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Qin X, He X, Chen L, Han Y, Yun Y, Wu J, Sha L, Borjigin G. Transcriptome analysis of adipose tissue in grazing cattle: Identifying key regulators of fat metabolism. Open Life Sci 2024; 19:20220843. [PMID: 38681730 PMCID: PMC11049749 DOI: 10.1515/biol-2022-0843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/05/2024] [Accepted: 02/20/2024] [Indexed: 05/01/2024] Open
Abstract
The taste and tenderness of meat are the main determinants of carcass quality in many countries. This study aimed to discuss the mechanisms of intramuscular fat deposition in grazing and house-breeding cattle. We performed transcriptome analysis to characterize messenger RNA and microRNA (miRNA) expression profiles. A total of 456 and 66 differentially expressed genes (DEGs) and differentially expressed (DE) miRNAs were identified in the adipose tissue of grazing and house-breeding cattle. Kyoto Encyclopedia of Genes and Genomes pathway analysis identified the association of DEGs with fatty acid metabolism, fatty acid degradation, peroxisome proliferator-activated receptors signaling pathway, adenosine monophosphate-activated protein kinase signaling pathway, adipocytokine signaling pathway, and the association of DE miRNAs with mitogen-activated protein kinase signaling pathway. Apolipoprotein L domain containing 1, pyruvate dehydrogenase kinase 4, and sphingosine-1-phosphate lyase 1 genes may be the key regulators of fat metabolism in grazing cattle. Finally, we found that miR-211 and miR-331-5p were negatively correlated with the elongation of very long-chain fatty acids protein 6 (ELOVL6), and miR-331-5p might be the new regulator involved in fat metabolism. The results indicated that ELOVL6 participated in various functions and pathways related to fat metabolism. Meanwhile, miR-331-5p, as a new regulator, might play an essential role in this process. Our findings laid a more in-depth and systematic research foundation for the formation mechanism and characteristics of adipose tissue in grazing cattle.
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Affiliation(s)
- Xia Qin
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
- Pharmacy and Materials School, Huainan Union University, Huainan232038, China
| | - Xige He
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Lu Chen
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Yunfei Han
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Yueying Yun
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Jindi Wu
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Lina Sha
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Gerelt Borjigin
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
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Matosinho CGR, Rosse IC, Fonseca PAS, de Oliveira FS, Dos Santos FG, Araújo FMG, de Matos Salim AC, Lopes BC, Arbex WA, Machado MA, Peixoto MGCD, da Silva Verneque R, Martins MF, da Silva MVGB, Oliveira G, Pires DEV, Carvalho MRS. Identification and in silico characterization of structural and functional impacts of genetic variants in milk protein genes in the Zebu breeds Guzerat and Gyr. Trop Anim Health Prod 2021; 53:524. [PMID: 34705124 DOI: 10.1007/s11250-021-02970-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/14/2021] [Indexed: 10/20/2022]
Abstract
Whole genome sequencing of bovine breeds has allowed identification of genetic variants in milk protein genes. However, functional repercussion of such variants at a molecular level has seldom been investigated. Here, the results of a multistep Bioinformatic analysis for functional characterization of recently identified genetic variants in Brazilian Gyr and Guzerat breeds is described, including predicted effects on the following: (i) evolutionary conserved nucleotide positions/regions; (ii) protein function, stability, and interactions; (iii) splicing, branching, and miRNA binding sites; (iv) promoters and transcription factor binding sites; and (v) collocation with QTL. Seventy-one genetic variants were identified in the caseins (CSN1S1, CSN2, CSN1S2, and CSN3), LALBA, LGB, and LTF genes. Eleven potentially regulatory variants and two missense mutations were identified. LALBA Ile60Val was predicted to affect protein stability and flexibility, by reducing the number the disulfide bonds established. LTF Thr546Asn is predicted to generate steric clashes, which could mildly affect iron coordination. In addition, LALBA Ile60Val and LTF Thr546Asn affect exonic splicing enhancers and silencers. Consequently, both mutations have the potential of affecting immune response at individual level, not only in the mammary gland. Although laborious, this multistep procedure for classifying variants allowed the identification of potentially functional variants for milk protein genes.
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Affiliation(s)
- Carolina Guimarães Ramos Matosinho
- Programa de Pós-Graduação Em GenéticaDepartamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31901-207, Brazil
| | - Izinara Cruz Rosse
- Programa de Pós-Graduação Em GenéticaDepartamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31901-207, Brazil
- Departamento de Farmácia, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Pablo Augusto Souza Fonseca
- Programa de Pós-Graduação Em GenéticaDepartamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31901-207, Brazil.
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G2W1, Canada.
| | - Francislon Silva de Oliveira
- Programa de Pós-Graduação Em GenéticaDepartamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31901-207, Brazil
- Grupo de Genômica E Biologia Computacional, Centro de Pesquisas René Rachou - Fiocruz Minas, Belo Horizonte, MG, 30190-00, Brazil
| | - Fausto Gonçalves Dos Santos
- Grupo de Genômica E Biologia Computacional, Centro de Pesquisas René Rachou - Fiocruz Minas, Belo Horizonte, MG, 30190-00, Brazil
| | - Flávio Marcos Gomes Araújo
- Grupo de Genômica E Biologia Computacional, Centro de Pesquisas René Rachou - Fiocruz Minas, Belo Horizonte, MG, 30190-00, Brazil
| | - Anna Christina de Matos Salim
- Grupo de Genômica E Biologia Computacional, Centro de Pesquisas René Rachou - Fiocruz Minas, Belo Horizonte, MG, 30190-00, Brazil
| | | | | | | | | | - Rui da Silva Verneque
- EPAMIG, Belo Horizonte, MG, 31170-495, Brazil
- Embrapa Gado de Leite, Juiz de Fora, MG, 36038-330, Brazil
| | | | | | - Guilherme Oliveira
- Grupo de Genômica E Biologia Computacional, Centro de Pesquisas René Rachou - Fiocruz Minas, Belo Horizonte, MG, 30190-00, Brazil
- Instituto Tecnológico Vale, Belém, PA, 66055-09, Brazil
| | - Douglas Eduardo Valente Pires
- School of Computing and Information Systems, University of Melbourne, Parkville, VIC, 3052, Australia
- Bio21 Institute, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Maria Raquel Santos Carvalho
- Programa de Pós-Graduação Em GenéticaDepartamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31901-207, Brazil
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In silico identification of variations in microRNAs with a potential impact on dairy traits using whole ruminant genome SNP datasets. Sci Rep 2021; 11:19580. [PMID: 34599210 PMCID: PMC8486775 DOI: 10.1038/s41598-021-98639-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 09/03/2021] [Indexed: 11/09/2022] Open
Abstract
MicroRNAs are small noncoding RNAs that have important roles in the lactation process and milk biosynthesis. Some polymorphisms have been studied in various livestock species from the perspective of pathology or production traits. To target variants that could be the causal variants of dairy traits, genetic variants of microRNAs expressed in the mammary gland or present in milk and localized in dairy quantitative trait loci (QTLs) were investigated in bovine, caprine, and ovine species. In this study, a total of 59,124 (out of 28 millions), 13,427 (out of 87 millions), and 4761 (out of 38 millions) genetic variants in microRNAs expressed in the mammary gland or present in milk were identified in bovine, caprine, and ovine species, respectively. A total of 4679 of these detected bovine genetic variants are located in dairy QTLs. In caprine species, 127 genetic variants are localized in dairy QTLs. In ovine species, no genetic variant was identified in dairy QTLs. This study leads to the detection of microRNA genetic variants of interest in the context of dairy production, taking advantage of whole genome data to identify microRNA genetic variants expressed in the mammary gland and localized in dairy QTLs.
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Differential expression of miRNAs and related mRNAs during heat stress in buffalo heifers. J Therm Biol 2021; 97:102904. [PMID: 33863422 DOI: 10.1016/j.jtherbio.2021.102904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 12/15/2022]
Abstract
The present experiment was aimed to study differential expression of miRNAs and related mRNAs during heat stress (HS) in buffalo heifers. Twelve Murrah buffalo heifers aged between 1.5 and 2.0 years, weighting between 250 and 300 Kg were randomly assigned into two equal groups. The animals were kept in the psychrometric chamber under Thermo-neutral (TN; THI = 72) and HS (THI = 87-90) conditions for 6 h every day between 1000 and 1600 h for 21 days. The blood sampling was done at 1500 h on 15th day of the experiment and physiological parameters viz. pulse rate (PR), respiratory rate (RR) and rectal temperature (RT) were recorded at 1500 h on day -5, -3, -1, 0, +1, +3, +5 with respect to blood sampling. PBMCs were used for extraction of miRNAs and total RNA; and first strand cDNA was synthesized. qPCR was performed for relative gene expression studies. Physiological, hematological (erythrocytic indices), biochemical (triglycerides, urea, ALT, AST, LDH), redox (SOD, ROS) and endocrine parameters (T4) altered significantly (P < 0.05) during HS as compared to TN. Out of eight targeted miRNAs only four were expressed in buffalo heifers. The relative expression of bta-mir-142, bta-mir-1248 and bta-mir-2332 was significantly (P < 0.05) up-regulated whereas expression of bta-mir-2478 was significantly (P < 0.05) down-regulated during HS as compared to TN. The relative expression of the predicted target genes i.e. HSF1, HSP60, HSP70, HSPA8 and HSP90 were significantly (P < 0.05) up-regulated whereas HSF4 expression was significantly (P < 0.05) down-regulated during HS as compared to TN. It can be concluded that a THI of 87-90 could lead to a moderate HS in buffalo heifers. Differential expression studies of miRNAs and related mRNAs in present study deciphers the role of miRNAs in the heat tolerance in buffalo heifers.
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Wang L, Zhang S, Cheng G, Mei C, Li S, Zhang W, Junjvlieke Z, Zan L. MiR-145 reduces the activity of PI3K/Akt and MAPK signaling pathways and inhibits adipogenesis in bovine preadipocytes. Genomics 2020; 112:2688-2694. [DOI: 10.1016/j.ygeno.2020.02.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/31/2020] [Accepted: 02/29/2020] [Indexed: 12/29/2022]
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Hanif Q, Farooq M, Amin I, Mansoor S, Zhang Y, Khan QM. In silico identification of conserved miRNAs and their selective target gene prediction in indicine (Bos indicus) cattle. PLoS One 2018; 13:e0206154. [PMID: 30365525 PMCID: PMC6203363 DOI: 10.1371/journal.pone.0206154] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 10/08/2018] [Indexed: 12/28/2022] Open
Abstract
The modern cattle was domesticated from aurochs, sharing its physiological traits into two subspecies Bos taurus and Bos indicus. MicroRNAs (miRNAs) are a class of non-coding short RNAs of ~22nt which have a key role in the regulation of many cellular and physiological processes in the animal. The current study was aimed to predict and annotate the potential mutations in indicine miRNAs throughout the genome using de novo and homology-based in silico approaches. Genome-wide mapping was performed in available indicine assembly by the homology-based approach and 768 miRNAs were recovered out of 808 reported taurine miRNAs belonging to 521 unique mature miRNA families. While 42 precursors were dropped due to lack of secondary miRNA structure, increasing stringency or decreasing similarity between the two genomes' miRNA. Increasing tendency of miRNAs incidence was observed on chr5, chr7, chr8, chr12 and chr21 with 19 polycistronic miRNA within 1-kilobase distance throughout the indicine genome. Notably, 12 miRNAs showed copy number variation. Eighteen miRNAs showed a mutation in their mature sequences in which eight were found in their seed region. Whilst in de novo based approach, 12 novel potential miRNAs on Y chromosome in indicine cattle along with a new miRNA (bind-miR-1264) on chrX were found. The final data set is annotated and explains the impending target genes that are responsible for enhanced immunity, heat tolerance and disease tolerance regulation in indicine. The study conforms to better understanding and perceptive approach towards indicine genome.
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Affiliation(s)
- Quratulain Hanif
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Bioinformatics and Computational Biology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, PK
| | - Muhammad Farooq
- Bioinformatics and Computational Biology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
| | - Imran Amin
- Bioinformatics and Computational Biology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
| | - Shahid Mansoor
- Bioinformatics and Computational Biology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
| | - Yi Zhang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qaiser Mahmood Khan
- Environmental Toxicology Laboratory, National Institute for Biotechnology and Genetic Engineering, (NIBGE), Faisalabad, Pakistan
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Baik M, Kang HJ, Park SJ, Na SW, Piao M, Kim SY, Fassah DM, Moon YS. TRIENNIAL GROWTH AND DEVELOPMENT SYMPOSIUM: Molecular mechanisms related to bovine intramuscular fat deposition in the longissimus muscle. J Anim Sci 2017; 95:2284-2303. [PMID: 28727015 DOI: 10.2527/jas.2016.1160] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The intramuscular fat (IMF) content of the LM, also known as marbling, is particularly important in determining the price of beef in Korea, Japan, and the United States. Deposition of IMF is influenced by both genetic (e.g., breed, gender, and genotype) and nongenetic factors (e.g., castration, nutrition, stressors, animal weight, and age). Castration of bulls markedly increases deposition of IMF, resulting in improved beef quality. Here, we present a comparative gene expression approach between bulls and steers. Transcriptomic and proteomic studies have demonstrated that the combined effects of increases in lipogenesis, fatty acid uptake, and fatty acid esterification and decreased lipolysis are associated with increased IMF deposition in the LM. Several peripheral tissues (LM, adipose tissues, and the liver) are involved in lipid metabolism. Therefore, understanding the significance of the tissue network in lipid metabolism is important. Here, we demonstrate that lipid metabolism in LM tissues is crucial for IMF deposition, whereas lipid metabolism in the liver plays only a minor role. Metabolism of body fat and IMF deposition in bovine species has similarities with these processes in metabolic diseases, such as obesity in humans and rodents. Extensive studies on metabolic diseases using epigenome modification (DNA methylation, histone modification, and microRNA), microbial metagenomics, and metabolomics have been performed in humans and rodents, and new findings have been reported using these technologies. The importance of applying "omics" fields (epigenomics, metagenomics, and metabolomics) to the study of IMF deposition in cattle is described. New information on the molecular mechanisms of IMF deposition may be used to design nutritional or genetic methods to manipulate IMF deposition and to modify fatty acid composition in beef cattle. Applying nutrigenomics could maximize the expression of genetic potential of economically important traits (e.g., marbling) in animals.
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Gong W, Huang Y, Xie J, Wang G, Yu D, Sun X. Genome-wide identification of novel microRNAs from genome sequences using computational approach in the mudskipper (Boleophthalmus pectinirostris). RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017040161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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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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Shi J, Sun G. Effect of pre-miRNA-1658 gene polymorphism on chicken growth and carcass traits. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:455-461. [PMID: 27503275 PMCID: PMC5394830 DOI: 10.5713/ajas.16.0305] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/30/2016] [Accepted: 08/04/2016] [Indexed: 12/17/2022]
Abstract
Objective Polymorphisms occurring in the precursor region of microRNAs (miRNAs) affect the target gene and alter the biogenesis of miRNAs, resulting in phenotypic variation. The purpose of the study was to investigate the genetic effects of rs16681031 (C>G) mutation in the precursor region of gga-miR-1658 on the economic traits of the Gushi-Anka chicken F2 resource population. Methods To explore the effect of miR-1658 polymorphisms on chicken economic traits, the SNP was genotyped by MassArray matrix-assisted laser desorption/ionization-time of flight mass spectrometry. The association between the SNP and chicken body size, growth and carcass traits was determined by linear mixed models. Results The SNP was not only significantly associated with body weight at the age of 6, 8, 10, 12 weeks, respectively, but also with the breadth of the chicken chest, body slanting length and pelvic breadth at 4 weeks, chest depth at 8 weeks of age, and body slanting length at 12 weeks (p<0.05), respectively. Conclusion Our data serve as a useful resource for further analysis of miRNA function, and represent a molecular genetic basis for poultry breeding.
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Affiliation(s)
- Jianzhou Shi
- Institute of Agricultural and Engineering, Nanyang Normal University, Nanyang, Henan 473061, China
| | - Guirong Sun
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, Zhengzhou 450002, China
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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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Wang HY, Lin ZL, Yu XF, Bao Y, Cui XS, Kim NH. Computational Prediction of Alzheimer's and Parkinson's Disease MicroRNAs in Domestic Animals. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 29:782-92. [PMID: 26954182 PMCID: PMC4852244 DOI: 10.5713/ajas.15.0413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/23/2015] [Accepted: 08/14/2015] [Indexed: 12/27/2022]
Abstract
As the most common neurodegenerative diseases, Alzheimer’s disease (AD) and Parkinson’s disease (PD) are two of the main health concerns for the elderly population. Recently, microRNAs (miRNAs) have been used as biomarkers of infectious, genetic, and metabolic diseases in humans but they have not been well studied in domestic animals. Here we describe a computational biology study in which human AD- and PD-associated miRNAs (ADM and PDM) were utilized to predict orthologous miRNAs in the following domestic animal species: dog, cow, pig, horse, and chicken. In this study, a total of 121 and 70 published human ADM and PDM were identified, respectively. Thirty-seven miRNAs were co-regulated in AD and PD. We identified a total of 105 unrepeated human ADM and PDM that had at least one 100% identical animal homolog, among which 81 and 54 showed 100% sequence identity with 241 and 161 domestic animal miRNAs, respectively. Over 20% of the total mature horse miRNAs (92) showed perfect matches to AD/PD-associated miRNAs. Pigs, dogs, and cows have similar numbers of AD/PD-associated miRNAs (63, 62, and 59). Chickens had the least number of perfect matches (34). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses suggested that humans and dogs are relatively similar in the functional pathways of the five selected highly conserved miRNAs. Taken together, our study provides the first evidence for better understanding the miRNA-AD/PD associations in domestic animals, and provides guidance to generate domestic animal models of AD/PD to replace the current rodent models.
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Affiliation(s)
- Hai Yang Wang
- Department of Animal Sciences, Chungbuk National University, Cheongju 362-763, Korea
| | - Zi Li Lin
- Department of Animal Sciences, Chungbuk National University, Cheongju 362-763, Korea
| | - Xian Feng Yu
- College of Animal Sciences, Jilin University, Changchun, Jilin 130062, China
| | - Yuan Bao
- College of Animal Sciences, Jilin University, Changchun, Jilin 130062, China
| | - Xiang-Shun Cui
- Department of Animal Sciences, Chungbuk National University, Cheongju 362-763, Korea
| | - Nam-Hyung Kim
- Department of Animal Sciences, Chungbuk National University, Cheongju 362-763, Korea.,College of Animal Sciences, Jilin University, Changchun, Jilin 130062, China
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Pan L, Wang X, Jin J, Yu X, Hu J. Bioinformatic identification and expression analysis of Nelumbo nucifera microRNA and their targets. APPLICATIONS IN PLANT SCIENCES 2015; 3:apps.1500046. [PMID: 26421251 PMCID: PMC4578376 DOI: 10.3732/apps.1500046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 08/12/2015] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Sacred lotus (Nelumbo nucifera) is a perennial aquatic herbaceous plant of ecological, ornamental, and economic importance. MicroRNAs (miRNAs) play an important role in plant development. However, reports of miRNAs and their role in sacred lotus have been limited. METHODS Using the homology search of known miRNAs with genome and transcriptome contig sequences, we employed a pipeline to identify miRNAs in N. nucifera. We also predicted the targets of these miRNAs. RESULTS We found 106 conserved miRNAs in N. nucifera, and 456 of their miRNA targets were annotated. Quantitative real-time PCR (qRT-PCR) analysis revealed the different expression levels of the 10 selected conserved miRNAs in tissues of young leaves, stems, and flowers of N. nucifera. Negative correlation of expression level between five miRNAs and their target genes was also revealed. DISCUSSION Combining bioinformatics and experiment analysis, we identified the miRNAs in N. nucifera. The results can be used as a workbench for further investigation of the roles of miRNAs in N. nucifera.
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Affiliation(s)
- Lei Pan
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan 430056, People’s Republic of China
| | - Xiaolei Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Jing Jin
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Xiaolu Yu
- Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan 430056, People’s Republic of China
| | - Jihong Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
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Chiang K, Shu J, Zempleni J, Cui J. Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs. PLoS One 2015; 10:e0128089. [PMID: 26030752 PMCID: PMC4451068 DOI: 10.1371/journal.pone.0128089] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 04/23/2015] [Indexed: 11/21/2022] Open
Abstract
With the advent of high throughput technology, a huge amount of microRNA information has been added to the growing body of knowledge for non-coding RNAs. Here we present the Dietary MicroRNA Databases (DMD), the first repository for archiving and analyzing the published and novel microRNAs discovered in dietary resources. Currently there are fifteen types of dietary species, such as apple, grape, cow milk, and cow fat, included in the database originating from 9 plant and 5 animal species. Annotation for each entry, a mature microRNA indexed as DM0000*, covers information of the mature sequences, genome locations, hairpin structures of parental pre-microRNAs, cross-species sequence comparison, disease relevance, and the experimentally validated gene targets. Furthermore, a few functional analyses including target prediction, pathway enrichment and gene network construction have been integrated into the system, which enable users to generate functional insights through viewing the functional pathways and building protein-protein interaction networks associated with each microRNA. Another unique feature of DMD is that it provides a feature generator where a total of 411 descriptive attributes can be calculated for any given microRNAs based on their sequences and structures. DMD would be particularly useful for research groups studying microRNA regulation from a nutrition point of view. The database can be accessed at http://sbbi.unl.edu/dmd/.
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Affiliation(s)
- Kevin Chiang
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Jiang Shu
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States of America
| | - Juan Cui
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States of America
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