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Zeng M, Yan S, Yang P, Li Q, Li J, Fan X, Liu X, Yao Y, Wang W, Chen R, Han G, Yang Y, Tang Z. Circular RNA transcriptome across multiple tissues reveal skeletal muscle-specific circPSME4 regulating myogenesis. Int J Biol Macromol 2023; 251:126322. [PMID: 37591436 DOI: 10.1016/j.ijbiomac.2023.126322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
There are significant differences in meat production, growth rate and other traits between Western commercial pigs and Chinese local pigs. Comparative transcriptome approaches have identified many coding and non-coding candidate genes associated various traits. However, the expression and function of circular RNAs (circRNAs) in different pig tissues are largely unknown. In this study, we conducted a comprehensive analysis of the genome-wide circRNA expression profile across ten tissues in Luchuan (a Chinese local breed) and Duroc (a Western commercial breed) pigs. We identified a total of 56,254 circRNAs, of which 42.9 % were not previously annotated. We found that 33.7 % of these circRNAs were differentially expressed. Enrichment analysis revealed that differentially expressed circRNAs might contribute to the phenotypic differentiation between Luchuan and Duroc pigs. We identified 538 tissue-specific circRNAs, most of which were specifically expressed in the brain and skeletal muscle. Competitive endogenous RNA network analysis suggested that skeletal muscle-specific circPSME4 was co-expressed with MYOD1 and targeted by ssc-miR-181d-3p. Functional analysis revealed that circPSME4 knockdown could promote the proliferation and differentiation of myoblasts. Together, our findings provide valuable resources of circRNAs for animal breeding and biomedical research. We demonstrated that circPSME4 is a novel regulator of skeletal muscle development.
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Affiliation(s)
- Mu Zeng
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Shanying Yan
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Peng Yang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Qiaowei Li
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; School of Veterinary Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Jiju Li
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xinhao Fan
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiaoqin Liu
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yilong Yao
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Wei Wang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ruipu Chen
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Guohao Han
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yalan Yang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
| | - Zhonglin Tang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
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Nguyen MT, Dash R, Jeong K, Lee W. Role of Actin-Binding Proteins in Skeletal Myogenesis. Cells 2023; 12:2523. [PMID: 37947600 PMCID: PMC10650911 DOI: 10.3390/cells12212523] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023] Open
Abstract
Maintenance of skeletal muscle quantity and quality is essential to ensure various vital functions of the body. Muscle homeostasis is regulated by multiple cytoskeletal proteins and myogenic transcriptional programs responding to endogenous and exogenous signals influencing cell structure and function. Since actin is an essential component in cytoskeleton dynamics, actin-binding proteins (ABPs) have been recognized as crucial players in skeletal muscle health and diseases. Hence, dysregulation of ABPs leads to muscle atrophy characterized by loss of mass, strength, quality, and capacity for regeneration. This comprehensive review summarizes the recent studies that have unveiled the role of ABPs in actin cytoskeletal dynamics, with a particular focus on skeletal myogenesis and diseases. This provides insight into the molecular mechanisms that regulate skeletal myogenesis via ABPs as well as research avenues to identify potential therapeutic targets. Moreover, this review explores the implications of non-coding RNAs (ncRNAs) targeting ABPs in skeletal myogenesis and disorders based on recent achievements in ncRNA research. The studies presented here will enhance our understanding of the functional significance of ABPs and mechanotransduction-derived myogenic regulatory mechanisms. Furthermore, revealing how ncRNAs regulate ABPs will allow diverse therapeutic approaches for skeletal muscle disorders to be developed.
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Affiliation(s)
- Mai Thi Nguyen
- Department of Biochemistry, Dongguk University College of Medicine, 123 Dongdae-ro, Gyeongju 38066, Republic of Korea; (M.T.N.); (K.J.)
| | - Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, 123 Dongdae-ro, Gyeongju 38066, Republic of Korea;
- Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu 42988, Republic of Korea
| | - Kyuho Jeong
- Department of Biochemistry, Dongguk University College of Medicine, 123 Dongdae-ro, Gyeongju 38066, Republic of Korea; (M.T.N.); (K.J.)
| | - Wan Lee
- Department of Biochemistry, Dongguk University College of Medicine, 123 Dongdae-ro, Gyeongju 38066, Republic of Korea; (M.T.N.); (K.J.)
- Channelopathy Research Center, Dongguk University College of Medicine, 32 Dongguk-ro, Ilsan Dong-gu, Goyang 10326, Republic of Korea
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Huang Y, Chen H, Gao X, Ren H, Gao S. Identification and functional analysis of miRNAs in skeletal muscle of juvenile and adult largemouth bass, Micropterus salmoides. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100985. [PMID: 35381488 DOI: 10.1016/j.cbd.2022.100985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/20/2022] [Accepted: 03/25/2022] [Indexed: 11/28/2022]
Abstract
MicroRNAs (miRNAs) are considered key regulators to post-transcriptionally regulate gene expression affecting multiple biological activities. However, the developmental process of fish skeletal muscles is regulated by complicated molecular mechanism that has not been completely well-described. In this study, two small RNAs libraries from skeletal muscle of juvenile as well as adult largemouth bass (LMB) were obtained and sequenced using deep sequencing to investigate the development-related miRNAs. We identified an overall number of 486 already recognized miRNAs in addition to 43 novel miRNAs. Comparison of two different skeletal muscle development stages led to the identification of 220 differently expressed miRNAs between juvenile and adult LMB containing 116 up-regulated as well as 104 down-regulated miRNAs. Of them, confirmation of some differently expressed miRNAs was performed via a stem-loop qRT-PCR, which exhibited differently expressed level in juvenile and adult LMB. Furthermore, GO and KEGG enrichment analyses of targets of differently-expressed miRNAs were carried out. Additionally, the analysis of miRNAs-targets interaction network showed that miR-181b-5p_R-1, miR-725 and miR-103 as the nodal miRNAs has over 20 target genes. Moreover, miR-103 could bind the 3'-UTR of actr8, which was validated via dual-luciferase reporter assay. It has been reasonably hypothesized that miR-103 may play a crucial role, which regulate skeletal muscle development of LMB. The present study provides the first identification of miRNA expression profiles at two different skeletal muscle development stages in LMB. Results may be valuable in interpreting the regulatory role miRNAs plays in the growth and developmental process of skeletal muscle and its possible use in LMB breeding.
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Affiliation(s)
- Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China.
| | - Haigang Chen
- Guangdong Province Key Laboratory of Fish Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Xiaochan Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Hongtao Ren
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
| | - Shiyang Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471023, China
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4
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Profiling and Functional Analysis of mRNAs during Skeletal Muscle Differentiation in Goats. Animals (Basel) 2022; 12:ani12081048. [PMID: 35454294 PMCID: PMC9024908 DOI: 10.3390/ani12081048] [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: 03/01/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 02/01/2023] Open
Abstract
Skeletal myogenesis is a complicated biological event that involves a succession of tightly controlled gene expressions. In order to identify novel regulators of this process, we performed mRNA-Seq studies of goat skeletal muscle satellite cells (MuSCs) cultured under proliferation (GM) and differentiation (DM1/DM5) conditions. A total of 19,871 goat genes were expressed during these stages, 198 of which represented novel transcripts. Notably, in pairwise comparisons at the different stages, 2551 differentially expressed genes (DEGs) were identified (p < 0.05), including 1560 in GM vs. DM1, 1597 in GM vs. DM5, and 959 in DM1 vs. DM5 DEGs. The time-series expression profile analysis clustered the DEGs into eight gene groups, three of which had significantly upregulated and downregulated patterns (p < 0.05). Functional enrichment analysis showed that DEGs were enriched for essential biological processes such as muscle structure development, muscle contraction, muscle cell development, striated muscle cell differentiation, and myofibril assembly, and were involved in pathways such as the MAPK, Wnt and PPAR signaling pathways. Moreover, the expression of eight DEGs (MYL2, DES, MYOG, FAP, PLK2, ADAM, WWC1, and PRDX1) was validated. These findings offer novel insights into the transcriptional regulation of skeletal myogenesis in goats.
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Li Y, Yang M, Lou A, Yun J, Ren C, Li X, Xia G, Nam K, Yoon D, Jin H, Seo K, Jin X. Integrated analysis of expression profiles with meat quality traits in cattle. Sci Rep 2022; 12:5926. [PMID: 35396568 PMCID: PMC8993808 DOI: 10.1038/s41598-022-09998-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 03/31/2022] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs) play a vital role in improving meat quality by binding to messenger RNAs (mRNAs). We performed an integrated analysis of miRNA and mRNA expression profiling between bulls and steers based on the differences in meat quality traits. Fat and fatty acids are the major phenotypic indices of meat quality traits to estimate between-group variance. In the present study, 90 differentially expressed mRNAs (DEGs) and 18 differentially expressed miRNAs (DEMs) were identified. Eighty-three potential DEG targets and 18 DEMs were used to structure a negative interaction network, and 75 matching target genes were shown in this network. Twenty-six target genes were designated as intersection genes, screened from 18 DEMs, and overlapped with the DEGs. Seventeen of these genes enriched to 19 terms involved in lipid metabolism. Subsequently, 13 DEGs and nine DEMs were validated using quantitative real-time PCR, and seven critical genes were selected to explore the influence of fat and fatty acids through hub genes and predict functional association. A dual-luciferase reporter and Western blot assays confirmed a predicted miRNA target (bta-miR-409a and PLIN5). These findings provide substantial evidence for molecular genetic controls and interaction among genes in cattle.
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Affiliation(s)
- Yunxiao Li
- College of Life Science, Shandong University, Qingdao, China
| | - Miaosen Yang
- Department of Chemistry, Northeast Electric Power University, Jilin, China
| | - Angang Lou
- Department of Veterinary Medicine, College of Agriculture, Yanbian University, Yanji, China
| | - Jinyan Yun
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin, China
| | - Chunyu Ren
- Animal Husbandry Bureau of Yanbian Autonomous Prefecture, Yanji, China
| | - Xiangchun Li
- Department of Veterinary Medicine, College of Agriculture, Yanbian University, Yanji, China
| | - Guangjun Xia
- Department of Veterinary Medicine, College of Agriculture, Yanbian University, Yanji, China
| | - Kichang Nam
- Department of Animal Science and Technology, College of Life Science and Natural Resources, Sunchon National University, Sunchon, South Korea
| | - Duhak Yoon
- Department of Animal Science, Kyungpook National University, Taegu, South Korea
| | - Haiguo Jin
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Kangseok Seo
- Department of Animal Science and Technology, College of Life Science and Natural Resources, Sunchon National University, Sunchon, South Korea.
| | - Xin Jin
- Engineering Research Center of North-East Cold Region Beef Cattle Science and Technology Innovation, Ministry of Education, Yanbian University, Yanji, China.
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Orzechowska K, Kopij G, Paukszto L, Dobrzyn K, Kiezun M, Jastrzebski J, Kaminski T, Smolinska N. Chemerin effect on transcriptome of the porcine endometrium during implantation determined by RNA-sequencing†. Biol Reprod 2022; 107:557-573. [PMID: 35349661 DOI: 10.1093/biolre/ioac063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/02/2022] [Accepted: 03/18/2022] [Indexed: 11/14/2022] Open
Abstract
It is well known that the body's metabolism and reproduction are closely related. Chemerin is one of many biologically active proteins secreted by the adipose tissue involved in the regulation of the energy homeostasis of the organism. In the present study, RNA-Sequencing (RNA-Seq) was performed to investigate the differentially expressed genes (DEGs), long non-coding RNAs (lncRNAs) and alternatively spliced (AS) transcripts in the cultured in vitro porcine endometrium exposed to chemerin for 24 hours (CHEM; 400 ng/ml) collected during the implantation period (15 to 16 days of gestation). High-throughput sequencing of transcriptomes was performed on the Illumina NovaSeq 6000 platform (Illumina, USA). In the current study, among all 130 DEGs, 58 were up-regulated and were 72 down-regulated in the CHEM-treated group. DEGs were assigned to 73 functional annotations. Twelve identified lncRNAs indicated a difference in the expression profile after CHEM administration. Additionally, we detected 386 differentially AS events encompassed 274 protein-coding genes and 2 lncRNAs. All AS events were divided into 5 alternative splicing types: alternative 3' splice site (A3SS), 5' splice site (A5SS), mutually exclusive exons (MXE), retention intron (RI), and skipping exon (SE). Within all AS events, we identified 42 A3SS, 43 A5SS, 53 MXE, 9 RI, and 239 SE. In summary, CHEM affects the transcriptomic profile of the porcine endometrium, controlling the expression of numerous genes, including those involved in the cell migration and adhesion, angiogenesis, inflammation, and steroidogenesis. It can be assumed that CHEM may be an important factor for a proper course of gestation and embryo development.
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Affiliation(s)
- Kinga Orzechowska
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Grzegorz Kopij
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Lukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Kamil Dobrzyn
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Marta Kiezun
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Jan Jastrzebski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Tadeusz Kaminski
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Nina Smolinska
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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Song J, Hao L, Zeng X, Yang R, Qiao S, Wang C, Yu H, Wang S, Jiao Y, Jia H, Liu S, Zhang Y. A Novel miRNA Y-56 Targeting IGF-1R Mediates the Proliferation of Porcine Skeletal Muscle Satellite Cells Through AKT and ERK Pathways. Front Vet Sci 2022; 9:754435. [PMID: 35372530 PMCID: PMC8968951 DOI: 10.3389/fvets.2022.754435] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
As a key regulator of gene transcription and post-transcriptional modification, miRNAs play a wide range of roles in skeletal muscle development. Skeletal muscle satellite cells contribute to postnatal growing muscle fibers. Thus, the goal of this study was to explore the effects of novel miRNA Y-56 on porcine skeletal muscle satellite cells (PSCs). We found that Y-56 was highly expressed in porcine muscle tissues, and its expression was higher in Bama Xiang pigs than in Landrace pigs. The EdU assay, cell counting kit-8, and flow cytometry results showed that Y-56 overexpression suppressed cell proliferation and cell cycle, whereas Y-56 inhibition resulted in the opposite consequences. The results of qRT-PCR and Western blot showed that Y-56 remarkably inhibited the expression levels of cyclin-dependent kinase 4 (CDK4), proliferating cell nuclear antigen (PCNA), and cyclin D1. We identified that IGF-1R was a direct target of Y-56 by dual-luciferase reporter assay. Moreover, IGF-1R overexpression promoted the proliferation and cell cycle process of PSCs and upregulated the expression of CDK4, PCNA, and cyclin D1. Conversely, IGF-1R knockdown had the opposite effect. Furthermore, IGF-1R overexpression partially reversed the inhibition of the cell proliferation and cell cycle process of PSCs and the downregulation of the expression of CDK4, PCNA, and Cyclin D1 caused by Y-56 overexpression. Finally, Y-56 inhibited the protein expression levels of p-AKT and p-ERK. Collectively, our findings suggested that Y-56 represses the proliferation and cell cycle process of PSCs by targeting IGF-1R-mediated AKT and ERK pathways.
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Affiliation(s)
- Jie Song
- College of Animal Science, Jilin University, Changchun, China
| | - Linlin Hao
- College of Animal Science, Jilin University, Changchun, China
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Rui Yang
- College of Animal Science, Jilin University, Changchun, China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chunli Wang
- College of Animal Science, Jilin University, Changchun, China
| | - Hao Yu
- College of Animal Science, Jilin University, Changchun, China
| | - Siyao Wang
- College of Animal Science, Jilin University, Changchun, China
| | - Yingying Jiao
- College of Animal Science, Jilin University, Changchun, China
| | - Hongyao Jia
- Department of Breast Surgery, The First Hospital of Jilin University, Jilin, China
| | - Songcai Liu
- College of Animal Science, Jilin University, Changchun, China
- *Correspondence: Songcai Liu
| | - Ying Zhang
- College of Animal Science, Jilin University, Changchun, China
- Ying Zhang
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8
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Cai S, Duo T, Wang X, Tong X, Luo C, Chen Y, Li J, Mo D. A Comparative Analysis of Metabolic Profiles of Embryonic Skeletal Muscle from Lantang and Landrace Pigs. Animals (Basel) 2022; 12:ani12040420. [PMID: 35203128 PMCID: PMC8868109 DOI: 10.3390/ani12040420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The pig is one of the most important domesticated meat animals. Some studies have revealed that pigs with low meat production show more intense myogenesis at the early stage of embryonic muscle development than pigs with high meat production. Here, by gas chromatography–mass spectrometry GC–MS based metabolomics, we concluded that the nucleotide metabolism and energy metabolism of the longissimuslumborum (LL) were increased in Lantang pigs compared with Landrace pigs, indicating rapid synthesis of nucleic acids and ATP to meet the material and energy requirements of rapid cell proliferation and differentiation in Lantang pigs. Abstract Elucidation of the complex regulation of porcine muscle development is key to increasing pork output and improving pork quality. However, the molecular mechanisms involved in early porcine embryonic muscle development in different pig breeds remain largely unknown. Here, GC–MS based metabolomics and metabolomic profiling was used to examine the longissimus lumborum (LL) of the Lantang (LT) and the Landrace (LR) pig at embryonic day 35 (E35). Metabolites showed clear separation between LT and LR, with 40 metabolites having higher abundances in LT and 14 metabolites having lower abundances in LT compared with LR. In addition, these metabolic changes were mainly associated with nucleotide metabolism and energy metabolism, such as purine metabolism, pyrimidine metabolism, the pentose phosphate pathway, and the TCA cycle. More interestingly, the contents of DNA, RNA, and ATP per unit mass of LL tissues were higher in LT, indicating rapid synthesis of nucleic acids and ATP, to meet both the material and energy requirements of rapid cell proliferation and differentiation. Furthermore, enzyme activity associated with the TCA cycle and pentose phosphate pathway, including α-ketoglutaric dehydrogenase (KGDH), malate dehydrogenase (MDH), pyruvate dehydrogenase (PDH), succinate dehydrogenase (SDH), and glucose-6-phosphate dehydrogenase (G6PDH), were higher in LT. Based on these results, we conclude that there are significant differences in nucleotide metabolism and energy metabolism of LL between LT and LR, and we speculate that the enhanced nucleic acid metabolism and energy metabolism in LT can meet the material and energy requirements of rapid cell proliferation and differentiation, making myogenesis more intense in LT compared to LR which might be the metabolic mechanism underlying the distinct skeletal muscle development in the two breeds.
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Affiliation(s)
- Shufang Cai
- State Key Laboratory of Livestock and Poultry Breeding & Guangdong Public Laboratory of Animal Breeding and Nutrition & Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.C.); (C.L.)
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
| | - Tianqi Duo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
| | - Xiaoyu Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
| | - Xian Tong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
| | - Chenglong Luo
- State Key Laboratory of Livestock and Poultry Breeding & Guangdong Public Laboratory of Animal Breeding and Nutrition & Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.C.); (C.L.)
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
| | - Jianhao Li
- State Key Laboratory of Livestock and Poultry Breeding & Guangdong Public Laboratory of Animal Breeding and Nutrition & Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.C.); (C.L.)
- Correspondence: (J.L.); (D.M.); Tel.: +86-020-38765361 (J.L.); +86-020-39332991 (D.M.)
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China; (T.D.); (X.W.); (X.T.); (Y.C.)
- Correspondence: (J.L.); (D.M.); Tel.: +86-020-38765361 (J.L.); +86-020-39332991 (D.M.)
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9
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Nguyen MT, Lee W. Role of MiR-325-3p in the Regulation of CFL2 and Myogenic Differentiation of C2C12 Myoblasts. Cells 2021; 10:cells10102725. [PMID: 34685705 PMCID: PMC8534702 DOI: 10.3390/cells10102725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 12/18/2022] Open
Abstract
Skeletal myogenesis is required to maintain muscle mass and integrity, and impaired myogenesis is causally linked to the etiology of muscle wasting. Recently, it was shown that excessive uptake of saturated fatty acids (SFA) plays a significant role in the pathogenesis of muscle wasting. Although microRNA (miRNA) is implicated in the regulation of myogenesis, the molecular mechanism whereby SFA-induced miRNAs impair myogenic differentiation remains largely unknown. Here, we investigated the regulatory roles of miR-325-3p on CFL2 expression and myogenic differentiation in C2C12 myoblasts. PA impeded myogenic differentiation, concomitantly suppressed CFL2 and induced miR-325-3p. Dual-luciferase analysis revealed that miR-325-3p directly targets the 3'UTR of CFL2, thereby suppressing the expression of CFL2, a crucial factor for actin dynamics. Transfection with miR-325-3p mimic resulted in the accumulation of actin filaments (F-actin) and nuclear Yes-associated protein (YAP) in myoblasts and promoted myoblast proliferation and cell cycle progression. Consequently, miR-325-3p mimic significantly attenuated the expressions of myogenic factors and thereby impaired the myogenic differentiation of myoblasts. The roles of miR-325-3p on CFL2 expression, F-actin modulation, and myogenic differentiation suggest a novel miRNA-mediated regulatory mechanism of myogenesis and PA-inducible miR-325-3p may be a critical mediator between obesity and muscle wasting.
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Affiliation(s)
- Mai Thi Nguyen
- Department of Biochemistry, Dongguk University College of Medicine, 123 Dongdae-ro, Gyeongju 38066, Korea;
| | - Wan Lee
- Department of Biochemistry, Dongguk University College of Medicine, 123 Dongdae-ro, Gyeongju 38066, Korea;
- Channelopathy Research Center, Dongguk University College of Medicine, 32 Dongguk-ro, Goyang 10326, Korea
- Correspondence: ; Tel.: +82-54-770-2409
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10
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Wang Y, Wang J, Hu H, Wang H, Wang C, Lin H, Zhao X. Dynamic transcriptome profiles of postnatal porcine skeletal muscle growth and development. BMC Genom Data 2021; 22:32. [PMID: 34488628 PMCID: PMC8419915 DOI: 10.1186/s12863-021-00984-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 08/02/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Skeletal muscle growth and development are closely associated with the quantity and quality of pork production. We performed a transcriptomic analysis of 12 Longissimus dorsi muscle samples from Tibetan piglets at four postnatal stages of 0, 14, 30, and 60 days using RNA sequencing. RESULTS According to the pairwise comparisons between the libraries of the muscle samples at the four postnatal stages, a total of 4115 differentially expressed genes (DEGs) were identified in terms of |log2(fold change)| ≥ 1 and an adjusted P value < 0.01. Short-time series expression miner (STEM) analysis of the DEGs identified eight significantly different expression profiles, which were divided into two clusters based on the expression pattern. DEGs in cluster I displayed a pattern of decreasing to a nadir, and then a rise, and the significantly enriched gene ontology (GO) terms detected using them were involved in multiple processes, of which the cell cycle, immunocyte activation and proliferation, as well as actin cytoskeleton organization, were the top three overrepresented processes based on the GO terms functional classification. DEGs in cluster II displayed a pattern of increasing to a peak, then declining, which mainly contributed to protein metabolism. Furthermore, besides the pathways related to immune system, a few diseases, and protein metabolism, the DEGs in clusters I and II were significantly enriched in pathways related to muscle growth and development, such as the Rap1, PI3K-Akt, AMPK, and mTOR signaling pathways. CONCLUSIONS This study revealed GO terms and pathways that could affect the postnatal muscle growth and development in piglets. In addition, this study provides crucial information concerning the molecular mechanisms of muscle growth and development as well as an overview of the piglet transcriptome dynamics throughout the postnatal period in terms of growth and development.
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Affiliation(s)
- Yanping Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Jiying Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Hongmei Hu
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Huaizhong Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Cheng Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Haichao Lin
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China
| | - Xueyan Zhao
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong Province, China.
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11
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Zhou Q, Zhang L. MicroRNA-183-5p protects human derived cell line SH-SY5Y cells from mepivacaine-induced injury. Bioengineered 2021; 12:3177-3187. [PMID: 34180760 PMCID: PMC8806725 DOI: 10.1080/21655979.2021.1946358] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
With the gradual recognition of the side effects of local anesthetics, the nerve injury caused by local anesthetics has received growing attention. This research intended to delve into miR-183-5p changes in mepivacaine-mediated SH-SY5Y cell injury, as well as its modulatory mechanism on cell apoptosis. RT-qPCR was adopted for assaying miR-183-5p and PDCD4 mRNA expression. Our team respectively transfected miR-183-5p mimic and inhibitor to enhance or inhibit miR-183-5p function. We employed Western blot for detecting PDCD4 protein levels, as well as flow cytometry and Hoechst 33342/PI double staining for determining cell apoptosis rate. Additionally, our crew applied an ELISA kit for measuring TNF-α, IL-1β, IL-6, and IL-8 contents. The level of reactive oxygen species (ROS) production was examined by the Image-iT LIVE Green ROS detection Kit. As well as dual-luciferase reporter experiment for verifying the targeting link of miR-183-5p with PDCD4. In mepivacaine-induced cell apoptosis in SH-SY5Y cells, miR-183-5p expression was down-regulated. TNF-α, IL-1β, IL-6, and IL-8 contents were elevated. The rate of apoptosis increased visibly, cleaved caspase-3 and Bax levels waxed, whereas Bcl-2 level waned. MiR-183-5p could alleviate the damaging impact of mepivacaine. Dual-luciferase reporter experiments demonstrated that miR-183-5p directly targeted PDCD4. Collectively, we concluded that a high concentration of mepivacaine can cause SH-SY5Y cell damage, miR-183-5p functions crucially in mepivacaine-mediated cell damage. This study provides a theoretical basis for elucidating the mechanism of mepivacaine-induced nerve cell damage, and overexpressed miR-183-5p likely become a novel strategy to combat mepivacaine-induced nerve damage.Abbreviations:miRNA: Micro RNA; PDCD4: Programmed Cell Death 4; MDA: Malondialdehyde; SOD: Superoxide Dismutase; ROS: Reactive Oxygen Species; WT: Wild Type; Mut: Mutant; UTR: Untranslated Region; IL-6: Interleukin-6; IL-1β: Interleukin-1β; TNF-α: Tumor Necrosis Factor-α; IL-8: Interleukin-8; COX-2: Cyclooxygenase-2; iNOS: inducible NOS; MEP: Mepivacaine.
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Affiliation(s)
- Qian Zhou
- Department of Anesthesiology, Jingzhou Central Hospital, Jinzhou, Hubei, China
| | - Ling Zhang
- Department of Anesthesiology, Jingzhou Central Hospital, Jinzhou, Hubei, China
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12
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Wan T, Liu X, Su Y, Zou J, Wu X, Jiang C, Cao C, Yao M, Zhou Y, Rong L, Li B, Wen L, Feng Q. Biological differentiation of traditional Chinese medicine from excessive to deficient syndromes in AIDS: Comparative microRNA microarray profiling and syndrome-specific biomarker identification. J Med Virol 2021; 93:3634-3646. [PMID: 33289096 DOI: 10.1002/jmv.26704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022]
Abstract
Traditional Chinese medicine (TCM) has been widely applied as a supplementary therapy of human immunodeficiency virus infection and acquired immunodeficiency syndrome (HIV/AIDS) in China. TCM has a positive effect on improving the quality of life, prolonging life, and ameliorating the symptoms of HIV/AIDS patients. Yang deficiency of spleen and kidney (YDSK) syndrome is a typical deficient TCM syndrome in AIDS patients, and accumulation of heat-toxicity (AHT) syndrome is a common excessive syndrome in the earlier stage of AIDS. Thus, accurate diagnosis of these two syndromes can improve the targeted treatment effect, and predict the prognosis of the disease. However, the scientific basis of TCM syndromes remains lacking, greatly hindering the accuracy of diagnosis and effectiveness of treatment. In this research, microRNA (miRNA) microarray and quantitative real-time polymerase chain reaction combined with bioinformatics were used for comparative analysis between YDSK and AHT patients. Significantly differential expressed miRNAs (SDE-miRNAs) of each TCM syndrome were identified, including hsa-miR-766-3p and hsa-miR-1260a and so on, as well hsa-miR-6124, hsa-let-7g-5p and so on, for YDSK and AHT, respectively. Biological differences were found between their SDE-miRNAs based on bioinformatics analyses, for example, ErbB signaling pathway mainly linked to AHT, while focal adhesion dominated in YDSK. Syndrome-specific SDE-miRNAs were further identified as potential biomarkers, including hsa-miR-30e-5p, hsa-miR-144-5p for YDSK and hsa-let-7g-5p, hsa-miR-126-3p for AHT, respectively. All of them have laid biological and clinical bases for TCM diagnosis and treatment of AIDS syndrome at the miRNA level, offering potential diagnostic indicators of immune reconstitution.
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Affiliation(s)
- Tingjun Wan
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xiyang Liu
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Yue Su
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Jiaxi Zou
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xi Wu
- Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Cen Jiang
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Chunhui Cao
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Mingyue Yao
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Yuyu Zhou
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Lijun Rong
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Baixue Li
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Li Wen
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Quansheng Feng
- Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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13
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Hu Z, Cao J, Zhang J, Ge L, Zhang H, Liu X. Skeletal Muscle Transcriptome Analysis of Hanzhong Ma Duck at Different Growth Stages Using RNA-Seq. Biomolecules 2021; 11:315. [PMID: 33669581 PMCID: PMC7927120 DOI: 10.3390/biom11020315] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 01/02/2023] Open
Abstract
As one of the most important poultry worldwide, ducks (Anas platyrhynchos) are raised mainly for meat and egg products, and muscle development in ducks is important for meat production. Therefore, an investigation of gene expression in duck skeletal muscle would significantly contribute to our understanding of muscle development. In this study, twenty-four cDNA libraries were constructed from breast and leg muscles of Hanzhong Ma ducks at day 17, 21, 27 of the embryo and postnatal at 6-month-old. High-throughput sequencing and bioinformatics were used to determine the abundances and characteristics of transcripts. A total of 632,172,628 (average 52,681,052) and 637,213,938 (average 53,101,162) reads were obtained from the sequencing data of breast and leg muscles, respectively. Over 71.63% and 77.36% of the reads could be mapped to the Anas platyrhynchos genome. In the skeletal muscle of Hanzhong duck, intron variant (INTRON), synonymous variant (SYNONYMOUS_CODING), and prime 3' UTR variant (UTR_3_PRIME) were the main single nucleotide polymorphisms (SNP) annotation information, and "INTRON", "UTR_3_PRIME", and downstream-gene variant (DOWNSTREAM) were the main insertion-deletion (InDel) annotation information. The predicted number of alternative splicing (AS) in all samples were mainly alternative 5' first exon (transcription start site)-the first exon splicing (TSS) and alternative 3' last exon (transcription terminal site)-the last exon splicing (TTS). Besides, there were 292 to 2801 annotated differentially expressed genes (DEGs) in breast muscle and 304 to 1950 annotated DEGs in leg muscle from different databases. It is worth noting that 75 DEGs in breast muscle and 49 DEGs in leg muscle were co-expressed at all developmental points of comparison, respectively. The RNA-Seq data were confirmed to be reliable by qPCR. The identified DEGs, such as CREBL2, RHEB, GDF6, SHISA2, MYLK2, ACTN3, RYR3, and STMN1, were specially highlighted, indicating their strong associations with muscle development in the Hanzhong Ma duck. KEGG pathway analysis suggested that regulation of actin cytoskeleton, oxidative phosphorylation, and focal adhesion were involved in the development of skeletal muscle. The findings from this study can contribute to future investigations of the growth and development mechanism in duck skeletal muscle.
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Affiliation(s)
| | | | | | | | | | - Xiaolin Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; (Z.H.); (J.C.); (J.Z.); (L.G.); (H.Z.)
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14
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Tan Y, Gan M, Shen L, Li L, Fan Y, Chen Y, Chen L, Niu L, Zhao Y, Jiang A, Jiang D, Zhang S, Zhu L. Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development. Int J Mol Sci 2021; 22:ijms22020503. [PMID: 33419093 PMCID: PMC7825455 DOI: 10.3390/ijms22020503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/28/2020] [Accepted: 01/01/2021] [Indexed: 11/16/2022] Open
Abstract
Gene transcripts or mRNAs and long noncoding RNAs (lncRNAs) are differentially expressed during porcine skeletal muscle development. However, only a few studies have been conducted on skeletal muscle transcriptome in pigs based on timepoints according to the growth curve for porcine. Here, we investigated gene expression in Qingyu pigs at three different growth stages: the inflection point with the maximum growth rate (MGI), the inflection point of the gradually increasing stage to the rapidly increasing stage (GRI), and the inflection point of the rapidly increasing stage to the slowly increasing stage (RSI). Subsequently, we explored gene expression profiles during muscle development at the MGI, GRI and RSI stages by Ribo-Zero RNA sequencing. Qingyu pigs reached the MGI, GRI and RSI stages at 156.40, 23.82 and 288.97 days of age with 51.73, 3.14 and 107.03 kg body weight, respectively. A total of 14,530 mRNAs and 11,970 lncRNAs were identified at the three stages, and 645, 323 differentially expressed genes (DEGs) and 696, 760 differentially expressed lncRNAs (DELs) were identified in the GRI vs. MGI, and RSI vs. MGI, comparisons. Functional enrichment analysis revealed that genes involved in immune system development and energy metabolism (mainly relate to amino acid, carbohydrate and lipid) were enriched at the GRI and MGI stages, respectively, whereas genes involved in lipid metabolism were enriched at the RSI stage. We further characterized G1430, an abundant lncRNA. The full-length sequence (316 nt) of lncRNA G1430 was determined by rapid amplification of cDNA ends (RACE). Subcellular distribution analysis by quantitative real-time PCR (qRT-PCR) revealed that G1430 is a cytoplasmic lncRNA. Binding site prediction and dual luciferase assay showed that lncRNA G1430 directly binds to microRNA 133a (miR-133a). Our findings provide the basis for further investigation of the regulatory mechanisms and molecular genetics of muscle development in pigs.
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Affiliation(s)
- Ya Tan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
- Institute of Animal Husbandry and Veterinary, Guizhou Academy of Agricultural Science, Guiyang 550005, China
| | - Mailin Gan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Linyuan Shen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
- Institute of Animal Husbandry and Veterinary, Guizhou Academy of Agricultural Science, Guiyang 550005, China
| | - Yuan Fan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Ying Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Lei Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Lili Niu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Ye Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Anan Jiang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Dongmei Jiang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
| | - Shunhua Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
- Correspondence: (S.Z.); (L.Z.); Tel.: +86-28-8629-1133 (S.Z. & L.Z.)
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (Y.T.); (M.G.); (L.S.); (L.L.); (Y.F.); (Y.C.); (L.C.); (L.N.); (Y.Z.); (A.J.); (D.J.)
- Correspondence: (S.Z.); (L.Z.); Tel.: +86-28-8629-1133 (S.Z. & L.Z.)
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15
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Iqbal A, Ping J, Ali S, Zhen G, Juan L, Kang JZ, Ziyi P, Huixian L, Zhihui Z. Role of microRNAs in myogenesis and their effects on meat quality in pig - A review. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2020; 33:1873-1884. [PMID: 32819078 PMCID: PMC7649413 DOI: 10.5713/ajas.20.0324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/02/2020] [Accepted: 08/16/2020] [Indexed: 02/02/2023]
Abstract
The demand for food is increasing day by day because of the increasing global population. Therefore, meat, the easiest and largely available source of protein, needs to be produced in large amounts with good quality. The pork industry is a significant shareholder in fulfilling the global meat demands. Notably, myogenesis- development of muscles during embryogenesis- is a complex mechanism which culminates in meat production. But the molecular mechanisms which govern the myogenesis are less known. The involvement of miRNAs in myogenesis and meat quality, which depends on factors such as myofiber composition and intramuscular fat contents which determine the meat color, flavor, juiciness, and water holding capacity, are being extrapolated to increase both the quantity and quality of pork. Various kinds of microRNAs (miRNAs), miR-1, miR-21, miR22, miR-27, miR-34, miR-127, miR-133, miR-143, miR-155, miR-199, miR-206, miR-208, miR-378, and miR-432 play important roles in pig skeletal muscle development. Further, the quality of meat also depends upon myofiber which is developed through the expression of different kinds of miRNAs at different stages. This review will focus on the mechanism of myogenesis, the role of miRNAs in myogenesis, and meat quality with a focus on the pig.
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Affiliation(s)
- Ambreen Iqbal
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Jiang Ping
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Shaokat Ali
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Gao Zhen
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Liu Juan
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Jin Zi Kang
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Pan Ziyi
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Lu Huixian
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Zhao Zhihui
- Department of Animal Breeding and Genetics, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
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16
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Zhang Y, Yao Y, Wang Z, Lu D, Zhang Y, Adetula AA, Liu S, Zhu M, Yang Y, Fan X, Chen M, Tang Y, Chen Y, Liu Y, Yi G, Tang Z. MiR-743a-5p regulates differentiation of myoblast by targeting Mob1b in skeletal muscle development and regeneration. Genes Dis 2020; 9:1038-1048. [PMID: 35685465 PMCID: PMC9170581 DOI: 10.1016/j.gendis.2020.11.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/26/2020] [Indexed: 01/21/2023] Open
Abstract
The microRNAs (miRNAs) play an important role in regulating myogenesis by targeting mRNA. However, the understanding of miRNAs in skeletal muscle development and diseases is unclear. In this study, we firstly performed the transcriptome profiling in differentiating C2C12 myoblast cells. Totally, we identified 187 miRNAs and 4260 mRNAs significantly differentially expressed that were involved in myoblast differentiation. We carried out validation of microarray data based on 5 mRNAs and 5 miRNAs differentially expressed and got a consistent result. Then we constructed and validated the significantly up- and down-regulated mRNA-miRNA interaction networks. Four interaction pairs (miR-145a-5p-Fscn1, miR-200c-5p-Tmigd1, miR-27a-5p-Sln and miR-743a-5p-Mob1b) with targeted relationships in differentiated myoblast cells were demonstrated. They are all closely related to myoblast development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated cell cycle signals important for exploring skeletal muscle development and disease. Functionally, we discovered that miR-743a targeting gene Mps One Binder Kinase Activator-Like 1B (Mob1b) gene in differentiated C2C12. The up-regulated miR-743a can promote the differentiation of C2C12 myoblast. While the down-regulated Mob1b plays a negative role in differentiation. In addition, the expression profile of miR-743a and Mob1b are consistent with skeletal muscle recovery after Cardiotoxin (CTX) injury. Our study revealed that miR-743a-5p regulates myoblast differentiation by targeting Mob1b involved in skeletal muscle development and regeneration. Our findings made a further exploration for mechanisms in myogenesis and might provide potential possible miRNA-based target therapies for skeletal muscle regeneration and disease in the near future.
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Affiliation(s)
- YongSheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
| | - YiLong Yao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
| | - ZiShuai Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
| | - Dan Lu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
| | - YuanYuan Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Adeyinka Abiola Adetula
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
| | - SiYuan Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
| | - Min Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
| | - YaLan Yang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
| | - XinHao Fan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
| | - MuYa Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
| | - YiJie Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
| | - Yun Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
| | - YuWen Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
| | - GuoQiang Yi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
| | - ZhongLin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
- Corresponding author. Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, PR China.
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17
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Wu S, Zhang J, Liu B, Huang Y, Li S, Wen H, Zhang M, Li J, Li Y, He F. Identification and Characterization of lncRNAs Related to the Muscle Growth and Development of Japanese Flounder ( Paralichthys olivaceus). Front Genet 2020; 11:1034. [PMID: 33033494 PMCID: PMC7510837 DOI: 10.3389/fgene.2020.01034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 08/11/2020] [Indexed: 01/28/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) play an important role in many life activities, but the expression pattern and function of lncRNAs in Japanese flounder skeletal muscle are unclear. In this study, 751 lncRNAs were selected from skeletal muscle in different development stages of the Japanese flounder [stage A: larval 7 days post hatching (dph); stage B: juvenile about 90 dph; stage C (female) and stage D (male): adult about 24 months] using coding potential analysis methods. In total, 232, 211, 194, 28, 29, and 14 differentially expressed lncRNAs and 9549, 8673, 9181, 1821, 1080, and 557 differentially expressed mRNAs were identified in comparisons of A versus B, A versus C, A versus D, B versus C, B versus D, and C versus D, respectively. We identified the cis- and trans-regulatory target genes of differentially expressed lncRNAs, and lncRNA-gene interaction networks were constructed using the Cytoscape program. In total, there were 200, 200, 200, 93, 47, and 11 cis-regulation relationships, and 29, 19, 24, 38, 8, and 47 trans-regulation relationships in the comparisons between A versus B, A versus C, A versus D, B versus C, B versus D, and C versus D, respectively. These results indicate that lncRNA may participate in the development of Japanese flounder skeletal muscle through cis- or trans-acting mechanisms, thus providing a scientific basis for further study of the biological function of lncRNA in Japanese flounder skeletal muscle. Based on these relationships, functional annotation of the related lncRNAs was performed by gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Differentially expressed genes associated with muscle development were enriched in multiple pairs of comparisons (e.g., differentially expressed genes LOC109640370, LOC109634180, LOC109643555, rusc1, and LOC109626999 were enriched in the actin-binding term, and differentially expressed genes LOC109640370, was, LOC109644970, LOC109643555, and itga9 were enriched in the regulation of the actin cytoskeleton pathway in the KEGG pathway analysis in the comparison of stages C and D). We predicted lncRNA-mRNA, miRNA-mRNA, and lncRNA-miRNA regulatory relationships and constructed interactive networks using Cytoscape software. Co-expression networks show that most lncRNAs interact with one or two predicted miRNAs involved in muscle growth and development. These results provide a basis for further study of the function of lncRNAs on skeletal muscle in different developmental stages of Japanese flounder.
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Affiliation(s)
- Shuxian Wu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Jingru Zhang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Binghua Liu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Yajuan Huang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Siping Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Haishen Wen
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Meizhao Zhang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Jifang Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Yun Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
| | - Feng He
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Fisheries College, Ocean University of China, Qingdao, China
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18
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Zhang X, Yao Y, Han J, Yang Y, Chen Y, Tang Z, Gao F. Longitudinal epitranscriptome profiling reveals the crucial role of N 6-methyladenosine methylation in porcine prenatal skeletal muscle development. J Genet Genomics 2020; 47:466-476. [PMID: 33268291 DOI: 10.1016/j.jgg.2020.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/03/2020] [Accepted: 07/31/2020] [Indexed: 11/30/2022]
Abstract
N6-methyladenosine (m6A) represents the most abundantly occurring mRNA modification and is involved in the regulation of skeletal muscle development. However, the status and function of m6A methylation in prenatal myogenesis remains unclear. In this study, we first demonstrated that knockdown of METTL14, an m6A methyltransferase, inhibited the differentiation and promoted the proliferation of C2C12 myoblast cells. Then, using a refined m6A-specific methylated RNA immunoprecipitation (RIP) with next generation sequencing (MeRIP-seq) method that is optimal for use with samples containing small amounts of RNA, we performed transcriptome-wide m6A profiling for six prenatal skeletal muscle developmental stages spanning two important waves of porcine myogenesis. The results revealed that, along with a continuous decrease in the mRNA expression of the m6A reader protein insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), the m6A methylome underwent highly dynamic changes across different development stages, with most of the affected genes being enriched in pathways related to skeletal muscle development. RNA immunoprecipitation confirmed that IGF2BP1 targets 76 genes involved in pathways associated with muscle development, including the key marker genes MYH2 and MyoG. Moreover, small interfering RNA (siRNA)-mediated knockdown of IGF2BP1 induced phenotypic changes in C2C12 myoblasts similar to those observed with knockdown of METTL14. In conclusion, we clarified the dynamics of m6A methylation and identified key genes involved in the regulatory network of porcine skeletal muscle development.
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Affiliation(s)
- Xinxin Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yilong Yao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Jinghua Han
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yalan Yang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yun Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Zhonglin Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Fei Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China; Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, DK-2000, Denmark.
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19
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Zhang H, Chen F, Liang Z, Wu Y, Pi J, Wang L, Du J, Shen J, Pan A, Pu Y. Analysis of miRNAs and their target genes associated with mucosal damage caused by transport stress in the mallard duck intestine. PLoS One 2020; 15:e0237699. [PMID: 32810175 PMCID: PMC7437463 DOI: 10.1371/journal.pone.0237699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 07/31/2020] [Indexed: 12/12/2022] Open
Abstract
Bowel health is an important factor for duck rearing that has been linked to feed uptake and growth and death rates. Because the regulatory networks associated with acute stress-mediated injury in the duck gastrointestinal tract have not clearly elucidated, we aimed to explore potential miRNA-mRNA pairs and their regulatory roles in oxidative stress injury caused by transport stress. Here, 1-day-old mallard ducklings from the same breeder flock were collected and transported for 8 h, whereas the control group was not being transported. Various parameters reflecting oxidative stress and the tissue appearance of the intestine were assessed. The data showed that the plasma T-AOC and SOD concentrations were decreased in the transported ducklings. The intestine of the transported ducklings also displayed significant damage. High-throughput sequencing of the intestine revealed 44 differentially expressed miRNAs and 75 differentially expressed genes, which constituted 344 miRNA-mRNA pairs. KEGG pathway analysis revealed that the metabolic, FoxO signaling, influenza A and TGF-β signaling pathways were mainly involved in the mechanism underlying the induction of intestinal damage induced by simulated transport stress in ducks. A miRNA-mRNA pair, miR-217-5p/CHRDL1, was selected to validate the miRNA-mRNA negative relationship, and the results showed that miR-217-5p could influence CHRDL1 expression. This study provides new useful information for future research on the regulatory network associated with mucosal damage in the duck intestine.
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Affiliation(s)
- Hao Zhang
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
| | - Fang Chen
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
| | - Zhenhua Liang
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
| | - Yan Wu
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
| | - Jinsong Pi
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
| | - Lixia Wang
- Institute of Animal Husbandry and Veterinary Sciences, Wuhan Academy of Agricultural Sciences, Wuhan, PR China
| | - Jinping Du
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
| | - Jie Shen
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
| | - Ailuan Pan
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
| | - Yuejin Pu
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, PR China
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20
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Salant GM, Tat KL, Goodrich JA, Kugel JF. miR-206 knockout shows it is critical for myogenesis and directly regulates newly identified target mRNAs. RNA Biol 2020; 17:956-965. [PMID: 32129700 DOI: 10.1080/15476286.2020.1737443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
The muscle specific miRNA, miR-206, is important for the process of myogenesis; however, studying the function of miR-206 in muscle development and differentiation still proves challenging because the complement of mRNA targets it regulates remains undefined. In addition, miR-206 shares close sequence similarity to miR-1, another muscle specific miRNA, making it hard to study the impact of miR-206 alone in cell culture models. Here we used CRISPR/Cas9 technology to knockout miR-206 in C2C12 muscle cells. We show that knocking out miR-206 significantly impairs and delays differentiation and myotube formation, revealing that miR-206 alone is important for myogenesis. In addition, we use an experimental affinity purification technique to identify new mRNA targets of miR-206 in C2C12 cells. We identified over one hundred mRNAs as putative miR-206 targets. Functional experiments on six of these targets indicate that Adam19, Bgn, Cbx5, Smarce1, and Spg20 are direct miR-206 targets in C2C12 cells. Our data show a unique and important role for miR-206 in myogenesis.
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Affiliation(s)
- Georgiana M Salant
- Department of Biochemistry, University of Colorado Boulder , Boulder, CO, USA
| | - Kimngan L Tat
- Department of Biochemistry, University of Colorado Boulder , Boulder, CO, USA
| | - James A Goodrich
- Department of Biochemistry, University of Colorado Boulder , Boulder, CO, USA
| | - Jennifer F Kugel
- Department of Biochemistry, University of Colorado Boulder , Boulder, CO, USA
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21
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Biological Differentiation of Dampness-Heat Syndromes in Chronic Hepatitis B: From Comparative MicroRNA Microarray Profiling to Biomarker Identification. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:7234893. [PMID: 32051688 PMCID: PMC6995329 DOI: 10.1155/2020/7234893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/11/2019] [Accepted: 12/18/2019] [Indexed: 11/26/2022]
Abstract
Increasing interest is aroused by traditional Chinese medicine (TCM) treatment of chronic hepatitis B (CHB) based on specific TCM syndrome. As the most common CHB syndromes, spleen-stomach dampness-heat (SSDH) syndrome and liver-gallbladder dampness-heat (LGDH) syndrome are still apt to be confused in TCM diagnosis, greatly hindering the stable exertion of TCM effectiveness. It is urgently needed to provide objective and biological evidences for differentiation and identification of the two significant syndromes. In this study, microRNA (miRNA) microarray analyses coupled with bioinformatics were employed for comparative miRNA profiling of SSDH and LGDH patients. It was found that the two syndromes had both the same and different significantly differentially expressed miRNAs (SDE-miRNAs). Commonness and specificity were also both found between their SDE-miRNA-based bioinformatics analyses, including Hierarchical Clustering, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and miRNA-GO/pathway networks. Furthermore, syndrome-specific SDE-miRNAs were identified as the potential biomarkers, including hsa-miR-1273g-3p and hsa-miR-4419b for SSDH as well as hsa-miR-129-1-3p and hsa-miR-129-2-3p for LGDH. All these laid biological and clinical bases for classification and diagnosis of the two significant CHB dampness-heat syndromes including SSDH and LGDH, providing more opportunities for better application of TCM efficacy and superiority in CHB treatment.
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22
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Xing K, Zhao X, Ao H, Chen S, Yang T, Tan Z, Wang Y, Zhang F, Liu Y, Ni H, Guo Y, Hou Z, Wang C. Transcriptome analysis of miRNA and mRNA in the livers of pigs with highly diverged backfat thickness. Sci Rep 2019; 9:16740. [PMID: 31727987 PMCID: PMC6856533 DOI: 10.1038/s41598-019-53377-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/31/2019] [Indexed: 12/19/2022] Open
Abstract
Fat deposition is very important in pig production, and its mechanism is not clearly understood. MicroRNAs (miRNAs) play critical roles in fat deposition and energy metabolism. In the current study, we investigated the mRNA and miRNA transcriptome in the livers of Landrace pigs with extreme backfat thickness to explore miRNA-mRNA regulatory networks related to lipid deposition and metabolism. A comparative analysis of liver mRNA and miRNA transcriptomes from pigs (four pigs per group) with extreme backfat thickness was performed. We identified differentially expressed genes from RNA-seq data using a Cufflinks pipeline. Seventy-one differentially expressed genes (DEGs), including twenty-eight well annotated on the porcine reference genome genes, were found. The upregulation genes in pigs with higher backfat thickness were mainly involved in fatty acid synthesis, and included fatty acid synthase (FASN), glucokinase (GCK), phosphoglycerate dehydrogenase (PHGDH), and apolipoprotein A4 (APOA4). Cytochrome P450, family 2, subfamily J, polypeptide 34 (CYP2J34) was lower expressed in pigs with high backfat thickness, and is involved in the oxidation of arachidonic acid. Moreover, 13 differentially expressed miRNAs were identified. Seven miRNAs were associated with fatty acid synthesis, lipid metabolism, and adipogenic differentiation. Based on comprehensive analysis of the transcriptome of both mRNAs and miRNAs, an important regulatory network, in which six DEGs could be regulated by differentially expressed miRNAs, was established for fat deposition. The negative correlate in the regulatory network including, miR-545-5p and GRAMD3, miR-338 and FASN, and miR-127, miR-146b, miR-34c, miR-144 and THBS1 indicate that direct suppressive regulation may be involved in lipid deposition and energy metabolism. Based on liver mRNA and miRNA transcriptomes from pigs with extreme backfat thickness, we identified 28 differentially expressed genes and 13 differentially expressed miRNAs, and established an important miRNA-mRNA regulatory network. This study provides new insights into the molecular mechanisms that determine fat deposition in pigs.
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Affiliation(s)
- Kai Xing
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xitong Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hong Ao
- State Key Laboratory for Animal Nutrition, Key Laboratory for Domestic Animal Genetic Resources and Breeding of the Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shaokang Chen
- Beijing General Station of Animal Husbandry, Beijing, 100125, China
| | - Ting Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhen Tan
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yuan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Fengxia Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yibing Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - HeMin Ni
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Yong Guo
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China.
| | - Zhuocheng Hou
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Chuduan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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23
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Chen M, Yao YL, Yang Y, Zhu M, Tang Y, Liu S, Li K, Tang Z. Comprehensive Profiles of mRNAs and miRNAs Reveal Molecular Characteristics of Multiple Organ Physiologies and Development in Pigs. Front Genet 2019; 10:756. [PMID: 31552085 PMCID: PMC6737989 DOI: 10.3389/fgene.2019.00756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/17/2019] [Indexed: 12/13/2022] Open
Abstract
The pig (Sus scrofa) is not only an important livestock animal but also widely used as a biomedical model. However, the understanding of the molecular characteristics of organs and of the developmental skeletal muscle of the pig is severely limited. Here, we performed a comprehensive transcriptome profiling of mRNAs and miRNAs across nine tissues and three skeletal muscle developmental stages in the Guizhou miniature pig. The reproductive organs (ovary and testis) had greater transcriptome complexity and activity than other tissues, and the highest transcriptome similarity was between skeletal muscle and heart (R = 0.79). We identified 1,819 mRNAs and 96 miRNAs to be tissue-specific in nine organs. Testis had the largest number of tissue-specific mRNAs (992) and miRNAs (40). Only 15 genes and two miRNAs were specifically expressed in skeletal muscle and fat, respectively. During postnatal skeletal muscle development, the mRNAs associated with focal adhesion, Notch signaling, protein digestion, and absorption pathways were up-regulated from D0 to D30 and then down-regulated from D30 and D240, while genes with opposing expression patterns were significantly enriched in the oxidative phosphorylation and proteasome pathways. The miRNAs mainly regulated genes associated with insulin, Wnt, fatty acid biosynthesis, Notch, MAPK, TGF-beta, insulin secretion, ECM-receptor interaction, focal adhesion, and calcium signaling pathways. We also identified 37 new miRNA-mRNA interaction pairs involved in skeletal muscle development. Overall, our data not only provide a rich resource for understanding pig organ physiology and development but also aid the study of the molecular functions of mRNA and miRNA in mammals.
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Affiliation(s)
- Muya Chen
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yi Long Yao
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yalan Yang
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Min Zhu
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yijie Tang
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Siyuan Liu
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kui Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonglin Tang
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Liang Y, Wang Y, Ma L, Zhong Z, Yang X, Tao X, Chen X, He Z, Yang Y, Zeng K, Kang R, Gong J, Ying S, Lei Y, Pang J, Lv X, Gu Y. Comparison of microRNAs in adipose and muscle tissue from seven indigenous Chinese breeds and Yorkshire pigs. Anim Genet 2019; 50:439-448. [PMID: 31328299 DOI: 10.1111/age.12826] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2019] [Indexed: 01/29/2023]
Abstract
Elucidation of the pig microRNAome is essential for interpreting functional elements of the genome and understanding the genetic architecture of complex traits. Here, we extracted small RNAs from skeletal muscle and adipose tissue, and we compared their expression levels between one Western breed (Yorkshire) and seven indigenous Chinese breeds. We detected the expression of 172 known porcine microRNAs (miRNAs) and 181 novel miRNAs. Differential expression analysis found 92 and 12 differentially expressed miRNAs in adipose and muscle tissue respectively. We found that different Chinese breeds shared common directional miRNA expression changes compared to Yorkshire pigs. Some miRNAs differentially expressed across multiple Chinese breeds, including ssc-miR-129-5p, ssc-miR-30 and ssc-miR-150, are involved in adipose tissue function. Functional enrichment analysis revealed that the target genes of the differentially expressed miRNAs are associated mainly with signaling pathways rather than metabolic and biosynthetic processes. The miRNA-target gene and miRNA-phenotypic traits networks identified many hub miRNAs that regulate a large number of target genes or phenotypic traits. Specifically, we found that intramuscular fat content is regulated by the greatest number of miRNAs in muscle tissue. This study provides valuable new candidate miRNAs that will aid in the improvement of meat quality and production.
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Affiliation(s)
- Y Liang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Y Wang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - L Ma
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, 610052, Sichuan Province China
| | - Z Zhong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - X Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - X Tao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - X Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Z He
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Y Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - K Zeng
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - R Kang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - J Gong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - S Ying
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Y Lei
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - J Pang
- Chengdu Biotechservice Institute, Chengdu, 610041, Sichuan Province China
| | - X Lv
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
| | - Y Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, Sichuan Province China
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Carvalho EB, Gionbelli MP, Rodrigues RTS, Bonilha SFM, Newbold CJ, Guimarães SEF, Silva W, Verardo LL, Silva FF, Detmann E, Duarte MS. Differentially expressed mRNAs, proteins and miRNAs associated to energy metabolism in skeletal muscle of beef cattle identified for low and high residual feed intake. BMC Genomics 2019; 20:501. [PMID: 31208329 PMCID: PMC6580615 DOI: 10.1186/s12864-019-5890-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 06/07/2019] [Indexed: 12/19/2022] Open
Abstract
Background Feed efficiency is one of the most important parameters that affect beef production costs. The energy metabolism of skeletal muscle greatly contributes to variations in feed efficiency. However, information regarding differences in proteins involved in the energy metabolism of the skeletal muscle in beef cattle divergently identified for feed efficiency is scarce. In this study, we aimed to investigate energy metabolism of skeletal muscle of Nellore beef cattle, identified for low and high residual feed intake using a proteomics approach. We further assessed the expression of candidate microRNAs as a one of the possible mechanisms controlling the biosynthesis of the proteins involved in energy metabolism that were differentially abundant between high and low residual feed intake animals. Results A greater abundance of 14–3-3 protein epsilon (P = 0.01) was observed in skeletal muscle of residual feed intake (RFI) high animals (RFI-High). Conversely, a greater abundance of Heat Shock Protein Beta 1 (P < 0.01) was observed in the skeletal muscle of RFI-Low cattle. A greater mRNA expression of YWHAE, which encodes the 14–3-3 protein epsilon, was also observed in the skeletal muscle of RFI-High animals (P = 0.01). A lower mRNA expression of HSPB1, which encodes the Heat Shock Protein Beta 1, was observed in the skeletal muscle of RFI-High animals (P = 0.01). The miR-665 was identified as a potential regulator of the 14–3-3 protein epsilon, and its expression was greater in RFI-Low animals (P < .001). A greater expression of miR-34a (P = 0.01) and miR-2899 (P < .001) was observed in the skeletal muscle of RFI-High animals, as both miRNAs were identified as potential regulators of HSPB1 expression. Conclusion Our results show that Nellore cattle divergently identified for feed efficiency by RFI present changes in the abundance of proteins involved in energy expenditure in skeletal muscle. Moreover, our data point towards that miR-665, miR34a and miR-2899 are likely involved in controlling both 14-3-3 epsilon and HSPB1 proteins identified as differentially abundant in the skeletal muscle of RFI-High and RFI-Low Nellore cattle. Electronic supplementary material The online version of this article (10.1186/s12864-019-5890-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa B Carvalho
- Department of Animal Science, Universidade Federal de Lavras, Lavras, MG, Brazil.,Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Mateus P Gionbelli
- Department of Animal Science, Universidade Federal de Lavras, Lavras, MG, Brazil
| | - Rafael T S Rodrigues
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil.,Department of Veterinary Sciences, Universidade Federal do Vale do São Francisco, Petrolina, PE, Brazil
| | - Sarah F M Bonilha
- Centro APTA Bovinos de Corte, Instituto de Zootecnia, Sertãozinho, SP, Brazil
| | | | - Simone E F Guimarães
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Walmir Silva
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Lucas L Verardo
- Department of Animal Science, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG, Brazil
| | - Fabyano F Silva
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Edenio Detmann
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Marcio S Duarte
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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26
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Sun L, Lu S, Bai M, Xiang L, Li J, Jia C, Jiang H. Integrative microRNA-mRNA Analysis of Muscle Tissues in Qianhua Mutton Merino and Small Tail Han Sheep Reveals Key Roles for oar-miR-655-3p and oar-miR-381-5p. DNA Cell Biol 2019; 38:423-435. [PMID: 30864845 DOI: 10.1089/dna.2018.4408] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The Qianhua Mutton Merino (QHMM) is a new variety of sheep (Ovis aries) with improved meat performance compared with the traditional Small Tail Han (STH) sheep variety. We recently reported the transcriptome profiling of longissimus muscle tissues between QHMM and STH sheep. In the present study, we aimed to evaluate key micro (mi)RNA-mRNA networks associated with sheep muscle growth and development. We used miRNA sequencing to obtain longissimus muscle miRNA profiles from QHMM and STH sheep. We identified a total of 153 known sheep miRNAs, of which 4 were differentially expressed (DE) between the 2 sheep varieties. We combined these results with mRNA library data to build an miRNA-mRNA network, including 26 target genes of the 4 DE miRNAs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that 26 target genes were significantly enriched in 86 biological processes, including muscle organogenesis, myoblast migration, cell proliferation, and adipose tissue development, and in 9 metabolic pathways, including carbohydrate, nucleotide, and amino acid metabolic pathways. oar-miR-655-3p and its target gene ACSM3 and oar-miR-381-5p and its target gene ABAT were selected for subsequent analysis based on GO and KEGG analyses. The binding sites of oar-miR-655-3p with ACSM3 and oar-miR-381-5p with ABAT were validated by a dual-luciferase reporter gene detection system. This represents the first integrative analysis of miRNA-mRNA networks in QHMM and STH muscles and suggests that DE miRNAs, especially oar-miR-655-3p and oar-miR-381-5p, play crucial roles in muscle growth and development.
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Affiliation(s)
- Limin Sun
- 1 College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Songyan Lu
- 2 Jilin Animal Disease Control Center, Changchun, China
| | - Man Bai
- 1 College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Lujie Xiang
- 1 College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Jiarong Li
- 1 College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Chao Jia
- 1 College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Huaizhi Jiang
- 1 College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
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27
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Aalijahan H, Ghorbian S. Long non-coding RNAs and cervical cancer. Exp Mol Pathol 2019; 106:7-16. [DOI: 10.1016/j.yexmp.2018.11.010] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 08/24/2018] [Accepted: 11/20/2018] [Indexed: 02/06/2023]
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28
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Identification and characterization of microRNAs in the liver of rainbow trout in response to heat stress by high-throughput sequencing. Gene 2018; 679:274-281. [DOI: 10.1016/j.gene.2018.09.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 08/30/2018] [Accepted: 09/06/2018] [Indexed: 01/30/2023]
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29
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Khanduri A, Sahu AR, Wani SA, Khan RIN, Pandey A, Saxena S, Malla WA, Mondal P, Rajak KK, Muthuchelvan D, Mishra B, Sahoo AP, Singh YP, Singh RK, Gandham RK, Mishra BP. Dysregulated miRNAome and Proteome of PPRV Infected Goat PBMCs Reveal a Coordinated Immune Response. Front Immunol 2018; 9:2631. [PMID: 30524425 PMCID: PMC6262310 DOI: 10.3389/fimmu.2018.02631] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 10/25/2018] [Indexed: 12/11/2022] Open
Abstract
In this study, the miRNAome and proteome of virulent Peste des petits ruminants virus (PPRV) infected goat peripheral blood mononuclear cells (PBMCs) were analyzed. The identified differentially expressed miRNAs (DEmiRNAs) were found to govern genes that modulate immune response based on the proteome data. The top 10 significantly enriched immune response processes were found to be governed by 98 genes. The top 10 DEmiRNAs governing these 98 genes were identified based on the number of genes governed by them. Out of these 10 DEmiRNAs, 7 were upregulated, and 3 were downregulated. These include miR-664, miR-2311, miR-2897, miR-484, miR-2440, miR-3533, miR-574, miR-210, miR-21-5p, and miR-30. miR-664 and miR-484 with proviral and antiviral activities, respectively, were upregulated in PPRV infected PBMCs. miR-210 that inhibits apoptosis was downregulated. miR-21-5p that decreases the sensitivity of cells to the antiviral activity of IFNs and miR-30b that inhibits antigen processing and presentation by primary macrophages were downregulated, indicative of a strong host response to PPRV infection. miR-21-5p was found to be inhibited on IPA upstream regulatory analysis of RNA-sequencing data. This miRNA that was also highly downregulated and was found to govern 16 immune response genes in the proteome data was selected for functional validation vis-a-vis TGFBR2 (TGF-beta receptor type-2). TGFBR2 that regulates cell differentiation and is involved in several immune response pathways was found to be governed by most of the identified immune modulating DEmiRNAs. The decreased luciferase activity in Dual Luciferase Reporter Assay indicated specific binding of miR-21-5p and miR-484 to their target thus establishing specific binding of the miRNAs to their targets.This is the first report on the miRNAome and proteome of virulent PPRV infected goat PBMCs.
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Affiliation(s)
- Alok Khanduri
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India.,DBT-National Institute of Animal Biotechnology, Hyderabad, India
| | - Sajad Ahmad Wani
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India.,The Ohio State University, Columbus, Ohio, OH, United States
| | - Raja Ishaq Nabi Khan
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Aruna Pandey
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Shikha Saxena
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Waseem Akram Malla
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Piyali Mondal
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Kaushal Kishor Rajak
- Division of Biological Products, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - D Muthuchelvan
- Division of Virology, ICAR-Indian Veterinary Research Institute (IVRI), Mukteswar, India
| | - Bina Mishra
- Division of Biological Products, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Aditya P Sahoo
- ICAR- Directorate of Foot and Mouth Disease, Mukteswar, India
| | - Yash Pal Singh
- ARIS Cell, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India.,DBT-National Institute of Animal Biotechnology, Hyderabad, India
| | - Bishnu Prasad Mishra
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, India
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30
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Zhang Q, Wang Q, Zhang Y, Cheng S, Hu J, Ma Y, Zhao X. Comprehensive Analysis of MicroRNA⁻Messenger RNA from White Yak Testis Reveals the Differentially Expressed Molecules Involved in Development and Reproduction. Int J Mol Sci 2018; 19:ijms19103083. [PMID: 30304826 PMCID: PMC6213350 DOI: 10.3390/ijms19103083] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 09/30/2018] [Accepted: 10/02/2018] [Indexed: 01/31/2023] Open
Abstract
Testis development is a vital and tightly regulated process in mammals. Understanding the biological mechanisms underlying testis development will benefit the animal reproduction industry. Expression changes in microRNA and messenger RNA in response to dynamic regulation effects have been associated with this process. However, very little is known about the roles of these molecules in yak development. Using whole-genome small RNA and messenger RNA sequencing, we performed a comprehensive analysis of the microRNA–messenger RNA interaction network expression in the testicles of Tianzhu white yaks during three developmental stages. Using Short Time-series Expression Miner analysis we identified 589 differentially expressed microRNAs (DERs) and 3383 differentially expressed messenger RNAs (DEGs) in the three age groups. A total of 93 unique DEGs are primarily involved in reproduction and testis development. Subsequently, four integration networks were constructed according to the DEGs and DERs in three biological processes. Nineteen DEGs were potentially regulated by 60 DERs, of which miR-574 and target gene AURKA played a crucial role in yak testis development and reproduction. The results of this study provide a basis for further exploration of the microRNA–messenger RNA interactions in testis development and reproduction and aid in uncovering the molecular mechanisms of spermatogenesis in male mammals.
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Affiliation(s)
- Quanwei Zhang
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China.
- College of Life science and Technology, Gansu Agriculture University, Lanzhou 730070, China.
| | - Qi Wang
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China.
| | - Yong Zhang
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China.
- College of Life science and Technology, Gansu Agriculture University, Lanzhou 730070, China.
| | - Shuru Cheng
- College of Animal Science and Technology, Gansu Agriculture University, Lanzhou 730070, China.
| | - Junjie Hu
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China.
| | - Youji Ma
- College of Animal Science and Technology, Gansu Agriculture University, Lanzhou 730070, China.
| | - Xingxu Zhao
- College of Veterinary Medicine, Gansu Agriculture University, Lanzhou 730070, China.
- College of Life science and Technology, Gansu Agriculture University, Lanzhou 730070, China.
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31
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A new approach of gene co-expression network inference reveals significant biological processes involved in porcine muscle development in late gestation. Sci Rep 2018; 8:10150. [PMID: 29977047 PMCID: PMC6033925 DOI: 10.1038/s41598-018-28173-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/14/2018] [Indexed: 12/28/2022] Open
Abstract
The integration of genetic information in the cellular and nuclear environments is crucial for deciphering the way in which the genome functions under different physiological conditions. Experimental techniques of 3D nuclear mapping, a high-flow approach such as transcriptomic data analyses, and statistical methods for the development of co-expressed gene networks, can be combined to develop an integrated approach for depicting the regulation of gene expression. Our work focused more specifically on the mechanisms involved in the transcriptional regulation of genes expressed in muscle during late foetal development in pig. The data generated by a transcriptomic analysis carried out on muscle of foetuses from two extreme genetic lines for birth mortality are used to construct networks of differentially expressed and co-regulated genes. We developed an innovative co-expression networking approach coupling, by means of an iterative process, a new statistical method for graph inference with data of gene spatial co-localization (3D DNA FISH) to construct a robust network grouping co-expressed genes. This enabled us to highlight relevant biological processes related to foetal muscle maturity and to discover unexpected gene associations between IGF2, MYH3 and DLK1/MEG3 in the nuclear space, genes that are up-regulated at this stage of muscle development.
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32
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Zhou X, Yang S, Yan F, He K, Zhao A. Genome-wide DNA methylation profiles of porcine ovaries in estrus and proestrus. Physiol Genomics 2018; 50:714-723. [PMID: 29775429 DOI: 10.1152/physiolgenomics.00052.2017] [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] [Indexed: 01/23/2023] Open
Abstract
DNA methylation is an important epigenetic modification involved in the estrous cycle and the regulation of reproduction. Here, we investigated the genome-wide profiles of DNA methylation in porcine ovaries in proestrus and estrus using methylated DNA immunoprecipitation sequencing. The results showed that DNA methylation was enriched in intergenic and intron regions. The methylation levels of coding regions were higher than those of the 5'- and 3'-flanking regions of genes. There were 4,813 differentially methylated regions (DMRs) of CpG islands in the estrus vs. proestrus ovarian genomes. Additionally, 3,651 differentially methylated genes (DMGs) were identified in pigs in estrus and proestrus. The DMGs were significantly enriched in biological processes and pathways related to reproduction and hormone regulation. We identified 90 DMGs associated with regulating reproduction in pigs. Our findings can serve as resources for DNA methylome research focused on porcine ovaries and further our understanding of epigenetically regulated reproduction in mammals.
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Affiliation(s)
- Xiaolong Zhou
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Lin'an, China
| | - Songbai Yang
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Lin'an, China
| | - Feifei Yan
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Lin'an, China
| | - Ke He
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Lin'an, China
| | - Ayong Zhao
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Lin'an, China
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33
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Liu Y, Zhang J, Xu Q, Kang X, Wang K, Wu K, Fang M. Integrated miRNA-mRNA analysis reveals regulatory pathways underlying the curly fleece trait in Chinese tan sheep. BMC Genomics 2018; 19:360. [PMID: 29751742 PMCID: PMC5948824 DOI: 10.1186/s12864-018-4736-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/26/2018] [Indexed: 12/26/2022] Open
Abstract
Background Tan sheep is an indigenous Chinese breed well known for its beautiful curly fleece. One prominent breed characteristic of this sheep breed is that the degree of curliness differs markedly between lambs and adults, but the molecular mechanisms regulating the shift are still not well understood. In this study, we identified 49 differentially expressed (DE) microRNAs (miRNAs) between Tan sheep at the two stages through miRNA-seq, and combined the data with that in our earlier Suppression Subtractive Hybridization cDNA (SSH) library study to elucidate the mechanisms underlying curly fleece formation. Results Thirty-six potential miRNA-mRNA target pairs were identified using computational methods, including 25 DE miRNAs and 10 DE genes involved in the MAPK signaling pathway, steroid biosynthesis and metabolic pathways. With the differential expressions between lambs and adults confirmed by qRT-PCR, some miRNAs were already annotated in the genome, but some were novel miRNAs. Inhibition of KRT83 expression by miR-432 was confirmed by both gene knockdown with siRNA and overexpression, which was consistent with the miRNAs and targets prediction results. Conclusion Our study represents the comprehensive analysis of mRNA and miRNA in Tan sheep and offers detailed insight into the development of curly fleece as well as the potential mechanisms controlling curly hair formation in humans. Electronic supplementary material The online version of this article (10.1186/s12864-018-4736-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yufang Liu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100194, Beijing, People's Republic of China.,College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, 056021, People's Republic of China
| | - Jibin Zhang
- Department of Cell and Molecular Biology, Beckman Research Institute of the City of Hope, Duarte, CA, 91010, USA
| | - Qiao Xu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100194, Beijing, People's Republic of China
| | - Xiaolong Kang
- College of Agriculture, Ningxia University, Yinchuan, 750021, People's Republic of China
| | - Kejun Wang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100194, Beijing, People's Republic of China
| | - Keliang Wu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100194, Beijing, People's Republic of China.
| | - Meiying Fang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, 100194, Beijing, People's Republic of China. .,Beijing Key Laboratory for Animal Genetic Improvement, Beijing, 100193, People's Republic of China.
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Ropka-Molik K, Pawlina-Tyszko K, Żukowski K, Piórkowska K, Żak G, Gurgul A, Derebecka N, Wesoły J. Examining the Genetic Background of Porcine Muscle Growth and Development Based on Transcriptome and miRNAome Data. Int J Mol Sci 2018; 19:ijms19041208. [PMID: 29659518 PMCID: PMC5979540 DOI: 10.3390/ijms19041208] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 03/29/2018] [Accepted: 04/03/2018] [Indexed: 12/13/2022] Open
Abstract
Recently, selection in pigs has been focused on improving the lean meat content in carcasses; this focus has been most evident in breeds constituting a paternal component in breeding. Such sire-breeds are used to improve the meat quantity of cross-breed pig lines. However, even in one breed, a significant variation in the meatiness level can be observed. In the present study, the comprehensive analysis of genes and microRNA expression profiles in porcine muscle tissue was applied to identify the genetic background of meat content. The comparison was performed between whole gene expression and miRNA profiles of muscle tissue collected from two sire-line pig breeds (Pietrain, Hampshire). The RNA-seq approach allowed the identification of 627 and 416 differentially expressed genes (DEGs) between pig groups differing in terms of loin weight between Pietrain and Hampshire breeds, respectively. The comparison of miRNA profiles showed differential expression of 57 microRNAs for Hampshire and 34 miRNAs for Pietrain pigs. Next, 43 genes and 18 miRNAs were selected as differentially expressed in both breeds and potentially related to muscle development. According to Gene Ontology analysis, identified DEGs and microRNAs were involved in the regulation of the cell cycle, fatty acid biosynthesis and regulation of the actin cytoskeleton. The most deregulated pathways dependent on muscle mass were the Hippo signalling pathway connected with the TGF-β signalling pathway and controlling organ size via the regulation of ubiquitin-mediated proteolysis, cell proliferation and apoptosis. The identified target genes were also involved in pathways such as the FoxO signalling pathway, signalling pathways regulating pluripotency of stem cells and the PI3K-Akt signalling pathway. The obtained results indicate molecular mechanisms controlling porcine muscle growth and development. Identified genes (SOX2, SIRT1, KLF4, PAX6 and genes belonging to the transforming growth factor beta superfamily) could be considered candidate genes for determining muscle mass in pigs.
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Affiliation(s)
- Katarzyna Ropka-Molik
- Department of Animal Molecular Biology, Laboratory of Genomics, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
| | - Klaudia Pawlina-Tyszko
- Department of Animal Molecular Biology, Laboratory of Genomics, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
| | - Kacper Żukowski
- Department of Cattle Breeding, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
| | - Katarzyna Piórkowska
- Department of Animal Molecular Biology, Laboratory of Genomics, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
| | - Grzegorz Żak
- Department of Cattle Breeding, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
| | - Artur Gurgul
- Department of Animal Molecular Biology, Laboratory of Genomics, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
| | - Natalia Derebecka
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland.
| | - Joanna Wesoły
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland.
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35
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Analysis of meat quality traits and gene expression profiling of pigs divergent in residual feed intake. Meat Sci 2018; 137:265-274. [DOI: 10.1016/j.meatsci.2017.11.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 09/08/2017] [Accepted: 11/16/2017] [Indexed: 11/19/2022]
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36
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Awan HM, Shah A, Rashid F, Wei S, Chen L, Shan G. Comparing two approaches of miR-34a target identification, biotinylated-miRNA pulldown vs miRNA overexpression. RNA Biol 2018; 15:55-61. [PMID: 29028450 PMCID: PMC5786020 DOI: 10.1080/15476286.2017.1391441] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/06/2017] [Accepted: 10/08/2017] [Indexed: 10/18/2022] Open
Abstract
microRNAs (miRNAs) are critical regulators of gene expression. For elucidating functional roles of miRNAs, it is critical to identify their direct targets. There are debates about whether pulldown of biotinylated miRNA mimics can be used to identify miRNA targets or not. Here we show that biotin-labelled miR-34a can be loaded to AGO2, and AGO2 immunoprecipitation can pulldown biotinylated miR-34a (Bio-miR pulldown). RNA-sequencing (RNA-seq) of the Bio-miR pulldown RNAs efficiently identified miR-34a mRNA targets, which could be verified with luciferase assays. In contrast to the approach of Bio-miR pulldown, RNA-seq of miR-34a overexpression samples had limited value in identifying direct targets of miR-34a. It seems that pulldown of 3'-Biotin-tagged miRNA can identify bona fide microRNA targets at least for miR-34a.
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Affiliation(s)
- Hassaan Mehboob Awan
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Abdullah Shah
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Farooq Rashid
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Shuai Wei
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Liang Chen
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ge Shan
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, China
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37
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Liang G, Yang Y, Niu G, Tang Z, Li K. Genome-wide profiling of Sus scrofa circular RNAs across nine organs and three developmental stages. DNA Res 2017; 24:523-535. [PMID: 28575165 PMCID: PMC5737845 DOI: 10.1093/dnares/dsx022] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 05/03/2017] [Indexed: 01/15/2023] Open
Abstract
The spatio-temporal expression patterns of Circular RNA (circRNA) across organs and developmental stages are critical for its function and evolution analysis. However, they remain largely unclear in mammals. Here, we comprehensively analysed circRNAs in nine organs and three skeletal muscles of Guizhou miniature pig (S. scrofa), a widely used biomedical model animal. We identified 5,934 circRNAs and analysed their molecular properties, sequence conservation, spatio-temporal expression pattern, potential function, and interaction with miRNAs. S. scrofa circRNAs show modest sequence conservation with human and mouse circRNAs, are flanked by long introns, exhibit low abundance, and are expressed dynamically in a spatio-temporally specific manner. S. scrofa circRNAs show the greatest abundance and complexity in the testis. Notably, 31% of circRNAs harbour well-conserved canonical miRNA seed matches, suggesting that some circRNAs act as miRNAs sponges. We identified 149 circRNAs potentially associated with muscle growth and found that their host genes were significantly involved in muscle development, contraction, chromatin modification, cation homeostasis, and ATP hydrolysis-coupled proton transport; moreover, this set of genes was markedly enriched in genes involved in tight junctions and the calcium signalling pathway. Finally, we constructed the first public S. scrofa circRNA database, allowing researchers to query comprehensive annotation, expression, and regulatory networks of circRNAs.
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Affiliation(s)
- Guoming Liang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.,Department of Pig Genomic Design and Breeding, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.,Shenzhen Key Laboratory of Phenotype Analysis and Utilization of Agricultural Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yalan Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.,Department of Pig Genomic Design and Breeding, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.,Shenzhen Key Laboratory of Phenotype Analysis and Utilization of Agricultural Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Guanglin Niu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhonglin Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.,Department of Pig Genomic Design and Breeding, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.,Shenzhen Key Laboratory of Phenotype Analysis and Utilization of Agricultural Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Kui Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.,Department of Pig Genomic Design and Breeding, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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38
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Integrated analysis of mRNA and miRNA expression profiles in livers of Yimeng black pigs with extreme phenotypes for backfat thickness. Oncotarget 2017; 8:114787-114800. [PMID: 29383120 PMCID: PMC5777732 DOI: 10.18632/oncotarget.21918] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/21/2017] [Indexed: 12/20/2022] Open
Abstract
Fat deposition is an important economic trait in farm animals as well as obesity related diseases in humans, and the liver is a central organ involved in regulating lipid synthesis and metabolism in mammals. In this study, the pig liver transcriptome of two groups (H and L) showing differences in backfat thickness were profiled using RNA-Seq and miRNA-Seq to further explore the molecular mechanism of fat deposition. A total of 238 differentially expressed genes (DEGs) and 58 differentially expressed miRNAs were identified between the H and L group. These genes and miRNAs were functionally related to lipid metabolism, including CYP1A1/2, HMGCS2, ACSS2, UBE2L6, miR-27a, and miR-31. Functional enrichment analysis revealed that genes associated with oxidative stress might be responsible for fat deposition in pigs. Two miRNA-mRNA interaction networks involved in lipid metabolism were identified, and these provided new insights into the molecular regulation that determines fat content in these pigs. Overall, our study furthers our understanding of the molecular mechanisms involved in fat deposition, and these results may help in the design of selection strategies to improve the quality of pork meat and to combat obesity in humans.
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39
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Dynamic transcriptomic analysis in hircine longissimus dorsi muscle from fetal to neonatal development stages. Funct Integr Genomics 2017; 18:43-54. [PMID: 28993898 DOI: 10.1007/s10142-017-0573-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 09/11/2017] [Indexed: 12/25/2022]
Abstract
Muscle growth and development from fetal to neonatal stages consist of a series of delicately regulated and orchestrated changes in expression of genes. In this study, we performed whole transcriptome profiling based on RNA-Seq of caprine longissimus dorsi muscle tissue obtained from prenatal stages (days 45, 60, and 105 of gestation) and neonatal stage (the 3-day-old newborn) to identify genes that are differentially expressed and investigate their temporal expression profiles. A total of 3276 differentially expressed genes (DEGs) were identified (Q value < 0.01). Time-series expression profile clustering analysis indicated that DEGs were significantly clustered into eight clusters which can be divided into two classes (Q value < 0.05), class I profiles with downregulated patterns and class II profiles with upregulated patterns. Based on cluster analysis, GO enrichment analysis found that 75, 25, and 8 terms to be significantly enriched in biological process (BP), cellular component (CC), and molecular function (MF) categories in class I profiles, while 35, 21, and 8 terms to be significantly enriched in BP, CC, and MF in class II profiles. KEGG pathway analysis revealed that DEGs from class I profiles were significantly enriched in 22 pathways and the most enriched pathway was Rap1 signaling pathway. DEGs from class II profiles were significantly enriched in 17 pathways and the mainly enriched pathway was AMPK signaling pathway. Finally, six selected DEGs from our sequencing results were confirmed by qPCR. Our study provides a comprehensive understanding of the molecular mechanisms during goat skeletal muscle development from fetal to neonatal stages and valuable information for future studies of muscle development in goats.
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40
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Sun S, Xuan F, Ge X, Zhu J, Zhang W. Dynamic mRNA and miRNA expression analysis in response to hypoxia and reoxygenation in the blunt snout bream (Megalobrama amblycephala). Sci Rep 2017; 7:12846. [PMID: 28993687 PMCID: PMC5634510 DOI: 10.1038/s41598-017-12537-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/12/2017] [Indexed: 12/24/2022] Open
Abstract
Adaptation to hypoxia is a complex process involving various pathways and regulation mechanisms. A better understanding of the genetic influence on these mechanisms could permit selection for hypoxia-sensitive fish. To aid this understanding, an integrated analysis of miRNA and mRNA expression was performed in Megalobrama amblycephala under four acute hypoxia and reoxygenation stages. A number of significantly differentially-expressed miRNAs and genes associated with oxidative stress were identified, and their functional characteristics were revealed by GO function and KEGG pathway analysis. They were found to be involved in HIF-1 pathways known to affect energy metabolism and apoptosis. MiRNA-mRNA interaction pairs were detected from comparison of expression between the four different stages. The function annotation results also showed that many miRNA-mRNA interaction pairs were likely to be involved in regulating hypoxia stress. As a unique resource for gene expression and regulation during hypoxia and reoxygenation, this study could provide a starting point for further studies to better understand the genetic background of hypoxia stress.
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Affiliation(s)
- Shengming Sun
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, Wuxi, 214081, P.R. China
| | - Fujun Xuan
- Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng City, Jiangsu Province, 224002, P.R. China
| | - Xianping Ge
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, Wuxi, 214081, P.R. China.
| | - Jian Zhu
- Key Laboratory of Genetic Breeding and Aquaculture Biology of Freshwater Fishes, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, Wuxi, 214081, P.R. China.
| | - Wuxiao Zhang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, P.R. China
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41
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Tao X, Liang Y, Yang X, Pang J, Zhong Z, Chen X, Yang Y, Zeng K, Kang R, Lei Y, Ying S, Gong J, Gu Y, Lv X. Transcriptomic profiling in muscle and adipose tissue identifies genes related to growth and lipid deposition. PLoS One 2017; 12:e0184120. [PMID: 28877211 PMCID: PMC5587268 DOI: 10.1371/journal.pone.0184120] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/18/2017] [Indexed: 11/23/2022] Open
Abstract
Growth performance and meat quality are important traits for the pig industry and consumers. Adipose tissue is the main site at which fat storage and fatty acid synthesis occur. Therefore, we combined high-throughput transcriptomic sequencing in adipose and muscle tissues with the quantification of corresponding phenotypic features using seven Chinese indigenous pig breeds and one Western commercial breed (Yorkshire). We obtained data on 101 phenotypic traits, from which principal component analysis distinguished two groups: one associated with the Chinese breeds and one with Yorkshire. The numbers of differentially expressed genes between all Chinese breeds and Yorkshire were shown to be 673 and 1056 in adipose and muscle tissues, respectively. Functional enrichment analysis revealed that these genes are associated with biological functions and canonical pathways related to oxidoreductase activity, immune response, and metabolic process. Weighted gene coexpression network analysis found more coexpression modules significantly correlated with the measured phenotypic traits in adipose than in muscle, indicating that adipose regulates meat and carcass quality. Using the combination of differential expression, QTL information, gene significance, and module hub genes, we identified a large number of candidate genes potentially related to economically important traits in pig, which should help us improve meat production and quality.
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Affiliation(s)
- Xuan Tao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Yan Liang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Xuemei Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Jianhui Pang
- Chengdu Biotechservice Institute, Chengdu, Sichuan, China
| | - Zhijun Zhong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Xiaohui Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Yuekui Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Kai Zeng
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Runming Kang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Yunfeng Lei
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Sancheng Ying
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Jianjun Gong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Yiren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
- * E-mail: (YRG); (XBL)
| | - Xuebin Lv
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
- * E-mail: (YRG); (XBL)
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42
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Zhao C, Zhang G, Yin S, Li Z, Wang Q, Chen S, Zhou G. Integrated analysis of mRNA-seq and miRNA-seq reveals the potential roles of sex-biased miRNA-mRNA pairs in gonad tissue of dark sleeper (Odontobutis potamophila). BMC Genomics 2017; 18:613. [PMID: 28806919 PMCID: PMC5557427 DOI: 10.1186/s12864-017-3995-9] [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: 07/29/2016] [Accepted: 08/01/2017] [Indexed: 01/16/2023] Open
Abstract
Background The dark sleeper (Odontobutis potamophila) is an important commercial fish species which shows a sexually dimorphic growth pattern. However, the lack of sex transcriptomic data is hindering further research and genetically selective breeding of the dark sleeper. In this study, integrated analysis of mRNA and miRNA was performed on gonad tissue to elucidate the molecular mechanisms of sex determination and differentiation in the dark sleeper. Results A total of 143 differentially expressed miRNAs and 16,540 differentially expressed genes were identified. Of these, 8103 mRNAs and 75 miRNAs were upregulated in testes, and 8437 mRNAs and 68 miRNAs were upregulated in ovaries. Integrated analysis of miRNA and mRNA expression profiles predicted more than 50,000 miRNA-mRNA interaction sites, and among them 27,583 negative miRNA-mRNA interactions. A number of sex related genes were targeted by sex-biased miRNAs. The relationship between 15 sex-biased genes and 15 sex-biased miRNAs verified by using qRT-PCR were described. Additionally, a number of SNPs were revealed through the transcriptome data. Conclusions The overall results of this study facilitate our understanding of the molecular mechanism underlying sex determination and differentiation and provide valuable genomic information for selective breeding of the dark sleeper. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3995-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cheng Zhao
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu, 210023, China.,Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu, 222005, China
| | - Guosong Zhang
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu, 210023, China.,Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu, 222005, China
| | - Shaowu Yin
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu, 210023, China. .,Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu, 222005, China.
| | - Zecheng Li
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu, 210023, China.,Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu, 222005, China
| | - Qintao Wang
- College of Life Sciences, Key Laboratory of Biodiversity and Biotechnology of Jiangsu Province, Nanjing Normal University, Nanjing, Jiangsu, 210023, China.,Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu, 222005, China
| | - Shuqiao Chen
- Nanjing Institute of Fisheries Science, Nanjing, Jiangsu, 210036, China
| | - Guoqin Zhou
- Nanjing Institute of Fisheries Science, Nanjing, Jiangsu, 210036, China
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43
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He D, Zou T, Gai X, Ma J, Li M, Huang Z, Chen D. MicroRNA expression profiles differ between primary myofiber of lean and obese pig breeds. PLoS One 2017; 12:e0181897. [PMID: 28759650 PMCID: PMC5536276 DOI: 10.1371/journal.pone.0181897] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 07/10/2017] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding small miRNAs ~22 nucleotides in length and play a vital role in muscle development by binding to messenger RNAs (mRNAs). Large White (LW, a lean type pig) and Meishan pigs (MS, a Chinese indigenous obese breed) have significant postnatal phenotype differences in growth rate, muscle mass and meat quality, and these differences are programmed during prenatal muscle development. Little research shed light directly on the miRNA transcriptome difference in prenatal muscles between these two distinct pig breeds. Myofiber phenotypes of LW and MS were measured at developmental stages of 35, 55 and 90 days post-conception (dpc), which revealed that the myogenesis process is more intense in MS than in LW at 35 dpc. To investigate the role of miRNAs involved in regulating muscle development at earlier stages of myogenesis and decipher the miRNAs transcriptome difference between LW and MS, here, the miRNAomes of longissimus dorsi muscle collected at 35 dpc from female LW and MS were analyzed by deep sequencing. Overall, 1147 unique miRNAs comprising 434 known miRNAs, 239 conserved miRNAs and 474 candidate miRNAs were identified. Expression analysis of the 10 most abundant miRNAs in every library indicated that functional miRNAome may be a small amount and tend to be greater expressed. These sets of miRNA may play house keeping roles that were involved in myogenesis. A total of 87 miRNAs were significantly differentially expressed between LW and MS (reads > 1000, P < 0.05). Gene ontology (GO) and KEGG pathway enrichment analysis revealed that the differentially expressed miRNAs (DE miRNAs) were associated mainly with muscle contraction, WNT, mTOR, and MAPK signaling pathways. Some myogenesis related miRNAs (miR-133, miR-1, miR-206 and miR-148a) are highly abundant in MS, while other miRNAs (let-7 family, miR-214, miR-181) highly expressed in LW. In addition, the expression patterns of miRNAs (miR-1, -133, -206) at three prenatal stages (35, 55 and 90 dpc) were determined using qRT-PCR. Notably, ssc-miR-133 was significantly more highly expressed in LW pigs skeletal muscle at all prenatal stages compared with its expression in LW pigs skeletal muscle. Taken together, the main functional miRNAs during muscle development are different between lean and obese pig breeds. The present study adds new information to existing data on porcine miRNAs and will be helpful to investigate the dominant (main functional) muscle-related miRNAs sets in different pig breeds.
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Affiliation(s)
- Dongting He
- Institute of Animal Nutrition, Sichuan Agricultural University, Chendu, Sichuan, People's Republic of China
| | - Tiande Zou
- Institute of Animal Nutrition, Sichuan Agricultural University, Chendu, Sichuan, People's Republic of China
| | - Xiangrong Gai
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, People's Republic of China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chendu, Sichuan, People's Republic of China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chendu, Sichuan, People's Republic of China
| | - Zhiqing Huang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chendu, Sichuan, People's Republic of China
| | - Daiwen Chen
- Institute of Animal Nutrition, Sichuan Agricultural University, Chendu, Sichuan, People's Republic of China
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44
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Pandey A, Sahu AR, Wani SA, Saxena S, Kanchan S, Sah V, Rajak KK, Khanduri A, Sahoo AP, Tiwari AK, Mishra B, Muthuchelvan D, Mishra BP, Singh RK, Gandham RK. Modulation of Host miRNAs Transcriptome in Lung and Spleen of Peste des Petits Ruminants Virus Infected Sheep and Goats. Front Microbiol 2017; 8:1146. [PMID: 28694795 PMCID: PMC5483481 DOI: 10.3389/fmicb.2017.01146] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/06/2017] [Indexed: 12/16/2022] Open
Abstract
Peste des petits ruminants (PPR) is one of the highly contagious viral disease, characterized by fever, sore mouth, conjunctivitis, gastroenteritis, and pneumonia, primarily affecting sheep and goats. Reports suggested variable host response in goats and sheep and this host response vis-a-vis the expression of microRNAs (miRNAs) has not been investigated. Here, miRNAs were sequenced and proteomics data were generated to identify the role of differentially expressed miRNA (DEmiRNA) in PPR virus (PPRV) infected lung and spleen tissues of sheep and goats. In lungs, 67 and 37 DEmiRNAs have been identified in goats and sheep, respectively. Similarly, in spleen, 50 and 56 DEmiRNAs were identified in goats and sheep, respectively. A total of 20 and 11 miRNAs were found to be common differentially expressed in both the species in PPRV infected spleen and lung, respectively. Six DEmiRNAs—miR-21-3p, miR-1246, miR-27a-5p, miR-760-3p, miR-320a, and miR-363 were selected based on their role in viral infections, apoptosis, and fold change. The target prediction analysis of these six selected DEmiRNAs from the proteome data generated, revealed involvement of more number of genes in lung and spleen of goats than in sheep. On gene ontology analysis of host target genes these DEmiRNAs were found to regulate several immune response signaling pathways. It was observed that the pathways viz. T cell receptor signaling, Rap1 signaling, Toll-like receptor signaling, and B cell receptor signaling governed by DEmiRNAs were more perturbed in goats than in sheep. The data suggests that PPRV-induced miR-21-3p, miR-320a, and miR-363 might act cooperatively to enhance viral pathogenesis in the lung and spleen of sheep by downregulating several immune response genes. The study gives an important insight into the molecular pathogenesis of PPR by identifying that the PPRV—Izatnagar/94 isolate elicits a strong host response in goats than in sheep.
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Affiliation(s)
- Aruna Pandey
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Amit R Sahu
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Sajad A Wani
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Shikha Saxena
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Sonam Kanchan
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Vaishali Sah
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Kaushal K Rajak
- Division of Biological Products, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Alok Khanduri
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Aditya P Sahoo
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Ashok K Tiwari
- Division of Biological Standardization, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Bina Mishra
- Division of Biological Products, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - D Muthuchelvan
- Division of Virology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, NainitalIndia
| | - Bishnu P Mishra
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Raj K Singh
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
| | - Ravi K Gandham
- Computational Biology and Genomics Facility Lab, Division of Veterinary Biotechnology, Indian Council of Agricultural Research-Indian Veterinary Research Institute, BareillyIndia
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45
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He J, Tian Y, Zhao Y, Liu Y, Tao Z, Li G, Niu D, Lu L, Lu Y. MiR-144 affects fatty acid composition by regulating ELOVL6 expression in duck hepatocytes. Cell Biol Int 2017; 41:691-696. [DOI: 10.1002/cbin.10753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 02/19/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Jun He
- Institute of Animal Husbandry and Veterinary Science; Zhejiang Academy Agricultural Sciences; Hangzhou 310021 China
- Department of Animal Science; Wenzhou Vocational College of Science & Technology; Wenzhou 325006 China
| | - Yong Tian
- Institute of Animal Husbandry and Veterinary Science; Zhejiang Academy Agricultural Sciences; Hangzhou 310021 China
| | - Yan Zhao
- Department of Animal Science; Wenzhou Vocational College of Science & Technology; Wenzhou 325006 China
| | - Yali Liu
- Institute of Animal Husbandry and Veterinary Science; Zhejiang Academy Agricultural Sciences; Hangzhou 310021 China
| | - Zhengrong Tao
- Institute of Animal Husbandry and Veterinary Science; Zhejiang Academy Agricultural Sciences; Hangzhou 310021 China
| | - Guoqin Li
- Institute of Animal Husbandry and Veterinary Science; Zhejiang Academy Agricultural Sciences; Hangzhou 310021 China
| | - Dong Niu
- College of Animal Science; Zhejiang University; Hangzhou 310021 China
| | - Lizhi Lu
- Institute of Animal Husbandry and Veterinary Science; Zhejiang Academy Agricultural Sciences; Hangzhou 310021 China
| | - Yingru Lu
- Department of Emergency Medicine; First Affiliated Hospital of Wenzhou Medical University; Wenzhou 325000 China
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Comparative analysis of DNA methylome and transcriptome of skeletal muscle in lean-, obese-, and mini-type pigs. Sci Rep 2017; 7:39883. [PMID: 28045116 PMCID: PMC5206674 DOI: 10.1038/srep39883] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/29/2016] [Indexed: 02/07/2023] Open
Abstract
DNA methylation plays a pivotal role in biological processes by affecting gene expression. However, how DNA methylation mediates phenotype difference of skeletal muscle between lean-, obese-, and mini-type pigs remains unclear. We systematically carried out comparative analysis of skeletal muscle by integrating analysis of genome-wide DNA methylation, mRNA, lncRNA and miRNA profiles in three different pig breeds (obese-type Tongcheng, lean-type Landrace, and mini-type Wuzhishan pigs). We found that the differentially methylated genes (DMGs) were significantly associated with lipid metabolism, oxidative stress and muscle development. Among the identified DMGs, 253 genes were related to body-size and obesity. A set of lncRNAs and mRNAs including UCP3, FHL1, ANK1, HDAC4, and HDAC5 exhibited inversely changed DNA methylation and expression level; these genes were associated with oxidation reduction, fatty acid metabolism and cell proliferation. Gene regulatory networks involved in phenotypic variation of skeletal muscle were related to lipid metabolism, cellular movement, skeletal muscle development, and the p38 MAPK signaling pathway. DNA methylation potentially influences the propensity for obesity and body size by affecting gene expression in skeletal muscle. Our findings provide an abundant information of epigenome and transcriptome that will be useful for animal breeding and biomedical research.
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Liu X, Trakooljul N, Hadlich F, Muráni E, Wimmers K, Ponsuksili S. MicroRNA-mRNA regulatory networking fine-tunes the porcine muscle fiber type, muscular mitochondrial respiratory and metabolic enzyme activities. BMC Genomics 2016; 17:531. [PMID: 27485725 PMCID: PMC4970254 DOI: 10.1186/s12864-016-2850-8] [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: 04/29/2016] [Accepted: 06/20/2016] [Indexed: 02/02/2023] Open
Abstract
Background MicroRNAs (miRNAs) are small non-coding RNAs that play critical roles in diverse biological processes via regulation of gene expression including in skeletal muscles. In the current study, miRNA expression profile was investigated in longissimus muscle biopsies of malignant hyperthermia syndrome-negative Duroc and Pietrain pigs with distinct muscle metabolic properties in order to explore the regulatory role of miRNAs related to mitochondrial respiratory activity and metabolic enzyme activity in skeletal muscle. Results A comparative analysis of the miRNA expression profile between Duroc and Pietrain pigs was performed, followed by integration with mRNA profiles based on their pairwise correlation and computational target prediction. The identified target genes were enriched in protein ubiquitination pathway, stem cell pluripotency and geranylgeranyl diphosphate biosynthesis, as well as skeletal and muscular system development. Next, we analyzed the correlation between individual miRNAs and phenotypical traits including muscle fiber type, mitochondrial respiratory activity, metabolic enzyme activity and adenosine phosphate concentrations, and constructed the regulatory miRNA-mRNA networks associated with energy metabolism. It is noteworthy that miR-25 targeting BMPR2 and IRS1, miR-363 targeting USP24, miR-28 targeting HECW2 and miR-210 targeting ATP5I, ME3, MTCH1 and CPT2 were highly associated with slow-twitch oxidative fibers, fast-twitch oxidative fibers, ADP and ATP concentration suggesting an essential role of the miRNA-mRNA regulatory networking in modulating the mitochondrial energy expenditure in the porcine muscle. In the identified miRNA-mRNA network, a tight relationship between mitochondrial and ubiquitin proteasome system at the level of gene expression was observed. It revealed a link between these two systems contributing to energy metabolism of skeletal muscle under physiological conditions. Conclusions We assembled miRNA-mRNA regulatory networks based on divergent muscle properties between different pig breeds and further with the correlation analysis of expressed genes and phenotypic measurements. These complex networks relate to muscle fiber type, metabolic enzyme activity and ATP production and may contribute to divergent muscle phenotypes by fine-tuning the expression of genes. Altogether, the results provide an insight into a regulatory role of miRNAs in muscular energy metabolisms and may have an implication on meat quality and production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2850-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xuan Liu
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Nares Trakooljul
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Frieder Hadlich
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Eduard Muráni
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
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48
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Yang Y, Zhou R, Mu Y, Hou X, Tang Z, Li K. Genome-wide analysis of DNA methylation in obese, lean, and miniature pig breeds. Sci Rep 2016; 6:30160. [PMID: 27444743 PMCID: PMC4957084 DOI: 10.1038/srep30160] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 06/28/2016] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is a crucial epigenetic modification involved in diverse biological processes. There is significant phenotypic variance between Chinese indigenous and western pig breeds. Here, we surveyed the genome-wide DNA methylation profiles of blood leukocytes from three pig breeds (Tongcheng, Landrace, and Wuzhishan) by methylated DNA immunoprecipitation sequencing. The results showed that DNA methylation was enriched in gene body regions and repetitive sequences. LINE/L1 and SINE/tRNA-Glu were the predominant methylated repeats in pigs. The methylation level in the gene body regions was higher than in the 5' and 3' flanking regions of genes. About 15% of CpG islands were methylated in the pig genomes. Additionally, 2,807, 2,969, and 5,547 differentially methylated genes (DMGs) were identified in the Tongcheng vs. Landrace, Tongcheng vs. Wuzhishan, and Landrace vs. Wuzhishan comparisons, respectively. A total of 868 DMGs were shared by the three contrasts. The DMGs were significantly enriched in development- and metabolism-related biological processes and pathways. Finally, we identified 32 candidate DMGs associated with phenotype variance in pigs. Our research provides a DNA methylome resource for pigs and furthers understanding of epigenetically regulated phenotype variance in mammals.
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Affiliation(s)
- Yalan Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Rong Zhou
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yulian Mu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xinhua Hou
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhonglin Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Kui Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
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49
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Yang Y, Tang Z, Fan X, Xu K, Mu Y, Zhou R, Li K. Transcriptome analysis revealed chimeric RNAs, single nucleotide polymorphisms and allele-specific expression in porcine prenatal skeletal muscle. Sci Rep 2016; 6:29039. [PMID: 27352850 PMCID: PMC4926253 DOI: 10.1038/srep29039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/14/2016] [Indexed: 01/28/2023] Open
Abstract
Prenatal skeletal muscle development genetically determines postnatal muscle characteristics such as growth and meat quality in pigs. However, the molecular mechanisms underlying prenatal skeletal muscle development remain unclear. Here, we performed the first genome-wide analysis of chimeric RNAs, single nuclear polymorphisms (SNPs) and allele-specific expression (ASE) in prenatal skeletal muscle in pigs. We identified 14,810 protein coding genes and 163 high-confidence chimeric RNAs expressed in prenatal skeletal muscle. More than 94.5% of the chimeric RNAs obeyed the canonical GT/AG splice rule and were trans-splicing events. Ten and two RNAs were aligned to human and mouse chimeric transcripts, respectively. We detected 106,457 high-quality SNPs (6,955 novel), which were mostly (89.09%) located within QTLs for production traits. The high proportion of non-exonic SNPs revealed the incomplete annotation status of the current swine reference genome. ASE analysis revealed that 11,300 heterozygous SNPs showed allelic imbalance, whereas 131 ASE variants were located in the chimeric RNAs. Moreover, 4 ASE variants were associated with various economically relevant traits of pigs. Taken together, our data provide a source for studies of chimeric RNAs and biomarkers for pig breeding, while illuminating the complex transcriptional events underlying prenatal skeletal muscle development in mammals.
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Affiliation(s)
- Yalan Yang
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, P.R.China
| | - Zhonglin Tang
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, P.R.China
| | - Xinhao Fan
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Kui Xu
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Yulian Mu
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Rong Zhou
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Kui Li
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, P.R.China
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50
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He J, Wang W, Lu L, Tian Y, Niu D, Ren J, Dong L, Sun S, Zhao Y, Chen L, Shen J, Li X. Analysis of miRNAs and their target genes associated with lipid metabolism in duck liver. Sci Rep 2016; 6:27418. [PMID: 27272010 PMCID: PMC4897641 DOI: 10.1038/srep27418] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/18/2016] [Indexed: 02/06/2023] Open
Abstract
Fat character is an important index in duck culture that linked to local flavor, feed cost and fat intake for costumers. Since the regulation networks in duck lipid metabolism had not been reported very clearly, we aimed to explore the potential miRNA-mRNA pairs and their regulatory roles in duck lipid metabolism. Here, Cherry-Valley ducks were selected and treated with/without 5% oil added in feed for 2 weeks, and then fat content determination was performed on. The data showed that the fat contents and the fatty acid ratios of C17:1 and C18:2 were up-regulated in livers of oil-added ducks, while the C12:0 ratio was down-regulated. Then 21 differential miRNAs, including 10 novel miRNAs, were obtain from the livers by sequencing, and 73 target genes involved in lipid metabolic processes of these miRNAs were found, which constituted 316 miRNA-mRNA pairs. Two miRNA-mRNA pairs including one novel miRNA and one known miRNA, N-miR-16020-FASN and gga-miR-144-ELOVL6, were selected to validate the miRNA-mRNA negative relation. And the results showed that N-mir-16020 and gga-miR-144 could respectively bind the 3′-UTRs of FASN and ELOVL6 to control their expressions. This study provides new sights and useful information for future research on regulation network in duck lipid metabolism.
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Affiliation(s)
- Jun He
- Department of Animal Science, Wenzhou Vocational College of Science &Technology, Wenzhou 325006, P.R. China.,Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy Agricultural Sciences, Hangzhou 310021, P.R. China
| | - Weiqun Wang
- Department of Human Nutrition, Kansas State University, Manhattan, Kansas, 66506, USA
| | - Lizhi Lu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy Agricultural Sciences, Hangzhou 310021, P.R. China
| | - Yong Tian
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy Agricultural Sciences, Hangzhou 310021, P.R. China
| | - Dong Niu
- College of Animal Science, Zhejiang University, Hangzhou 310021, P.R. China
| | - Jindong Ren
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy Agricultural Sciences, Hangzhou 310021, P.R. China.,Zhejiang Zhuowang Agriculture Sci-Tech Limited Co., Huzhou 313014, P.R. China
| | - Liyan Dong
- Department of Animal Science, Wenzhou Vocational College of Science &Technology, Wenzhou 325006, P.R. China.,Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy Agricultural Sciences, Hangzhou 310021, P.R. China
| | - Siwei Sun
- Department of Animal Science, Wenzhou Vocational College of Science &Technology, Wenzhou 325006, P.R. China
| | - Yan Zhao
- Department of Animal Science, Wenzhou Vocational College of Science &Technology, Wenzhou 325006, P.R. China
| | - Li Chen
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy Agricultural Sciences, Hangzhou 310021, P.R. China
| | - Jianliang Shen
- Zhejiang Zhuowang Agriculture Sci-Tech Limited Co., Huzhou 313014, P.R. China
| | - Xiuhong Li
- Department of Animal Science, Wenzhou Vocational College of Science &Technology, Wenzhou 325006, P.R. China
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