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Liu C, Yang P, Wang X, Xiang B, E G, Huang Y. Candidate circRNAs related to skeletal muscle development in Dazu black goats. Anim Biotechnol 2024; 35:2286609. [PMID: 38032316 DOI: 10.1080/10495398.2023.2286609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Circular RNA (CircRNA), as a classical noncoding RNA, has been proven to regulate skeletal muscle development (SMD). However, the molecular genetic basis of circRNA regulation in muscle cells remains unclear. In this study, the expression patterns of circRNAs in the longissimus dorsi muscle at embryonic day 75 and postnatal day 1 in DBGs were investigated to identify the key circRNAs that play an important role in SMD in goats. A total of 140 significantly and differentially expressed circRNAs (DEcircRNAs) were identified among the groups at different developmental stages. Among the 116 host genes (HGs) of DEcircRNAs, 76 were significantly and differentially expressed, which was confirmed by previous RNA_seq data. Furthermore, the expression pattern of 10 DEcircRNAs with RT-qPCR was verified, which showed 80% concordance rate with that of RNA_seq datasets. Moreover, the authenticity of seven randomly selected DEcircRNAs was verified by PCR Sanger sequencing. Based on the functional annotation results, among the 76 significantly and differentially expressed HGs, 74 were enriched in 845 GO terms, whereas 35 were annotated to 85 KEGG pathways. The results of this study could provide a comprehensive understanding of the genetic basis of circRNAs involved in SMD and muscle growth.
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Affiliation(s)
- Chengli Liu
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Pu Yang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Xiao Wang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Baiju Xiang
- Chongqing Academy of Animal Sciences, Chongqing, China
| | - Guangxin E
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
| | - Yongfu Huang
- College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing, China
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Guo W, Ciwang R, Wang L, Zhang S, Liu N, Zhao J, Zhou L, Li H, Gao X, He J. CircRNA-5335 Regulates the Differentiation and Proliferation of Sheep Preadipocyte via the miR-125a-3p/STAT3 Pathway. Vet Sci 2024; 11:70. [PMID: 38393088 PMCID: PMC10891738 DOI: 10.3390/vetsci11020070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/17/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
The content of intramuscular fat (IMF) from preadipocytes is proportional to meat quality in livestock. However, the roles of circRNAs in IMF deposition in sheep are not well known. In this study, we show that circRNA-5335/miR-125a-3p/STAT3 play a crucial adjective role in the proliferation and differentiation of sheep preadipocytes. In this study, we characterized the roles of differentially expressed circRNA-5335/miR-125a-3p/STAT3, which were screened from sheep of different months of age and based on sequencing data. Firstly, the expression profiles of circRNA-5335/miR-125a-3p/STAT3 were identified during the differentiation of preadipocytes in vitro by RT-qPCR and WB. Then, the targeting relationship of the circRNA-5335/miR-125a-3p/STAT3 was verified by dual-luciferase reporter assays. The results of RT-qPCR, CCK8, EdU and Oil Red O staining assay showed that miR-125a-3p suppressed the differentiation and raised the proliferation of preadipocytes by targeting STAT3. As a competing endogenous RNA, the downregulation of circRNA-5335 decreased the expression of STAT3 by increasing miR-125a-3p, which inhibited the differentiation of preadipocytes and promoted proliferation. Our present study demonstrates the functional significance of circRNA-5335/miR-125a-3p/STAT3 in the differentiation of sheep preadipocytes, and provides novel insights into exploring the mechanism of IMF.
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Affiliation(s)
- Wei Guo
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Renzeng Ciwang
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China
| | - Lei Wang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Shuer Zhang
- Shandong Animal Husbandry Chief Station, Jinan 250100, China
| | - Nan Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Jinshan Zhao
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Lisheng Zhou
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Hegang Li
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaoxiao Gao
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Jianning He
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
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Zhu W, Huang Y, Yu C. The emerging role of circRNAs on skeletal muscle development in economical animals. Anim Biotechnol 2023; 34:2778-2792. [PMID: 36052979 DOI: 10.1080/10495398.2022.2118130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
CircRNAs are a novel type of closed circular molecules formed through a covalent bond lacking a 5'cap and 3' end tail, which mainly arise from mRNA precursor. They are widely distributed in plants and animals and are characterized by stable structure, high conservativeness in cells or tissues, and showed the expression specificity at different stages of development in different tissues. CircRNAs have been gradually attracted wide attention with the development of RNA sequencing, which become a new research hotspot in the field of RNA. CircRNAs play an important role in gene expression regulation. Presently, the related circRNAs research in the regulation of animal muscle development is still at the initial stage. In this review, the formation, properties, biological functions of circRNAs were summarized. The recent research progresses of circRNAs in skeletal muscle growth and development from economic animals including livestock, poultry and fishes were introduced. Finally, we proposed a prospective for further studies of circRNAs in muscle development, and we hope our research could provide new ideas, some theoretical supports and helps for new molecular genetic markers exploitation and animal genetic breeding in future.
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Affiliation(s)
- Wenwen Zhu
- Animal Diseases and Public Health Engineering Research Center of Henan Province, Luoyang Polytechnic, Luoyang, China
| | - Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Chuan Yu
- Animal Diseases and Public Health Engineering Research Center of Henan Province, Luoyang Polytechnic, Luoyang, China
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Hou X, Zhang R, Yang M, Niu N, Zong W, Yang L, Li H, Hou R, Wang X, Wang L, Liu X, Shi L, Zhao F, Wang L, Zhang L. Characteristics of Transcriptome and Metabolome Concerning Intramuscular Fat Content in Beijing Black Pigs. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15874-15883. [PMID: 37847170 DOI: 10.1021/acs.jafc.3c02669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
To study the characteristics of genes and metabolites related to intramuscular fat (IMF) content with less influence by breed background and individual differences, the skeletal muscle samples from 40 Beijing black pigs with either high or low IMF content were used to perform transcriptome and metabolome analyses. About 99 genes (twofold-change) were differentially expressed. Up-regulated genes in the high IMF pigs were mainly related to fat metabolism. The key genes in charge of IMF deposition are ADIPOQ, CIDEC, CYP4B1, DGAT2, LEP, OPRL1, PLIN1, SCD, and THRSP. KLHL40, TRAFD1, and HSPA6 were novel candidate genes for the IMF trait due to their high abundances. In the low IMF pigs, the differentially expressed genes involved in virus resistance were up-regulated. About 16 and 18 differential metabolites (1.5 fold-change) were obtained in the positive and negative modes, respectively. Pigs with low IMF had weaker fatty acid oxidation due to the down-regulation of various carnitines. Differentially expressed genes were more important in determining IMF deposition than differential metabolites because relatively few differential metabolites were obtained, and they were merely the products under the physiological status of diverged IMF content. This study provided valuable information for further studies on IMF deposition.
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Affiliation(s)
- Xinhua Hou
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Run Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Man Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Naiqi Niu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Wencheng Zong
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Liyu Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Huihui Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Renda Hou
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xiaoqing Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Ligang Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xin Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Lijun Shi
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Fuping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Lixian Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Longchao Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
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Qi K, Dou Y, Li C, Liu Y, Song C, Li X, Wang K, Qiao R, Li X, Yang F, Han X. CircGUCY2C regulates cofilin 1 by sponging miR-425-3p to promote the proliferation of porcine skeletal muscle satellite cells. Arch Anim Breed 2023; 66:285-298. [PMID: 38039333 PMCID: PMC10655074 DOI: 10.5194/aab-66-285-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 09/07/2023] [Indexed: 12/03/2023] Open
Abstract
Circular ribonucleic acids (or circRNAs) are an emerging class of endogenous noncoding RNAs that are involved in physiological and pathological processes. Increasing evidence suggests that circRNAs play an important regulatory role in skeletal muscle development and meat quality regulation. In this study, it was found that circGUCY2C exhibits a high expression level in the longissimus dorsi muscle. It shows resistance to RNase R and additionally promotes the mRNA expression of cyclin-dependent kinase 2 (CDK2) and proliferating cell nuclear antigen (PCNA). Specifically, it was observed that the overexpression of circGUCY2C could promote the transition of porcine skeletal muscle satellite cells into the S and G2 phases of the cell cycle and that it regulates the proliferation of porcine skeletal muscle satellite cells. In contrast, miR-425-3p plays the opposite role and has an inhibitory effect on the proliferation of porcine skeletal muscle satellite cells. MiR-425-3p has been described as a target of circGUCY2C; consequently, the depletion of miR-425-3p promoted the proliferation of porcine skeletal muscle satellite cells. CFL1 (cofilin 1) is a target of miR-425-3p, and circGUCY2C upregulated CFL1 expression by inhibiting miR-425-3p. Collectively, our research outcomes demonstrate that circGUCY2C significantly influences the proliferation of porcine skeletal muscle satellite cells by selectively targeting the miR-425-3p-CFL1 axis, and our work partially clarified the role of circGUCY2C in porcine skeletal muscle satellite cells. Thus, the study provides new insight into the function of circGUCY2C and adds to the knowledge of the post-transcriptional regulation of pork quality.
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Affiliation(s)
- Kunlong Qi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yaqing Dou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Chenlei Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yingke Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Chenglei Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
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Bordonaro S, Chessari G, Mastrangelo S, Senczuk G, Chessa S, Castiglioni B, Tumino S, Marletta D, Criscione A. Genome-wide population structure, homozygosity, and heterozygosity patterns of Nero Siciliano pig in the framework of Italian and cosmopolitan breeds. Anim Genet 2023; 54:591-605. [PMID: 37381662 DOI: 10.1111/age.13344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/30/2023]
Abstract
Analysis of genomic data is becoming more and more common for the effective management of livestock breeding programmes, even in the case of local populations. In this work, the genome-wide data of Nero Siciliano pig breed were compared to that of wild boar, Italian local and cosmopolitan breeds to investigate its genetic structure, and runs of homozygosity (ROH) and heterozygosity patterns. The Nero Siciliano has been reported to have the highest rate of genetic diversity among the Italian breeds, and a genetic variability comparable to that of the cosmopolitan breeds. Analyses of genomic structure and relationships underlined its proximity to wild boar, and an internal substructure probably linked to different family lines. The breed showed a low value of inbreeding estimated from ROH, and the highest diversity index among the Italian breeds, even if lower than that of the cosmopolitans. Four ROH islands in three chromosomes (SSC8, SSC11, and SSC14) and one heterozygosity-rich region (SSC1) were identified in Nero Siciliano, highlighting genomic regions related to productive QTL. Across breeds, SSC8 and SSC14 were the chromosomes with most ROH islands, with Mora Romagnola and wild boar showing the highest level of autozygosity. Chromosomes SSC2, SSC6, SSC8 and SSC13 showed the majority of runs of heterozygosity regions, mainly found in the cosmopolitan pig breeds, which reported several genes associated with health-related QTL. The outlined results can help to better identify the genomic profile of this local breed in order to plan matings, maintain adequate internal diversity and exploit the production system.
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Affiliation(s)
- Salvatore Bordonaro
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Giorgio Chessari
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, Università del Molise, Campobasso, Italy
| | - Stefania Chessa
- Dipartimento di Scienze Veterinarie, Università di Torino, Torino, Italy
| | - Bianca Castiglioni
- Istituto di Biologia e Biotecnologia Agraria, National Research Council, Lodi, Italy
| | - Serena Tumino
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Andrea Criscione
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
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Yang Y, Wang X, Wang S, Chen Q, Li M, Lu S. Identification of Potential Sex-Specific Biomarkers in Pigs with Low and High Intramuscular Fat Content Using Integrated Bioinformatics and Machine Learning. Genes (Basel) 2023; 14:1695. [PMID: 37761835 PMCID: PMC10531182 DOI: 10.3390/genes14091695] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/17/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Intramuscular fat (IMF) content is a key determinant of pork quality. Controlling the genetic and physiological factors of IMF and the expression patterns of various genes is important for regulating the IMF content and improving meat quality in pig breeding. Growing evidence has suggested the role of genetic factors and breeds in IMF deposition; however, research on the sex factors of IMF deposition is still lacking. The present study aimed to identify potential sex-specific biomarkers strongly associated with IMF deposition in low- and high-IMF pig populations. The GSE144780 expression dataset of IMF deposition-related genes were obtained from the Gene Expression Omnibus. Initially, differentially expressed genes (DEGs) were detected in male and female low-IMF (162 DEGs, including 64 up- and 98 down-regulated genes) and high-IMF pigs (202 DEGs, including 147 up- and 55 down-regulated genes). Moreover, hub genes were screened via PPI network construction. Furthermore, hub genes were screened for potential sex-specific biomarkers using the least absolute shrinkage and selection operator machine learning algorithm, and sex-specific biomarkers in low-IMF (troponin I (TNNI1), myosin light chain 9(MYL9), and serpin family C member 1(SERPINC1)) and high-IMF pigs (CD4 molecule (CD4), CD2 molecule (CD2), and amine oxidase copper-containing 2(AOC2)) were identified, and then verified by quantitative real-time PCR (qRT-PCR) in semimembranosus muscles. Additionally, the gene set enrichment analysis and single-sample gene set enrichment analysis of hallmark gene sets were collectively performed on the identified biomarkers. Finally, the transcription factor-biomarker and lncRNA-miRNA-mRNA (biomarker) networks were predicted. The identified potential sex-specific biomarkers may provide new insights into the molecular mechanisms of IMF deposition and the beneficial foundation for improving meat quality in pig breeding.
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Affiliation(s)
| | | | | | | | | | - Shaoxiong Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.Y.); (X.W.); (S.W.); (Q.C.); (M.L.)
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Peng O, Xia Y, Wei Y, Zeng S, Zou C, Hu F, Xu Q, Huang Y, Geng R, Hu G, Cao Y, Zhang H. Integrative transcriptomic profiling of mRNA, miRNA, circRNA, and lncRNA in alveolar macrophages isolated from PRRSV-infected porcine. Front Immunol 2023; 14:1258778. [PMID: 37691924 PMCID: PMC10491896 DOI: 10.3389/fimmu.2023.1258778] [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: 07/14/2023] [Accepted: 08/09/2023] [Indexed: 09/12/2023] Open
Abstract
Introduction The porcine reproductive and respiratory syndrome virus (PRRSV) continues to pose a significant threat to the global swine industry, attributed largely to its immunosuppressive properties and the chronic nature of its infection. The absence of effective vaccines and therapeutics amplifies the urgency to deepen our comprehension of PRRSV's intricate pathogenic mechanisms. Previous transcriptomic studies, although informative, are partially constrained by their predominant reliance on in vitro models or lack of long-term infections. Moreover, the role of circular RNAs (circRNAs) during PRRSV invasion is yet to be elucidated. Methods In this study, we employed an in vivo approach, exposing piglets to a PRRSV challenge over varied durations of 3, 7, or 21 days. Subsequently, porcine alveolar macrophages were isolated for a comprehensive transcriptomic investigation, examining the expression patterns of mRNAs, miRNAs, circRNAs, and long non-coding RNAs (lncRNAs). Results Differentially expressed RNAs from all four categories were identified, underscoring the dynamic interplay among these RNA species during PRRSV infection. Functional enrichment analyses indicate that these differentially expressed RNAs, as well as their target genes, play a pivotal role in immune related pathways. For the first time, we integrated circRNAs into the lncRNA-miRNA-mRNA relationship, constructing a competitive endogenous RNA (ceRNA) network. Our findings highlight the immune-related genes, CTLA4 and SAMHD1, as well as their associated miRNAs, lncRNAs, and circRNAs, suggesting potential therapeutic targets for PRRS. Importantly, we corroborated the expression patterns of selected RNAs through RT-qPCR, ensuring consistency with our transcriptomic sequencing data. Discussion This study sheds lights on the intricate RNA interplay during PRRSV infection and provides a solid foundation for future therapeutic strategizing.
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Affiliation(s)
- Ouyang Peng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yu Xia
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Wei
- College of Animal Science and Technology/Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, China
| | - Siying Zeng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chuangchao Zou
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Fangyu Hu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qiuping Xu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yihui Huang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Rui Geng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Guangli Hu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yongchang Cao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hao Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Wang Y, Cheng J, Xu C, Jin J, Bao W, Wu S, Wu Z. Genome-wide analysis of circRNA regulation during spleen development of Chinese indigenous breed Meishan pigs. BMC Genomics 2023; 24:477. [PMID: 37612620 PMCID: PMC10463621 DOI: 10.1186/s12864-023-09612-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/22/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Numerous circular RNAs (circRNAs) have been recently identified in porcine tissues and cell types. Nevertheless, their significance in porcine spleen development is yet unelucidated. Herein, we reported an extensive overlook of circRNA expression profile during spleen development in Meishan pigs. RESULTS Overall, 39,641 circRNAs were identified from 6,914 host genes. Among them, many circRNAs are up- or down-regulated at different time points of pig spleen development. Using WGCNA analysis, we revealed two essential modules for protein-coding genes and circRNAs. Subsequent correlation analysis revealed 67 circRNAs/co-expressed genes that participated in immnue-associated networks. Furthermore, a competing endogenous RNA (ceRNA) network analysis of circRNAs revealed that 12 circRNAs modulated CD226, MBD2, SAMD3, SIT1, SRP14, SYTL3 gene expressions via acting as miRNA sponges. Moreover, the circRNA_21767/miR-202-3p axis regulated SIT1 expression in a ceRNA manner, which is critical for the immune-based regulation of spleen development in Meishan pigs. CONCLUSIONS Overall, our results demonstrated that the circRNAs were differentially expressed during different stages of porcine spleen development, meanwhile the circRNAs interacted with immune-related genes in a ceRNA-based fashion. Moreover, we presented biomedical researchers with RNAseqTools, a user-friendly and powerful software for the visualization of transcriptome profile data.
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Affiliation(s)
- Yifu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Jinhua Cheng
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Chao Xu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Jian Jin
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Wenbin Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Shenglong Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Zhengchang Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.
- International Research Laboratory of Prevention and Control of Important Animal Infectious Diseases and Zoonotic Diseases of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou, 225009, China.
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10
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Qi K, Dou Y, Zhang Z, Wei Y, Song C, Qiao R, Li X, Yang F, Wang K, Li X, Han X. Expression Profile and Regulatory Properties of m6A-Modified circRNAs in the Longissimus Dorsi of Queshan Black and Large White Pigs. Animals (Basel) 2023; 13:2190. [PMID: 37443988 DOI: 10.3390/ani13132190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/21/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
It is well known that N6-methyladenosine (m6A) is the most abundant modification in linear RNA molecules, but many circRNA molecules have now been found to have a wide range of m6A modification sites as well. However, there are few relevant studies and information on the expression profile and functional regulatory properties of m6A-modified circRNAs (m6A-circRNAs) in longissimus dorsi. In this study, a total of 12 putative m6A-circRNAs were identified and characterized in the longissimus dorsi of Queshan Black and Large White pigs-8 of them were significantly more expressed in the longissimus dorsi of Queshan Black than in Large White pigs, while the other 4 were the opposite. These 12 putative m6A-circRNAs were also found to act as miRNA sponge molecules to regulate fat deposition by constructing the ceRNA regulatory network. Enrichment analysis also revealed that the 12 m6A-circRNAs parent genes and their adsorbed miRNA target genes were widely involved in fat deposition and cell proliferation and differentiation-related pathways, such as the HIF-1 signaling pathway, the pentose phosphate pathway, the MAPK signaling pathway, the glycosphingolipid biosynthesis-lacto and neolacto series, and the TNF signaling pathway, suggesting that the analyzed m6A-circRNAs may be largely involved in the formation of pork quality. These results provide new information to study the regulatory properties of m6A-circRNAs in the formation of pork quality.
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Affiliation(s)
- Kunlong Qi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yaqing Dou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhe Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yilin Wei
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Chenglei Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
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11
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Yu Z, Xu X, Ai N, Wang K, Zhang P, Li X, LiuFu S, Liu X, Jiang J, Gu J, Gao N, Ma H. Integrated analysis of circRNA, lncRNA, miRNA and mRNA to reveal the ceRNA regulatory network of postnatal skeletal muscle development in Ningxiang pig. Front Cell Dev Biol 2023; 11:1185823. [PMID: 37465009 PMCID: PMC10350537 DOI: 10.3389/fcell.2023.1185823] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/22/2023] [Indexed: 07/20/2023] Open
Abstract
Introduction: The development of skeletal muscle is regulated by regulatory factors of genes and non-coding RNAs (ncRNAs). Methods: The objective of this study was to understand the transformation of muscle fiber type in the longissimus dorsi muscle of male Ningxiang pigs at four different growth stages (30, 90, 150, and 210 days after birth, n = 3) by histological analysis and whole transcriptome sequencing. Additionally, the study investigated the expression patterns of various RNAs involved in muscle fiber transformation and constructed a regulatory network for competing endogenous RNA (ceRNA) that includes circular RNA (circRNA)/long non-coding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA). Results: Histomorphology analysis showed that the diameter of muscle fiber reached its maximum at 150 days after birth. The slow muscle fiber transformation showed a pattern of initial decrease followed by an increase. 29,963 circRNAs, 2,683 lncRNAs, 986 miRNAs and 22,411 mRNAs with expression level ≥0 were identified by whole transcriptome sequencing. Furthermore, 642 differentially expressed circRNAs (DEc), 505 differentially expressed lncRNAs (DEl), 316 differentially expressed miRNAs (DEmi) and 6,090 differentially expressed mRNAs (DEm) were identified by differential expression analysis. Functions of differentially expressed mRNA were identified by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). GO enrichment analysis indicates that 40 known genes and 6 new genes are associated with skeletal muscle development. Additionally, KEGG analysis shows that these genes regulate skeletal muscle development via MAPK, FoxO, Hedgehog, PI3K-Akt, Notch, VEGF and other signaling pathways. Through protein-protein interaction (PPI) and transcription factor prediction (TFP), the action mode of skeletal muscle-related genes was explored. PPI analysis showed that there were stable interactions among 19 proteins, meanwhile, TFP analysis predicted 22 transcription factors such as HMG20B, MYF6, MYOD1 and MYOG, and 12 of the 19 interacting proteins were transcription factors. The regulatory network of ceRNA related to skeletal muscle development was constructed based on the correlation of various RNA expression levels and the targeted binding characteristics with miRNA. The regulatory network included 31 DEms, 59 miRNAs, 667 circRNAs and 224 lncRNAs. conclusion: Overall, the study revealed the role of ceRNA regulatory network in the transformation of skeletal muscle fiber types in Ningxiang pigs, which contributes to the understanding of ceRNA regulatory network in Ningxiang pigs during the skeletal muscle development period.
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Affiliation(s)
- Zonggang Yu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xueli Xu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Nini Ai
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Kaiming Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Peiwen Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xintong Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Sui LiuFu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xiaolin Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Jun Jiang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Jingjing Gu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Ning Gao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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12
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Liu Y, Wei Y, Dou Y, Li C, Song C, Zhang Z, Qi K, Li X, Qiao R, Wang K, Li X, Yang F, Han X. Effect of miR-149-5p on intramuscular fat deposition in pigs based on metabolomics and transcriptomics. BMC Genomics 2023; 24:293. [PMID: 37259030 DOI: 10.1186/s12864-023-09382-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/15/2023] [Indexed: 06/02/2023] Open
Abstract
As one of the important traits in pig production, meat quality has important research significance and value. Intramuscular fat (IMF) content is one of the most important factors affecting pork quality. Many experimental studies have shown that IMF content is closely related to the flavor, tenderness, and juiciness of pork. Therefore, it is of great significance to study the mechanism of porcine IMF deposition. Previous research indicated that miR-149-5p promoted the proliferation of porcine intramuscular (IM) preadipocytes and decreased their ability to differentiate, albeit the exact mechanism of action is unknown. In vitro, foreign pigs showed increased miR-149-5p expression and reduced fat deposition when compared to Queshan Black pigs. This study conducted metabolomics and transcriptomics analyses of porcine IM preadipocytes overexpressing miR-149-5p to verify their effects on lipid formation. According to metabolomics analysis, the overexpression of miR-149-5p has significantly altered the lipid, organic acid, and organic oxygen metabolites of porcine IM preadipocytes. Specially speaking, it has changed 115 metabolites, including 105 up-regulated and 10 down-regulated ones, as well as the composition of lipid, organic acid, and organic oxygen metabolism-related metabolites. RNA-seq analysis showed that overexpression of miR-149-5p significantly altered 857 genes, of which 442 were up-regulated, and 415 were down-regulated, with enrichment to MAPK, IL-17, PI3K-Akt, and ErbB signaling pathways. We found that overexpression of miR-149-5p inhibited adipogenic differentiation by changing cAMP signaling pathway in porcine IM preadipocytes. In addition, the overexpression of miR-149-5p may affect the transport of Cu2+ by targeting ATP7A and inhibiting adipogenic differentiation. These findings elucidate the regulatory function of miR-149-5p in porcine IM preadipocytes, which may be a key target for controlling pork quality.
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Affiliation(s)
- Yingke Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yilin Wei
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yaqing Dou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Chenlei Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Chenglei Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhe Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Kunlong Qi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
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13
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Dou Y, Wei Y, Zhang Z, Li C, Song C, Liu Y, Qi K, Li X, Li X, Qiao R, Wang K, Yang F, Han X. Transcriptome-wide analysis of RNA m 6A methylation regulation of muscle development in Queshan Black pigs. BMC Genomics 2023; 24:239. [PMID: 37142996 PMCID: PMC10161540 DOI: 10.1186/s12864-023-09346-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 04/28/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) refers to the methylation modification of N6 position of RNA adenine, a dynamic reversible RNA epigenetic modification that plays an important regulatory role in a variety of life processes. In this study, we used MeRIP-Seq and RNA-Seq of the longissimus dorsi (LD) muscle of adult (QA) and newborn (QN) Queshan Black pigs to screen key genes with m6A modification involved in muscle growth by bioinformatics analysis. RESULTS A total of 23,445 and 25,465 m6A peaks were found in the whole genomes of QA and QN, respectively. Among them, 613 methylation peaks were significantly different (DMPs) and 579 genes were defined as differentially methylated genes (DMGs). Compared with the QN group, there were 1,874 significantly differentially expressed genes (DEGs) in QA group, including 620 up-regulated and 1,254 down-regulated genes. In order to investigate the relationship between m6A and mRNA expression in the muscle of Queshan Black pigs at different periods, a combined analysis of MeRIP-Seq and RNA-Seq showed that 88 genes were significantly different at both levels. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes results showed that DEGs and DMGs were mainly involved in skeletal muscle tissue development, FoxO signaling pathway, MAPK signaling pathway, insulin signaling pathway, PI3K-Akt signaling pathway, and Wnt signaling pathway. Four DEGs (IGF1R, CCND2, MYOD1 and FOS) and four DMGs (CCND2, PHKB, BIN1 and FUT2), which are closely related to skeletal muscle development, were selected as candidate genes for verification, and the results were consistent with the sequencing results, which indicated the reliability of the sequencing results. CONCLUSIONS These results lay the foundation for understanding the specific regulatory mechanisms of growth in Queshan Black pigs, and provide theoretical references for further research on the role of m6A in muscle development and breed optimization selection.
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Affiliation(s)
- Yaqing Dou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yilin Wei
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhe Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Chenlei Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Chenglei Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yingke Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Kunlong Qi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Feng Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
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14
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Gong Y, Lin Z, Wang Y, Liu Y. Research progress of non-coding RNAs regulation on intramuscular adipocytes in domestic animals. Gene 2023; 860:147226. [PMID: 36736503 DOI: 10.1016/j.gene.2023.147226] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/07/2023] [Accepted: 01/20/2023] [Indexed: 02/05/2023]
Abstract
Intramuscular fat (IMF) is the main determinant of the economic value of domestic animal meat, and has a vital impact on the sensory quality characteristics, while the content of IMF is mainly determined by the size and number of intramuscular adipocytes. In recent years, due to the development of sequencing technology and omics technology, a large number of non-coding RNAs have been identified in intramuscular adipocytes. Non-coding RNAs are a kind of RNA regulatory factors with biological functions but without translation function, which mainly include microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). These non-coding RNAs regulate the key genes of intramuscular adipocyte growth and development at post-transcriptional level through a variety of regulatory mechanisms, and affect the number and size of intramuscular adipocytes, thus affecting the content of IMF. Here, the review summarizes the candidate non-coding RNAs (miRNAs, lncRNAs, circRNAs) and genes involved in the regulation of intramuscular adipocytes, the related regulation mechanism and signaling pathways, in order to provide reference for further clarifying the molecular regulation mechanism of non-coding RNAs on intramuscular adipocytes in domestic animals.
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Affiliation(s)
- Yanrong Gong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhongzhen Lin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yiping Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
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15
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Yun J, Huang X, Liu C, Shi M, Li W, Niu J, Cai C, Yang Y, Gao P, Guo X, Li B, Lu C, Cao G. Genome-wide analysis of circular RNA-mediated ceRNA regulation in porcine skeletal muscle development. BMC Genomics 2023; 24:196. [PMID: 37046223 PMCID: PMC10099641 DOI: 10.1186/s12864-023-09284-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 03/30/2023] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND As a diverse and abundant class of endogenous RNAs, circular RNAs (circRNAs) participate in various biological processes including cell proliferation and apoptosis. Nevertheless, few researchers have investigated the role of circRNAs in muscle development in cultivated pigs. RESULTS In this study, we used RNA-seq to construct circRNA expression profiles in skeletal muscle of Jinfen White pigs at the age of 1, 90, and 180 days. Among the 16,990 identified circRNAs, 584 circRNAs were differentially expressed. Moreover, the enrichment analysis of DE circRNA host genes showed that they were mainly involved in muscle contraction, muscle organ development and muscle system processes, as well as AMPK and cAMP-related signal pathways. We also constructed a circRNA-miRNA-mRNA co-expression network to find key circRNAs which many involved in the regulation of porcine skeletal muscle development through the competitive endogenous RNA (ceRNA) mechanism. It is noteworthy that circ_0018595/miR-1343/PGM1 axis may play a regulatory role in the development of porcine skeletal muscle. CONCLUSIONS This study identified the circRNAs and present the circRNA expression profile in the development of pigs, revealed that DE circRNA host genes participate in different cell fates and enriched the porcine ceRNA network. Thus, this work will become a valuable resource for further in-depth study of the regulatory mechanism of circRNA in the development of porcine skeletal muscle.
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Affiliation(s)
- Jiale Yun
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Xiaoyu Huang
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Chang Liu
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Mingyue Shi
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Wenxia Li
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Jin Niu
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Chunbo Cai
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Yang Yang
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Pengfei Gao
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Xiaohong Guo
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Bugao Li
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China
| | - Chang Lu
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China.
| | - Guoqing Cao
- College of Animal Science, Shanxi Agricultural University, Taigu, 030801, China.
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16
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Fan Y, Zhang Z, Deng K, Kang Z, Guo J, Zhang G, Zhang Y, Wang F. CircUBE3A promotes myoblasts proliferation and differentiation by sponging miR-28-5p to enhance expression. Int J Biol Macromol 2023; 226:730-745. [PMID: 36526061 DOI: 10.1016/j.ijbiomac.2022.12.064] [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: 06/20/2022] [Revised: 11/18/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022]
Abstract
circRNAs have been found to be involved in the regulatory network of skeletal muscle development in studies. However, their precise functions and regulatory mechanisms remain unknown. The expression patterns and alterations of circRNAs in the longissimus dorsi muscle of two major developmental stages of goats (D75 fetus and D1 kid) were studied using high-throughput sequencing technology and bioinformatics tools in this study. In kid skeletal muscles, 831 differently expressed circRNAs were found, comprising 486 up-regulated circRNAs and 345 down-regulated circRNAs. In skeletal muscle, we focused on the highly expressed and variably expressed circUBE3A. CircUBE3A levels were discovered to be much higher in kid skeletal muscle and differentiated myoblasts. Knocking down circUBE3A resulted in a significant increase in cell proliferation and differentiation in goat myoblasts. CircUBE3A specifically binds to and inhibits miR-28-5p, boosting the expression of Hydroxyacyl Coenzyme A Dehydrogenase Beta (HADHB) and contributing to goat myoblast proliferation and differentiation, according to the mechanistic investigation. The above results indicated that circUBE3A could regulate HADHB expression by targeting miR-28-5p, consequently increasing goat myoblast proliferation and differentiation. Our findings offer fresh perspectives on goat breeding and growth regulation, as well as substantial theoretical basis.
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Affiliation(s)
- Yixuan Fan
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhen Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Kaiping Deng
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziqi Kang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinjing Guo
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Guomin Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanli Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Wang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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17
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Identification and Functional Prediction of Long Non-Coding RNA in Longissimus Dorsi Muscle of Queshan Black and Large White Pigs. Genes (Basel) 2023; 14:genes14010197. [PMID: 36672938 PMCID: PMC9858627 DOI: 10.3390/genes14010197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Long non-coding RNA (lncRNA) participates in the regulation of various biological processes, but its function and characteristics in intramuscular fat (IMF) deposition in different breeds of pigs have not been fully understood. IMF content is one of the important factors affecting pork quality. In the present study, the differentially expressed lncRNAs (DE lncRNAs) and their target genes were screened by comparing Queshan Black (QS) and Large White (LW) pigs based on RNA-seq. The results displayed 55 DE lncRNAs between QS and LW, 29 upregulated and 26 downregulated, with 172 co-located target genes, and 6203 co-expressed target genes. The results of GO and KEGG analysis showed that the target genes of DE lncRNAs were involved in multiple pathways related to lipogenesis and lipid metabolism, such as the lipid biosynthetic process, protein phosphorylation, activation of MAPK activity, and the Jak-STAT signaling pathway. By constructing regulatory networks, lincRNA-ZFP42-ACTC1, lincRNA-AMY2-STAT1, and/or lincRNA-AMY2/miR-204/STAT1 were sieved, and the results indicate that lncRNA could participate in IMF deposition through direct regulation or ceRNA. These findings provide a basis for analyzing the molecular mechanism of IMF deposition in pigs and lay a foundation for developing and utilizing high-quality resources of local pig breeds.
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18
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Construction and Comprehensive Analysis of miRNAs and Target mRNAs in Longissimus dorsi Muscle of Queshan Black and Large White Pigs. Life (Basel) 2022; 12:life12111814. [DOI: 10.3390/life12111814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/23/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
A miRNA-mRNA combination analysis was performed on the longissimus dorsi muscle of adult Queshan Black and Large White pigs by RNA-seq technology to reveal the molecular mechanism affecting pork quality traits. The sequencing results showed that 39 miRNAs were differentially expressed between Queshan Black and Large White pigs, which targeted 5234 mRNAs, and 15 differentially expressed miRNAs targeted 86 differentially expressed mRNAs. The qRT-PCR results showed that miRNAs showed similar expression patterns to RNA-seq. The GO analysis indicated that differentially expressed miRNAs with differential target mRNAs were primarily involved in biological processes such as phospholipase activity, MAP-kinase scaffold activity, lipase activity, and regulation of the extent of cell growth. The KEGG analysis also revealed that such mRNAs were significantly enriched in the ECM-receptor interaction, sphingolipid metabolism, apoptosis, PI3K-Akt signaling pathway, and AMPK signaling pathway. In addition, software predictions showed that 17 (13 of which were upregulated and four were downregulated) of 39 differentially expressed miRNAs targeted 118 negatively correlated expression mRNAs. The upregulated miRNAs contained 103 negatively correlated target mRNAs, whereas the downregulated miRNAs contained 15 negatively correlated target mRNAs. The GO analysis showed that such mRNAs were primarily involved in MAP-kinase scaffold activity, myoblast development, and peptidyl-lysine methylation, and the KEGG analysis showed significant enrichment in ECM-receptor interaction and focal adhesion. The functional enrichment analysis of miRNA target genes revealed that miR-328 was screened out as a key miRNA, and preliminary functional validation was performed. Moreover, the overexpressed miR-328 could affect the expression of proliferation-related genes, such as CDK2, CDK4, CCNB1, CCND1, CCNE1, and PCNA. These results indicated that miR-328 may regulate fat deposition and affect meat quality by influencing related pathways. This study revealed that the miRNA−mRNA regulatory axis affects fat deposition and skeletal muscle development, which provides a theoretical basis for further study on the molecular mechanism of meat quality.
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19
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Ding Y, Hou Y, Ling Z, Chen Q, Xu T, Liu L, Yu N, Ni W, Ding X, Zhang X, Zheng X, Bao W, Yin Z. Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes. Int J Mol Sci 2022; 23:12596. [PMID: 36293455 PMCID: PMC9603960 DOI: 10.3390/ijms232012596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 11/27/2022] Open
Abstract
Intramuscular fat (IMF) content is vital for pork quality, serving an important role in economic performance in pig industry. Non-coding RNAs, with mRNAs, are involved in IMF deposition; however, their functions and regulatory mechanisms in porcine IMF remain elusive. This study assessed the whole transcriptome expression profiles of the Longissimus dorsi muscle of pigs with high (H) and low (L) IMF content to identify genes implicated in porcine IMF adipogenesis and their regulatory functions. Hundreds of differentially expressed RNAs were found to be involved in fatty acid metabolic processes, lipid metabolism, and fat cell differentiation. Furthermore, combing co-differential expression analyses, we constructed competing endogenous RNAs (ceRNA) regulatory networks, showing crosstalk among 30 lncRNAs and 61 mRNAs through 20 miRNAs, five circRNAs and 11 mRNAs through four miRNAs, and potential IMF deposition-related ceRNA subnetworks. Functional lncRNAs and circRNAs (such as MSTRG.12440.1, ENSSSCT00000066779, novel_circ_011355, novel_circ_011355) were found to act as ceRNAs of important lipid metabolism-related mRNAs (LEP, IP6K1, FFAR4, CEBPA, etc.) by sponging functional miRNAs (such as ssc-miR-196a, ssc-miR-200b, ssc-miR10391, miR486-y). These findings provide potential regulators and molecular regulatory networks that can be utilized for research on IMF traits in pigs, which would aid in marker-assisted selection to improve pork quality.
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Affiliation(s)
- Yueyun Ding
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Yinhui Hou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Zijing Ling
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Qiong Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Tao Xu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Lifei Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Na Yu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Wenliang Ni
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Xiaoling Ding
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Xiaodong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Xianrui Zheng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
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20
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Jiang Y, Liu J, Liu H, Zhang W, Li X, Liu L, Zhou M, Wang J, Su S, Ding X, Wang C. miR-381-3p Inhibits Intramuscular Fat Deposition through Targeting FABP3 by ceRNA Regulatory Network. BIOLOGY 2022; 11:biology11101497. [PMID: 36290402 PMCID: PMC9598794 DOI: 10.3390/biology11101497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/07/2022] [Accepted: 10/07/2022] [Indexed: 01/24/2023]
Abstract
Intramuscular fat (IMF) deposition is an important determinant of pork quality and a complex process facilitated by non-coding ceRNAs. In this study, 52 Berkshire × Anqing Sixwhite crossbred pigs were slaughtered to measure eight carcass and pork quality traits. Whole-transcriptome sequencing analysis was performed using longissimus dorsi samples of six low- and high-IMF samples; 34 ceRNA networks, based on 881, 394, 158 differentially expressed (DE) lncRNAs, miRNAs, and mRNAs, were constructed. Following weighted gene co-expression network analysis between the low and high IMF, only one ceRNA, lncRNA4789/miR-381-3p/FABP3, that showed similar DE trend in longissimus dorsi tissue was retained. Dual-luciferase reporter assays further indicated that FABP3 was a direct, functional target of miR-381-3p, where miR-381-3p overexpression inhibited the mRNA and protein expression of FABP3. In addition, overexpressed lncRNA4789 attenuated the effect of miR-381-3p on FABP3 by sponging miR-381-3p. Cell function verification experiment demonstrated that miR-381-3p suppressed IMF deposition by inhibiting preadipocyte cell differentiation and lipid droplet deposition via the suppression of FABP3 expression in the peroxisome proliferator-activated receptor signalling pathway, whereas lncRNA4789 rescued FABP3 expression by sponging miR-381-3p. Our study may aid in identifying novel molecular markers for its optimization in IMF which is of importance in breeding for improving pork quality.
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Affiliation(s)
- Yao Jiang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- National Animal Husbandry Service, Beijing 100125, China
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jiali Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huatao Liu
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wei Zhang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiaojin Li
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Linqing Liu
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Mei Zhou
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Jieru Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Shiguang Su
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xiangdong Ding
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chonglong Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Correspondence:
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21
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Liu Y, Dou Y, Qi K, Li C, Song C, Li X, Li X, Qiao R, Wang K, Han X. CircSETBP1 Acts as a MiR-149-5p Sponge to Promote Intramuscular Fat Deposition by Regulating CRTCs. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12841-12851. [PMID: 36165804 DOI: 10.1021/acs.jafc.2c05697] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Circular RNAs (circRNAs) appear to be crucial in the process of adipogenesis according to mounting data. CircSETBP1 is a newly discovered circRNA associated with adipogenesis. Sequencing verification and RNase R treatment have confirmed the circular nature of circSETBP1 in porcine tissue. The precise function and mechanism of circSETBP1 in adipocyte biology are still unclear. Cell counting kit-8 (CCK8), Oil red O staining, and quantitative real-time polymerase chain reaction (qRT-PCR) were employed in this investigation to reveal the functions of circSETBP1 and miR-149-5p in the growth and development of porcine intramuscular (IM) preadipocytes. CircSETBP1 overexpression accelerated cell differentiation while reducing cell proliferation. The opposite outcome was produced by overexpressing miR-149-5p. Meanwhile, circSETBP1 down-regulated the expression of miR-149-5p and miR-149-5p restrained the expression of CRTC1/CRTC2. CircSETBP1 was directly targeted by miR-149-5p, and CRTC1/CRTC2 were the target genes of miR-149-5p using bioinformatic analysis, the dual-Luciferase reporter system, and qRT-PCR. In conclusion, circSETBP1 controls the proliferation and differentiation of porcine IM preadipocytes and 3T3-L1 cells by regulating the miR-149-5p/CRTCs axis. The results of this study not only illuminate the molecular mechanism of circSETBP1/miR-149-5p involved in the deposition of porcine intramuscular fat (IMF), but they also provide a significant theoretical reference for raising quality of pork.
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Affiliation(s)
- Yingke Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yaqing Dou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Kunlong Qi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Chenlei Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Chenglei Song
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xinjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiuling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
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22
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Characteristics and Expression of circ_003628 and Its Promoted Effect on Proliferation and Differentiation of Skeletal Muscle Satellite Cells in Goats. Animals (Basel) 2022; 12:ani12192524. [PMID: 36230263 PMCID: PMC9559657 DOI: 10.3390/ani12192524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/18/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Circular RNAs (circRNAs) are new regulators of the development of skeletal muscle in mammals. Herein, circ_003628 in Longissimus dorsi muscle tissue of goats, previously found by RNA-seq, was selected to construct an expression profile in different caprine tissues, and investigate the effect on proliferation and differentiation of caprine skeletal muscle satellite cells (SMSCs), using RT-qPCR, EdU, CCK-8 and immunofluorescence assays. The results showed that circ_003628 had the highest expression level both in the longissimus dorsi muscle among nine caprine tissues collected, and on day 6 after differentiation during SMSCs differentiation periods. The interfering of circ_003628 inhibited the viability, proliferation, and differentiation of goat SMSCs. Abstract In our previous a study, circ_003628 was one of the most highly expressed circular RNAs (circRNAs) in the Longissimus dorsi muscle of goats found by RNA-seq, suggesting that the circRNA may be important for caprine muscle growth and development. However, there have been no reports describing the molecular mechanisms by which circ_003628 regulates the activities of goat skeletal muscle satellite cells (SMSCs). In this study, reverse transcriptase-PCR (RT-PCR) and DNA sequencing were used to validate the authenticity of circ_003628, and its characteristics, expression profile and effect on goat SMSCs were also studied using real-time quantitative-PCR (RT-qPCR), EdU, CCK-8 and immunofluorescence assays. Circ_003628 is partially originated from 13 exons, 12 introns and 3′-untranslated regions (UTR) of caprine Myosin Heavy Chain 1 (MYH1), and 25 exons and 5′ UTR of Myosin Heavy Chain 4 (MYH4), as well as intergenic sequences between the two genes. A total of 77.07% of circ_003628 were located in the nuclei of goat SMSCs, while 22.93% were expressed in the cytoplasm. The circRNAs were only expressed in triceps brachii, quadriceps femoris and longissimus dorsi muscle tissues in nine caprine tissues investigated, with the highest expression level in longissimus dorsi muscle. The expression level of circ_003628 gradually increased during differentiation periods of goat SMSCs and reached the maximum on day 6 after differentiation. The small interfering RNA of circ_003628 (named si-circ_003628) inhibited the viability and proliferation of goat SMSCs, and also decreased the expression of four cell proliferation marker genes: paired box 7 (Pax7), cyclin-dependent kinase 2 (CDK2), CDK4 and CyclinD1 in goat SMSCs. Transfection of si-circ_003628 significantly decreased the area of MyHC-labeled myotubes of goat SMSCs, as well as the expression levels of three differentiation marker genes: myosin heavy chain (MyHC), myogenin (MyoG), and myocyte enhancer factor 2C (MEF2C). These results suggest that circ_003628 promotes the viability, proliferation, and differentiation of goat SMSCs, and they also provide an improved understanding of the roles of circ_003628 in skeletal muscle growth and development in goats.
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23
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Comparative Transcriptomic Analysis of mRNAs, miRNAs and lncRNAs in the Longissimus dorsi Muscles between Fat-Type and Lean-Type Pigs. Biomolecules 2022; 12:biom12091294. [PMID: 36139132 PMCID: PMC9496231 DOI: 10.3390/biom12091294] [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: 06/26/2022] [Revised: 09/05/2022] [Accepted: 09/09/2022] [Indexed: 11/24/2022] Open
Abstract
In pigs, meat quality and production are two important traits affecting the pig industry and human health. Compared to lean-type pigs, fat-type pigs contain higher intramuscular fat (IMF) contents, better taste and nutritional value. To uncover genetic factors controlling differences related to IMF in pig muscle, we performed RNA-seq analysis on the transcriptomes of the Longissimus dorsi (LD) muscle of Laiwu pigs (LW, fat-type pigs) and commercial Duroc × Landrace × Yorkshire pigs (DLY, lean-type pigs) at 150 d to compare the expression profiles of mRNA, miRNA and lncRNA. A total of 225 mRNAs, 12 miRNAs and 57 lncRNAs were found to be differentially expressed at the criteria of |log2(foldchange)| > 1 and q < 0.05. The mRNA expression of LDHB was significantly higher in the LD muscle of LW compared to DLY pigs with log2(foldchange) being 9.66. Using protein interaction prediction method, we identified more interactions of estrogen-related receptor alpha (ESRRA) associated with upregulated mRNAs, whereas versican (VCAN) and proenkephalin (PENK) were associated with downregulated mRNAs in LW pigs. Integrated analysis on differentially expressed (DE) mRNAs and miRNAs in the LD muscle between LW and DLY pigs revealed two network modules: between five upregulated mRNA genes (GALNT15, FKBP5, PPARGC1A, LOC110258214 and LOC110258215) and six downregulated miRNA genes (ssc-let-7a, ssc-miR190-3p, ssc-miR356-5p, ssc-miR573-5p, ssc-miR204-5p and ssc-miR-10383), and between three downregulated DE mRNA genes (IFRD1, LOC110258600 and LOC102158401) and six upregulated DE miRNA genes (ssc-miR1379-3p, ssc-miR1379-5p, ssc-miR397-5p, ssc-miR1358-5p, ssc-miR299-5p and ssc-miR1156-5p) in LW pigs. Based on the mRNA and ncRNA binding site targeting database, we constructed a regulatory network with miRNA as the center and mRNA and lncRNA as the target genes, including GALNT15/ssc-let-7a/LOC100523888, IFRD1/ssc-miR1379-5p/CD99, etc., forming a ceRNA network in the LD muscles that are differentially expressed between LW and DLY pigs. Collectively, these data may provide resources for further investigation of molecular mechanisms underlying differences in meat traits between lean- and fat-type pigs.
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24
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Li B, He Y, Wu W, Tan X, Wang Z, Irwin DM, Wang Z, Zhang S. Circular RNA Profiling Identifies Novel circPPARA that Promotes Intramuscular Fat Deposition in Pigs. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4123-4137. [PMID: 35324170 DOI: 10.1021/acs.jafc.1c07358] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Intramuscular fat (IMF) content plays an important role in pork quality. Circular RNAs (circRNAs) implicate various biological processes; however, the regulatory mechanisms and functions of circRNAs in porcine IMF remains elusive. Hence, the study assessed the circRNA expression profiling in the longissimus dorsi muscle of pigs with high (H) and low (L) IMF content to unravel their regulatory functions in improving meat quality. The RNA sequencing analysis identified 29,732 circRNAs from six sampled pigs, most of which were exon-derived. In the muscle, 336 were differentially expressed (DE) between the H and L IMF groups; 196 circRNAs were upregulated, and 140 were downregulated. Subsequent qRT-PCR validation of 10 DE circRNAs revealed expression patterns consistent with the RNA-seq data. Gene ontology and KEGG enrichment analysis revealed that most significantly enriched DE circRNAs' host genes were linked to lipid metabolism and adipogenesis processes. The circRNA-miRNA regulatory network analysis found several circRNAs targeting miRNAs associated with adipogenesis. Finally, a novel circRNA, circPPARA, was identified with the expression positively correlated with the IMF content. Detailed analysis revealed that circPPARA was formed via head-to-tail splicing and was more stable than the linear PPARA, predominantly located in the cytoplasm. Functional studies using overexpression and siRNA constructs demonstrated that circPPARA promotes differentiation and hinders the proliferation of porcine intramuscular preadipocytes. Moreover, the dual-luciferase assay revealed that circPPARA adsorbed miR-429 and miR-200b, thereby promoting intramuscular adipogenesis in pigs. Our results identified a candidate circRNA, circPPARA, that affects porcine IMF content. The study provides knowledge of the regulatory functions of circRNAs in intramuscular adipogenesis and abundant resource for future research on circRNAs in pigs.
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Affiliation(s)
- Bojiang Li
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Yu He
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Wangjun Wu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaofan Tan
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Zichenhan Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Zhe Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
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