muscle quality traits in rainbow trout. Sci Rep 2017; 7:9078. [PMID: 28831113 PMCID: PMC5567286 DOI: 10.1038/s41598-017-09515-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/25/2017] [Indexed: 02/01/2023] Open
Abstract
The role of microRNA expression and genetic variation in microRNA-binding sites of target genes on growth and muscle quality traits is poorly characterized. We used RNA-Seq approach to investigate their importance on 5 growth and muscle quality traits: whole body weight (WBW), muscle yield, muscle crude-fat content, muscle shear force and whiteness. Phenotypic data were collected from 471 fish, representing 98 families (~5 fish/family) from a growth-selected line. Muscle microRNAs and mRNAs were sequenced from 22 families showing divergent phenotypes. Ninety microRNAs showed differential expression between families with divergent phenotypes, and their expression was strongly associated with variation in phenotypes. A total of 204 single nucleotide polymorphisms (SNPs) present in 3′ UTR of target genes either destroyed or created novel illegitimate microRNA target sites; of them, 78 SNPs explained significant variation in the aforementioned 5 muscle traits. Majority of the phenotype-associated SNPs were present in microRNA-binding sites of genes involved in energy metabolism and muscle structure. These findings suggest that variation in microRNA expression and/or sequence variation in microRNA binding sites in target genes play an important role in mediating differences in fish growth and muscle quality phenotypes.
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Affiliation(s)
- Bam Dev Paneru
- Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, United States
| | - Rafet Al-Tobasei
- Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, United States
| | - Brett Kenney
- Division of Animal and Nutritional Science, West Virginia University, Morgantown, 26506-6108, West Virginia, United States
| | - Timothy D Leeds
- The National Center for Cool and Cold Water Aquaculture, USDA Agricultural Research Service, Kearneysville, WV, 25430, United States
| | - Mohamed Salem
- Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, United States. .,Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, United States.
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24
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Tan Z, Du J, Shen L, Liu C, Ma J, Bai L, Jiang Y, Tang G, Li M, Li X, Zhang S, Zhu L. miR-199a-3p affects adipocytes differentiation and fatty acid composition through targeting SCD. Biochem Biophys Res Commun 2017; 492:82-88. [PMID: 28803985 DOI: 10.1016/j.bbrc.2017.08.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 08/09/2017] [Indexed: 12/11/2022]
Abstract
Body fat mass is closely associated to diseases related to obesity. MicroRNAs (miRNAs, miR) are important regulatory molecules that function as post-transcriptional gene regulators of adipocyte development. In the current study, we revealed that reduced expression of miR-199a-3p in adipose tissue resulting from high fat diet (HFD)-induced obesity in mice. Overexpression of miR-199a-3p promoted adipocyte proliferation by regulating the expression of regulating factors of the cell cycle. Furthermore, miR-199a-3p blunted lipid accumulation in 3T3-L1 adipocytes. This was accompanied by a marked decrease in the expression of adipocyte-specific genes involved in lipogenic transcription, fatty acid synthesis, and fatty acid transportation. Furthermore, the fatty acid oxidation process was enhanced. Luciferase activity assays confirmed that miR-199a-3p regulates adipocyte differentiation by directly targeting the 3'-untranslated region (3'-UTR) of stearoyl-CoA desaturase (SCD). Moreover, miR-199a-3p regulates fatty acid composition by decreasing the ratio of unsaturated fatty acids (UFAs) in adipocytes transfected with miR-199a-3p mimics. These results suggest that miR-199a-3p may promote adipocyte proliferation, while also repressing adipocyte differentiation by down-regulating SCD and changing fatty acid composition during adipogenesis.
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Affiliation(s)
- Zhendong Tan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jingjing Du
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Chendong Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jideng Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lin Bai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanzhi Jiang
- College of Life and Science, Sichuan Agricultural University, Chengdu 611130, China
| | - Guoqing Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Shunhua Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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25
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Guo Y, Zhang X, Huang W, Miao X. Identification and characterization of differentially expressed miRNAs in subcutaneous adipose between Wagyu and Holstein cattle. Sci Rep 2017; 7:44026. [PMID: 28272430 PMCID: PMC5341059 DOI: 10.1038/srep44026] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/02/2017] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are important post-transcriptional regulators involved in animal adipogenesis, however, their roles in bovine fat deposition remain poorly understood. In the present study, we conducted a comparative RNA sequencing to identify the key miRNAs involved in beef lipid accumulation by comparing the backfat small RNA samples between Wagyu (high intramuscular fat) and Holstein (moderate intramuscular fat) cattle. Fifteen miRNAs such as bta-miR-142-3p, bta-miR-379, bta-miR-196a, bta-miR-196b, bta-miR-30f and bta-miR-2887 were identified to have a higher expression level in Wagyu cattle compared with Holstein, whereas bta-miR-320a, bta-miR-874 and bta-miR-1247-3p had a lower expression level in Wagyu. Furthermore, a total of 1345 potential target genes of differentially expressed miRNAs were predicted using bioinformatics tools, in which PPARα and RXRα were known to play a critical role in adipocyte differentiation and lipid metabolism. In conclusion, the present study constructed a high-throughput RNA sequencing screen and successfully identified miRNAs such as bta-miR-874, bta-miR-320a and bta-miR-196b which may affect beef fat deposition. The present findings may provide a theoretical foundation for the utilization of beef cattle germplasm resources.
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Affiliation(s)
- Yuntao Guo
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiuxiu Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wanlong Huang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiangyang Miao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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26
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Guan L, Hu X, Liu L, Xing Y, Zhou Z, Liang X, Yang Q, Jin S, Bao J, Gao H, Du M, Li J, Zhang L. bta-miR-23a involves in adipogenesis of progenitor cells derived from fetal bovine skeletal muscle. Sci Rep 2017; 7:43716. [PMID: 28255176 PMCID: PMC5334644 DOI: 10.1038/srep43716] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/27/2017] [Indexed: 12/30/2022] Open
Abstract
Intramuscular fat deposition or marbling is essential for high quality beef. The molecular mechanism of adipogenesis in skeletal muscle remains largely unknown. In this study, we isolated Platelet-derived growth factor receptor α (PDGFRα) positive progenitor cells from fetal bovine skeletal muscle and induced into adipocytes. Using miRNAome sequencing, we revealed that bta-miR-23a was an adipogenic miRNA mediating bovine adipogenesis in skeletal muscle. The expression of bta-miR-23a was down-regulated during differentiation of PDGFRα+ progenitor cells. Forced expression of bta-miR-23a mimics reduced lipid accumulation and inhibited the key adipogenic transcription factor peroxisome proliferative activated receptor gamma (PPARγ) and CCAAT/enhancer binding protein alpha (C/EBPα). Whereas down-regulation of bta-miR-23a by its inhibitors increased lipid accumulation and expression of C/EBPα, PPARγ and fatty acid-binding protein 4 (FABP4). Target prediction analysis revealed that ZNF423 was a potential target of bta-miR-23a. Dual-luciferase reporter assay revealed that bta-miR-23a directly targeted the 3′-UTR of ZNF423. Together, our data showed that bta-miR-23a orchestrates early intramuscular adipogeneic commitment as an anti-adipogenic regulator which acts by targeting ZNF423.
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Affiliation(s)
- Long Guan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xin Hu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Li Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Yishen Xing
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhengkui Zhou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xingwei Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi High Education Laboratory for Animal Reproduction and Biotechnology, Guangxi University, Guangxi 530004, China
| | - Qiyuan Yang
- Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA
| | - Shengyun Jin
- Animal Husbandry Station of Wulagai, Wulagai 026321, China
| | - Jinshan Bao
- Animal Husbandry Station of Wulagai, Wulagai 026321, China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Min Du
- Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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27
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Integrating miRNA and mRNA Expression Profiling Uncovers miRNAs Underlying Fat Deposition in Sheep. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1857580. [PMID: 28293627 PMCID: PMC5331317 DOI: 10.1155/2017/1857580] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 12/05/2016] [Accepted: 12/15/2016] [Indexed: 01/01/2023]
Abstract
MicroRNAs (miRNAs) are endogenous, noncoding RNAs that regulate various biological processes including adipogenesis and fat metabolism. Here, we adopted a deep sequencing approach to determine the identity and abundance of miRNAs involved in fat deposition in adipose tissues from fat-tailed (Kazakhstan sheep, KS) and thin-tailed (Tibetan sheep, TS) sheep breeds. By comparing HiSeq data of these two breeds, 539 miRNAs were shared in both breeds, whereas 179 and 97 miRNAs were uniquely expressed in KS and TS, respectively. We also identified 35 miRNAs that are considered to be putative novel miRNAs. The integration of miRNA-mRNA analysis revealed that miRNA-associated targets were mainly involved in the gene ontology (GO) biological processes concerning cellular process and metabolic process, and miRNAs play critical roles in fat deposition through their ability to regulate fundamental pathways. These pathways included the MAPK signaling pathway, FoxO and Wnt signaling pathway, and focal adhesion. Taken together, our results define miRNA expression signatures that may contribute to fat deposition and lipid metabolism in sheep.
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28
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Vailati-Riboni M, Farina G, Batistel F, Heiser A, Mitchell MD, Crookenden MA, Walker CG, Kay JK, Meier S, Roche JR, Loor JJ. Far-off and close-up dry matter intake modulate indicators of immunometabolic adaptations to lactation in subcutaneous adipose tissue of pasture-based transition dairy cows. J Dairy Sci 2017; 100:2334-2350. [PMID: 28088407 DOI: 10.3168/jds.2016-11790] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/13/2016] [Indexed: 12/21/2022]
Abstract
The common practice of increasing dietary energy density during the close-up dry period (last ∼3 wk prepartum) has been recently associated with a higher incidence of metabolic disorders after calving. Despite these reports, over-feeding of metabolizable energy (ME) during the far-off, nonlactating period is a common management policy aimed at achieving optimum calving body condition score (BCS) in pasture-based systems, as cows are generally thinner than total mixed ration cows at the end of lactation. Our hypothesis was that both far-off and close-up overfeeding influence the peripartum adipose tissue changes associated with energy balance and inflammatory state. Sixty mid-lactation, grazing dairy cows of mixed age and breed were randomly allocated to 1 of 2 groups that were managed through late lactation to achieve a low and high BCS (approximately 4.25 and 5.0 on a 10-point scale) at dry-off. The low BCS cows were then overfed ME to ensure that they achieved the same BCS as the higher BCS group by calving. Within each rate of BCS gain treatment, cows were offered 65, 90, or 120% of their pre-calving ME requirements for 3 wk pre-calving in a 2 × 3 factorial arrangement of treatments (i.e., 10 cows/treatment). Subcutaneous adipose tissue was collected via biopsy at -1, 1, and 4 wk relative to parturition. Quantitative PCR was used to measure mRNA and microRNA expression of targets related to adipogenesis and inflammation. Cows overfed in the far-off period had increased expression of miR-143 and miR-378 prepartum (-1 wk) indicating greater adipogenesis, consistent with their rapid gain in BCS following dry-off. Furthermore, the lower postpartum expression of IL6, TNF, TLR4, TLR9, and miR-145, and a higher abundance of miR-99a indicated lower body fat mobilization in early lactation in the same group. In the close-up period, feeding either 65 or 120% of ME requirements caused changes in FASN, IL1B, IL6R, TLR9, and the microRNA miR-143, miR-155, and miR-378. Their respective expression patterns indicate a tentative negative-feedback mechanism in metabolically compromised, feed-restricted cows, and a possible immune-related stimulation of lipolysis in apparently static adipocytes in overfed cows. Data from cows fed 90% of ME requirements indicate the existence of a balance between lipolytic (inflammatory-related) and anti-lipolytic signals, to prime the mobilization machinery in light of imminent lactation. Overall, results indicate that far-off dry cow nutrition influences peripartum adipose tissue metabolism, with neither strategy negatively affecting the physiological adaptation to lactation. Furthermore, to ensure a favorable transition, cows should be subjected to a small feed restriction in the close-up period, irrespective of far-off nutritional management.
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Affiliation(s)
- M Vailati-Riboni
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana 61801
| | - G Farina
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana 61801; Dipartimento di Scienze Veterinarie per la salute, la produzione animale e la sicurezza alimentare (VESPA), Università di Milano, Milan, Italy 20122
| | - F Batistel
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana 61801
| | - A Heiser
- AgResearch, Hopkirk Research Institute, Grasslands Research Centre, Palmerston North, New Zealand 4442
| | - M D Mitchell
- University of Queensland, Centre for Clinical Research, Royal Brisbane and Women's Hospital Campus, Herston, Queensland, Australia 4029
| | - M A Crookenden
- DairyNZ Limited, c/o University of Auckland, 3A Symonds St., Auckland, New Zealand 1010
| | - C G Walker
- DairyNZ Limited, c/o University of Auckland, 3A Symonds St., Auckland, New Zealand 1010
| | - J K Kay
- DairyNZ Limited, Private Bag 3221, Hamilton, New Zealand 3240
| | - S Meier
- DairyNZ Limited, Private Bag 3221, Hamilton, New Zealand 3240
| | - J R Roche
- DairyNZ Limited, Private Bag 3221, Hamilton, New Zealand 3240
| | - J J Loor
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana 61801.
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29
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Jahuey-Martínez FJ, Parra-Bracamonte GM, Sifuentes-Rincón AM, Martínez-González JC, Gondro C, García-Pérez CA, López-Bustamante LA. Genomewide association analysis of growth traits in Charolais beef cattle1. J Anim Sci 2016; 94:4570-4582. [DOI: 10.2527/jas.2016-0359] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- F. J. Jahuey-Martínez
- Centro de Biotecnología Genómica-Instituto Politécnico Nacional, Reynosa, Tamaulipas, México, 88710
| | - G. M. Parra-Bracamonte
- Centro de Biotecnología Genómica-Instituto Politécnico Nacional, Reynosa, Tamaulipas, México, 88710
| | - A. M. Sifuentes-Rincón
- Centro de Biotecnología Genómica-Instituto Politécnico Nacional, Reynosa, Tamaulipas, México, 88710
| | - J. C. Martínez-González
- Universidad Autónoma de Tamaulipas-Facultad de Ingeniería y Ciencias, Victoria, Tamaulipas, México, 87749
| | - C. Gondro
- The Centre for Genetic Analyses and Applications, University of New England, Armidale, NSW, Australia, 2351
| | - C. A. García-Pérez
- Centro de Biotecnología Genómica-Instituto Politécnico Nacional, Reynosa, Tamaulipas, México, 88710
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30
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Mobley CB, Mumford PW, McCarthy JJ, Miller ME, Young KC, Martin JS, Beck DT, Lockwood CM, Roberts MD. Whey protein-derived exosomes increase protein synthesis and hypertrophy in C 2-C 12 myotubes. J Dairy Sci 2016; 100:48-64. [PMID: 28341051 DOI: 10.3168/jds.2016-11341] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 09/01/2016] [Indexed: 12/29/2022]
Abstract
We sought to examine potential amino acid independent mechanisms whereby hydrolyzed whey protein (WP) affects muscle protein synthesis (MPS) and anabolism in vitro. Specifically, we tested (1) whether 3-h and 6-h treatments of WP, essential amino acids, or l-leucine (Leu) affected MPS, and whether 6-h treatments with low-, medium-, or high doses of WP versus Leu affected MPS; (2) whether knockdown of the primary Leu transporter affected WP- and Leu-mediated changes in MPS, mammalian target of rapamycin (mTOR) signaling responses, or both, following 6-h treatments; (3) whether exosomes isolated from WP (WP-EXO) affected MPS, mTOR signaling responses, or both, compared with untreated (control) myotubes, following 6-h, 12-h, and 24-h treatments, and whether they affected myotube diameter following 24-h and 48-h treatments. For all treatments, 7-d post-differentiated C2C12 myotubes were examined. In experiment 1, 6-h WP treatments increased MPS compared with control (+46%), Leu (+24%), and essential amino acids (+25%). Moreover, the 6-h low-, medium-, and high WP treatments increased MPS by approximately 40 to 50% more than corresponding Leu treatments. In experiment 2 (LAT short hairpin RNA-transfected myotubes), 6-h WP treatments increased MPS compared with control (+18%) and Leu (+19%). In experiment 3, WP-EXO treatments increased MPS over controls at 12h (+18%) and 24h (+45%), and myotube diameters increased with 24-h (+24%) and 48-h (+40%) WP-EXO treatments compared with controls. The WP-EXO treatments did not appear to operate through mTOR signaling; instead, they increased mRNA and protein levels o eukaryotic initiation factor 4A. Bovine-specific microRNA following 24-h WP-EXO treatments were enriched in myotubes (chiefly miR-149-3p, miR-2881), but were not related to hypertrophic gene targets. To summarize, hydrolyzed WP-EXO increased skeletal MPS and anabolism in vitro, and this may be related to an unknown mechanism that increases translation initiation factors rather than enhancing mTOR signaling or the involvement of bovine-specific microRNA.
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Affiliation(s)
| | | | - John J McCarthy
- Department of Physiology, University of Kentucky Medical College of Medicine, Lexington 40506
| | - Michael E Miller
- Harrison School of Pharmacy, Auburn University, Auburn, AL 36849
| | - Kaelin C Young
- School of Kinesiology, Auburn University, Auburn, AL 36849; Department of Cellular Biology and Physiology, Edward Via College of Osteopathic Medicine, Auburn Campus, Auburn, AL 36849
| | - Jeffrey S Martin
- School of Kinesiology, Auburn University, Auburn, AL 36849; Department of Cellular Biology and Physiology, Edward Via College of Osteopathic Medicine, Auburn Campus, Auburn, AL 36849
| | - Darren T Beck
- School of Kinesiology, Auburn University, Auburn, AL 36849; Department of Cellular Biology and Physiology, Edward Via College of Osteopathic Medicine, Auburn Campus, Auburn, AL 36849
| | | | - Michael D Roberts
- School of Kinesiology, Auburn University, Auburn, AL 36849; Department of Cellular Biology and Physiology, Edward Via College of Osteopathic Medicine, Auburn Campus, Auburn, AL 36849.
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31
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Wei Y, Cui YF, Tong HL, Zhang WW, Yan YQ. MicroRNA-2400 promotes bovine preadipocyte proliferation. Biochem Biophys Res Commun 2016; 478:1054-9. [PMID: 27514450 DOI: 10.1016/j.bbrc.2016.08.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 08/06/2016] [Indexed: 11/27/2022]
Abstract
MicroRNAs (miRNAs) play critical roles in the proliferation of bovine preadipocytes. miR-2400 is a novel and unique miRNA from bovines. In the present study, we separated and identified preadipocytes from bovine samples. miR-2400 overexpression increased the rate of preadipocyte proliferation, which was analyzed with a combination of EdU and flow cytometry. Simultaneously, functional genes related to proliferation (PCNA, CCND2, CCNB1) were also increased, which was detected by real-time PCR. Furthermore, luciferase reporter assays showed that miR-2400 bound directly to the 3'untranslated regions (3'UTRs) of PRDM11 mRNA. These data suggested that miR-2400 could promote preadipocyte proliferation by targeting PRDM11.
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Affiliation(s)
- Yao Wei
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Ya Feng Cui
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Hui Li Tong
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Wei Wei Zhang
- College of Life Sciences and Agriculture & Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Yun Qin Yan
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
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32
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An X, Ma K, Zhang Z, Zhao T, Zhang X, Tang B, Li Z. miR-17, miR-21, and miR-143 Enhance Adipogenic Differentiation from Porcine Bone Marrow-Derived Mesenchymal Stem Cells. DNA Cell Biol 2016; 35:410-6. [PMID: 27093346 DOI: 10.1089/dna.2015.3182] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bone marrow-derived mesenchymal stem cells (BMSCs) have multilineage differentiation abilities toward adipocytes and osteoblasts. Recently, numerous studies have focused on the roles of microRNAs (miRNAs) in the process of adipogenic differentiation of human and mouse cells. However, the role of miRNAs in adipogenic differentiation process of porcine BMSCs (pBMSCs) remains unclear. In this study, pBMSCs were induced to differentiate into adipocytes using a chemical approach, and the roles of miR-17, miR-21, and miR-143 in this process were investigated. Our results showed that pBMSCs could be chemically induced to differentiate into adipocytes and that the expression of miR-17, miR-21, and miR-143 increased during differentiation. Then, overexpression of mimics of miR-17, miR-21, and miR-143 increased the number of oil red O-positive cells of adipocyte differentiation. The expression levels of CCAAT/enhancer-binding protein alpha (C/EBPα) mRNA showed increases of 1.8-, 1.5-, and 1.2-fold in the groups expressing mimics of miR-21, miR-17, and miR-143, respectively, at day 20. These results demonstrate that miR-17, miR-21, and miR-143 are involved in and promote the adipogenic differentiation of pBMSCs. This study provides an experimental basis for establishing a stable and efficient adipogenic differentiation model for applications in cell therapy and tissue engineering.
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Affiliation(s)
- Xinglan An
- 1 College of Animal Science, Jilin University , Changchun, China .,2 State & Local Joint Engineering Laboratory for Animal Models of Human Diseases, Academy of Translational Medicine, First Hospital, Jilin University , Changchun, China
| | - Kuiying Ma
- 1 College of Animal Science, Jilin University , Changchun, China
| | - Zhiren Zhang
- 1 College of Animal Science, Jilin University , Changchun, China
| | - Tianchuang Zhao
- 3 College of Veterinary Medicine, Jilin University , Changchun, China
| | - Xueming Zhang
- 3 College of Veterinary Medicine, Jilin University , Changchun, China
| | - Bo Tang
- 3 College of Veterinary Medicine, Jilin University , Changchun, China
| | - Ziyi Li
- 1 College of Animal Science, Jilin University , Changchun, China .,2 State & Local Joint Engineering Laboratory for Animal Models of Human Diseases, Academy of Translational Medicine, First Hospital, Jilin University , Changchun, China
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An X, Song Y, Hou J, Li G, Zhao H, Wang J, Cao B. Identification and profiling of microRNAs in the ovaries of polytocous and monotocous goats during estrus. Theriogenology 2016; 85:769-80. [DOI: 10.1016/j.theriogenology.2015.09.056] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 01/11/2023]
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Moisá SJ, Shike DW, Shoup L, Loor JJ. Maternal Plane of Nutrition During Late-Gestation and Weaning Age Alter Steer Calf Longissimus Muscle Adipogenic MicroRNA and Target Gene Expression. Lipids 2015; 51:123-38. [PMID: 26597919 DOI: 10.1007/s11745-015-4092-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 11/02/2015] [Indexed: 12/15/2022]
Abstract
The main objective was to evaluate if different planes of maternal nutrition during late gestation and weaning age alter microRNA (miRNA) and target gene expression in offspring longissimus muscle (LM). Early (EW) and normal weaned (NW) Angus × Simmental calves (n = 30) born to cows that were grazing endophyte-infected tall fescue and red clover pastures with no supplement [low plane of nutrition (LPN)], or supplemented with 2.3 and 9.1 kg of dried distiller's grains with solubles and soy hulls [medium and high plane of nutrition (MPN, HPN), respectively] during the last 105 ± 11 days of gestation were used. Biopsies of LM were harvested at 78 (early weaning), 187 (normal weaning) and 354 days of age. Results indicate a role of pro-adipogenic miRNA in the control of adipogenesis in LM of NW-MPN steers between 78 and 187 days of age through upregulation of (1) miR-103 which inhibits CAV1, a protein that destabilizes INSR and leads to insulin resistance; (2) miR-143 which inhibits DLK1, a protein that inhibits adipocyte differentiation; and (3) miR-21 which impairs TGFBR2-induced inhibition of adipocyte differentiation. Among the studied anti-adipogenic miRNA, cow plane of nutrition resulted in downregulation of miR-34a expression in MPN steers compared with HPN and LPN at 78 days of age. Data for miR-34a provided a potential sign of epigenetic regulation of LM in beef offspring due to the cow plane of nutrition during late gestation.
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Affiliation(s)
- Sonia J Moisá
- Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | - Daniel W Shike
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | - Lindsay Shoup
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA
| | - Juan J Loor
- Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois, Urbana, IL, USA. .,Department of Animal Sciences, University of Illinois, Urbana, IL, USA. .,Division of Nutritional Sciences, Illinois Informatics Institute, University of Illinois, Urbana, IL, USA.
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Vailati-Riboni M, Kanwal M, Bulgari O, Meier S, Priest NV, Burke CR, Kay JK, McDougall S, Mitchell MD, Walker CG, Crookenden M, Heiser A, Roche JR, Loor JJ. Body condition score and plane of nutrition prepartum affect adipose tissue transcriptome regulators of metabolism and inflammation in grazing dairy cows during the transition period. J Dairy Sci 2015; 99:758-70. [PMID: 26601585 DOI: 10.3168/jds.2015-10046] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/08/2015] [Indexed: 01/11/2023]
Abstract
Recent studies demonstrating a higher incidence of metabolic disorders after calving have challenged the management practice of increasing dietary energy density during the last ~3 wk prepartum. Despite our knowledge at the whole-animal level, the tissue-level mechanisms that are altered in response to feeding management prepartum remain unclear. Our hypothesis was that prepartum body condition score (BCS), in combination with feeding management, plays a central role in the peripartum changes associated with energy balance and inflammatory state. Twenty-eight mid-lactation grazing dairy cows of mixed age and breed were randomly allocated to 1 of 4 treatment groups in a 2 × 2 factorial arrangement: 2 prepartum BCS categories (4.0 and 5.0, based on a 10-point scale; BCS4, BCS5) obtained via differential feeding management during late-lactation, and 2 levels of energy intake during the 3 wk preceding calving (75 and 125% of estimated requirements). Subcutaneous adipose tissue was harvested via biopsy at -1, 1, and 4 wk relative to parturition. Quantitative polymerase chain reaction was used to measure mRNA and microRNA (miRNA) expression of targets related to fatty acid metabolism (lipogenesis, lipolysis), adipokine synthesis, and inflammation. Both prepartum BCS and feeding management had a significant effect on mRNA and miRNA expression throughout the peripartum period. Overfed BCS5 cows had the greatest prepartum expression of fatty acid synthase (FASN) and an overall greater expression of leptin (LEP); BCS5 was also associated with greater overall adiponectin (ADIPOQ) and peroxisome proliferator-activated receptor gamma (PPARG), whereas overfeeding upregulated expression of proadipogenic miRNA. Higher postpartum expression of chemokine ligand 5 (CCL5) and the cytokines interleukin 6 (IL6) and tumor necrosis factor (TNF) was detected in overfed BCS5 cows. Feed-restricted BCS4 cows had the highest overall interleukin 1 (IL1B) expression. Prepartum feed restriction resulted in greater chemokine ligand 2 (CCL2) expression. Overall, changes in mRNA expression were consistent with the expression pattern of inflammation-related miRNA. These data shed light on molecular mechanisms underlying the effect of prepartum BCS and feeding management on metabolic and inflammatory status of adipose tissue during the peripartum period. Data support the use of a controlled feed restriction prepartum in optimally conditioned cows, as well as the use of a higher level of dietary energy in under-conditioned cows.
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Affiliation(s)
- M Vailati-Riboni
- Department of Animal Sciences, University of Illinois, Urbana 61801
| | - M Kanwal
- Department of Animal Sciences, University of Illinois, Urbana 61801
| | - O Bulgari
- Department of Animal Sciences, University of Illinois, Urbana 61801; Department of Molecular and Translational Medicine, University of Brescia, Brescia 25123, Italy
| | - S Meier
- DairyNZ Limited, Private Bag 3221, Hamilton 3240, New Zealand
| | - N V Priest
- DairyNZ Limited, Private Bag 3221, Hamilton 3240, New Zealand
| | - C R Burke
- DairyNZ Limited, Private Bag 3221, Hamilton 3240, New Zealand
| | - J K Kay
- DairyNZ Limited, Private Bag 3221, Hamilton 3240, New Zealand
| | - S McDougall
- Cognosco, Anexa Animal Health, PO Box 21, Morrinsville 3300, New Zealand
| | - M D Mitchell
- University of Queensland, Centre for Clinical Research, Royal Brisbane & Women's Hospital Campus, Herston, Queensland 4029, Australia
| | - C G Walker
- DairyNZ Limited, Private Bag 3221, Hamilton 3240, New Zealand
| | - M Crookenden
- DairyNZ Limited, Private Bag 3221, Hamilton 3240, New Zealand
| | - A Heiser
- AgResearch, Hopkirk Research Institute, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - J R Roche
- DairyNZ Limited, Private Bag 3221, Hamilton 3240, New Zealand
| | - J J Loor
- Department of Animal Sciences, University of Illinois, Urbana 61801.
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Sun J, Aswath K, Schroeder SG, Lippolis JD, Reinhardt TA, Sonstegard TS. MicroRNA expression profiles of bovine milk exosomes in response to Staphylococcus aureus infection. BMC Genomics 2015; 16:806. [PMID: 26475455 PMCID: PMC4609085 DOI: 10.1186/s12864-015-2044-9] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 10/09/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Milk exosomes are a rich source of microRNAs (miRNAs) that are protected from degradation. Ingestion of milk and subsequent absorption of miRNAs into recipient cells by endocytosis may play a role in the regulation of neonatal innate and adaptive immunity. In contrast, the miRNA content of milk exosomes may also be indicative of a lactating animal's health; whereby, the presence or absence of specific miRNAs could serve as biomarkers for early detection of bacterial infection that can lead to mastitis. In the present study, we therefore analyzed and compared miRNA expression profiles of milk exosomes from four Holstein cows obtained during mid-lactation prior to and after infection (48 h) of the mammary gland with Staphylococcus aureus. METHODS Milk exosomes, purified from control and S. aureus infected cows, were extracted for RNA. Following preparation indexed libraries from both groups the samples were subjected to next generation sequencing. RESULTS Next generation sequencing of eight, unpooled small RNA libraries derived from milk exosomes produced about 60.5 million high-quality, bovine-specific sequence reads for comparison of miRNA expression between treatments. Sequence identity analysis showed the miRNAs make up about 13 % of the average RNA content of these exosomes. Although 417 known bovine miRNAs were identified, miRNAs represented the least diverse class of RNA accounting for only 1 % of all unique sequences. The 20 most prevalent unique sequences within this class accounted for about 90 % of the total miRNA-associated reads across samples. Non-annotated, unique reads provided evidence for another 303 previously unknown bovine miRNAs. Expression analyses found 14 known bovine microRNAs significantly differed in frequency between exosomes from infected and control animals. CONCLUSIONS Our survey of miRNA expression from uninfected milk exosomes and those produced in response to infection provides new and comprehensive information supporting a role for delivery into milk of specific miRNAs involved in immune response. In particular, bta-miR-142-5p, and -223 are potential biomarkers for early detection of bacterial infection of the mammary gland. Additionally, 22 mammary-expressed genes involved in regulation of host immune processes and response to inflammation were identified as potential binding targets of the differentially expressed miRNAs.
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Affiliation(s)
- Jiajie Sun
- Animal Genomics and Improvement Laboratory, USDA-ARS, BARC-East, Beltsville, MD, 20705, USA.
| | - Kshama Aswath
- School of Systems Biology, George Mason University, 10900 University Boulevard, Manassas, VA, 20110, USA.
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, USDA-ARS, BARC-East, Beltsville, MD, 20705, USA.
| | - John D Lippolis
- Ruminant Diseases and Immunology Unit, National Animal Disease Center, USDA/ARS, Ames, IA, 50010, USA.
| | - Timothy A Reinhardt
- Ruminant Diseases and Immunology Unit, National Animal Disease Center, USDA/ARS, Ames, IA, 50010, USA.
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, USDA-ARS, BARC-East, Beltsville, MD, 20705, USA. .,Acceligen Inc., 1246 University Avenue W, St. Paul, MN, 55104, USA.
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Ibeagha-Awemu EM, Zhao X. Epigenetic marks: regulators of livestock phenotypes and conceivable sources of missing variation in livestock improvement programs. Front Genet 2015; 6:302. [PMID: 26442116 PMCID: PMC4585011 DOI: 10.3389/fgene.2015.00302] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 09/11/2015] [Indexed: 12/30/2022] Open
Abstract
Improvement in animal productivity has been achieved over the years through careful breeding and selection programs. Today, variations in the genome are gaining increasing importance in livestock improvement strategies. Genomic information alone, however, explains only a part of the phenotypic variance in traits. It is likely that a portion of the unaccounted variance is embedded in the epigenome. The epigenome encompasses epigenetic marks such as DNA methylation, histone tail modifications, chromatin remodeling, and other molecules that can transmit epigenetic information such as non-coding RNA species. Epigenetic factors respond to external or internal environmental cues such as nutrition, pathogens, and climate, and have the ability to change gene expression leading to emergence of specific phenotypes. Accumulating evidence shows that epigenetic marks influence gene expression and phenotypic outcome in livestock species. This review examines available evidence of the influence of epigenetic marks on livestock (cattle, sheep, goat, and pig) traits and discusses the potential for consideration of epigenetic markers in livestock improvement programs. However, epigenetic research activities on farm animal species are currently limited partly due to lack of recognition, funding and a global network of researchers. Therefore, considerable less attention has been given to epigenetic research in livestock species in comparison to extensive work in humans and model organisms. Elucidating therefore the epigenetic determinants of animal diseases and complex traits may represent one of the principal challenges to use epigenetic markers for further improvement of animal productivity.
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Affiliation(s)
- Eveline M. Ibeagha-Awemu
- Dairy and Swine Research and Development Centre, Agriculture and Agri-Food CanadaSherbrooke, QC, Canada
| | - Xin Zhao
- Department of Animal Science, McGill University, Ste-Anne-De-BellevueQC, Canada
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Wang XL, Zhang T, Wang J, Zhang DB, Zhao F, Lin XW, Wang Z, Shi P, Pang XN. MiR-378b Promotes Differentiation of Keratinocytes through NKX3.1. PLoS One 2015; 10:e0136049. [PMID: 26313654 PMCID: PMC4551849 DOI: 10.1371/journal.pone.0136049] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/29/2015] [Indexed: 02/07/2023] Open
Abstract
MicroRNA (miRNA) is a kind of short non-coding RNA, involved in various cellular processes. During keratinocyte differentiation, miRNAs act as important regulators. In this study, we demonstrated by microarray assay that the expression of miR-378b significantly increased during keratinocytes differentiation. Our findings showed that miR-378b could inhibit proliferation, migration and differentiation in keratinocytes. Luciferase reporter assays showed that miR-378b directly target NKX3.1. Silencing of NKX3.1 could coincide with the effects of miR-24 overexpression. In conclusion, our results demonstrate miR-378b promote keratinocytes differentiation by targeting NKX3.1. Manipulation of miR-378b may afford a new strategy to clinic treatment of skin injury and repair.
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Affiliation(s)
- Xi-liang Wang
- Key Laboratory of Cell Biology, Ministry of Public Health of China, Department of Stem Cells and Regenerative Medicine, China Medical University, Shenyang, 110122, China
| | - Tao Zhang
- Key Laboratory of Cell Biology, Ministry of Public Health of China, Department of Stem Cells and Regenerative Medicine, China Medical University, Shenyang, 110122, China
| | - Jing Wang
- Department of Anus and Intestine Surgery, the First Affiliated Hospital, China Medical University, Shenyang, 110001, China
| | - Dian-bao Zhang
- Key Laboratory of Cell Biology, Ministry of Public Health of China, Department of Stem Cells and Regenerative Medicine, China Medical University, Shenyang, 110122, China
| | - Feng Zhao
- Key Laboratory of Cell Biology, Ministry of Public Health of China, Department of Stem Cells and Regenerative Medicine, China Medical University, Shenyang, 110122, China
| | - Xue-wen Lin
- Key Laboratory of Cell Biology, Ministry of Public Health of China, Department of Stem Cells and Regenerative Medicine, China Medical University, Shenyang, 110122, China
| | - Zhe Wang
- Department of Blood Transfusion, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Ping Shi
- Department of General Practice, the First Affiliated Hospital, China Medical University, Shenyang, 110001, China
| | - Xi-ning Pang
- Key Laboratory of Cell Biology, Ministry of Public Health of China, Department of Stem Cells and Regenerative Medicine, China Medical University, Shenyang, 110122, China
- * E-mail:
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Hausman GJ, Basu U, Wei S, Hausman DB, Dodson MV. Preadipocyte and adipose tissue differentiation in meat animals: influence of species and anatomical location. Annu Rev Anim Biosci 2015; 2:323-51. [PMID: 25384146 DOI: 10.1146/annurev-animal-022513-114211] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Early in porcine adipose tissue development, the stromal-vascular (SV) elements control and dictate the extent of adipogenesis in a depot-dependent manner. The vasculature and collagen matrix differentiate before overt adipocyte differentiation. In the fetal pig, subcutaneous (SQ) layer development is predictive of adipocyte development, as the outer, middle, and inner layers of dorsal SQ adipose tissue develop and maintain layered morphology throughout postnatal growth of SQ adipose tissue. Bovine and ovine fetuses contain brown adipose tissue but SQ white adipose tissue is poorly developed structurally. Fetal adipose tissue differentiation is associated with the precocious expression of several genes encoding secreted factors and key transcription factors like peroxisome proliferator activated receptor (PPAR)γ and CCAAT/-enhancer-binding protein. Identification of adipocyte-associated genes differentially expressed by age, depot, and species in vivo and in vitro has been achieved using single-gene analysis, microarrays, suppressive subtraction hybridization, and next-generation sequencing applications. Gene polymorphisms in PPARγ, cathepsins, and uncoupling protein 3 have been associated with back fat accumulation. Genome scans have mapped several quantitative trait loci (QTL) predictive of adipose tissue-deposition phenotypes in cattle and pigs.
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40
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Bae IS, Chung KY, Yi J, Kim TI, Choi HS, Cho YM, Choi I, Kim SH. Identification of reference genes for relative quantification of circulating microRNAs in bovine serum. PLoS One 2015; 10:e0122554. [PMID: 25826387 PMCID: PMC4380332 DOI: 10.1371/journal.pone.0122554] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 02/22/2015] [Indexed: 02/06/2023] Open
Abstract
Circulating microRNAs in body fluids have been implicated as promising biomarkers for physiopathology disorders. Currently, the expression levels of circulating microRNAs are estimated by reverse transcription quantitative real-time polymerase chain reaction. Use of appropriate reference microRNAs for normalization is critical for accurate microRNA expression analysis. However, no study has systematically investigated reference genes for evaluating circulating microRNA expression in cattle. In this study, we describe the identification and characterization of appropriate reference microRNAs for use in the normalization of circulating microRNA levels in bovine serum. We evaluated the expression stability of ten candidate reference genes in bovine serum by using reverse transcription quantitative real-time polymerase chain reaction. Data were analyzed using geNorm, NormFinder, and BestKeeper statistical algorithms. The results consistently showed that a combination of miR-93 and miR-127 provided the most stably expressed reference. The suitability of these microRNAs was validated, and even when compared among different genders or breeds, the combination of miR-93 and miR-127 was ranked as the most stable microRNA reference. Therefore, we conclude that this combination is the optimal endogenous reference for reverse transcription quantitative real-time polymerase chain reaction-based detection of microRNAs in bovine serum. The data presented in this study are crucial to successful biomarker discovery and validation for the diagnosis of physiopathological conditions in cattle.
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Affiliation(s)
- In-Seon Bae
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Ki Yong Chung
- National Institute of Animal Science, RDA, Pyeongchang, Gangwon, Republic of Korea
| | - Jongmin Yi
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Tae Il Kim
- National Institute of Animal Science, RDA, Pyeongchang, Gangwon, Republic of Korea
| | - Hwa-Sik Choi
- Department of Biomedical Laboratory Science, Shinhan University, Uijeongbu, Gyeonggi, Republic of Korea
| | - Young-Moo Cho
- National Institute of Animal Science, RDA, Pyeongchang, Gangwon, Republic of Korea
| | - Inho Choi
- Bovine Genome Resources Bank, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
| | - Sang Hoon Kim
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
- * E-mail:
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Bu D, Nan X, Wang F, Loor J, Wang J. Identification and characterization of microRNA sequences from bovine mammary epithelial cells. J Dairy Sci 2015; 98:1696-705. [DOI: 10.3168/jds.2014-8217] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 11/22/2014] [Indexed: 11/19/2022]
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Krist B, Florczyk U, Pietraszek-Gremplewicz K, Józkowicz A, Dulak J. The Role of miR-378a in Metabolism, Angiogenesis, and Muscle Biology. Int J Endocrinol 2015; 2015:281756. [PMID: 26839547 PMCID: PMC4709675 DOI: 10.1155/2015/281756] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/30/2015] [Indexed: 02/06/2023] Open
Abstract
MicroRNA-378a (miR-378a, previously known as miR-378) is one of the small noncoding RNA molecules able to regulate gene expression at posttranscriptional level. Its two mature strands, miR-378a-3p and miR-378a-5p, originate from the first intron of the peroxisome proliferator-activated receptor gamma, coactivator 1 beta (ppargc1b) gene encoding PGC-1β. Embedding in the sequence of this transcriptional regulator of oxidative energy metabolism implies involvement of miR-378a in metabolic pathways, mitochondrial energy homeostasis, and related biological processes such as muscle development, differentiation, and regeneration. On the other hand, modulating the expression of proangiogenic factors such as vascular endothelial growth factor, angiopoietin-1, or interleukin-8, influencing inflammatory reaction, and affecting tumor suppressors, such as SuFu and Fus-1, miR-378a is considered as a part of an angiogenic network in tumors. In the latter, miR-378a can evoke broader actions by enhancing cell survival, reducing apoptosis, and promoting cell migration and invasion. This review describes the current knowledge on miR-378a linking oxidative/lipid metabolism, muscle biology, and blood vessel formation.
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Affiliation(s)
- Bart Krist
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30–387 Krakow, Poland
| | - Urszula Florczyk
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30–387 Krakow, Poland
| | - Katarzyna Pietraszek-Gremplewicz
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30–387 Krakow, Poland
| | - Alicja Józkowicz
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30–387 Krakow, Poland
| | - Jozef Dulak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30–387 Krakow, Poland
- *Jozef Dulak:
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Hausman GJ, Basu U, Du M, Fernyhough-Culver M, Dodson MV. Intermuscular and intramuscular adipose tissues: Bad vs. good adipose tissues. Adipocyte 2014; 3:242-55. [PMID: 26317048 DOI: 10.4161/adip.28546] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 03/11/2014] [Accepted: 03/14/2014] [Indexed: 12/23/2022] Open
Abstract
Human studies of the influence of aging and other factors on intermuscular fat (INTMF) were reviewed. Intermuscular fat increased with weight loss, weight gain, or with no weight change with age in humans. An increase in INTMF represents a similar threat to type 2 diabetes and insulin resistance as does visceral adipose tissue (VAT). Studies of INTMF in animals covered topics such as quantitative deposition and genetic relationships with other fat depots. The relationship between leanness and higher proportions of INTMF fat in pigs was not observed in human studies and was not corroborated by other pig studies. In humans, changes in muscle mass, strength and quality are associated with INTMF accretion with aging. Gene expression profiling and intrinsic methylation differences in pigs demonstrated that INTMF and VAT are primarily associated with inflammatory and immune processes. It seems that in the pig and humans, INTMF and VAT share a similar pattern of distribution and a similar association of components dictating insulin sensitivity. Studies on intramuscular (IM) adipocyte development in meat animals were reviewed. Gene expression analysis and genetic analysis have identified candidate genes involved in IM adipocyte development. Intramuscular (IM) adipocyte development in human muscle is only seen during aging and some pathological circumstance. Several genetic links between human and meat animal adipogenesis have been identified. In pigs, the Lipin1 and Lipin 2 gene have strong genetic effects on IM accumulation. Lipin1 deficiency results in immature adipocyte development in human lipodystrophy. In humans, overexpression of Perilipin 2 (PLIN2) facilitates intramyocellular lipid accretion whereas in pigs PLIN2 gene expression is associated with IM deposition. Lipins and perilipins may influence intramuscular lipid regardless of species.
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Dodson MV, Du M, Wang S, Bergen WG, Fernyhough-Culver M, Basu U, Poulos SP, Hausman GJ. Adipose depots differ in cellularity, adipokines produced, gene expression, and cell systems. Adipocyte 2014; 3:236-41. [PMID: 26317047 PMCID: PMC4550680 DOI: 10.4161/adip.28321] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/20/2014] [Accepted: 02/21/2014] [Indexed: 12/28/2022] Open
Abstract
The race to manage the health concerns related to excess fat deposition has spawned a proliferation of clinical and basic research efforts to understand variables including dietary uptake, metabolism, and lipid deposition by adipocytes. A full appreciation of these variables must also include a depot-specific understanding of content and location in order to elucidate mechanisms governing cellular development and regulation of fat deposition. Because adipose tissue depots contain various cell types, differences in the cellularity among and within adipose depots are presently being documented to ascertain functional differences. This has led to the possibility of there being, within any one adipose depot, cellular distinctions that essentially result in adipose depots within depots. The papers comprising this issue will underscore numerous differences in cellularity (development, histogenesis, growth, metabolic function, regulation) of different adipose depots. Such information is useful in deciphering adipose depot involvement both in normal physiology and in pathology. Obesity, diabetes, metabolic syndrome, carcass composition of meat animals, performance of elite athletes, physiology/pathophysiology of aging, and numerous other diseases might be altered with a greater understanding of adipose depots and the cells that comprise them-including stem cells-during initial development and subsequent periods of normal/abnormal growth into senescence. Once thought to be dormant and innocuous, the adipocyte is emerging as a dynamic and influential cell and research will continue to identify complex physiologic regulation of processes involved in adipose depot physiology.
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Affiliation(s)
- Michael V Dodson
- Department of Animal Sciences; Washington State University; Pullman, WA USA
| | - Min Du
- Department of Animal Sciences; Washington State University; Pullman, WA USA
| | - Songbo Wang
- Department of Animal Sciences; Washington State University; Pullman, WA USA
- College of Animal Science; South China Agricultural University; Guangzhou, PR China
| | - Werner G Bergen
- Program in Cellular and Molecular Biosciences/Department of Animal Sciences; Auburn University; Auburn, AL USA
| | | | | | | | - Gary J Hausman
- Department of Animal and Dairy Science; University of Georgia; Athens, GA USA
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Lin QZ, Yin RX, Guo T, Wu J, Sun JQ, Shen SW, Shi GY, Wu JZ, Liu CW, Pan SL. Association of the ST3GAL4 rs11220462 polymorphism and serum lipid levels in the Mulao and Han populations. Lipids Health Dis 2014; 13:123. [PMID: 25086711 PMCID: PMC4237880 DOI: 10.1186/1476-511x-13-123] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 07/24/2014] [Indexed: 01/10/2023] Open
Abstract
Background A previous genome-wide association study has displayed the association of the ST3 beta-galactoside alpha-2,3-sialytransferase 4 (ST3GAL4) gene variant and lipid traits in the individuals of European ancestry, but the reproducibility of this association has not been detected in the Chinese population. The present study was undertaken to detect the association of ST3GAL4 rs11220462 single nucleotide polymorphism (SNP) and several environmental factors with serum lipid profiles in the Mulao and Han populations. Methods A total of 700 unrelated individuals of Mulao nationality and 694 subjects of Han nationality were randomly selected from our previous stratified randomized samples. Genotypes of the SNP were determined via polymerase chain reaction and restriction fragment length polymorphism in combination with gel electrophoresis, and then verified by direct sequencing. Results Serum apolipoprotein (Apo) B levels were higher and the ApoAI/ApoB ratio was lower in Mulao than in Han (P < 0.05-0.01). There were no significant differences in the genotypic and allelic frequencies of the ST3GAL4 rs11220462 SNP between the two ethnic groups or between males and females. The A allele carriers in both Mulao males and females had higher total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and ApoB levels than the A allele non-carriers (P < 0.05-0.01). The subjects with AA genotype in Han males but not in females had higher TC and triglyceride (TG) levels than the subjects with AG or GG genotype (P < 0.01 for each). Multiple linear regression analyses showed that the levels of TC, LDL-C and ApoB in Mulao females; TC and LDL-C in Mulao males; and TC in Han males were correlated with the genotypes (P < 0.05-0.001). Serum lipid parameters were also associated with several environmental factors in both ethnic groups (P < 0.05 -0.001). Conclusions The association of ST3GAL4 rs11220462 SNP and serum lipid levels was different between the Mulao and Han populations, suggesting that there may be a racial/ethnic-specific association, and/or sex-specific association between the ST3GAL4 rs11220462 SNP and serum lipid parameters in some ethnic groups.
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Affiliation(s)
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, 22 Shuangyong Road, Nanning 530021 Guangxi, People's Republic of China.
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Sun J, Zhang B, Lan X, Zhang C, Lei C, Chen H. Comparative transcriptome analysis reveals significant differences in MicroRNA expression and their target genes between adipose and muscular tissues in cattle. PLoS One 2014; 9:e102142. [PMID: 25006962 PMCID: PMC4090223 DOI: 10.1371/journal.pone.0102142] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 06/13/2014] [Indexed: 12/17/2022] Open
Abstract
The posttranscriptional gene regulation mediated by microRNAs (miRNAs) plays an important role in various species. However, to date limited miRNAs have been reported between fat and muscle tissues in beef cattle. In this paper, 412 known and 22 novel miRNAs in backfat as well as 334 known and 10 novel miRNAs in longissimus thoracis were identified in the Chinese Qinchuan beef cattle. Bta-miR-199a-3p, -154c, -320a and -432 were expressed at higher levels in backfat tissue, while bta-miR-1, -133a, -206, and -378 were also significantly enriched in muscle tissue. Functional analysis revealed that fat-enriched miRNAs targeted PRKAA1/2, PPARA and PPARG genes to modulate lipid and fatty acid metabolism, and muscle-enriched miRNAs targeted CSRP3 gene to present function involved in skeletal and muscular system development. The results obtained may help in the design of new selection strategies to improve beef quality.
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Affiliation(s)
- Jiajie Sun
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Bowen Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Chunlei Zhang
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
- * E-mail:
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Meale SJ, Romao JM, He ML, Chaves AV, McAllister TA, Guan LL. Effect of diet on microRNA expression in ovine subcutaneous and visceral adipose tissues. J Anim Sci 2014; 92:3328-37. [PMID: 24893997 DOI: 10.2527/jas.2014-7710] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Knowledge of the molecular mechanisms that regulate ovine adipogenesis is very limited. MicroRNAs (miRNA) have been reported as one of the regulatory mechanisms of adipogenesis. This study aimed to compare the expression of miRNA related to ovine adipogenesis in different adipose depots and to investigate whether their expression is affected by dietary fatty acid composition. We also investigated the role of miRNA in adipogenic gene regulation. Subcutaneous and visceral adipose tissue samples were collected at slaughter from 12 Canadian Arcott lambs fed a barley-based finishing diet where an algae meal (DHA-Gold; Schizochytrium spp.) replaced flax oil and barley grain at 0 or 3% DM (n = 6). Total RNA from each tissue was subjected to quantitative real time (qRT-) PCR analysis to determine the expression of 15 selected miRNA including 11 identified from bovine adipose tissues and 4 conserved between bovine and ovine species. MicroRNAs were differentially expressed according to diet in each tissue depot (miR-142-5p and miR-376d) in visceral and miR-142-5p, miR-92a, and miR-378 in subcutaneous adipose tissue; P ≤ 0.05) and in each tissue depot depending on diet (miR-101, miR-106, miR-136, miR-16b, miR-196a-1, miR-2368*, miR-2454, miR-296, miR-376d, miR-378, and miR-92a in both control and DHA-G diets and miR-478 in control; P ≤ 0.05). Six miRNA were subjected to functional analysis and 3 genes of interest (ACSL1, PPARα, and C/EBPα) were validated by qRT-PCR. Both diet and tissue depot affected expression levels of all 3 genes (P < 0.05). miR-101, miR-106, and miR-136 were negatively correlated with their respective predicted gene targets C/EBPα, PPARα, and ACSL1 in subcutaneous adipose tissue of lambs fed DHA-G. Yet miR-142-5p and miR-101 showed no correlation with ACSL1 or C/EBPα. The variability in expression patterns of miRNA across adipose depots reflects the tissue specific nature of adipogenic regulation. Although the examined miRNA appear to be conserved across ruminant species, our results indicate the presence of ovine specific regulatory mechanisms that can be influenced by diet.
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Affiliation(s)
- S J Meale
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta T1J 4B1, Canada
| | - J M Romao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - M L He
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta T1J 4B1, Canada
| | - A V Chaves
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - T A McAllister
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta T1J 4B1, Canada
| | - L L Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
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Romao JM, He ML, McAllister TA, Guan LL. Effect of age on bovine subcutaneous fat proteome: molecular mechanisms of physiological variations during beef cattle growth. J Anim Sci 2014; 92:3316-27. [PMID: 24894005 DOI: 10.2527/jas.2013-7423] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Fat deposition influences both meat quality and animal productivity. However, it is not clear how fat development is regulated in growing and fattening beef cattle. This study characterized proteomic changes in subcutaneous adipose tissue from steers fed a high-grain diet in an effort to understand the molecular mechanisms of fat development during feedlot production. Eight British-Continental crossbred steers had two subcutaneous adipose tissue biopsies at 12 and 15 mo of age. Protein expression in fat samples was profiled using liquid chromatography-tandem mass spectrometry (LC-MS/MS). During the finishing period, steers increased subcutaneous adipose tissue mass with concomitant changes in the proteome profile, but the nature of these changes varied among steers. The expression of 123 out of 627 identified proteins differed (P <: 0.05) between 2 ages. Functional analyses on differentially expressed proteins revealed that 20.2% of them were associated with cellular growth and proliferation of adipose tissue. There were 17 out of 108 differentially expressed proteins associated with lipid metabolism, which were acyl-CoA synthetase medium-chain family member 1 (ACSM1), annexin A1 (ANXA1), apolipoprotein C-III (APOC3), apolipoprotein H (beta-2-glycoprotein I; APOH), EH-domain containing 1 (EHD1), coagulation factor II (thrombin; F2), gelsolin (GSN), lamin A/C (LMNA), mitogen-activated protein kinase kinase 1 (MAP2K1), myosin, heavy chain 9, non-muscle (MYH9), orosomucoid 1 (ORM1), protein disulfide isomerase family A, member 3 (PDIA3), retinol binding protein 4, plasma (RBP4), renin binding protein (RENBP), succinate dehydrogenase complex, subunit A, flavoprotein (Fp; SDHA), serpin peptidase inhibitor, clade C (antithrombin), member 1 (SERPINC1), and serpin peptidase inhibitor, clade G (C1 inhibitor), member 1 (SERPING1). Further analysis of the expression levels of proteins associated with lipid metabolism indicated a downregulation in the synthesis of fatty acids at the cellular level at 15 compared to 12 mo of age. These results suggest that even though adipose tissue expanded, fat anabolism was reduced in adipocytes during growth, revealing a coordinated balance between subcutaneous fat mass and the cellular abundance of lipogenic proteins to control the rate of fat deposition in growing beef cattle. The findings observed in this study expand our understanding on how proteome of bovine adipose tissue is regulated during growth, which might help the development in the future of new strategies to manipulate adiposity in beef cattle in a manner that improves meat quality and animal productivity.
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Affiliation(s)
- J M Romao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - M L He
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - T A McAllister
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - L L Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2R3, Canada
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Abstract
Adipocyte differentiation, termed adipogenesis, is a complicated process in which pluripotent mesenchymal stem cells differentiate into mature adipocytes. The process of adipocyte differentiation is tightly regulated by a number of transcription factors, hormones and signaling pathway molecules. Recent studies have demonstrated that microRNAs, which belong to small noncoding RNA species, are also involved in adipocyte differentiation. In vivo and in vitro studies have revealed that various microRNAs affect adipogenesis by targeting several adipogenic transcription factors and key signaling molecules. In this review, we will summarize the roles of microRNAs in adipogenesis and their target genes associated with each stage of adipocyte differentiation.
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Affiliation(s)
- You Hwa Son
- Seoul National University School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Sojeong Ka
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - A Young Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Jae Bum Kim
- Seoul National University School of Biological Sciences, Seoul National University, Seoul, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
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The miRNAome of the postpartum dairy cow liver in negative energy balance. BMC Genomics 2014; 15:279. [PMID: 24725334 PMCID: PMC4023597 DOI: 10.1186/1471-2164-15-279] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 04/08/2014] [Indexed: 01/01/2023] Open
Abstract
Background Negative energy balance (NEB) is an altered metabolic state in high yielding cows that occurs during the first few weeks postpartum when energy demands for lactation and maintenance exceed the energy supply from dietary intake. NEB can, in turn, lead to metabolic disorders and to reduced fertility. Alterations in the expression of more than 700 hepatic genes have previously been reported in a study of NEB in postpartum dairy cows. miRNAs (microRNA) are known to mediate many alterations in gene expression post transcriptionally. To study the hepatic miRNA content of postpartum dairy cows, including their overall abundance and differential expression, in mild NEB (MNEB) and severe NEB (SNEB), short read RNA sequencing was carried out. To identify putative targets of differentially expressed miRNAs among differentially expressed hepatic genes reported previously in dairy cows in SNEB computational target identification was employed. Results Our results indicate that the dairy cow liver expresses 53 miRNAs at a lower threshold of 10 reads per million. Of these, 10 miRNAs accounted for greater than 95% of the miRNAome (miRNA content). Of the highly expressed miRNAs, miR-122 constitutes 75% followed by miR-192 and miR-3596. Five out of thirteen let-7 miRNA family members are also among the highly expressed miRNAs. miR-143, down-regulated in SNEB, was found to have 4 putative up-regulated gene targets associated with SNEB including LRP2 (low density lipoprotein receptor-related protein 2), involved in lipid metabolism and up-regulated in SNEB. Conclusions This is the first liver miRNA-seq profiling study of moderate yielding dairy cows in the early postpartum period. Tissue specific miR-122 and liver enriched miR-192 are two of the most abundant miRNAs in the postpartum dairy cow liver. miR-143 is significantly down-regulated in SNEB and putative targets of miRNA-143 which are up-regulated in SNEB, include a gene involved in lipid metabolism.
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