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1
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Sindhu P, Magotra A, Sindhu V, Chaudhary P. Unravelling the impact of epigenetic mechanisms on offspring growth, production, reproduction and disease susceptibility. ZYGOTE 2024; 32:190-206. [PMID: 39291610 DOI: 10.1017/s0967199424000224] [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] [Indexed: 09/19/2024]
Abstract
Epigenetic mechanisms, such as DNA methylation, histone modifications and non-coding RNA molecules, play a critical role in gene expression and regulation in livestock species, influencing development, reproduction and disease resistance. DNA methylation patterns silence gene expression by blocking transcription factor binding, while histone modifications alter chromatin structure and affect DNA accessibility. Livestock-specific histone modifications contribute to gene expression and genome stability. Non-coding RNAs, including miRNAs, piRNAs, siRNAs, snoRNAs, lncRNAs and circRNAs, regulate gene expression post-transcriptionally. Transgenerational epigenetic inheritance occurs in livestock, with environmental factors impacting epigenetic modifications and phenotypic traits across generations. Epigenetic regulation revealed significant effect on gene expression profiling that can be exploited for various targeted traits like muscle hypertrophy, puberty onset, growth, metabolism, disease resistance and milk production in livestock and poultry breeds. Epigenetic regulation of imprinted genes affects cattle growth and metabolism while epigenetic modifications play a role in disease resistance and mastitis in dairy cattle, as well as milk protein gene regulation during lactation. Nutri-epigenomics research also reveals the influence of maternal nutrition on offspring's epigenetic regulation of metabolic homeostasis in cattle, sheep, goat and poultry. Integrating cyto-genomics approaches enhances understanding of epigenetic mechanisms in livestock breeding, providing insights into chromosomal structure, rearrangements and their impact on gene regulation and phenotypic traits. This review presents potential research areas to enhance production potential and deepen our understanding of epigenetic changes in livestock, offering opportunities for genetic improvement, reproductive management, disease control and milk production in diverse livestock species.
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Affiliation(s)
- Pushpa Sindhu
- Department of Animal Genetics and Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Ankit Magotra
- Department of Animal Genetics and Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Vikas Sindhu
- Department of Animal Nutrition, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Pradeep Chaudhary
- Department of Animal Genetics and Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
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2
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Yue Y, Ge Z, Guo Z, Wang Y, Yang G, Sun S, Li X. Screening of lncRNA profiles during intramuscular adipogenic differentiation in longissimus dorsi and semitendinosus muscles in pigs. Anim Biotechnol 2023; 34:4616-4626. [PMID: 36794392 DOI: 10.1080/10495398.2023.2176319] [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] [Indexed: 02/17/2023]
Abstract
Intramuscular fat content is an important factor that determines meat quality in pigs. In recent years, epigenetic regulation has increasingly studied the physiological model of intramuscular fat. Although long noncoding RNAs (lncRNAs) play essential roles in various biological processes, their role in intramuscular fat deposition in pigs remains largely unknown. In this study, intramuscular preadipocytes in the longissimus dorsi and semitendinosus of Large White pigs were isolated and induced into adipogenic differentiation in vitro. High-throughput RNA-seq was carried out to estimate the expression of lncRNAs at 0, 2 and 8 days post-differentiation. At this stage, 2135 lncRNAs were identified. KEGG analysis showed that the differentially expressed lncRNAs were common in pathways involved with adipogenesis and lipid metabolism. lnc_000368 was found to gradually increase during the adipogenic process. Reverse-transcription quantitative polymerase chain reaction and a western blot revealed that the knockdown of lnc_000368 significantly repressed the expression of adipogenic genes and lipolytic genes. As a result, lipid accumulation in porcine intramuscular adipocytes was impaired by the silencing of lnc_000368. Overall, our study identified a genome-wide lncRNA profile related to porcine intramuscular fat deposition, and the results suggest that lnc_000368 is a potential target gene that might be targeted in pig breeding in the future.
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Affiliation(s)
- Yanru Yue
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Shaanxi, P. R. China
| | - Zihao Ge
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Shaanxi, P. R. China
| | - Zhicheng Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Shaanxi, P. R. China
| | - Yuhe Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Shaanxi, P. R. China
| | - Gongshe Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Shaanxi, P. R. China
| | - Shiduo Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Shaanxi, P. R. China
| | - Xiao Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Shaanxi, P. R. China
- Key Laboratory of Livestock Biology, Northwest A & F University, Xianyang, China
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3
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Chai J, Wang N, Chen L, Bai J, Zhang J, Zhang G, An J, Zhang T, Tong X, Wu Y, Li M, Jin L. Identification of a Novel Long Non-Coding RNA G8110 That Modulates Porcine Adipogenic Differentiation and Inflammatory Responses. Int J Mol Sci 2023; 24:16799. [PMID: 38069122 PMCID: PMC10706401 DOI: 10.3390/ijms242316799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/14/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been extensively studied, and their crucial roles in adipogenesis, lipid metabolism, and gene expression have been revealed. However, the exact regulatory or other mechanisms by which lncRNAs influence the functioning of mesenteric adipose tissue (MAT) remain largely unknown. In this paper, we report the identification of a new lncRNA, named G8110, from the MAT of Bama pigs. The coordinated expression levels of lncRNA G8110 and NFE2L1 were significantly decreased in the MAT of obese Bama pigs compared with those in the MAT of lean pigs. Using a bone mesenchymal stem cell adipogenic differentiation model, we found that lncRNA G8110 played a role in adipocyte differentiation by positively regulating NFE2L1. We also found that lncRNA G8110 inhibited the formation of intracellular lipid synthesis, promoted lipid metabolism, and inhibited the expression of inflammatory cytokines. Our findings regarding lipid synthesis may further promote the role of lncRNAs in driving adipose tissue remodeling and maintaining metabolic health.
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Affiliation(s)
- Jin Chai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (N.W.); (J.B.); (J.Z.); (G.Z.); (J.A.); (T.Z.); (X.T.); (Y.W.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Ning Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (N.W.); (J.B.); (J.Z.); (G.Z.); (J.A.); (T.Z.); (X.T.); (Y.W.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Chen
- Chongqing Academy of Animal Science, Chongqing 402460, China;
- National Center of Technology Innovation for Pigs, Chongqing 402460, China
- Key Laboratory of Animal Resource Evaluation and Utilization (Pigs), Ministry of Agriculture and Rural Affairs, Chongqing 402160, China
| | - Jingyi Bai
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (N.W.); (J.B.); (J.Z.); (G.Z.); (J.A.); (T.Z.); (X.T.); (Y.W.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaman Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (N.W.); (J.B.); (J.Z.); (G.Z.); (J.A.); (T.Z.); (X.T.); (Y.W.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Geng Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (N.W.); (J.B.); (J.Z.); (G.Z.); (J.A.); (T.Z.); (X.T.); (Y.W.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiahua An
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (N.W.); (J.B.); (J.Z.); (G.Z.); (J.A.); (T.Z.); (X.T.); (Y.W.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tingting Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (N.W.); (J.B.); (J.Z.); (G.Z.); (J.A.); (T.Z.); (X.T.); (Y.W.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xingyan Tong
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (N.W.); (J.B.); (J.Z.); (G.Z.); (J.A.); (T.Z.); (X.T.); (Y.W.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yifan Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (N.W.); (J.B.); (J.Z.); (G.Z.); (J.A.); (T.Z.); (X.T.); (Y.W.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingzhou Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (N.W.); (J.B.); (J.Z.); (G.Z.); (J.A.); (T.Z.); (X.T.); (Y.W.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Long Jin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (J.C.); (N.W.); (J.B.); (J.Z.); (G.Z.); (J.A.); (T.Z.); (X.T.); (Y.W.)
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Sichuan Agricultural University, Chengdu 611130, China
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4
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Ru W, Zhang S, Liu J, Liu W, Huang B, Chen H. Non-Coding RNAs and Adipogenesis. Int J Mol Sci 2023; 24:9978. [PMID: 37373126 PMCID: PMC10298535 DOI: 10.3390/ijms24129978] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/26/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Adipogenesis is regarded as an intricate network in which multiple transcription factors and signal pathways are involved. Recently, big efforts have focused on understanding the epigenetic mechanisms and their involvement in the regulation of adipocyte development. Multiple studies investigating the regulatory role of non-coding RNAs (ncRNAs) in adipogenesis have been reported so far, especially lncRNA, miRNA, and circRNA. They regulate gene expression at multiple levels through interactions with proteins, DNA, and RNA. Exploring the mechanism of adipogenesis and developments in the field of non-coding RNA may provide a new insight to identify therapeutic targets for obesity and related diseases. Therefore, this article outlines the process of adipogenesis, and discusses updated roles and mechanisms of ncRNAs in the development of adipocytes.
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Affiliation(s)
- Wenxiu Ru
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (W.R.); (W.L.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China;
| | - Sihuan Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China;
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming 650212, China;
| | - Wujun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (W.R.); (W.L.)
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming 650212, China;
| | - Hong Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (W.R.); (W.L.)
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5
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Identification and Functional Prediction of Long Non-Coding RNA in Longissimus Dorsi Muscle of Queshan Black and Large White Pigs. Genes (Basel) 2023; 14:genes14010197. [PMID: 36672938 PMCID: PMC9858627 DOI: 10.3390/genes14010197] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Long non-coding RNA (lncRNA) participates in the regulation of various biological processes, but its function and characteristics in intramuscular fat (IMF) deposition in different breeds of pigs have not been fully understood. IMF content is one of the important factors affecting pork quality. In the present study, the differentially expressed lncRNAs (DE lncRNAs) and their target genes were screened by comparing Queshan Black (QS) and Large White (LW) pigs based on RNA-seq. The results displayed 55 DE lncRNAs between QS and LW, 29 upregulated and 26 downregulated, with 172 co-located target genes, and 6203 co-expressed target genes. The results of GO and KEGG analysis showed that the target genes of DE lncRNAs were involved in multiple pathways related to lipogenesis and lipid metabolism, such as the lipid biosynthetic process, protein phosphorylation, activation of MAPK activity, and the Jak-STAT signaling pathway. By constructing regulatory networks, lincRNA-ZFP42-ACTC1, lincRNA-AMY2-STAT1, and/or lincRNA-AMY2/miR-204/STAT1 were sieved, and the results indicate that lncRNA could participate in IMF deposition through direct regulation or ceRNA. These findings provide a basis for analyzing the molecular mechanism of IMF deposition in pigs and lay a foundation for developing and utilizing high-quality resources of local pig breeds.
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6
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Corral A, Alcala M, Carmen Duran-Ruiz M, Arroba AI, Ponce-Gonzalez JG, Todorčević M, Serra D, Calderon-Dominguez M, Herrero L. Role of long non-coding RNAs in adipose tissue metabolism and associated pathologies. Biochem Pharmacol 2022; 206:115305. [DOI: 10.1016/j.bcp.2022.115305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022]
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7
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Yang Y, Wu Y, Ji M, Rong X, Zhang Y, Yang S, Lu C, Cai C, Gao P, Guo X, Li B, Cao G. The long non-coding RNA lncMYOZ2 mediates an AHCY/MYOZ2 axis to promote adipogenic differentiation in porcine preadipocytes. BMC Genomics 2022; 23:700. [PMID: 36221052 PMCID: PMC9552422 DOI: 10.1186/s12864-022-08923-9] [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: 05/13/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play a vital role in regulating adipogenesis. However, the associated regulatory mechanisms have yet to be described in detail in pig. In this study, we demonstrate a critical role for lncMYOZ2 in adipogenesis from porcine preadipocytes. Specifically, lncMYOZ2 was more abundant in the adipose tissue of Mashen (fat-type) pigs than for Large White (lean-type) pigs, and knockdown of this lncRNA significantly inhibited the differentiation of porcine preadipocytes into adipocytes. Mechanistically, we used RNA pull-down and RIP assays to establish that lncMYOZ2 interacts with adenosylhomocysteinase (AHCY). Moreover, lncMYOZ2 knockdown increased promoter methylation of the target gene MYOZ2 and lowered its expression. Finally, we describe a positive regulatory role for MYOZ2 in adipogenesis. Collectively, these findings establish lncMYOZ2 as an important epigenetic regulator of adipogenesis via the aforementioned AHCY/MYOZ2 pathway, and provide insights into the role of lncRNAs in porcine adipose development.
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Affiliation(s)
- Yang Yang
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Yiqi Wu
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Mengting Ji
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Xiaoyin Rong
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Yanwei Zhang
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Shuai Yang
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Chang Lu
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Chunbo Cai
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Pengfei Gao
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Xiaohong Guo
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Bugao Li
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Guoqing Cao
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China.
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8
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Rashidmayvan M, Sahebi R, Ghayour-Mobarhan M. Long non-coding RNAs: a valuable biomarker for metabolic syndrome. Mol Genet Genomics 2022; 297:1169-1183. [PMID: 35854006 DOI: 10.1007/s00438-022-01922-1] [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: 03/27/2022] [Accepted: 06/25/2022] [Indexed: 10/17/2022]
Abstract
Long non-coding RNAs (lncRNAs) have become important regulators of gene expression because they affect a wide range of biological processes, such as cell growth, death, differentiation, and aging. More and more evidence suggests that lncRNAs play a role in maintaining metabolic homeostasis. When certain lncRNAs are out of balance, metabolic disorders like diabetes, obesity, and heart disease get worse. In this review, we talk about what we know about how lncRNAs control metabolism, with a focus on diseases caused by long-term inflammation and the characteristics of the metabolic syndrome. We looked at lncRNAs and their molecular targets in the pathogenesis of signaling pathways. We also talked about how lncRNAs are becoming more and more interesting as diagnostic and therapeutic targets for improving metabolic homeostasis.
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Affiliation(s)
- Mohammad Rashidmayvan
- Department of Nutrition, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Sahebi
- Metabolic Syndrome Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Ghayour-Mobarhan
- Department of Nutrition, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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9
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Zhang Y, Tian Z, Ye H, Sun X, Zhang H, Sun Y, Mao Y, Yang Z, Li M. Emerging functions of circular RNA in the regulation of adipocyte metabolism and obesity. Cell Death Dis 2022; 8:268. [PMID: 35595755 PMCID: PMC9122900 DOI: 10.1038/s41420-022-01062-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 05/04/2022] [Accepted: 05/10/2022] [Indexed: 02/08/2023]
Abstract
As noncoding RNAs, circular RNAs (circRNAs) are covalently enclosed endogenous biomolecules in eukaryotes that have tissue specificity and cell specificity. circRNAs were once considered a rare splicing byproduct. With the development of high-throughput sequencing, it has been confirmed that they are expressed in thousands of mammalian genes. To date, only a few circRNA functions and regulatory mechanisms have been verified. Adipose is the main tissue for body energy storage and energy supply. Adipocyte metabolism is a physiological process involving a series of genes and affects biological activities in the body, such as energy metabolism, immunity, and signal transmission. When adipocyte formation is dysregulated, it will cause a series of diseases, such as atherosclerosis, obesity, fatty liver, and diabetes. In recent years, many noncoding RNAs involved in adipocyte metabolism have been revealed. This review provides a comprehensive overview of the basic structure and biosynthetic mechanism of circRNAs, and further discusses the circRNAs related to adipocyte formation in adipose tissue and liver. Our review will provide a reference for further elucidating the genetic regulation mechanism of circRNAs involved in adipocyte metabolism.
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Affiliation(s)
- Yuanyuan Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China.,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Zhichen Tian
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China.,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Haibo Ye
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China.,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Xiaomei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China.,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Huiming Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China.,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Yujia Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China.,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Yongjiang Mao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China.,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China
| | - Zhangping Yang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China. .,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China.
| | - Mingxun Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, 225009, Yangzhou, Jiangsu, China. .,Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, Jiangsu, China.
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10
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Fernández-Barroso MÁ, García-Casco JM, Núñez Y, Ramírez-Hidalgo L, Matos G, Muñoz M. Understanding the role of myoglobin content in Iberian pigs fattened in an extensive system through analysis of the transcriptome profile. Anim Genet 2022; 53:352-367. [PMID: 35355298 PMCID: PMC9314091 DOI: 10.1111/age.13195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 01/31/2022] [Accepted: 03/11/2022] [Indexed: 11/30/2022]
Abstract
Meat color is the first perceived sensory feature and one of the most important quality traits. Myoglobin is the main pigment in meat, giving meat its characteristic cherry‐red color, highly appreciated by the consumers. In the current study, we used the RNA‐seq technique to characterize the longissimus dorsi muscle transcriptome in two groups of Iberian pigs with divergent breeding values for myoglobin content. As a result, we identified 57 differentially expressed genes and transcripts (DEGs). Moreover, we have validated the RNA‐seq expression of a set of genes by quantitative PCR (qPCR). Functional analyses revealed an enrichment of DEGs in biological processes related to oxidation (HBA1), lipid metabolism (ECH1, PLA2G10, PLD2), inflammation (CHST1, CD209, PLA2G10), and immune system (CD209, MX2, LGALS3, LGALS9). The upstream analysis showed a total of five transcriptional regulatory factors and eight master regulators that could moderate the expression of some DEGs, highlighting SPI1 and MAPK1, since they regulate the expression of DEGs involved in immune defense and inflammatory processes. Iberian pigs with high myoglobin content also showed higher expression of the HBA1 gene and both molecules, myoglobin and hemoglobin, have been described as having a protective effect against oxidative and inflammatory processes. Therefore, the HBA1 gene is a very promising candidate gene to harbor polymorphisms underlying myoglobin content, whereby further studies should be carried out for its potential use in an Iberian pig selection program.
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Affiliation(s)
- Miguel Ángel Fernández-Barroso
- Centro Nacional de I+D del Cerdo Ibérico, INIA-CSIC, Zafra, Spain.,Departamento de Mejora Genética Animal, INIA-CSIC, Madrid, Spain
| | - Juan María García-Casco
- Centro Nacional de I+D del Cerdo Ibérico, INIA-CSIC, Zafra, Spain.,Departamento de Mejora Genética Animal, INIA-CSIC, Madrid, Spain
| | - Yolanda Núñez
- Departamento de Mejora Genética Animal, INIA-CSIC, Madrid, Spain
| | | | - Gema Matos
- Sánchez Romero Carvajal-Jabugo, SRC, Huelva, Spain
| | - María Muñoz
- Departamento de Mejora Genética Animal, INIA-CSIC, Madrid, Spain
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11
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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: 1.0] [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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12
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Zhan S, Xue Y, Yang L, Li D, Dai H, Zhong T, Wang L, Dai D, Li L, Zhang H. Transcriptome analysis reveals long non-coding natural antisense transcripts involved in muscle development in fetal goat (Capra hircus). Genomics 2022; 114:110284. [DOI: 10.1016/j.ygeno.2022.110284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 11/24/2021] [Accepted: 01/31/2022] [Indexed: 11/16/2022]
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13
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Zhai B, Zhao Y, Fan S, Yuan P, Li H, Li S, Li Y, Zhang Y, Huang H, Li H, Kang X, Li G. Differentially Expressed lncRNAs Related to the Development of Abdominal Fat in Gushi Chickens and Their Interaction Regulatory Network. Front Genet 2022; 12:802857. [PMID: 35003230 PMCID: PMC8740130 DOI: 10.3389/fgene.2021.802857] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/29/2021] [Indexed: 01/03/2023] Open
Abstract
Chickens are one of the most important sources of meat worldwide, and the growth status of abdominal fat is closely related to production efficiency. Long noncoding RNAs (lncRNAs) play an important role in lipid metabolism and deposition regulation. However, research on the expression profile of lncRNAs related to the development of abdominal fat in chickens after hatching and their interaction regulatory networks is still lacking. To characterize the lncRNA expression profile during the development of chicken abdominal fat, abdominal adipose tissues from 6-, 14-, 22-, and 30-week-old Chinese Gushi chickens were herein used to construct 12 cDNA libraries, and a total of 3,827 new lncRNAs and 5,466 previously annotated lncRNAs were revealed. At the same time, based on the comparative analysis of five combinations, 276 differentially expressed lncRNAs (DE-lncRNAs) were screened. Functional enrichment analysis showed that the predicted target genes of these DE-lncRNAs were significantly enriched in pathways related to the posttranscriptional regulation of gene expression, negative regulation of cell proliferation, cell adhesion and other biological processes, glycosphingolipid biosynthesis, PPAR signaling, fatty acid degradation, fatty acid synthesis and others. In addition, association analysis of the lncRNA transcriptome profile was performed, and DE-lncRNA-related lncRNA-mRNA, lncRNA-miRNA and lncRNA-miRNA-mRNA interaction regulatory networks were constructed. The results showed that DE-lncRNA formed a complex network with PPAR pathway components, including PPARD, ACOX1, ADIPOQ, CPT1A, FABP5, ASBG2, LPL, PLIN2 and related miRNAs, including mir-200b-3p, mir-130b-3p, mir-215-5p, mir-122-5p, mir-223 and mir-125b-5p, and played an important regulatory role in biological processes such as lipid metabolism, adipocyte proliferation and differentiation. This study described the dynamic expression profile of lncRNAs in the abdominal fat of Gushi chickens for the first time and constructed the DE-lncRNA interaction regulatory network. The results expand the number of known lncRNAs in chicken abdominal fat and provide valuable resources for further elucidating the posttranscriptional regulatory mechanism of chicken abdominal fat development or deposition.
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Affiliation(s)
- Bin Zhai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Yinli Zhao
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
| | - Shengxin Fan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Pengtao Yuan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Hongtai Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Shuaihao Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Yuanfang Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Yanhua Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China.,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, China
| | - Hetian Huang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China.,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, China
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China.,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China.,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China.,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, China
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14
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Su XH, He HY, Fang C, Liu LL, Liu WJ. Transcriptome profiling of LncRNAs in sheep tail fat deposition. Anim Biotechnol 2021:1-11. [PMID: 34865605 DOI: 10.1080/10495398.2021.2002882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
LncRNAs have recently received special attention due to their critical role in many important biological processes. There are few reports on its regulatory function in sheep fat deposition. In this study, two sheep populations with different tail types in Xinjiang, Bashibai sheep (fat-tailed) and the hybrid population of Bashibai sheep and wild argali (small-tailed) were selected for whole transcriptome sequencing from their tail tissues. First, 728 differentially expressed LncRNAs of tail fat between Bashibai and F2 sheep were identified by RNA-seq. Second, the tissue expression profile and relative expression difference between Bashibai and F2 sheep of 2 of 728 DE LncRNAs were analyzed by RT-PCR. LncRNA-MSTRG.24995 was highly expressed in tail fat, while lncRNA-MSTRG.36913 was highly expressed in subcutaneous fat. In addition, the expressions of LncRNA-MSTRG.24995 and LncRNA-MSTRG.36913 in tail fat of F2 sheep were significantly lower than that of Bashibai sheep, while those patterns in longissimus dorsi, quadriceps femoris and rumen were reversed. Third, the expression pattern of target genes FASN and THRSP in each tissue was similar with that of corresponding LncRNAs. The LncRNA-MSTRG.24995 directly affects tail fat deposition by FASN gene, while the LncRNA-MSTRG.36913 indirectly affects that by THRSP gene. This will help us to understand molecular mechanism of fat tail deposition from transcriptomic perspectives.
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Affiliation(s)
- Xiao-Hui Su
- Faculty of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Hai-Ying He
- Faculty of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Chao Fang
- Faculty of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Ling-Ling Liu
- Faculty of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Wu-Jun Liu
- Faculty of Animal Science, Xinjiang Agricultural University, Urumqi, China
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15
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Yi X, He Z, Tian T, Kou Z, Pang W. LncIMF2 promotes adipogenesis in porcine intramuscular preadipocyte through sponging MiR-217. Anim Biotechnol 2021; 34:268-279. [PMID: 34346296 DOI: 10.1080/10495398.2021.1956509] [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] [Indexed: 01/22/2023]
Abstract
Intramuscular fat is positively related to meat quality including tenderness, flavor, and juiciness. Long noncoding RNA (LncRNA) plays a vital role in regulating adipogenesis. However, it is largely unknown about lncRNAs associated with porcine intramuscular adipocyte adipogenesis. In the present study, we focus on a novel LncRNA, which is named lncIMF2, associated with adipogenesis by our previous RNA-sequence analysis and bioinformatics analysis. We demonstrated LncIMF2 knockdown inhibited the proliferation of porcine intramuscular adipocytes while expression of cell cycle-related genes was decreased. Besides, we found LncIMF2 knockdown inhibited expression of adipogenic differentiation marker genes including PPARγ (Peroxisome proliferator-activated reporter gamma) and ATGL (Adipose triglyceride lipase). Similarly, overexpression of LncIMF2 promotes proliferation and differentiation of porcine intramuscular preadipocytes. Moreover, we proved that IncIMF2 acts as a molecular sponge for MicroRNA-217 (miR-217), which has been found associated with adipogenesis, thereby affecting the expression of the miR-217 target gene. Collectively, our findings will contribute to a deeper understanding of the role of LncRNA in pig IMF deposition for the improvement of meat quality.
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Affiliation(s)
- XuDong Yi
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Shaanxi, P.R. China
| | - ZhaoZhao He
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Shaanxi, P.R. China
| | - TingTing Tian
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Shaanxi, P.R. China
| | - ZhongYun Kou
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Shaanxi, P.R. China
| | - WeiJun Pang
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Shaanxi, P.R. China
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16
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Rey F, Urrata V, Gilardini L, Bertoli S, Calcaterra V, Zuccotti GV, Cancello R, Carelli S. Role of long non-coding RNAs in adipogenesis: State of the art and implications in obesity and obesity-associated diseases. Obes Rev 2021; 22:e13203. [PMID: 33443301 PMCID: PMC8244036 DOI: 10.1111/obr.13203] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/11/2020] [Accepted: 12/13/2020] [Indexed: 12/14/2022]
Abstract
Obesity is an evolutionary, chronic, and relapsing disease that consists of a pathological accumulation of adipose tissue able to increase morbidity for high blood pressure, type 2 diabetes, metabolic syndrome, and obstructive sleep apnea in adults, children, and adolescents. Despite intense research over the last 20 years, obesity remains today a disease with a complex and multifactorial etiology. Recently, long non-coding RNAs (lncRNAs) are emerging as interesting new regulators as different lncRNAs have been found to play a role in early and late phases of adipogenesis and to be implicated in obesity-associated complications onset. In this review, we discuss the most recent advances on the role of lncRNAs in adipocyte biology and in obesity-associated complications. Indeed, more and more researchers are focusing on investigating the underlying roles that these molecular modulators could play. Even if a significant number of evidence is correlation-based, with lncRNAs being differentially expressed in a specific disease, recent works are now focused on deeply analyzing how lncRNAs can effectively modulate the disease pathogenesis onset and progression. LncRNAs possibly represent new molecular markers useful in the future for both the early diagnosis and a prompt clinical management of patients with obesity.
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Affiliation(s)
- Federica Rey
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy.,Pediatric Clinical Research Center Fondazione "Romeo ed Enrica Invernizzi", University of Milan, Milan, Italy
| | - Valentina Urrata
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy.,Pediatric Clinical Research Center Fondazione "Romeo ed Enrica Invernizzi", University of Milan, Milan, Italy
| | - Luisa Gilardini
- Obesity Unit-Laboratory of Nutrition and Obesity Research, Department of Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Simona Bertoli
- Obesity Unit-Laboratory of Nutrition and Obesity Research, Department of Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, Milan, Italy.,International Center for the Assessment of Nutritional Status (ICANS), Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Valeria Calcaterra
- Pediatrics and Adolescentology Unit, Department of Internal Medicine, University of Pavia, Pavia, Italy.,Department of Pediatrics, Children's Hospital "V. Buzzi", Milan, Italy
| | - Gian Vincenzo Zuccotti
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy.,Pediatric Clinical Research Center Fondazione "Romeo ed Enrica Invernizzi", University of Milan, Milan, Italy.,Department of Pediatrics, Children's Hospital "V. Buzzi", Milan, Italy
| | - Raffaella Cancello
- Obesity Unit-Laboratory of Nutrition and Obesity Research, Department of Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Stephana Carelli
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy.,Pediatric Clinical Research Center Fondazione "Romeo ed Enrica Invernizzi", University of Milan, Milan, Italy
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17
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Björk C, Subramanian N, Liu J, Acosta JR, Tavira B, Eriksson AB, Arner P, Laurencikiene J. An RNAi Screening of Clinically Relevant Transcription Factors Regulating Human Adipogenesis and Adipocyte Metabolism. Endocrinology 2021; 162:6272286. [PMID: 33963396 PMCID: PMC8197287 DOI: 10.1210/endocr/bqab096] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 12/13/2022]
Abstract
CONTEXT Healthy hyperplasic (many but smaller fat cells) white adipose tissue (WAT) expansion is mediated by recruitment, proliferation and/or differentiation of new fat cells. This process (adipogenesis) is controlled by transcriptional programs that have been mostly identified in rodents. OBJECTIVE A systemic investigation of adipogenic human transcription factors (TFs) that are relevant for metabolic conditions has not been revealed previously. METHODS TFs regulated in WAT by obesity, adipose morphology, cancer cachexia, and insulin resistance were selected from microarrays. Their role in differentiation of human adipose tissue-derived stem cells (hASC) was investigated by RNA interference (RNAi) screen. Lipid accumulation, cell number, and lipolysis were measured for all screened factors (148 TFs). RNA (RNAseq), protein (Western blot) expression, insulin, and catecholamine responsiveness were examined in hASC following siRNA treatment of selected target TFs. RESULTS Analysis of TFs regulated by metabolic conditions in human WAT revealed that many of them belong to adipogenesis-regulating pathways. The RNAi screen identified 39 genes that affected fat cell differentiation in vitro, where 11 genes were novel. Of the latter JARID2 stood out as being necessary for formation of healthy fat cell metabolic phenotype by regulating expression of multiple fat cell phenotype-specific genes. CONCLUSION This comprehensive RNAi screening in hASC suggests that a large proportion of WAT TFs that are impacted by metabolic conditions might be important for hyperplastic adipose tissue expansion. The screen also identified JARID2 as a novel TF essential for the development of functional adipocytes.
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Affiliation(s)
- Christel Björk
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, SE-14186, Sweden
| | - Narmadha Subramanian
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, SE-14186, Sweden
| | - Jianping Liu
- Karolinska High Throughput Center, Department of Medical Biochemistry and Biophysics (MBB), Division of Functional Genomics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Juan Ramon Acosta
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, SE-14186, Sweden
| | - Beatriz Tavira
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, SE-14186, Sweden
| | - Anders B Eriksson
- Karolinska High Throughput Center, Department of Medical Biochemistry and Biophysics (MBB), Division of Functional Genomics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Peter Arner
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, SE-14186, Sweden
| | - Jurga Laurencikiene
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, SE-14186, Sweden
- Correspondence: Jurga Laurencikiene, PhD, Karolinska Institutet, Lipid laboratory, Dept. of Medicine Huddinge (MedH), NEO, Hälsovägen 9/Blickagången 16, 14183 Huddinge, Sweden.
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18
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Wang L, Xie Y, Chen W, Zhang Y, Zeng Y. The role of long noncoding RNAs in livestock adipose tissue deposition - A review. Anim Biosci 2021; 34:1089-1099. [PMID: 33902176 PMCID: PMC8255878 DOI: 10.5713/ab.21.0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/29/2021] [Indexed: 11/27/2022] Open
Abstract
With the development of sequencing technology, numerous, long noncoding RNAs (lncRNAs) have been discovered and annotated. Increasing evidence has shown that lncRNAs play an essential role in regulating many biological and pathological processes, especially in cancer. However, there have been few studies on the roles of lncRNAs in livestock production. In animal products, meat quality and lean percentage are vital economic traits closely related to adipose tissue deposition. However, adipose tissue accumulation is also a pivotal contributor to obesity, diabetes, atherosclerosis, and many other diseases, as demonstrated by human studies. In livestock production, the mechanism by which lncRNAs regulate adipose tissue deposition is still unclear. In addition, the phenomenon that different animal species have different adipose tissue accumulation abilities is not well understood. In this review, we summarize the characteristics of lncRNAs and their four functional archetypes and review the current knowledge about lncRNA functions in adipose tissue deposition in livestock species. This review could provide theoretical significance to explore the functional mechanisms of lncRNAs in adipose tissue accumulation in animals.
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Affiliation(s)
- Lixue Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yuhuai Xie
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Wei Chen
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yu Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yongqing Zeng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong 271018, China
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19
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Hongfang G, Khan R, Raza SHA, Nurgulsim K, Suhail SM, Rahman A, Ahmed I, Ijaz A, Ahmad I, Linsen Z. Transcriptional regulation of adipogenic marker genes for the improvement of intramuscular fat in Qinchuan beef cattle. Anim Biotechnol 2020; 33:776-795. [PMID: 33151113 DOI: 10.1080/10495398.2020.1837847] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The intramuscular fat content plays a crucial role in meat quality traits. Increasing the degree of adipogenesis in beef cattle leads to an increase in the content of intramuscular fat. Adipogenesis a complex biochemical process which is under firm genetic control. Over the last three decades, the Qinchuan beef cattle have been extensively studied for the improvement of meat production and quality traits. In this study, we reviewed the literature regarding adipogenesis and intramuscular fat deposition. Then, we summarized the research conducted on the transcriptional regulation of key adipogenic marker genes, and also reviewed the roles of adipogenic marker genes in adipogenesis of Qinchuan beef cattle. This review will elaborate our understanding regarding transcriptional regulation which is a vital physiological process regulated by a cascade of transcription factors (TFs), key target marker genes, and regulatory proteins. This synergistic action of TFs and target genes ensures the accurate and diverse transmission of the genetic information for the accomplishment of central physiological processes. This information will provide an insight into the transcriptional regulation of the adipogenic marker genes and its role in bovine adipogenesis for the breed improvement programs especially for the trait of intramuscular fat deposition.
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Affiliation(s)
- Guo Hongfang
- Medical College of Xuchang University, Xuchang City, Henan Province, P. R. China
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China.,Department of Livestock Management, Breeding and Genetics, The University of Agriculture, Peshawar, Pakistan
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Kaster Nurgulsim
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Syed Muhammad Suhail
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture, Peshawar, Pakistan
| | - Abdur Rahman
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture, Peshawar, Pakistan
| | - Ijaz Ahmed
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture, Peshawar, Pakistan
| | - Asim Ijaz
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture, Peshawar, Pakistan
| | - Iftikhar Ahmad
- Department of Livestock Management, Breeding and Genetics, The University of Agriculture, Peshawar, Pakistan
| | - Zan Linsen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P. R. China
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20
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He L, He Q, Qiao L, Huang S, Dai Z, Yang T, Liu L, Zhao Z. LncWNT3‐IT affects the proliferation of Sertoli cells by regulating the expression of the WNT3 gene in goat testis. Reprod Domest Anim 2020; 55:1061-1071. [DOI: 10.1111/rda.13738] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 05/28/2020] [Indexed: 01/16/2023]
Affiliation(s)
- Lina He
- College of Animal Science and Technology Southwest University Chongqing China
| | - Qijie He
- College of Animal Science and Technology Southwest University Chongqing China
| | - Lei Qiao
- College of Animal Science and Technology Southwest University Chongqing China
| | - Siyi Huang
- College of Animal Science and Technology Southwest University Chongqing China
| | - Zinuo Dai
- College of Animal Science and Technology Southwest University Chongqing China
| | - Tianyuan Yang
- College of Animal Science and Technology Southwest University Chongqing China
| | - Lingbin Liu
- College of Animal Science and Technology Southwest University Chongqing China
| | - Zhongquan Zhao
- College of Animal Science and Technology Southwest University Chongqing China
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21
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A Newly Identified LncRNA LncIMF4 Controls Adipogenesis of Porcine Intramuscular Preadipocyte through Attenuating Autophagy to Inhibit Lipolysis. Animals (Basel) 2020; 10:ani10060926. [PMID: 32466602 PMCID: PMC7341528 DOI: 10.3390/ani10060926] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/18/2020] [Accepted: 05/18/2020] [Indexed: 01/12/2023] Open
Abstract
Simple Summary Compared with lean-type pigs, the intramuscular fat content of fat-type Bamei pigs was greater. LncRNA, as a vital regular, plays an important role in numerous biological processes. However, there were a few studies on the role of lncRNAs during IMF development in pigs. Based on these, lncRNA sequencing in intramuscular adipocytes was performed to explore the effects of lncRNA on intramuscular fat deposition. RNA sequencing analysis of intramuscular adipocyte from Bamei pig (fat-type) and Yorkshire pig (lean-type) indicated that, a novel lncRNA, lncIMF4, was associated with intramuscular adipogenesis. In addition, further researches showed that knockdown lncIMF4 promoted proliferation and adipogenic differentiation of porcine intramuscular adipocytes, whereas inhibited autophagy. Moreover, knockdown lncIMF4 facilitated intramuscular adipogenesis through attenuating autophagy to repress the lipolysis. Our findings will contribute to better understand the mechanism of lncRNA controlling adipogenesis in pig. Furthermore, it also provides a new perspective to study the role of lncRNA in regulating porcine intramuscular adipogenesis for promoting pork quality. Abstract Intramuscular fat (IMF) is implicated in juiciness, tenderness, and flavor of pork. Meat quality of Chinese fat-type pig is much better than that of lean-type pig because of its higher IMF content. LncRNA is a vital regulator that contributes to adipogenesis. However, it is unknown about the regulation of lncRNA on IMF content. Here, by RNA sequence analysis of intramuscular adipocyte from Bamei pig (fat-type) and Yorkshire pig (lean-type), we found that a novel lncRNA, lncIMF4, was associated with adipogenesis. LncIMF4, abundant in adipose, differently expressed along with intramuscular preadipocyte proliferation and differentiation. Meanwhile, it is located both in cytoplasm and nucleus. Besides, lncIMF4 knockdown promoted proliferation and differentiation of porcine intramuscular preadipocytes, whereas inhibited autophagy. Moreover, lncIMF4 knockdown facilitated intramuscular adipogenesis through attenuating autophagy to repress the lipolysis. Our findings will contribute to understand better the mechanism of lncRNA controlling intramuscular adipogenesis for promoting pork quality.
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22
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Wang H, Zhong J, Zhang C, Chai Z, Cao H, Wang J, Zhu J, Wang J, Ji Q. The whole-transcriptome landscape of muscle and adipose tissues reveals the ceRNA regulation network related to intramuscular fat deposition in yak. BMC Genomics 2020; 21:347. [PMID: 32381004 PMCID: PMC7203869 DOI: 10.1186/s12864-020-6757-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 04/27/2020] [Indexed: 02/07/2023] Open
Abstract
Background The Intramuscular fat (IMF) content in meat products, which is positively correlated with meat quality, is an important trait considered by consumers. The regulation of IMF deposition is species specific. However, the IMF-deposition-related mRNA and non-coding RNA and their regulatory network in yak (Bos grunniens) remain unknown. High-throughput sequencing technology provides a powerful approach for analyzing the association between transcriptome-related differences and specific traits in animals. Thus, the whole transcriptomes of yak muscle and adipose tissues were screened and analyzed to elucidate the IMF deposition-related genes. The muscle tissues were used for IMF content measurements. Results Significant differences were observed between the 0.5- and 2.5-year-old yaks. Several mRNAs, miRNAs, lncRNAs and circRNAs were generally expressed in both muscle and adipose tissues. Between the 0.5- and 2.5-year-old yaks, 149 mRNAs, 62 miRNAs, 4 lncRNAs, and 223 circRNAs were differentially expressed in muscle tissue, and 72 mRNAs, 15 miRNAs, 9 lncRNAs, and 211 circRNAs were differentially expressed in adipose tissue. KEGG annotation revelved that these differentially expressed genes were related to pathways that maintain normal biological functions of muscle and adipose tissues. Moreover, 16 mRNAs, 5 miRNAs, 3 lncRNAs, and 5 circRNAs were co-differentially expressed in both types of tissue. We suspected that these co-differentially expressed genes were involved in IMF-deposition in the yak. Additionally, LPL, ACADL, SCD, and FASN, which were previously shown to be associated with the IMF content, were identified in the competing endogenous RNA (ceRNA) regulatory network that was constructed on the basis of the IMF deposition-related genes. Three ceRNA subnetworks also revealed that TCONS-00016416 and its target SIRT1 “talk” to each other through the same miR-381-y and miR-208 response elements, whereas TCONS-00061798 and its target PRKCA, and TCONS-00084092 and its target LPL “talk” to each other through miR-122-x and miR-499-y response elements, respectively. Conclusion Taken together, our results reveal the potential mRNA and noncoding RNAs involved in IMF deposition in the yak, providing a useful resource for further research on IMF deposition in this animal species.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China. .,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.
| | - Chengfu Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, the Tibet Academy of Agricultural and Animal Husbandry Science , Lhasa, Tibet, 850000, People's Republic of China
| | - Zhixin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Hanwen Cao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, the Tibet Academy of Agricultural and Animal Husbandry Science , Lhasa, Tibet, 850000, People's Republic of China
| | - Jikun Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Jiangjiang Zhu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Qiumei Ji
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, the Tibet Academy of Agricultural and Animal Husbandry Science , Lhasa, Tibet, 850000, People's Republic of China.
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23
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Lackey DE, Reis FCG, Isaac R, Zapata RC, El Ouarrat D, Lee YS, Bandyopadhyay G, Ofrecio JM, Oh DY, Osborn O. Adipocyte PU.1 knockout promotes insulin sensitivity in HFD-fed obese mice. Sci Rep 2019; 9:14779. [PMID: 31611602 PMCID: PMC6791934 DOI: 10.1038/s41598-019-51196-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 09/26/2019] [Indexed: 12/27/2022] Open
Abstract
Insulin resistance is a key feature of obesity and type 2 diabetes. PU.1 is a master transcription factor predominantly expressed in macrophages but after HFD feeding PU.1 expression is also significantly increased in adipocytes. We generated adipocyte specific PU.1 knockout mice using adiponectin cre to investigate the role of PU.1 in adipocyte biology, insulin and glucose homeostasis. In HFD-fed obese mice systemic glucose tolerance and insulin sensitivity were improved in PU.1 AKO mice and clamp studies indicated improvements in both adipose and liver insulin sensitivity. At the level of adipose tissue, macrophage infiltration and inflammation was decreased and glucose uptake was increased in PU.1 AKO mice compared with controls. While PU.1 deletion in adipocytes did not affect the gene expression of PPARg itself, we observed increased expression of PPARg target genes in eWAT from HFD fed PU.1 AKO mice compared with controls. Furthermore, we observed decreased phosphorylation at serine 273 in PU.1 AKO mice compared with fl/fl controls, indicating that PPARg is more active when PU.1 expression is reduced in adipocytes. Therefore, in obesity the increased expression of PU.1 in adipocytes modifies the adipocyte PPARg cistrome resulting in impaired glucose tolerance and insulin sensitivity.
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Affiliation(s)
- Denise E Lackey
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Felipe C G Reis
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Roi Isaac
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Rizaldy C Zapata
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Dalila El Ouarrat
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Yun Sok Lee
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Gautam Bandyopadhyay
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Jachelle M Ofrecio
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Da Young Oh
- Touchstone Diabetes Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas, USA
| | - Olivia Osborn
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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24
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Huang J, Zheng Q, Wang S, Wei X, Li F, Ma Y. High-Throughput RNA Sequencing Reveals NDUFC2-AS lncRNA Promotes Adipogenic Differentiation in Chinese Buffalo ( Bubalus bubalis L). Genes (Basel) 2019; 10:genes10090689. [PMID: 31500202 PMCID: PMC6770997 DOI: 10.3390/genes10090689] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/02/2019] [Accepted: 09/05/2019] [Indexed: 12/21/2022] Open
Abstract
The buffalo (Bubalus bubalis L.) is prevalent in China and the increasing demand for meat production has changed its role from being a beast of burden to a meat source. The low fat deposition level has become one of the main barriers for its use in meat production. It is urgent to reveal factors involved in fat deposition in buffalo. This study performed RNA sequencing to investigate both long noncoding RNAs (lncRNAs) and mRNAs of adipose tissues in young and adult buffalos. A total of 124 lncRNAs and 2008 mRNAs showed differential expression patterns between young and adult samples. Coexpression analysis and functional enrichment revealed 585 mRNA–lncRNA pairs with potential function in fat deposition. After validation by qRT-PCR, we focused on a lncRNA transcribed from the ubiquinone oxidoreductase subunit C2 (NDUFC2) antisense (AS) strand which showed high correlation with thyroid hormone responsive protein (THRSP). NDUFC2-AS lncRNA is highly expressed in adipose tissue and maturation adipocytes and mainly exists in the nucleus. Functional assays demonstrated that NDUFC2-AS lncRNA promotes adipogenic differentiation by upregulating the expression levels of THRSP and CCAAT enhancer binding protein alpha (C/EBPα) in buffalo. These results indicate that NDUFC2-AS lncRNA promotes fat deposition in buffalo.
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Affiliation(s)
- Jieping Huang
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Qiuzhi Zheng
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Shuzhe Wang
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Xuefeng Wei
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Fen Li
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan 464000, China.
- School of Agriculture, Ningxia University, Yinchuan, Ningxia 750021, China.
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25
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Guo M, Liu T, Zhang S, Yang L. RASSF1-AS1, an antisense lncRNA of RASSF1A, inhibits the translation of RASSF1A to exacerbate cardiac fibrosis in mice. Cell Biol Int 2019; 43:1163-1173. [PMID: 30571844 DOI: 10.1002/cbin.11085] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Cardiac fibrosis is associated with various cardiovascular diseases and can eventually lead to heart failure. Dysregulation of long non-coding RNAs (lncRNAs) are recognized as one of the key mechanisms of cardiac diseases. However, the roles and underlying mechanisms of lncRNAs in cardiac fibrosis have not been explicitly defined. Here, we investigated the role of an antisense (AS) lncRNA from the Ras association domain-containing protein 1 isoform A (RASSF1A) gene locus, named RASSF1-AS1, in the development of cardiac fibrosis. Cardiac fibrosis mouse model was established by isoproterenol injection. We found that RASSF1A protein was downregulated, whereas RASSF1-AS1 was markedly upregulated during cardiac fibrosis. Overexpression and knockdown of mouse primary cardiac fibroblasts showed that RASSF1-AS1 negatively regulated RASSF1A expression at the post-transcriptional level. According to the landscape analysis and sense-AS binding evaluation, RASSF1-AS1 partially overlaps with RASSF1A messenger RNA (mRNA) at the exon2 region. RNA pull-down and luciferase activity assays confirmed that RASSF1-AS1 directly bound to RASSF1A mRNA and suppressed its translation. Furthermore, wild-type RASSF1-AS1 had a promoting effect on nuclear factor-κB activation and cardiac fibrosis, but mutated RASSF1-AS1, in which the binding region was deleted, had no effect. In conclusion, RASSF1-AS1 inhibits the translation of RASSF1A to exacerbate cardiac fibrosis in mice, indicating a potential application of RASSF1-AS1 as a therapy target for cardiac fibrosis.
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Affiliation(s)
- Min Guo
- Department of Geriatric, Shandong Energy Zibo Mining Group Co. Ltd. Central Hospital, 133 Zikuang Road, Zichuan District, Zibo, Shandong, 255120, P.R. China
| | - Tangyu Liu
- Department of Cardiovascular Medicine, Shandong Energy Zibo Mining Group Co. Ltd. Central Hospital, 133 Zikuang Road, Zichuan District, Zibo, Shandong, 255120, P.R. China
| | - Shujie Zhang
- Department of Geriatric, Shandong Energy Zibo Mining Group Co. Ltd. Central Hospital, 133 Zikuang Road, Zichuan District, Zibo, Shandong, 255120, P.R. China
| | - Longbiao Yang
- Department of Orthopedics, Shandong Energy Zibo Mining Group Co. Ltd. Central Hospital, 133 Zikuang Road, Zichuan District, Zibo, Shandong, 255120, P.R. China
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26
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Ding Y, Qian L, Wang L, Wu C, Li D, Zhang X, Yin Z, Wang Y, Zhang W, Wu X, Ding J, Yang M, Zhang L, Shang J, Wang C, Gao Y. Relationship among porcine lncRNA TCONS_00010987, miR-323, and leptin receptor based on dual luciferase reporter gene assays and expression patterns. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 33:219-229. [PMID: 31480192 PMCID: PMC6946967 DOI: 10.5713/ajas.19.0065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 06/11/2019] [Indexed: 12/12/2022]
Abstract
Objective Considering the physiological and clinical importance of leptin receptor (LEPR) in regulating obesity and the fact that porcine LEPR expression is not known to be controlled by lncRNAs and miRNAs, we aim to characterize this gene as a potential target of SSC-miR-323 and the lncRNA TCONS_00010987. Methods Bioinformatics analyses revealed that lncRNA TCONS_00010987 and LEPR have SSC-miR-323-binding sites and that LEPR might be a target of lncRNA TCONS_00010987 based on cis prediction. Wild-type and mutant TCONS_00010987-target sequence fragments and wild-type and mutant LEPR 3′-UTR fragments were generated and cloned into pmiR-RB-REPORTTM-Control vectors to construct respective recombinant plasmids. HEK293T cells were co-transfected with the SSC-miR-323 mimics or a negative control with constructs harboring the corresponding binding sites and relative luciferase activities were determined. Tissue expression patterns of lncRNA TCONS_00010987, SSC-miR-323, and LEPR in Anqing six-end-white (AQ, the obese breed) and Large White (LW, the lean breed) pigs were detected by real-time quantitative polymerase chain reaction; backfat expression of LEPR protein was detected by western blotting. Results Target gene fragments were successfully cloned, and the four recombinant vectors were constructed. Compared to the negative control, SSC-miR-323 mimics significantly inhibited luciferase activity from the wild-type TCONS_00010987-target sequence and wild-type LEPR-3′-UTR (p<0.01 for both) but not from the mutant TCONS_00010987-target sequence and mutant LEPR-3′-UTR (p>0.05 for both). Backfat expression levels of TCONS_ 00010987 and LEPR in AQ pigs were significantly higher than those in LW pigs (p<0.01), whereas levels of SSC-miR-323 in AQ pigs were significantly lower than those in LW pigs (p<0.05). LEPR protein levels in the backfat tissues of AQ pigs were markedly higher than those in LW pigs (p<0.01). Conclusion LEPR is a potential target of SSC-miR-323, and TCONS_00010987 might act as a sponge for SSC-miR-323 to regulate LEPR expression.
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Affiliation(s)
- Yueyun Ding
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Li Qian
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Li Wang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Chaodong Wu
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - DengTao Li
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xiaodong Zhang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Zongjun Yin
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yuanlang Wang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Wei Zhang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xudong Wu
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Jian Ding
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Min Yang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Liang Zhang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Jinnan Shang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Chonglong Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China
| | - Yafei Gao
- Anhui Haoxiang Agriculture and Animal Husbandry Co. LTD, Bozhou, Anhui 236700, China
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27
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Wei S, Li A, Zhang L, Du M. GROWTH AND DEVELOPMENT SYMPOSIUM: STEM AND PROGENITOR CELLS IN ANIMAL GROWTH: Long noncoding RNAs in adipogenesis and adipose development of meat animals12. J Anim Sci 2019; 97:2644-2657. [PMID: 30959518 DOI: 10.1093/jas/skz114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/05/2019] [Indexed: 12/22/2022] Open
Abstract
Sequencing technology, especially next-generation RNA sequencing, has greatly facilitated the identification and annotation of long noncoding RNAs (lncRNAs). In mammals, a large number of lncRNAs have been identified, which regulate various biological processes. An increasing number of lncRNAs have been identified which could function as key regulators of adipogenesis (adipocyte formation), a key step of the development of adipose tissue. Because proper adipose tissue development is a key factor affecting animal growth efficiency, lean/fat ratio, and meat quality, summarizing the roles and recent advances of lncRNAs in adipogenesis is needed in order to develop strategies to effectively manage fat deposition. In this review, we updated lncRNAs contributed to the regulation of adipogenesis, focusing on their roles in fat development of farm animals.
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Affiliation(s)
- Shengjuan Wei
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Anning Li
- Department of Animal Sciences, Washington State University, Pullman, WA
| | - Lifan Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Min Du
- Department of Animal Sciences, Washington State University, Pullman, WA
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28
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Cai R, Tang G, Zhang Q, Yong W, Zhang W, Xiao J, Wei C, He C, Yang G, Pang W. A Novel lnc-RNA, Named lnc-ORA, Is Identified by RNA-Seq Analysis, and Its Knockdown Inhibits Adipogenesis by Regulating the PI3K/AKT/mTOR Signaling Pathway. Cells 2019; 8:cells8050477. [PMID: 31109074 PMCID: PMC6562744 DOI: 10.3390/cells8050477] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/16/2019] [Accepted: 05/16/2019] [Indexed: 12/17/2022] Open
Abstract
Obesity is closely associated with numerous adipogenic regulatory factors, including coding and non-coding genes. Long noncoding RNAs (lncRNAs) play a major role in adipogenesis. However, differential expression profiles of lncRNAs in inguinal white adipose tissue (iWAT) between wild-type (WT) and ob/ob mice, as well as their roles in adipogenesis, are not well understood. Here, a total of 2809 lncRNAs were detected in the iWAT of WT and ob/ob mice by RNA-Sequencing (RNA-Seq), including 248 novel lncRNAs. Of them, 46 lncRNAs were expressed differentially in WT and ob/ob mice and were enriched in adipogenesis signaling pathways as determined by KEGG enrichment analysis, including the PI3K/AKT/mTOR and cytokine-cytokine receptor interaction signaling pathways. Furthermore, we focused on one novel lncRNA, which we named lnc-ORA (obesity-related lncRNA), which had a seven-fold higher expression in ob/ob mice than in WT mice. Knockdown of lnc-ORA inhibited preadipocyte proliferation by decreasing the mRNA and protein expression levels of cell cycle markers. Interestingly, lnc-ORA knockdown inhibited adipocyte differentiation by regulating the PI3K/AKT/mTOR signaling pathway. In summary, these findings contribute to a better understanding of adipogenesis in relation to lncRNAs and provide novel potential therapeutic targets for obesity-related metabolic diseases.
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Affiliation(s)
- Rui Cai
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Guorong Tang
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Que Zhang
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Wenlong Yong
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Wanrong Zhang
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Junying Xiao
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Changsheng Wei
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Chun He
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Gongshe Yang
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Weijun Pang
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
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29
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Sun L, Lin JD. Function and Mechanism of Long Noncoding RNAs in Adipocyte Biology. Diabetes 2019; 68:887-896. [PMID: 31010880 PMCID: PMC6477904 DOI: 10.2337/dbi18-0009] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/19/2019] [Indexed: 12/17/2022]
Abstract
The last two decades have witnessed an explosion of interest in adipocyte biology, coinciding with the upsurge of obesity and metabolic syndrome. Now we have new perspectives on the distinct developmental origins of white, brown, and beige adipocytes and their role in metabolic physiology and disease. Beyond fuel metabolism, adipocytes communicate with the immune system and other tissues by releasing diverse paracrine and endocrine factors to orchestrate adipose tissue remodeling and maintain systemic homeostasis. Significant progress has been made in delineating the regulatory networks that govern different aspects of adipocyte biology. Here we provide an overview on the emerging role of long noncoding RNAs (lncRNAs) in the regulation of adipocyte development and metabolism and discuss the implications of the RNA-protein regulatory interface in metabolic control.
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Affiliation(s)
- Lei Sun
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, Singapore
| | - Jiandie D Lin
- Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI
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30
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Junjvlieke Z, Mei CG, Khan R, Zhang WZ, Hong JY, Wang L, Li SJ, Zan LS. Transcriptional regulation of bovine elongation of very long chain fatty acids protein 6 in lipid metabolism and adipocyte proliferation. J Cell Biochem 2019; 120:13932-13943. [PMID: 30945346 DOI: 10.1002/jcb.28667] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 02/03/2019] [Accepted: 02/14/2019] [Indexed: 12/19/2022]
Abstract
The elongation of very long chain fatty acids protein 6 (ELOVL6) gene encodes a key enzyme that plays a role in lipogenesis through the catalytic elongation of both saturated and monounsaturated fatty acids. Previous studies have described the high expression of bovine ELOVL6 in adipose tissues. However, transcriptional regulation and the functional role of ELOVL6 in lipid metabolism and adipocyte proliferation remain unexplored. Here, a 1.5 kb fragment of the 5'-untranslated region promoter region of ELOVL6 was amplified from the genomic DNA of Qinchuan cattle and sequenced. The core promoter region was identified through unidirectional 5'-end deletion of the promoter plasmid vector. In silico analysis predicted important transcription factors that were then validated through site-directed mutation and small interfering RNA interference with an electrophoretic mobility shift assay. We found that the binding of KLF6 and PU.1 transcription factors occurred in the region -168/+69. Both perform a vital regulatory function in the transcription of bovine ELOVL6. Overexpression of ELOVL6 significantly upregulated the expression of peroxisome proliferator activated receptor γ (PPARγ), but inhibited the expression of fatty acid-binding protein 4 (FABP4), while silencing of ELOVL6 negatively regulated the messenger RNA expression level of PPARγ, FABP4, ACSL, and FATP1. In addition, ELOVL6 promotes adipocyte proliferation by regulating the cell-cycle genes' expression. Taken together, these findings provide useful information about the transcriptional regulation and functional mechanisms of bovine ELOVL6 in lipid metabolism and adipocyte proliferation in Qinchuan cattle.
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Affiliation(s)
- Zainaguli Junjvlieke
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Chu-Gang Mei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Wen-Zhen Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jie-Yun Hong
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Li Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Shi-Jun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Lin-Sen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi, China
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31
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Comprehensive Analysis of Differentially Expressed mRNA, lncRNA and circRNA and Their ceRNA Networks in the Longissimus Dorsi Muscle of Two Different Pig Breeds. Int J Mol Sci 2019; 20:ijms20051107. [PMID: 30836719 PMCID: PMC6429497 DOI: 10.3390/ijms20051107] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 12/22/2022] Open
Abstract
Circular RNA (circRNA) and long non-coding RNA (lncRNA) are known to participate in adipogenesis and myogenic differentiation, but their impact on porcine muscle traits is not well understood. We compared their expressional profiles in the longissimus dorsi muscle of Chinese Huainan pigs (HN, the fat type) and Western commercial Duroc×(Landrace×Yorkshire) (DLY, the thin type) pigs, and 854 mRNAs, 233 lncRNAs, and 66 circRNAs (p < 0.05 and ｜log₂FoldChange｜>1) were found to be differentially expressed. The differentially expressed mRNA and circRNA parental genes were enriched in the Wnt signaling pathway (adipogenesis), the transition between fast and slow fibers (myogenic differentiation), and alanine, aspartate and glutamate metabolism (pork flavor). The potential lncRNAs/circRNAs-miRNAs-mRNAs regulatory networks shared MYOD1, PPARD, miR-423-5p and miR-874, which were associated with skeletal muscle muscular proliferation, differentiation/regeneration and adipogenesis. Taken together, these differentially expressed non-coding RNAs may be involved in the molecular basis of muscle traits, acting as the competing endogenous RNA (ceRNA) for miRNAs.
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32
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Zhang X, Yang Q, Ding T, Xu J, Yan Z, Men Y, Xin W, Xu H. Retracted Article: Gm5820, an antisense RNA of FGF1, suppresses FGF1 expression at the posttranscriptional level to inactivate the ERK/STAT3 pathway and alleviates neuropathic pain in mice. RSC Adv 2019; 9:28364-28376. [PMID: 35529622 PMCID: PMC9071159 DOI: 10.1039/c9ra03791h] [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: 05/20/2019] [Accepted: 09/02/2019] [Indexed: 11/21/2022] Open
Abstract
Emerging evidence reveals that lncRNAs play important roles in various pathological processes, but precious little indicates their regulatory role in neuropathic pain.
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Affiliation(s)
- Xin Zhang
- Department of Pain
- Huaihe Hospital of Henan University
- Kaifeng 475000
- China
| | - Qing Yang
- Department of Anesthesiology
- Huaihe Hospital of Henan University
- Kaifeng 475000
- China
| | - Tao Ding
- Department of Anesthesiology
- Huaihe Hospital of Henan University
- Kaifeng 475000
- China
| | - Jingyu Xu
- Department of Pain
- Huaihe Hospital of Henan University
- Kaifeng 475000
- China
| | - Zeng Yan
- Department of Anesthesiology
- Huaihe Hospital of Henan University
- Kaifeng 475000
- China
| | - Yanhua Men
- Department of Anesthesiology
- Huaihe Hospital of Henan University
- Kaifeng 475000
- China
| | - Wenqi Xin
- Department of Anesthesiology
- Huaihe Hospital of Henan University
- Kaifeng 475000
- China
| | - Haixia Xu
- Department of Anesthesiology
- Huaihe Hospital of Henan University
- Kaifeng 475000
- China
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33
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Zhang X, Zhang P, Song D, Xiong S, Zhang H, Fu J, Gao F, Chen H, Zeng X. Expression profiles and characteristics of human lncRNA in normal and asthenozoospermia sperm†. Biol Reprod 2018; 100:982-993. [DOI: 10.1093/biolre/ioy253] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/16/2018] [Accepted: 12/01/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Xiaoning Zhang
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
- Jiangxi Provincial Key Laboratory of Reproductive Physiology and Pathology, Nanchang University, Nanchang, China
| | - Peng Zhang
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Dandan Song
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Suping Xiong
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | | | - Jianbo Fu
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Fengxin Gao
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Houyang Chen
- Reproductive Medical Center, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi, China
| | - Xuhui Zeng
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
- Jiangxi Provincial Key Laboratory of Reproductive Physiology and Pathology, Nanchang University, Nanchang, China
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34
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Wang GZ, Du K, Hu SQ, Chen SY, Jia XB, Cai MC, Shi Y, Wang J, Lai SJ. Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue. Lipids Health Dis 2018; 17:271. [PMID: 30486837 PMCID: PMC6263043 DOI: 10.1186/s12944-018-0915-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/15/2018] [Indexed: 02/06/2023] Open
Abstract
Background The rabbit is widely used as an important experimental model for biomedical research, and shows low adipose tissue deposition during growth. Long non-coding RNAs (lncRNAs) are associated with adipose growth, but little is known about the function of lncRNAs in the rabbit adipose tissue. Methods Deep RNA-sequencing and comprehensive bioinformatics analyses were used to characterize the lncRNAs of rabbit visceral adipose tissue (VAT) at 35, 85 and 120 days after birth. Differentially expressed (DE) lncRNAs were identified at the three growth stages by DESeq. The cis and trans prediction ways predicted the target genes of the DE lncRNAs. To explore the function of lncRNAs, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed on the candidate genes. Results A total of 991,157,544 clean reads were generated after RNA-Seq of the three growth stages, of which, 30,353 and 107 differentially expressed (DE) lncRNAs were identified. Compared to the protein-coding transcripts, the rabbit lncRNAs shared some characteristics such as shorter length and fewer exons. Cis and trans target gene prediction revealed, 43 and 64 DE lncRNAs respectively, corresponding to 72 and 20 protein-coding genes. GO enrichment and KEGG pathway analyses revealed that the candidate DE lncRNA target genes were involved in oxidative phosphorylation, glyoxylate and dicarboxylate metabolism, and other adipose growth-related pathways. Six DE lncRNAs were randomly selected and validated by q-PCR. Conclusions This study is the first to profile the potentially functional lncRNAs in the adipose tissue growth in rabbits, and contributes to our understanding of mammalian adipogenesis. Electronic supplementary material The online version of this article (10.1186/s12944-018-0915-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guo-Ze Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.,College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Kun Du
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shen-Qiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xian-Bo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ming-Cheng Cai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Shi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China
| | - Song-Jia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, China.
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35
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Sun Y, Chen X, Qin J, Liu S, Zhao R, Yu T, Chu G, Yang G, Pang W. Comparative Analysis of Long Noncoding RNAs Expressed during Intramuscular Adipocytes Adipogenesis in Fat-Type and Lean-Type Pigs. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:12122-12130. [PMID: 30339027 DOI: 10.1021/acs.jafc.8b04243] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The meat quality of local breed pigs is more tender and juicier than the imported varieties. The important reason is that the intramuscular fat content is high. Even through modest sequence conservation and evolution, the expression pattern and function of long noncoding RNAs (lncRNAs) seem to be conserved. In spite of that, analysis of lncRNAs associated with intramuscular fat development remains unknown to us in porcine. Here, we systematically investigated lncRNAs of intramuscular adipocytes of fat local Bamei pigs and lean Large White pigs to consider the function of lncRNAs on intramuscular fat development. We selected three piglets of both breeds separately to isolate intramuscular preadipocytes, performed RNA sequencing across four stages (0, 2, 4, and 8 d) during the intramuscular preadipocytes differentiation, and identified 1932 lncRNAs (760 novel). In addition, we have screened lnc_000414 closely related to fat synthesis. This lncRNA function as an inhibitor in the proliferation of porcine intramuscular adipocytes. These novel findings will provide new targets for improving pork quality and making pig breeding better.
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Affiliation(s)
- Yunmei Sun
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Xiaochang Chen
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Jin Qin
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Shuge Liu
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Rui Zhao
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Taiyong Yu
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Guiyan Chu
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Gongshe Yang
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Weijun Pang
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi 712100 , China
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36
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Chen X, Sun Y, Cai R, Wang G, Shu X, Pang W. Long noncoding RNA: multiple players in gene expression. BMB Rep 2018; 51:280-289. [PMID: 29636120 PMCID: PMC6033065 DOI: 10.5483/bmbrep.2018.51.6.025] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Indexed: 01/13/2023] Open
Abstract
Previously considered as a component of transcriptional noise, long noncoding RNAs (lncRNAs) were neglected as a therapeutic target, however, recently increasing evidence has shown that lncRNAs can participate in numerous biological processes involved in genetic regulation including epigenetic, transcriptional, and post-transcriptional regulation. In this review, we discuss the fundamental functions of lncRNAs at different regulatory levels and their roles in metabolic balance. Typical examples are introduced to illustrate their diverse molecular mechanisms. The comprehensive investigation and identification of key lncRNAs will not only contribute to insights into diseases, such as breast cancer and type II diabetes, but also provide promising therapeutic targets for related diseases. [BMB Reports 2018; 51(6): 280-289].
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Affiliation(s)
- Xiaochang Chen
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Yunmei Sun
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Rui Cai
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Guoqiang Wang
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Xiaoyan Shu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan Province 621010, China
| | - Weijun Pang
- Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province 712100, China
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37
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Abstract
Long noncoding RNAs (lncRNAs) are an important group of pervasive noncoding RNAs (>200nt) proposed to be crucial regulators of numerous physiological and pathological processes. Through interactions with RNA, chromatin, and protein, lncRNAs modulate mRNA stability, chromatin structure, and the function of proteins (including transcription factors). In addition, to their well-known roles in the modulation of cell growth, apoptosis, neurological disease progression and cancer metastasis, these large molecules have also been identified as likely mediators of lipid metabolism. In particular, lncRNAs orchestrate adipogenesis; fatty acid, cholesterol, and phospholipid metabolism and transport; and the formation of high-density and low-density lipoproteins (HDLs and LDLs). LncRNAs also appear to target several transcription factors that play essential roles in the regulation of lipid metabolism, such as liver X receptors (LXRs), sterol regulatory element binding proteins (SREBPs), and peroxisome proliferator-activated receptor γ (PPARγ). Better understanding the regulatory roles of lncRNAs in dyslipidemia, atherosclerosis, and adipogenesis will reveal appropriate strategies to treat these diseases. In this review, we review recent progress in lncRNA-mediated regulation of lipid metabolism, as well as its role in the regulation of adipogenesis.
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38
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Chen C, Cui Q, Zhang X, Luo X, Liu Y, Zuo J, Peng Y. Long non-coding RNAs regulation in adipogenesis and lipid metabolism: Emerging insights in obesity. Cell Signal 2018; 51:47-58. [PMID: 30071290 DOI: 10.1016/j.cellsig.2018.07.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/27/2018] [Accepted: 07/29/2018] [Indexed: 12/15/2022]
Abstract
Obesity is a widespread health problem that brings about various adipose tissue dysfunctions. The balance of energy storage and energy expenditure is critical for normal fat accumulation and lipid metabolism. Therefore, understanding the molecular basis of adipogenesis and thermogenesis is essential to maintain adipose development and lipid homeostasis. Increasing evidence demonstrated that lncRNAs (long non-coding RNAs), a class of non-protein coding RNAs of >200 nucleotides in length, are identified as key regulators in obesity-related biological processes through diverse regulatory mechanisms. In this review, we concentrate on recent and relevant studies on the roles of lncRNAs in regulation of white adipogenesis, brown adipocyte differentiation and lipid metabolism. In addition, the diagnostic and therapeutic potential of lncRNAs is highlighted, and that will make recommendations for the future application of lncRNAs in the treatment of obesity.
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Affiliation(s)
- Chen Chen
- Hunan Institute of Animal & Veterinary Science, Changsha, 410131, PR China.
| | - Qingming Cui
- Hunan Institute of Animal & Veterinary Science, Changsha, 410131, PR China
| | - Xing Zhang
- Hunan Institute of Animal & Veterinary Science, Changsha, 410131, PR China
| | - Xuan Luo
- Hunan Institute of Animal & Veterinary Science, Changsha, 410131, PR China
| | - Yingying Liu
- Hunan Institute of Animal & Veterinary Science, Changsha, 410131, PR China
| | - Jianbo Zuo
- Hunan Institute of Animal & Veterinary Science, Changsha, 410131, PR China
| | - Yinglin Peng
- Hunan Institute of Animal & Veterinary Science, Changsha, 410131, PR China.
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39
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Kong F, Deng X, Kong X, Du Y, Li L, Zhu H, Wang Y, Xie D, Guha S, Li Z, Guan M, Xie K. ZFPM2-AS1, a novel lncRNA, attenuates the p53 pathway and promotes gastric carcinogenesis by stabilizing MIF. Oncogene 2018; 37:5982-5996. [PMID: 29985481 PMCID: PMC6226322 DOI: 10.1038/s41388-018-0387-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 04/02/2018] [Accepted: 05/05/2018] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) are implicated to be involved in the pathogenesis of many cancers. Herein we report on our discovery of a novel lncRNA, ZFPM2 antisense RNA 1 (ZFPM2-AS1), and its critical role in gastric carcinogenesis. ZFPM2-AS1 expression in gastric cancer specimens was analyzed using Gene Expression Omnibus data set and validated in 73 paired gastric tumor and normal adjacent gastric tissue specimens using qRT-PCR. The effect of ZFPM2-AS1 expression on proliferation and apoptosis in gastric cancer cells was assessed by altering its expression in vitro and in vivo. Mechanistic investigation was carried out using cell and molecular biological approaches. ZFPM2-AS1 expression was higher in gastric tumors than in normal gastric tissue. Also, increased ZFPM2-AS1 expression in gastric cancer specimens was associated with tumor size, depth of tumor invasion, differentiation grade, and TNM stage. High ZFPM2-AS1 expression predicted markedly reduced overall and disease-free survival in gastric cancer patients. Functional experiments demonstrated that ZFPM2-AS1 expression promoted proliferation and suppressed apoptosis of gastric cancer cells in vitro and promoted tumor growth in vivo. This effect is associated with attenuated nuclear translocation of p53. Mechanistic experiments demonstrated that tumor-activated ZFPM2-AS1 could bind to and protect the degradation of macrophage migration inhibitory factor (MIF), a potent destabilizer of p53. Knockdown of MIF expression diminished ZFPM2-AS1's impact on p53 expression in gastric cancer cells. Our findings demonstrated that ZFPM2-AS1 regulates gastric cancer progression and revealed a novel ZFPM2-AS1/MIF/p53 signaling axis, shedding light on the molecular mechanisms underlying the tumorigenicity of certain malignant gastric cells.
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Affiliation(s)
- Fanyang Kong
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China.,Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xuan Deng
- Department of Laboratory Medicine, Huashan Hospital Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Xiangyu Kong
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China.,Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yiqi Du
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Lei Li
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Huiyun Zhu
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Yuxin Wang
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Dacheng Xie
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shivani Guha
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Zhaoshen Li
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China.
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital Shanghai Medical College, Fudan University, Shanghai, People's Republic of China.
| | - Keping Xie
- Department of Gastroenterology, Hepatology & Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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40
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Integrated analysis of long noncoding RNA and mRNA expression profile in children with obesity by microarray analysis. Sci Rep 2018; 8:8750. [PMID: 29884798 PMCID: PMC5993825 DOI: 10.1038/s41598-018-27113-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 05/30/2018] [Indexed: 12/29/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have an important role in adipose tissue function and energy metabolism homeostasis, and abnormalities may lead to obesity. To investigate whether lncRNAs are involved in childhood obesity, we investigated the differential expression profile of lncRNAs in obese children compared with non-obese children. A total number of 1268 differentially expressed lncRNAs and 1085 differentially expressed mRNAs were identified. Gene Ontology (GO) and pathway analysis revealed that these lncRNAs were involved in varied biological processes, including the inflammatory response, lipid metabolic process, osteoclast differentiation and fatty acid metabolism. In addition, the lncRNA-mRNA co-expression network and the protein-protein interaction (PPI) network were constructed to identify hub regulatory lncRNAs and genes based on the microarray expression profiles. This study for the first time identifies an expression profile of differentially expressed lncRNAs in obese children and indicated hub lncRNA RP11-20G13.3 attenuated adipogenesis of preadipocytes, which is conducive to the search for new diagnostic and therapeutic strategies of childhood obesity.
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41
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Liu P, Jin L, Zhao L, Long K, Song Y, Tang Q, Ma J, Wang X, Tang G, Jiang Y, Zhu L, Li X, Li M. Identification of a novel antisense long non-coding RNA PLA2G16-AS that regulates the expression of PLA2G16 in pigs. Gene 2018; 671:78-84. [PMID: 29860067 DOI: 10.1016/j.gene.2018.05.114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/28/2018] [Accepted: 05/30/2018] [Indexed: 02/06/2023]
Abstract
Natural antisense transcripts (NATs) are widely present in mammalian genomes and act as pivotal regulator molecules to control gene expression. However, studies on the NATs of pigs are relatively rare. Here, we identified a novel antisense transcript, designated PLA2G16-AS, transcribed from the phospholipase A2 group XVI locus (PLA2G16) in the porcine genome, which is a well-known regulatory molecule of fat deposition. PLA2G16-AS and PLA2G16 were dominantly expressed in porcine adipose tissue, and were differentially expressed between Tibetan pigs and Rongchang pigs. In addition, PLA2G16-AS has a weak sequence conservation among different vertebrates. PLA2G16-AS was also shown to form an RNA-RNA duplex with PLA2G16, and to regulate PLA2G16 expression at the mRNA level. Moreover, the overexpression of PLA2G16-AS increased the stability of PLA2G16 mRNA in porcine cells. We envision that our findings of a NAT for a regulatory gene associated with lipolysis might further our understanding of the molecular regulation of fat deposition.
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Affiliation(s)
- Pengliang Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Long Jin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Lirui Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Keren Long
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Yang Song
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Qianzi Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Jideng Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Xun Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Guoqing Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Xuewei Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Mingzhou Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China.
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42
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Cai R, Sun Y, Qimuge N, Wang G, Wang Y, Chu G, Yu T, Yang G, Pang W. Adiponectin AS lncRNA inhibits adipogenesis by transferring from nucleus to cytoplasm and attenuating Adiponectin mRNA translation. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:420-432. [DOI: 10.1016/j.bbalip.2018.01.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/22/2017] [Accepted: 01/08/2018] [Indexed: 02/06/2023]
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43
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Zou C, Li L, Cheng X, Li C, Fu Y, Fang C, Li C. Identification and Functional Analysis of Long Intergenic Non-coding RNAs Underlying Intramuscular Fat Content in Pigs. Front Genet 2018; 9:102. [PMID: 29662503 PMCID: PMC5890112 DOI: 10.3389/fgene.2018.00102] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/13/2018] [Indexed: 12/12/2022] Open
Abstract
Intramuscular fat (IMF) content is an important trait that can affect pork quality. Previous studies have identified many genes that can regulate IMF. Long intergenic non-coding RNAs (lincRNAs) are emerging as key regulators in various biological processes. However, lincRNAs related to IMF in pig are largely unknown, and the mechanisms by which they regulate IMF are yet to be elucidated. Here we reconstructed 105,687 transcripts and identified 1,032 lincRNAs in pig longissimus dorsi muscle (LDM) of four stages with different IMF contents based on published RNA-seq. These lincRNAs show typical characteristics such as shorter length and lower expression compared with protein-coding genes. Combined with methylation data, we found that both the promoter and genebody methylation of lincRNAs can negatively regulate lincRNA expression. We found that lincRNAs exhibit high correlation with their protein-coding neighbors in expression. Co-expression network analysis resulted in eight stage-specific modules, gene ontology and pathway analysis of them suggested that some lincRNAs were involved in IMF-related processes, such as fatty acid metabolism and peroxisome proliferator-activated receptor signaling pathway. Furthermore, we identified hub lincRNAs and found six of them may play important roles in IMF development. This work detailed some lincRNAs which may affect of IMF development in pig, and facilitated future research on these lincRNAs and molecular assisted breeding for pig.
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Affiliation(s)
- Cheng Zou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Long Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Xiaofang Cheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Cencen Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Yuhua Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Chengchi Fang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Changchun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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Zhu XX, Yan YW, Chen D, Ai CZ, Lu X, Xu SS, Jiang S, Zhong GS, Chen DB, Jiang YZ. Long non-coding RNA HoxA-AS3 interacts with EZH2 to regulate lineage commitment of mesenchymal stem cells. Oncotarget 2018; 7:63561-63570. [PMID: 27566578 PMCID: PMC5325385 DOI: 10.18632/oncotarget.11538] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/15/2016] [Indexed: 01/15/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play an important role in gene regulation and are involving in diverse cellular processes. However, their roles in reprogramming of gene expression profiles during lineage commitment and maturation of mesenchymal stem cells (MSCs) remain poorly understood. In the current study, we characterize the expression of a lncRNA, HoxA-AS3, during the differentiation of MSCs. We showed that HoxA-AS3 is increased upon adipogenic induction of MSCs, while HoxA-AS3 remains unaltered during osteogenic induction. Silencing of HoxA-AS3 in MSCs resulted in decreased adipogenesis and expression of adipogenic markers, PPARG, CEBPA, FABP4 and ADIPOQ. Conversely, knockdown of HoxA-AS3 expression in MSCs exhibited an enhanced osteogenesis and osteogenic markers expression, including RUNX2, SP7, COL1A1, IBSP, BGLAP and SPP1. Mechanistically, HoxA-AS3 interacts with Enhancer Of Zeste 2 (EZH2) and is required for H3 lysine-27 trimethylation (H3K27me3) of key osteogenic transcription factor Runx2. Our data reveal that HoxA-AS3 acts as an epigenetic switch that determines the lineage specification of MSC.
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Affiliation(s)
- Xin-Xing Zhu
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Ya-Wei Yan
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Demeng Chen
- School of Dentistry, University of California, Los Angeles, CA, USA
| | - Chun-Zhi Ai
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Xifeng Lu
- Department of Physiology, Center for Diabetes, Obesity and Metabolism, Shenzhen University Health Science Center, Shenzhen University, Shenzhen, Guangdong, China
| | - Shan-Shan Xu
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Shan Jiang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Gen-Shen Zhong
- Henan Key Laboratory of Neural Regeneration and Repairment, The First affiliated Hospital of Xinxiang Medical University, Weihui, Henan, China
| | - Dong-Bao Chen
- Department of Obstetrics and Gynecology, University of California, Irvine, CA, USA
| | - Yi-Zhou Jiang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
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PU.1-deficient mice are resistant to thioacetamide-induced hepatic fibrosis: PU.1 finely regulates Sirt1 expression via transcriptional promotion of miR-34a and miR-29c in hepatic stellate cells. Biosci Rep 2017; 37:BSR20170926. [PMID: 29162670 PMCID: PMC5725609 DOI: 10.1042/bsr20170926] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 11/18/2017] [Accepted: 11/21/2017] [Indexed: 12/13/2022] Open
Abstract
PU box binding protein (PU.1) is a critical transcription factor involved in many pathological processes. However, its exact role in activation of hepatic stellate cells (HSCs) and liver fibrosis was rarely reported. Here, we found that, in HSCs of PU.1+/− mice, Sirt1 mRNA expression was not changed but Sirt1 protein was significantly increased, suggesting its promoting role in Sirt1 translation. We then isolated HSCs from wild-type (WT) and PU.1+/− mice, and the pcDNA-PU.1 expression vector was transfected into PU.1+/− HSCs. We checked the levels of miR-34a and miR-29c, two Sirt1-targetting miRNAs, and protein levels of PU.1 and Sirt1. The results showed that miR-34a/-29c were significantly reduced and Sirt1 protein was increased in PU.1+/− HSCs, compared with WT HSCs. Besides, PU.1 overexpression inversed the reduction in miR-34a/-29c levels and the increase in Sirt1 protein in both PU.1+/- HSCs and WT HSCs. Additionally, ChIP-quantitive real-time PCR (qPCR) assay comfirmed that PU.1 was directly bound to both the promoter regions of miR-34a and miR-29c. Importantly, PU.1 overexpression promoted the proliferation, migration, activation, oxidative stress and inflammatory response in WT HSCs, while the promotion could be inversed by either overexpression of Sirt1 or inhibition of miR-34a/-29c. Moreover, animal model of liver fibrosis was established by intraperitoneal injections of thioacetamide (TAA) in WT and PU.1+/− mice, respectively. Compared with the WT mice, PU.1+/− mice displayed a lower fibrotic score, less collagen content, better liver function, and lower levels of oxidative stress and inflammatory response. In conclusion, PU.1 suppresses Sirt1 translation via transcriptional promotion of miR-34a/-29c, thus promoting Sirt1-mediated HSC activation and TAA-induced hepatic fibrosis.
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Long Non-Coding RNAs in Metabolic Organs and Energy Homeostasis. Int J Mol Sci 2017; 18:ijms18122578. [PMID: 29189723 PMCID: PMC5751181 DOI: 10.3390/ijms18122578] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/20/2017] [Accepted: 11/24/2017] [Indexed: 12/15/2022] Open
Abstract
Single cell organisms can surprisingly exceed the number of human protein-coding genes, which are thus not at the origin of the complexity of an organism. In contrast, the relative amount of non-protein-coding sequences increases consistently with organismal complexity. Moreover, the mammalian transcriptome predominantly comprises non-(protein)-coding RNAs (ncRNA), of which the long ncRNAs (lncRNAs) constitute the most abundant part. lncRNAs are highly species- and tissue-specific with very versatile modes of action in accordance with their binding to a large spectrum of molecules and their diverse localization. lncRNAs are transcriptional regulators adding an additional regulatory layer in biological processes and pathophysiological conditions. Here, we review lncRNAs affecting metabolic organs with a focus on the liver, pancreas, skeletal muscle, cardiac muscle, brain, and adipose organ. In addition, we will discuss the impact of lncRNAs on metabolic diseases such as obesity and diabetes. In contrast to the substantial number of lncRNA loci in the human genome, the functionally characterized lncRNAs are just the tip of the iceberg. So far, our knowledge concerning lncRNAs in energy homeostasis is still in its infancy, meaning that the rest of the iceberg is a treasure chest yet to be discovered.
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Liu W, Ma C, Yang B, Yin C, Zhang B, Xiao Y. LncRNA Gm15290 sponges miR-27b to promote PPARγ-induced fat deposition and contribute to body weight gain in mice. Biochem Biophys Res Commun 2017; 493:1168-1175. [PMID: 28943435 DOI: 10.1016/j.bbrc.2017.09.114] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 09/20/2017] [Indexed: 11/15/2022]
Abstract
We found that Gm15290 was one of the most upregulated lncRNAs in the adipose of ob/ob mice through lncRNA microarray analysis. Then, manipulations of overexpression and silencing in mouse primary adipocytes showed that Gm15290 positively regulated adipogenesis, manifested by increasing lipid deposition and upregulating adipogenic genes including PPARγ, C/EBPα, and aP2. However, overexpression of mutant Gm15290 (at the binding site of miR-27c) did not have an promoting effect on adipogenesis. Additionally, Gm15290 was found to potentially interact with miR-27b that had been identified as a PPARγ targeting miRNA, and we verified their interaction by luciferase activity and RNA pull down assays. Furthermore, inhibition of Gm15290, by injection of the Gm15290 siRNA, decreased the body weight gain and mass of adipose tissues, including iWAT and eWAT, in mice fed with HFD. In conclusion, Gm15290 sponges miR-27b to increase fat deposition and body weight in HFD-fed mice.
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Affiliation(s)
- Weihua Liu
- Pediatrics Department, The Second Affiliated Hospital of Xi'an Jiaotong University, China; Pediatrics Department, The First Hospital of Xi'an, China
| | - Chunli Ma
- Pediatrics Department, Baoji People's Hospital, China
| | - Bin Yang
- Pediatrics Department, Chang'an District Maternal and Child Health Care of Xi'an, China
| | - Chunyan Yin
- Pediatrics Department, The Second Affiliated Hospital of Xi'an Jiaotong University, China
| | - Beining Zhang
- Pediatrics Department, The First Hospital of Xi'an, China
| | - Yanfeng Xiao
- Pediatrics Department, The Second Affiliated Hospital of Xi'an Jiaotong University, China.
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Zou C, Li S, Deng L, Guan Y, Chen D, Yuan X, Xia T, He X, Shan Y, Li C. Transcriptome Analysis Reveals Long Intergenic Noncoding RNAs Contributed to Growth and Meat Quality Differences between Yorkshire and Wannanhua Pig. Genes (Basel) 2017; 8:genes8080203. [PMID: 28820450 PMCID: PMC5575666 DOI: 10.3390/genes8080203] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 08/12/2017] [Accepted: 08/14/2017] [Indexed: 01/28/2023] Open
Abstract
There are major differences between Yorkshire (lean-type) and Wannanhua pig (fat-type) in terms of growth performance and meat quality. Long intergenic noncoding RNAs (lincRNAs) are a class of regulators that are involved in numerous biological processes and widely identified in many species. However, the role of lincRNAs in pig is largely unknown, and the mechanisms by which they affect growth and meat quality are elusive. In this study, we used published data to identify 759 lincRNAs in porcine longissimus dorsi muscle. These putative lincRNAs shared many features with mammalian lincRNAs, such as shorter length and fewer exons. Gene ontology and pathway analysis indicated that many potential target genes (PTGs) of lincRNAs were involved in muscle growth-related and meat quality-related biological processes. Moreover, we constructed a co-expression network between differentially expressed lincRNAs (DELs) and their PTGs, and found a potential mechanism that most DELs can use to upregulate their PTGs, which may finally contribute to the growth and meat quality differences between the two breeds through an unknown manner. This work details some lincRNAs and their PTGs related to muscle growth or meat quality, and facilitates future research on the roles of lincRNAs in these two types of pig, as well as molecular-assisted breeding for pig.
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Affiliation(s)
- Cheng Zou
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Sha Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Lulu Deng
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yang Guan
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Dake Chen
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiongkun Yuan
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Tianrui Xia
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xinglin He
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yawei Shan
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Changchun Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Yu L, Tai L, Zhang L, Chu Y, Li Y, Zhou L. Comparative analyses of long non-coding RNA in lean and obese pig. Oncotarget 2017; 8:41440-41450. [PMID: 28589911 PMCID: PMC5522191 DOI: 10.18632/oncotarget.18269] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 05/15/2017] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES Current studies have revealed that long non-coding RNA plays a crucial role in fat metabolism. However, the difference of lncRNA between lean (Duroc) and obese (Luchuan) pig remain undefined. Here, we investigated the expressional profile of lncRNA in these two pigs and discussed the relationship between lncRNA and fat deposition. MATERIALS AND METHODS The Chinese Luchuan pig has a dramatic differences in backfat thickness as compared with Duroc pig. In this study, 4868 lncRNA transcripts (including 3235 novel transcripts) were identified. We determined that patterns of differently expressed lncRNAs and mRNAs are strongly tissue-specific. The differentially expressed lncRNAs in adipose tissue have 794 potential target genes, which are involved in adipocytokine signaling pathways, the PI3k-Akt signaling pathway, and calcium signaling pathways. In addition, differentially expressed lncRNAs were located to 13 adipose-related quantitative trait loci which include 65 QTL_ID. Subsequently, lncRNA and mRNA in the same QTL_ID were analyzed and their co-expression in two QTL_ID were confirmed by qPCR. CONCLUSIONS Our study provides an insight into mechanism behind the fat metabolic differences between the two breeds and lays an important groundwork for further research regarding the regulatory role of lncRNA in obesity development.
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Affiliation(s)
- Lin Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Lina Tai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Lifang Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Yi Chu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Yixing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Lei Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
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Ni Y, Huang H, Chen Y, Cao M, Zhou H, Zhang Y. Investigation of Long Non-coding RNA Expression Profiles in the Substantia Nigra of Parkinson's Disease. Cell Mol Neurobiol 2017; 37:329-338. [PMID: 27151187 DOI: 10.1007/s10571-016-0373-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 12/17/2015] [Indexed: 01/18/2023]
Abstract
Genetics is considered as an important risk factor in the pathological changes of Parkinson's disease (PD). Substantia nigra (SN) is thought to be the most vulnerable area in this process. In recent decades, however, few related long non-coding RNAs (lncRNAs) in the SN of PD patients had been identified and the functions of those lncRNAs had been studied even less. In this study, we sought to investigate the lncRNA expression profiles and their potential functions in the SN of PD patients. We screened lncRNA expression profiles in the SN of PD patients using the lncRNA mining approach from the ArrayExpress database, which included GSE20295. The samples were from 11 of PD and 14 of normal tissue samples. We identified 87 lncRNAs that were altered significantly in the SN during the occurrence of PD. Among these lncRNAs, lncRNA AL049437 and lncRNA AK021630 varied most dramatically. AL049437 was up-regulated in the PD samples, while AK021630 was down-regulated. Based on the results, we focused on the potential roles of the two lncRNAs in the pathogenesis of PD by the knockdown of the expression of AL049437 or AK021630 in human neuroblastoma SH-SY5Y cell line. Results indicated that the reduction in AL049437 level increased cell viability, mitochondrial transmembrane potential (Δψm), mitochondrial mass, and tyrosine hydroxylase (TyrH) secretion. By contrast, the knockdown of AK021630 resulted in the opposite effect. Based on these results, we speculated that lncRNA AL049437 likely contributed to the risk of PD, while lncRNA AK021630 likely inhibited the occurrence of PD.
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Affiliation(s)
- Yaohui Ni
- Department of Neurology, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu Province, China
| | - Hua Huang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu Province, China
| | - Yaqin Chen
- Department of Neurology, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu Province, China
| | - Maohong Cao
- Department of Neurology, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu Province, China
| | - Hongzhi Zhou
- Department of Neurology, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu Province, China
| | - Yuanyuan Zhang
- Department of Neurology, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu Province, China.
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