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Xue Q, Huang Y, Cheng C, Wang Y, Liao F, Duan Q, Wang X, Miao C. Progress in epigenetic regulation of milk synthesis, with particular emphasis on mRNA regulation and DNA methylation. Cell Cycle 2023; 22:1675-1693. [PMID: 37409592 PMCID: PMC10446801 DOI: 10.1080/15384101.2023.2225939] [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: 03/29/2023] [Revised: 04/29/2023] [Accepted: 05/26/2023] [Indexed: 07/07/2023] Open
Abstract
Inadequate milk secretion and a lack of nutrients in humans and mammals are serious problems. It is of great significance to clarify the mechanisms of milk synthesis and treatment methods. Epigenetic modification, represented by RNA methylation, is an important way of gene expression regulation that profoundly affects human gene expression and participates in various physiological and pathological mechanisms. Epigenetic disorders also have an important impact on the production and secretion of milk. This review systematically summarized the research results of epigenetics in the process of lactation in PubMed, Web of Science, NSTL, and other databases and reviewed the effects of epigenetics on human and mammalian lactation, including miRNAs, circRNAs, lncRNAs, DNA methylations, and RNA methylations. The abnormal expression of miRNAs was closely related to the synthesis and secretion of milk fat, milk protein, and other nutrients in the milk of cattle, sheep, and other mammals. MiRNAs are also involved in the synthesis of human milk and the secretion of nutrients. CircRNAs and lncRNAs mainly target miRNAs and regulate the synthesis of nutrients in milk by ceRNA mechanisms. The abnormal expression of DNA and RNA methylation also has an important impact on milk synthesis. Epigenetic modification has the potential to regulate the milk synthesis of breast epithelial cells. Analyzing the mechanisms of human and mammalian milk secretion deficiency and nutrient deficiency from the perspective of epigenetics will provide a new perspective for the treatment of postpartum milk deficiency in pregnant women and mammalian milk secretion deficiency.
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Affiliation(s)
- Qiuyun Xue
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Yurong Huang
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Chenglong Cheng
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Yuting Wang
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Faxue Liao
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
| | - Qiangjun Duan
- Department of Experimental (Practical Training) Teaching Center, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Xiao Wang
- Department of Clinical Nursing, School of Nursing, Anhui University of Chinese Medicine, Hefei, China
| | - Chenggui Miao
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
- Institute of Rheumatism, Anhui University of Chinese Medicine, Hefei, China
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2
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Ojo OE, Kreuzer-Redmer S. MicroRNAs in Ruminants and Their Potential Role in Nutrition and Physiology. Vet Sci 2023; 10:vetsci10010057. [PMID: 36669058 PMCID: PMC9867202 DOI: 10.3390/vetsci10010057] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/09/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
The knowledge of how diet choices, dietary supplements, and feed intake influence molecular mechanisms in ruminant nutrition and physiology to maintain ruminant health, is essential to attain. In the present review, we focus on the role of microRNAs in ruminant health and disease; additionally, we discuss the potential of circulating microRNAs as biomarkers of disease in ruminants and the state of technology for their detection, also considering the major difficulties in the transition of biomarker development from bench to clinical practice. MicroRNAs are an inexhaustible class of endogenous non-protein coding small RNAs of 18 to 25 nucleotides that target either the 3' untranslated (UTR) or coding region of genes, ensuring a tight post-transcriptionally controlled regulation of gene expression. The development of new "omics" technologies facilitated a fresh perspective on the nutrition-to-gene relationship, incorporating more extensive data from molecular genetics, animal nutrition, and veterinary sciences. MicroRNAs might serve as important regulators of metabolic processes and may present the inter-phase between nutrition and gene regulation, controlled by the diet. The development of biomarkers holds the potential to revolutionize veterinary practice through faster disease detection, more accurate ruminant health monitoring, enhanced welfare, and increased productivity. Finally, we summarize the latest findings on how microRNAs function as biomarkers, how technological paradigms are reshaping this field of research, and how platforms are being used to identify novel biomarkers. Numerous studies have demonstrated a connection between circulating microRNAs and ruminant diseases such as mastitis, tuberculosis, foot-and-mouth disease, fasciolosis, and metabolic disorders. Therefore, the identification and analysis of a small number of microRNAs can provide crucial information about the stage of a disease, etiology, and prognosis.
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The Role of microRNAs in the Mammary Gland Development, Health, and Function of Cattle, Goats, and Sheep. Noncoding RNA 2021; 7:ncrna7040078. [PMID: 34940759 PMCID: PMC8708473 DOI: 10.3390/ncrna7040078] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 02/07/2023] Open
Abstract
Milk is an integral and therefore complex structural element of mammalian nutrition. Therefore, it is simple to conclude that lactation, the process of producing milk, is as complex as the mammary gland, the organ responsible for this biochemical activity. Nutrition, genetics, epigenetics, disease pathogens, climatic conditions, and other environmental variables all impact breast productivity. In the last decade, the number of studies devoted to epigenetics has increased dramatically. Reports are increasingly describing the direct participation of microRNAs (miRNAs), small noncoding RNAs that regulate gene expression post-transcriptionally, in the regulation of mammary gland development and function. This paper presents a summary of the current state of knowledge about the roles of miRNAs in mammary gland development, health, and functions, particularly during lactation. The significance of miRNAs in signaling pathways, cellular proliferation, and the lipid metabolism in agricultural ruminants, which are crucial in light of their role in the nutrition of humans as consumers of dairy products, is discussed.
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4
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Lu Q, Chen Z, Ji D, Mao Y, Jiang Q, Yang Z, Loor JJ. Progress on the Regulation of Ruminant Milk Fat by Noncoding RNAs and ceRNAs. Front Genet 2021; 12:733925. [PMID: 34790222 PMCID: PMC8591074 DOI: 10.3389/fgene.2021.733925] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/23/2021] [Indexed: 12/11/2022] Open
Abstract
Milk fat is not only a key factor affecting the quality of fresh milk but also a major target trait forbreeding. The regulation of milk fat involves multiple genes, network regulation and signal transduction. To explore recent discoveries of pathway regulation, we reviewed the published literature with a focus on functional noncoding RNAs and epigenetic regulation in ruminants. Results indicate that miRNAs play key roles in the regulation of milk fat synthesis and catabolism in ruminants. Although few data are available, merging evidence indicates that lncRNAs and circRNAs act on milk fat related genes through indirect action with microRNAs or RNAs in the ceRNA network to elicit positive effects on transcription. Although precise regulatory mechanisms remain unclear, most studies have focused on the regulation of the function of target genes through functional noncoding RNAs. Data to help identify factors that can regulate their own expression and function or to determine whether self-regulation involves positive and/or negative feedback are needed. Despite the growing body of research on the role of functional noncoding RNA in the control of ruminant milk fat, most data are still not translatable for field applications. Overall, the understanding of mechanisms whereby miRNA, lncRNA, circRNA, and ceRNA regulate ruminant milk fat remains an exciting area of research.
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Affiliation(s)
- QinYue Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| | - Zhi Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| | - Dejun Ji
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| | - Yongjiang Mao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| | - Qianming Jiang
- Mammalian Nutrition Physiology Genomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL, United States
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, China
| | - Juan J Loor
- Mammalian Nutrition Physiology Genomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL, United States
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Cai W, Li C, Li J, Song J, Zhang S. Integrated Small RNA Sequencing, Transcriptome and GWAS Data Reveal microRNA Regulation in Response to Milk Protein Traits in Chinese Holstein Cattle. Front Genet 2021; 12:726706. [PMID: 34712266 PMCID: PMC8546187 DOI: 10.3389/fgene.2021.726706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/21/2021] [Indexed: 01/04/2023] Open
Abstract
Milk protein is one of the most important economic traits in the dairy industry. Yet, the regulatory network of miRNAs for the synthesis of milk protein in mammary is poorly understood. Samples from 12 Chinese Holstein cows with three high ( ≥ 3.5%) and three low ( ≤ 3.0%) phenotypic values for milk protein percentage in lactation and non-lactation were examined through deep small RNA sequencing. We characterized 388 known and 212 novel miRNAs in the mammary gland. Differentially expressed analysis detected 28 miRNAs in lactation and 52 miRNAs in the non-lactating period with a highly significant correlation with milk protein concentration. Target prediction and correlation analysis identified some key miRNAs and their targets potentially involved in the synthesis of milk protein. We analyzed for enrichments of GWAS signals in miRNAs and their correlated targets. Our results demonstrated that genomic regions harboring DE miRNA genes in lactation were significantly enriched with GWAS signals for milk protein percentage traits and that enrichments within DE miRNA targets were significantly higher than in random gene sets for the majority of milk production traits. This integrated study on the transcriptome and posttranscriptional regulatory profiles between significantly differential phenotypes of milk protein concentration provides new insights into the mechanism of milk protein synthesis, which should reveal the regulatory mechanisms of milk secretion.
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Affiliation(s)
- Wentao Cai
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Department of Animal and Avian Science, University of Maryland, College Park, MD, United States
| | - Cong Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiuzhou Song
- Department of Animal and Avian Science, University of Maryland, College Park, MD, United States
| | - Shengli Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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6
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Liu L, Fang C, Sun Y, Liu W. Evaluation of key miRNAs during early pregnancy in Kazakh horse using RNA sequencing. PeerJ 2021; 9:e10796. [PMID: 33665012 PMCID: PMC7908884 DOI: 10.7717/peerj.10796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/28/2020] [Indexed: 12/25/2022] Open
Abstract
Background miRNA has an important role in cell differentiation, biological development, and physiology. Milk production is an important quantitative trait in livestock and miRNA plays a role in the amount of milk produced. Methods The role of regulatory miRNAs involved in equine milk production is not fully understood. We constructed two miRNA libraries for Kazakh horse milk production from higher-producing (H group) and lower-producing (L group) individuals, and used RNA-Seq technology to identify the differentially expressed miRNAs between the two milk phenotypes of Kazakh horses. Results A total of 341 known and 333 novel miRNAs were detected from the H and L groups, respectively. Eighty-three differentially expressed miRNAs were identified between the H and L group s, of which 32 were known miRNAs (27 were up-regulated, five were down-regulated) and 51 were novel miRNAs (nine were up-regulated, 42 were down-regulated). A total of 2,415 genes were identified. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that these genes were annotated to mammary gland development, mammary gland morphogenesis, tissue development and PI3K-Akt signaling pathways, insulin signaling pathway and TGF-beta signaling pathway, among others. Five miRNAs (miR-199a-3p, miR143, miR145, miR221, miR486-5p) were identified as affecting horse milk production and these five miRNAs were validated using qRT-PCR. Conclusions We described a methodology for the transcriptome-wide profiling of miRNAs in milk, which may help the design of new intervention strategies to improve the milk yield of Kazakh horses.
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Affiliation(s)
- LingLing Liu
- College of Animal Science, Xinjiang Agriculture University, Urumqi, Xinjiang, China
| | - Chao Fang
- Department of Animal Production, Farah Research Centre from the Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - YinZe Sun
- College of Animal Science, Xinjiang Agriculture University, Urumqi, Xinjiang, China
| | - WuJun Liu
- College of Animal Science, Xinjiang Agriculture University, Urumqi, Xinjiang, China
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7
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Ivanova E, Le Guillou S, Hue-Beauvais C, Le Provost F. Epigenetics: New Insights into Mammary Gland Biology. Genes (Basel) 2021; 12:genes12020231. [PMID: 33562534 PMCID: PMC7914701 DOI: 10.3390/genes12020231] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/23/2021] [Accepted: 01/28/2021] [Indexed: 12/14/2022] Open
Abstract
The mammary gland undergoes important anatomical and physiological changes from embryogenesis through puberty, pregnancy, lactation and involution. These steps are under the control of a complex network of molecular factors, in which epigenetic mechanisms play a role that is increasingly well described. Recently, studies investigating epigenetic modifications and their impacts on gene expression in the mammary gland have been performed at different physiological stages and in different mammary cell types. This has led to the establishment of a role for epigenetic marks in milk component biosynthesis. This review aims to summarize the available knowledge regarding the involvement of the four main molecular mechanisms in epigenetics: DNA methylation, histone modifications, polycomb protein activity and non-coding RNA functions.
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Ji Z, He R, Chao T, Xuan R, Liu S, Wang G, Wang J. chi-miR-143-3p Promotes Apoptosis of Mammary Gland Epithelial Cells from Dairy Goats by Targeting Ndfip1. DNA Cell Biol 2019; 38:1188-1196. [PMID: 31603699 DOI: 10.1089/dna.2019.4830] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The mammary gland is an important organ for lactation in dairy goats. Mammary gland development and lactation functions are primarily regulated by natural hormones and certain crucial regulatory factors. Nedd4 family-interacting protein 1 (Ndfip1) can specifically bind to neural precursor cell-expressed, developmentally downregulated protein 4 (Nedd4) family members to participate in ubiquitination, which in turn regulates a range of biological processes in the body. However, the effects of Ndfip1 expression regulation at the post-transcriptional level on the development of mammary gland cells have not been previously reported. To study the regulation of Ndfip1 at post-transcriptional level, the overexpression and interference vectors of Ndfip1 were constructed, and co-transfected into the primary mammary gland epithelial cells cultured in vitro with miR-143 mimics and inhibitor. Dual luciferase reporter gene system, real-time quantitative polymerase chain reaction, western blotting, cholecystokinin octapeptide assays, and flow cytometry were used to identify their regulation and function. As a result, Ndfip1 was targeted and regulated by miR-143, which influences the development of mammary gland epithelial cells in dairy goats cultured in vitro. This study will lay an experimental foundation for further understanding the functions of Ndfip1 and miR-143.
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Affiliation(s)
- Zhibin Ji
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Rongyan He
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Tianle Chao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Rong Xuan
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Shuang Liu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Guizhi Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
| | - Jianmin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, P.R. China
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Cai W, Li C, Liu S, Zhou C, Yin H, Song J, Zhang Q, Zhang S. Genome Wide Identification of Novel Long Non-coding RNAs and Their Potential Associations With Milk Proteins in Chinese Holstein Cows. Front Genet 2018; 9:281. [PMID: 30105049 PMCID: PMC6077245 DOI: 10.3389/fgene.2018.00281] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 07/09/2018] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as a novel class of regulatory molecules involved in various biological processes. However, their role in milk performance is unknown. Here, whole transcriptome RNA sequencing was used to generate the lncRNA transcriptome profiles in mammary tissue samples from 6 Chinese Holstein cows with 3 extremely high and 3 low milk protein percentage phenotypes. In this study, 6,450 lncRNA transcripts were identified through 5 stringent steps and filtration by coding potential. In total, 31 lncRNAs and 18 novel genes were identified to be differentially expressed in high milk protein samples (HP) relative to low milk protein samples (LP), respectively. Differentially expressed lncRNAs were selected to predict target genes through bioinformatics analysis, followed by the integration of differentially expressed mRNA data, gene function, gene ontology (GO) and pathway, genome wide association study (GWAS) and quantitative trait locus (QTL) information, as well as network analysis to further characterize potential interactions. Several lncRNAs were found (such as XLOC_059976) that could be used as candidate markers for milk protein content prediction. This is the first study to perform global expression profiling of lncRNAs and mRNAs related to milk protein traits in dairy cows. These results provide important information and insights into the synthesis of milk proteins, and potential targets for the future improvement of milk quality.
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Affiliation(s)
- Wentao Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Cong Li
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shuli Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chenghao Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hongwei Yin
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiuzhou Song
- Department of Animal and Avian Science, University of Maryland, College Park, MD, United States
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shengli Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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10
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Ma L, Qiu H, Chen Z, Li L, Zeng Y, Luo J, Gou D. miR-25 modulates triacylglycerol and lipid accumulation in goat mammary epithelial cells by repressing PGC-1beta. J Anim Sci Biotechnol 2018; 9:48. [PMID: 29946461 PMCID: PMC6004671 DOI: 10.1186/s40104-018-0262-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 04/25/2018] [Indexed: 12/31/2022] Open
Abstract
Background The goat (Caprahircus) is one of the most important livestock animals. Goat milk fat is an important component in the nutritional quality of goat milk. Growing evidence points to the critical roles of microRNAs (miRNAs) in lipid metabolism. Results Using a highly sensitive method of S-poly(T) plus for miRNAs detection, we analyze the expression patterns of 715 miRNAs in goat mammary gland tissues at different stages of lactation. We observed that miR-25 expression had an inverse relationship with milk production. Overexpression of miR-25 significantly repressed triacylglycerol synthesis and lipid droplet accumulation. To explore the regulatory mechanism of miR-25 in milk lipid metabolism, we analyzed its putative target genes with bioinformatics analysis followed by 3′-UTR assays. Peroxisome proliferative activated receptor gamma coactivator 1 beta (PGC-1beta), a key regulator of lipogenics was identified as a direct target of miR-25 with three specific sites within its 3′-UTR. In addition, miR-25 mimics in goat mammary epithelial cells reduced the expressions of genes involved in lipid metabolism. Conclusions Taken together, our results show miR-25 is potentially involved in lipid metabolism and we reveal the function of the miR-25/PGC-1beta regulatory axis during lactation. Electronic supplementary material The online version of this article (10.1186/s40104-018-0262-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Liuan Ma
- 1Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Huiling Qiu
- 1Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 Guangdong China.,Biomedical Engineering, Health and Environmental Engineering, Shenzhen Technology University, Shenzhen, 518000 Guangdong China
| | - Zhi Chen
- 3Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Li Li
- 1Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Yan Zeng
- 1Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Jun Luo
- 3Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Deming Gou
- 4Present Address: Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 Guangdong China
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Osorio JS, Vailati-Riboni M, Palladino A, Luo J, Loor JJ. Application of nutrigenomics in small ruminants: Lactation, growth, and beyond. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2017.06.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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12
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Co-Expression Network and Pathway Analyses Reveal Important Modules of miRNAs Regulating Milk Yield and Component Traits. Int J Mol Sci 2017; 18:ijms18071560. [PMID: 28718798 PMCID: PMC5536048 DOI: 10.3390/ijms18071560] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 07/05/2017] [Accepted: 07/05/2017] [Indexed: 01/01/2023] Open
Abstract
Co-expression network analyses provide insights into the molecular interactions underlying complex traits and diseases. In this study, co-expression network analysis was performed to detect expression patterns (modules or clusters) of microRNAs (miRNAs) during lactation, and to identify miRNA regulatory mechanisms for milk yield and component traits (fat, protein, somatic cell count (SCC), lactose, and milk urea nitrogen (MUN)) via miRNA target gene enrichment analysis. miRNA expression (713 miRNAs), and milk yield and components (Fat%, Protein%, lactose, SCC, MUN) data of nine cows at each of six different time points (day 30 (D30), D70, D130, D170, D230 and D290) of an entire lactation curve were used. Four modules or clusters (GREEN, BLUE, RED and TURQUOISE) of miRNAs were identified as important for milk yield and component traits. The GREEN and BLUE modules were significantly correlated (|r| > 0.5) with milk yield and lactose, respectively. The RED and TURQUOISE modules were significantly correlated (|r| > 0.5) with both SCC and lactose. In the GREEN module, three abundantly expressed miRNAs (miR-148a, miR-186 and miR-200a) were most significantly correlated to milk yield, and are probably the most important miRNAs for this trait. DDR1 and DDHX1 are hub genes for miRNA regulatory networks controlling milk yield, while HHEX is an important transcription regulator for these networks. miR-18a, miR-221/222 cluster, and transcription factors HOXA7, and NOTCH 3 and 4, are important for the regulation of lactose. miR-142, miR-146a, and miR-EIA17-14144 (a novel miRNA), and transcription factors in the SMAD family and MYB, are important for the regulation of SCC. Important signaling pathways enriched for target genes of miRNAs of significant modules, included protein kinase A and PTEN signaling for milk yield, eNOS and Noth signaling for lactose, and TGF β, HIPPO, Wnt/β-catenin and cell cycle signaling for SCC. Relevant enriched gene ontology (GO)-terms related to milk and mammary gland traits included cell differentiation, G-protein coupled receptor activity, and intracellular signaling transduction. Overall, this study uncovered regulatory networks in which miRNAs interacted with each other to regulate lactation traits.
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Hou J, An X, Song Y, Cao B, Yang H, Zhang Z, Shen W, Li Y. Detection and comparison of microRNAs in the caprine mammary gland tissues of colostrum and common milk stages. BMC Genet 2017; 18:38. [PMID: 28464792 PMCID: PMC5414302 DOI: 10.1186/s12863-017-0498-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 03/30/2017] [Indexed: 01/21/2023] Open
Abstract
Background MicroRNAs (miRNAs) have a great influence on various physiological functions. A lot of high-throughput sequencing (HTS) research on miRNAs has been executed in the caprine mammary gland at different lactation periods (common milk lactation and dry period), but little is known about differentially expressed miRNAs in the caprine mammary gland of colostrum and peak lactation periods. Result This study identified 131 differentially expressed miRNAs (P < 0.05 and log2 colostrum normalized expression (NE)/peak lactation NE > 1 or log2 colostrum NE/peak lactation NE < −1), including 57 known miRNAs and 74 potential novel miRNAs in the colostrum and peak lactation libraries. In addition, compared with differentially expressed miRNAs in the peak lactation period, 45 miRNAs in the colostrum lactation period were remarkably upregulated, whereas 86 miRNAs were markedly downregulated (P < 0.05 and log2 colostrum NE/peak lactation NE > 1 or log2 colostrum NE/peak lactation NE < −1). The expressions of 10 randomly selected miRNAs was analyzed through stem-loop real-time quantitative PCR (RT-qPCR). Their expression patterns were the same with Solexa sequencing results. Pathway analysis suggested that oestrogen, endocrine, adipocytokine, oxytocin and MAPK signalling pathways act on the development of mammary gland and milk secretion importantly. In addition, the miRNA-target-network showed that the bta-miR-574 could influence the development of mammary gland and lactation by leptin receptor (LEPR), which was in the adipocytokine signalling pathway. Chr5_3880_mature regulated mammary gland development and lactation through Serine/threonine-protein phosphatase (PPP1CA), which was in the oxytocin signalling pathway. Conclusions Our finding suggested that the profiles of miRNAs were related to the physiological functions of mammary gland in the colostrum and peak lactation periods. The biological features of these miRNAs may help to clarify the molecular mechanisms of lactation and the development of caprine mammary gland. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0498-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jinxing Hou
- Animal Engineering Branch, Yangling Vocational & Technical College, No. 10 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xiaopeng An
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yuxuan Song
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Binyun Cao
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Heping Yang
- Animal Engineering Branch, Yangling Vocational & Technical College, No. 10 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Zhou Zhang
- Animal Engineering Branch, Yangling Vocational & Technical College, No. 10 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Wenzheng Shen
- Animal Engineering Branch, Yangling Vocational & Technical College, No. 10 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yunpu Li
- Animal Engineering Branch, Yangling Vocational & Technical College, No. 10 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China.
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14
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Do DN, Li R, Dudemaine PL, Ibeagha-Awemu EM. MicroRNA roles in signalling during lactation: an insight from differential expression, time course and pathway analyses of deep sequence data. Sci Rep 2017; 7:44605. [PMID: 28317898 PMCID: PMC5357959 DOI: 10.1038/srep44605] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/09/2017] [Indexed: 01/30/2023] Open
Abstract
The study examined microRNA (miRNA) expression and regulatory patterns during an entire bovine lactation cycle. Total RNA from milk fat samples collected at the lactogenesis (LAC, day1 [D1] and D7), galactopoiesis (GAL, D30, D70, D130, D170 and D230) and involution (INV, D290 and when milk production dropped to 5 kg/day) stages from 9 cows was used for miRNA sequencing. A total of 475 known and 238 novel miRNAs were identified. Fifteen abundantly expressed miRNAs across lactation stages play regulatory roles in basic metabolic, cellular and immunological functions. About 344, 366 and 209 miRNAs were significantly differentially expressed (DE) between GAL and LAC, INV and GAL, and INV and LAC stages, respectively. MiR-29b/miR-363 and miR-874/miR-6254 are important mediators for transition signals from LAC to GAL and from GAL to INV, respectively. Moreover, 58 miRNAs were dynamically DE in all lactation stages and 19 miRNAs were significantly time-dependently DE throughout lactation. Relevant signalling pathways for transition between lactation stages are involved in apoptosis (PTEN and SAPK/JNK), intracellular signalling (protein kinase A, TGF-β and ERK5), cell cycle regulation (STAT3), cytokines, hormones and growth factors (prolactin, growth hormone and glucocorticoid receptor). Overall, our data suggest diverse, temporal and physiological signal-dependent regulatory and mediator functions for miRNAs during lactation.
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Affiliation(s)
- Duy N Do
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, 2000 College Street, Sherbrooke, Quebec, J1M 0C8, Canada.,Department of Animal Science, McGill University, 21111, Lakeshore Road, Ste-Anne-de Bellevue, Quebec, J1M 0C8, Canada
| | - Ran Li
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, 2000 College Street, Sherbrooke, Quebec, J1M 0C8, Canada.,College of Animal Science and Technology, Northwest A&F University, Xinong road 22, Shaanxi, 712100, China
| | - Pier-Luc Dudemaine
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, 2000 College Street, Sherbrooke, Quebec, J1M 0C8, Canada
| | - Eveline M Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, 2000 College Street, Sherbrooke, Quebec, J1M 0C8, Canada
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15
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Yang Y, Pan Q, Sun B, Yang R, Fang X, Liu X, Yu X, Zhao Z. miR-29b Targets LPL and TDG Genes and Regulates Apoptosis and Triglyceride Production in MECs. DNA Cell Biol 2016; 35:758-765. [DOI: 10.1089/dna.2016.3443] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Yuwei Yang
- College of Animal Science, Jilin University, Changchun, People's Republic of China
| | - Qiqi Pan
- College of Animal Science, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Boxing Sun
- College of Animal Science, Jilin University, Changchun, People's Republic of China
| | - Runjun Yang
- College of Animal Science, Jilin University, Changchun, People's Republic of China
| | - Xibi Fang
- College of Animal Science, Jilin University, Changchun, People's Republic of China
| | - Xin Liu
- College of Animal Science, Jilin University, Changchun, People's Republic of China
| | - Xianzhong Yu
- Department of Biological Sciences, Clemson University, Clemson, South Carolina
| | - Zhihui Zhao
- College of Animal Science, Jilin University, Changchun, People's Republic of China
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16
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Morammazi S, Masoudi AA, Vaez Torshizi R, Pakdel A. Changes in the Expression of the Prolactin Receptor (PRLR) Gene in Different Physiological Stages in the Mammary Gland of the Iranian Adani Goat. Reprod Domest Anim 2016; 51:585-90. [PMID: 27333814 DOI: 10.1111/rda.12723] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 05/29/2016] [Indexed: 01/28/2023]
Abstract
The actions of prolactin hormone are mediated by prolactin receptor (PRLR), and proliferation and differentiation of secretory mammary epithelium are dependent on the presence of its receptors. To understand the PRLR expression pattern in mammary gland of dairy goat during different lactation stages, in this study, we first estimated the milk yield breeding value by multitrait random regression model and then compared the expression of the gene in different physiological stage of mammary gland between high- and low-breeding value groups. We assayed the transcription level of the gene by quantitative real-time PCR method, and its outcomes were analysed by a statistical model containing breeding value groups, sampling times and their interactions as fixed effects. The results indicated that the expression levels of PRLR gene were significantly upregulated in the drying stage (p < 0.01). The transcription pattern of the gene was significantly different between the two breeding value groups (p < 0.01), so that the amount of PRLR mRNA was significantly higher in the low-breeding value groups of animals in the lactation stage (p < 0.01). Based on the results of this study, it could be suggested that the abundance of PRLR transcripts in mammary gland of goat might be changed by some physiological, environmental and genetic factors. Nucleotide variations in the promoter region might be resulted in various transcription activities of the gene which should be studied in a complementary research.
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Affiliation(s)
- S Morammazi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - A A Masoudi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - R Vaez Torshizi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - A Pakdel
- Department of Animal Science, Faculty of Agriculture, Isfahan University of Technology, Isfahan, Iran
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17
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Wang H, Luo J, Zhang T, Tian H, Ma Y, Xu H, Yao D, Loor JJ. MicroRNA-26a/b and their host genes synergistically regulate triacylglycerol synthesis by targeting the INSIG1 gene. RNA Biol 2016; 13:500-10. [PMID: 27002347 DOI: 10.1080/15476286.2016.1164365] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The microRNA-26 (miR-26) family is known to control adipogenesis in non-ruminants. The genomic loci of miR-26a and miR-26b have been localized in the introns of genes encoding for the proteins of the C-terminal domain RNA polymerase II polypeptide A small phosphatase (CTDSP) family. Insulin-induced gene 1 (INSIG1) encodes a protein with a key role in the regulation of lipogenesis in rodent liver. In the present study, we investigated the synergistic function of the miR-26 family and their host genes in goat mammary epithelial cells (GMEC). Downregulation of miR-26a/b and their host genes in GMEC decreased the expression of genes relate to fatty acid synthesis (PPARG, LXRA, SREBF1, FASN, ACACA, GPAM, LPIN1, DGAT1 and SCD1), triacylglycerol accumulation and unsaturated fatty acid synthesis. Luciferase reporter assays confirmed INSIG1 as a direct target of miR-26a/b. Furthermore, inhibition of the CTDSP family also downregulated the expression of INSIG1. Taken together, our findings highlight a functional association of miR-26a/b, their host genes and INSIG1, and provide new insights into the regulatory network controlling milk fat synthesis in GMEC. The data indicate that targeting this network via nutrition might be important for regulating milk fat synthesis in ruminants.
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Affiliation(s)
- Hui Wang
- a Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University , Yangling , Shaanxi , PR China
| | - Jun Luo
- a Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University , Yangling , Shaanxi , PR China
| | - Tianying Zhang
- a Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University , Yangling , Shaanxi , PR China
| | - Huibin Tian
- a Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University , Yangling , Shaanxi , PR China
| | - Yue Ma
- a Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University , Yangling , Shaanxi , PR China
| | - Huifen Xu
- a Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University , Yangling , Shaanxi , PR China
| | - Dawei Yao
- a Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University , Yangling , Shaanxi , PR China
| | - Juan J Loor
- b Mammalian NutriPhysioGenomics , Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois , Urbana , USA
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