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Arikawa LM, Mota LFM, Schmidt PI, Frezarim GB, Fonseca LFS, Magalhães AFB, Silva DA, Carvalheiro R, Chardulo LAL, Albuquerque LGD. Genome-wide scans identify biological and metabolic pathways regulating carcass and meat quality traits in beef cattle. Meat Sci 2024; 209:109402. [PMID: 38056170 DOI: 10.1016/j.meatsci.2023.109402] [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: 04/25/2023] [Revised: 10/19/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
Genome association studies (GWAS) provides knowledge about the genetic architecture of beef-related traits that allow linking the target phenotype to genomic information aiding breeding decision. Thus, the present study aims to uncover the genetic mechanism involved in carcass (REA: rib eye area, BF: backfat thickness, and HCW: hot carcass weight) and meat quality traits (SF: shear-force, MARB: marbling score, and IMF: intramuscular fat content) in Nellore cattle. For this, 6910 young bulls with phenotypic information and 23,859 animals genotyped with 435 k markers were used to perform the weighted single-step GBLUP (WssGBLUP) approach, considering two iterations. The top 10 genomic regions explained 8.13, 11.81, and 9.58% of the additive genetic variance, harboring a total of 119, 143, and 95 positional candidate genes for REA, BF, and HCW, respectively. For meat quality traits, the top 10 windows explained a large proportion of the total genetic variance for SF (14.95%), MARB (17.56%), and IMF (21.41%) surrounding 92, 155, and 111 candidate genes, respectively. Relevant candidate genes (CAST, PLAG1, XKR4, PLAGL2, AQP3/AQP7, MYLK2, WWOX, CARTPT, and PLA2G16) are related to physiological aspects affecting growth, carcass, meat quality, feed intake, and reproductive traits by signaling pathways controlling muscle control, key signal metabolic molecules INS / IGF-1 pathway, lipid metabolism, and adipose tissue development. The GWAS results provided insights into the genetic control of the traits studied and the genes found are potential candidates to be used in the improvement of carcass and meat quality traits.
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Affiliation(s)
- Leonardo Machestropa Arikawa
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil.
| | - Lucio Flavio Macedo Mota
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Patrícia Iana Schmidt
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Gabriela Bonfá Frezarim
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Larissa Fernanda Simielli Fonseca
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Ana Fabrícia Braga Magalhães
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil; University of Jequitinhonha and Mucuri Valleys, Department of Animal Science, Rod. MG 367, Diamantina, MG 39100-000, Brazil
| | - Delvan Alves Silva
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil; University of Viçosa, Department of Animal Science, Av. PH Rolfs, Viçosa, MG 36570-900, Brazil
| | - Roberto Carvalheiro
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil
| | - Luis Artur Loyola Chardulo
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil; National Council for Science and Technological Development, Brasilia, DF 71605-001, Brazil
| | - Lucia Galvão de Albuquerque
- São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Department of Animal Science, Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, SP 14884-900, Brazil; National Council for Science and Technological Development, Brasilia, DF 71605-001, Brazil.
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2
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Qubi W, Zheng J, Wang Y, Xu G, Li Y, Xiong Y, Wang Y, Liu W, Lin Y. Goat miR-92a-3p Targets APOL6 Gene to Regulate the Differentiation of Intramuscular Precursor Adipocytes. Genes (Basel) 2023; 15:57. [PMID: 38254947 PMCID: PMC10815674 DOI: 10.3390/genes15010057] [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: 12/09/2023] [Revised: 12/23/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
The quality of lamb meat is positively correlated with intramuscular fat content. In recent years, a large number of studies have shown that miRNAs play an important role in the proliferation and differentiation of adipocytes. In this study, we aimed to explore the effect of miR-92a-3p on the differentiation of goat intramuscular preadipocytes. The results showed that the expression level of miR-92a-3p was low in the early stage of differentiation, reached the highest level on the third day of differentiation, and then decreased. And miR-92a-3p can inhibit the accumulation of lipid droplets and down-regulate the determinants of adipogenic differentiation. Mechanistically, by predicting target genes, we found that miR-92a-3p affects the differentiation of goat intramuscular preadipocytes and the accumulation of lipid droplets by regulating the expression of goat gene APOL6. This study provides important new information to better understand the relationship between miRNAs and the differentiation of goat intramuscular preadipocytes, thus providing a new reference for goat intramuscular adipogenesis.
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Affiliation(s)
- Wuqie Qubi
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu 610041, China; (W.Q.); (J.Z.); (Y.W.); (Y.L.); (Y.X.); (Y.W.); (W.L.)
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu 610041, China
- College of Animal & Veterinary Science, Southwest Minzu University, Chengdu 610041, China
| | - Jianying Zheng
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu 610041, China; (W.Q.); (J.Z.); (Y.W.); (Y.L.); (Y.X.); (Y.W.); (W.L.)
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu 610041, China
- College of Animal & Veterinary Science, Southwest Minzu University, Chengdu 610041, China
| | - Youli Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu 610041, China; (W.Q.); (J.Z.); (Y.W.); (Y.L.); (Y.X.); (Y.W.); (W.L.)
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu 610041, China
- College of Animal & Veterinary Science, Southwest Minzu University, Chengdu 610041, China
| | - Guishan Xu
- College of Animal Science and Technology, Tarim University, Alar 843301, China;
| | - Yanyan Li
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu 610041, China; (W.Q.); (J.Z.); (Y.W.); (Y.L.); (Y.X.); (Y.W.); (W.L.)
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu 610041, China
- College of Animal & Veterinary Science, Southwest Minzu University, Chengdu 610041, China
| | - Yan Xiong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu 610041, China; (W.Q.); (J.Z.); (Y.W.); (Y.L.); (Y.X.); (Y.W.); (W.L.)
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu 610041, China
- College of Animal & Veterinary Science, Southwest Minzu University, Chengdu 610041, China
| | - Yong Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu 610041, China; (W.Q.); (J.Z.); (Y.W.); (Y.L.); (Y.X.); (Y.W.); (W.L.)
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu 610041, China
- College of Animal & Veterinary Science, Southwest Minzu University, Chengdu 610041, China
| | - Wei Liu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu 610041, China; (W.Q.); (J.Z.); (Y.W.); (Y.L.); (Y.X.); (Y.W.); (W.L.)
- College of Animal & Veterinary Science, Southwest Minzu University, Chengdu 610041, China
| | - Yaqiu Lin
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu 610041, China; (W.Q.); (J.Z.); (Y.W.); (Y.L.); (Y.X.); (Y.W.); (W.L.)
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu 610041, China
- College of Animal & Veterinary Science, Southwest Minzu University, Chengdu 610041, China
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Zhao W, Liu X, Li C, Qin X, Ren S, Cao S, Zhou G. Bovine C-X-C Motif Chemokine Ligand 14 Expression Is Regulated by Alternative Polyadenylation and MicroRNAs. Animals (Basel) 2023; 13:3075. [PMID: 37835681 PMCID: PMC10571712 DOI: 10.3390/ani13193075] [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: 08/01/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Alternative polyadenylation (APA), including APA that occurs only in the 3' UTR (3' UTR-APA), is an important post-transcriptional regulatory mechanism that leads to distinct 3' UTRs for some genes, increasing the complexity of the transcriptome. The post-transcriptional events regulating the expression of bovine, the C-X-C motif chemokine ligand 14 (CXCL14) gene, remains largely unknown. Here, we find that the bovine CXCL14 gene produces two different lengths of mRNA isoforms due to 3' UTR-APA, and the short and long 3' UTR is 126 bp and 1155 bp, respectively. We found that the expression level of the short isoform was significantly higher than that of the long isoform by luciferase assays and overexpression of different CXCL14 3' UTR-APA isoforms. Moreover, using luciferase assay and site-directed mutagenesis experiments, the results showed that the long CXCL14 3' UTR-APA isoform is downregulated by miR-17-5p, miR-150, and miR-217. However, because the short isoform lacks the true target of miR-17-5p, miR-150, and miR-217 in its 3' UTR and thus escapes the inhibitory effect of these microRNAs, its expression level is significantly higher than that of the long isoform. Finally, we demonstrate that the short CXCL14 3' UTR-APA isoform promotes preadipocyte proliferation by cell counting kit 8 (CCK8) assays. Collectively, our results show that the CXCL14 gene is post-transcriptionally regulated through APA and microRNAs.
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Affiliation(s)
| | | | | | | | | | | | - Guoli Zhou
- College of Life Science, Liaocheng University, Liaocheng 252000, China; (W.Z.); (X.L.)
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Ling X, Wang Q, Zhang J, Zhang G. Genome-Wide Analysis of the KLF Gene Family in Chicken: Characterization and Expression Profile. Animals (Basel) 2023; 13:ani13091429. [PMID: 37174466 PMCID: PMC10177326 DOI: 10.3390/ani13091429] [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: 03/06/2023] [Revised: 04/08/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
The kruppel-like factor (KLF) gene family is a group of transcription factors containing highly conserved zinc-finger motifs, which play a crucial role in cell proliferation and differentiation. Chicken has been widely used as a model animal for analyzing gene function, however, little is known about the function of the KLF gene family in chickens. In this study, we performed genome-wide studies of chicken KLF genes and analyzed their biological and expression characteristics. We identified 13 KLF genes from chickens. Our phylogenetic, motif, and conserved domain analyses indicate that the KLF gene family has remained conserved through evolution. Synteny analysis showed the collinear relationship among KLFs, which indicated that they had related biomolecular functions. Interaction network analysis revealed that KLFs worked with 20 genes in biological processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that KLF2 was involved in Apelin and Forkhead Box O (FOXO) signaling pathways. Moreover, qPCR showed that 13 KLF genes were expressed in the nine selected tissues and displayed various gene expression patterns in chickens. RNA-seq showed that KLF3 and KLF10 genes were differentially expressed in the normal and high-fat diet fed groups, and KLF4, KLF5, KLF6, KLF7, KLF9, KLF12, and KLF13 genes were differentially expressed between undifferentiated and differentiated chicken preadipocytes. Besides, RNA-seq also showed that KLF genes displayed different expression patterns in muscle at 11 and 16 embryonic days old, and in 1-day-old chickens. These results indicated that the KLF genes were involved in the development of muscle and fat in chickens. Our findings provide some valuable reference points for the subsequent study of the function of KLF genes.
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Affiliation(s)
- Xuanze Ling
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225000, China
| | - Qifan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225000, China
| | - Jin Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225000, China
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225000, China
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5
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Zhang Y, Chen J, He S, Xiao Y, Liu A, Zhang D, Li X. Systematic identification of aberrant non-coding RNAs and their mediated modules in rotator cuff tears. Front Mol Biosci 2022; 9:940290. [PMID: 36111133 PMCID: PMC9470226 DOI: 10.3389/fmolb.2022.940290] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/05/2022] [Indexed: 11/25/2022] Open
Abstract
Background: Rotator cuff tears (RCT) is the most common cause of shoulder dysfunction, however, its molecular mechanisms remain unclear. Non-coding RNAs(ncRNAs), such as long ncRNA (lncRNA), microRNA (miRNA) and circular RNA (circRNA), are involved in a variety of diseases, but little is known about their roles in RCT. Therefore, the purpose of this study is to identify dysregulated ncRNAs and understand how they influence RCT. Methods: We performed RNA sequencing and miRNA sequencing on five pairs of torn supraspinatus muscles and matched unharmed subscapularis muscles to identify RNAs dysregulated in RCT patients. To better comprehend the fundamental biological processes, we carried out enrichment analysis of these dysregulated mRNAs or the co-expressed genes of dysregulated ncRNAs. According to the competing endogenous RNA (ceRNA) theory, we finally established ceRNA networks to explore the relationship among dysregulated RNAs in RCT. Results: A total of 151 mRNAs, 38 miRNAs, 20 lncRNAs and 90 circRNAs were differentially expressed between torn supraspinatus muscles and matched unharmed subscapularis muscles, respectively. We found that these dysregulated mRNAs, the target mRNAs of these dysregulated miRNAs or the co-expressed mRNAs of these dysregulated ncRNAs were enriched in muscle structure development, actin-mediated cell contraction and actin binding. Then we constructed and analyzed the ceRNA network and found that the largest module in the ceRNA network was associated with vasculature development. Based on the topological properties of the largest module, we identified several important ncRNAs including hsa_circ_0000722, hsa-miR-129-5p and hsa-miR-30c-5p, whose interacting mRNAs related to muscle diseases, fat and inflammation. Conclusion: This study presented a systematic dissection of the expression profile of mRNAs and ncRNAs in RCT patients and revealed some important ncRNAs which may contribute to the development of RCT. Such results could provide new insights for further research on RCT.
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Affiliation(s)
- Yichong Zhang
- Department of Orthopedics and Trauma, Key Laboratory of Trauma and Neural Regeneration (Ministry of Education/Peking University), Peking University People’s Hospital, Beijing, China
| | - Jianhai Chen
- Department of Orthopedics and Trauma, Key Laboratory of Trauma and Neural Regeneration (Ministry of Education/Peking University), Peking University People’s Hospital, Beijing, China
| | - Shengyuan He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Aiyu Liu
- Central Laboratory, Peking University People’s Hospital, Beijing, China
| | - Dianying Zhang
- Department of Orthopedics and Trauma, Key Laboratory of Trauma and Neural Regeneration (Ministry of Education/Peking University), Peking University People’s Hospital, Beijing, China
- *Correspondence: Dianying Zhang, ; Xia Li,
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
- *Correspondence: Dianying Zhang, ; Xia Li,
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Mármol-Sánchez E, Cirera S, Zingaretti LM, Jacobsen MJ, Ramayo-Caldas Y, Jørgensen CB, Fredholm M, Cardoso TF, Quintanilla R, Amills M. Modeling microRNA-driven post-transcriptional regulation using exon-intron split analysis in pigs. Anim Genet 2022; 53:613-626. [PMID: 35811409 DOI: 10.1111/age.13238] [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: 10/22/2021] [Revised: 04/23/2022] [Accepted: 06/16/2022] [Indexed: 11/27/2022]
Abstract
The contribution of microRNAs (miRNAs) to mRNA post-transcriptional regulation has often been explored by the post hoc selection of downregulated genes and determining whether they harbor binding sites for miRNAs of interest. This approach, however, does not discriminate whether these mRNAs are also downregulated at the transcriptional level. Here, we have characterized the transcriptional and post-transcriptional changes in mRNA expression in two porcine tissues: gluteus medius muscle of fasted and fed Duroc gilts and adipose tissue of lean and obese Duroc-Göttingen minipigs. Exon-intron split analysis of RNA-seq data allowed us to identify downregulated mRNAs with high post-transcriptional signals in fed or obese states, and we assessed whether they harbor binding sites for upregulated miRNAs in any of these two physiological states. We found 26 downregulated mRNAs with high post-transcriptional signals in the muscle of fed gilts and 21 of these were predicted targets of miRNAs upregulated in fed pigs. For adipose tissue, 44 downregulated mRNAs in obese minipigs displayed high post-transcriptional signals, and 25 of these were predicted targets of miRNAs upregulated in the obese state. These results suggest that the contribution of miRNAs to mRNA repression is more prominent in the skeletal muscle system. Finally, we identified several genes that may play relevant roles in the energy homeostasis of the pig skeletal muscle (DKK2 and PDK4) and adipose (SESN3 and ESRRG) tissues. By differentiating transcriptional from post-transcriptional changes in mRNA expression, exon-intron split analysis provides a valuable view of the regulation of gene expression, complementary to canonical differential expression analyses.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Susanna Cirera
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | | | - Mette Juul Jacobsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture, Barcelona, Spain
| | - Claus B Jørgensen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Merete Fredholm
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Tainã Figueiredo Cardoso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Empresa Brasileira de Pesquisa Agropecuária, Embrapa Pecuária Sudeste, São Carlos, Brazil
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture, Barcelona, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Barcelona, Spain
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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: 19] [Impact Index Per Article: 9.5] [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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8
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Pan S, Chen Y, Yan J, Li F, Chen X, Xu X, Xing H. The emerging roles and mechanisms of exosomal non-coding RNAs in the mutual regulation between adipose tissue and other related tissues in obesity and metabolic diseases. Front Endocrinol (Lausanne) 2022; 13:975334. [PMID: 36060952 PMCID: PMC9433671 DOI: 10.3389/fendo.2022.975334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/02/2022] [Indexed: 11/24/2022] Open
Abstract
Exosomes (EXs) are the major types of extracellular vesicles (EVs) of 30-100 nm diameter that can be secreted by most cells to the extracellular environment. EXs transport endogenous cargoes (proteins, lipids, RNAs, etc.) to target cells and thereby triggers the release of these bioactive components, which then play important roles in regulating numerous biological processes under both physiological and pathological conditions. Throughout the studies in recent years, growing evidences have shown that EXs-derived non-coding RNAs (EXs-ncRNAs) are emerging as key players in cell-to-cell communication between adipose tissue and other related tissues in obesity and metabolic diseases. In this review, we will summarize the recent findings about EXs-ncRNAs, especially focus on the following aspects: 1) the biogenesis of EXs and emerging roles of EXs-ncRNAs, 2) the role of EXs-ncRNAs (EXs-miRNAs, EXs-lncRNAs, EXs-circRNAs, etc.) that were secreted by adipose-related tissues in promoting the differentiation of preadipocytes into mature and fully functional adipocytes, and 3) the crosstalk between the adipose tissue derived EXs-ncRNAs and the development of insulin resistance, obesity and various cancers. This review aims to reveal the emerging roles and mechanisms of EXs-ncRNAs in the mutual regulation of adipose tissue and its related tissues in obesity and metabolic diseases, so as to provide references for elucidating the etiology of obesity and related metabolic diseases and screening novel therapeutic targets.
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Affiliation(s)
- Shifeng Pan
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Department of Animal Science, Washington State University, Pullman, WA, United States
- *Correspondence: Shifeng Pan,
| | - Yongfang Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Jie Yan
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Fei Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Xinyu Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Xingyu Xu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Hua Xing
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
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Lin W, Zhao J, Yan M, Li X, Yang K, Wei W, Zhang L, Chen J. SESN3 Inhibited SMAD3 to Relieve Its Suppression for MiR-124, Thus Regulating Pre-Adipocyte Adipogenesis. Genes (Basel) 2021; 12:genes12121852. [PMID: 34946801 PMCID: PMC8701261 DOI: 10.3390/genes12121852] [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: 10/16/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 12/29/2022] Open
Abstract
Sestrin-3, together with the other two members Sestrin-1 and Sestrin-2, belongs to the Sestrin family. The Sestrin protein family has been demonstrated to be involved in antioxidative, metabolic homeostasis, and even the development of nonalcoholic steatohepatitis (NASH). However, the adipogenic regulatory role of SESN3 in adipogenesis still needs to be further explored. In this study, we demonstrated SESN3 inhibited porcine pre-adipocyte proliferation, thus suppressing its adipogenesis. Meanwhile, SESN3 has been demonstrated to inhibit Smad3 thus protecting against NASH. Further, for our previous study, we found mmu-miR-124 involved in 3T3-L1 cell adipogenesis regulation. In this study, we also identified that ssc-miR-124 inhibited porcine pre-adipocyte proliferation, thus suppressing its adipogenesis, and the SMAD3 was an inhibitor of ssc-miR-124 by binding to its promoter. Furthermore, the ssc-miR-124 targeted porcine C/EBPα and GR and thus inhibited pre-adipocyte adipogenesis. In conclusion, SESN3 inhibited SMAD3, thus improving ssc-miR124, and then suppressed C/EBPα and GR to regulate pre-adipocytes adipogenesis.
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Affiliation(s)
| | | | | | | | | | | | | | - Jie Chen
- Correspondence: ; Tel.: +86-18759141669
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10
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Chan GCK, Than WH, Kwan BCH, Lai KB, Chan RCK, Ng JKC, Chow KM, Cheng PMS, Law MC, Leung CB, Li PKT, Szeto CC. Adipose expression of miR-130b and miR-17-5p with wasting, cardiovascular event and mortality in advanced chronic kidney disease patients. Nephrol Dial Transplant 2021; 37:1935-1943. [PMID: 34601609 DOI: 10.1093/ndt/gfab287] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND There were limited data on the association of adipose microRNA expression with body composition and adverse clinical outcomes in patients with advanced chronic kidney disease (CKD). We aimed to evaluate the association of adipose miR-130b and miR-17-5p expressions with body composition, functional state, cardiovascular outcome and mortality in incident dialysis patients. METHODS We performed a single-centre prospective cohort study. Patients who were planned for peritoneal dialysis were recruited. MiR-130b and miR-17-5p expressions were measured from subcutaneous and pre-peritoneal fat tissue obtained during peritoneal dialysis catheter insertion. Body composition and physical function were assessed by bioimpedance spectroscopy and Clinical Frailty Scale. Primary outcome was 2-year survival. Secondary outcomes were 2-year technique survival and major adverse cardiovascular event (MACE) rate. RESULTS Adipose expression of miR-130b and miR-17-5p correlated with parameters of muscle mass including intracellular water (miR-130b: r = 0.191, P = 0.02; miR-17-5p: r = 0.211, P = 0.013) and lean tissue mass (miR-130b: r = 0.180, P = 0.03; miR-17-5p: r = 0.176, P = 0.004). miR-130b expression predicted frailty significantly (P = 0.016). Adipose miR-17-5p expression predicted 2-year all-cause survival (P = 0.020) and technique survival (P = 0.036), while miR-130b expression predicted incidence of major adverse cardiovascular events (P = 0.015). CONCLUSIONS Adipose miR-130b and miR-17-5p expressions correlated with body composition parameters, frailty, and predicted cardiovascular events and mortality in advanced CKD patients.
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Affiliation(s)
- Gordon Chun-Kau Chan
- Carol & Richard Yu Peritoneal Dialysis Research Centre, Department of Medicine & Therapeutics, The Chinese University of Hong Kong
| | - Win Hlaing Than
- Carol & Richard Yu Peritoneal Dialysis Research Centre, Department of Medicine & Therapeutics, The Chinese University of Hong Kong
| | - Bonnie Ching-Ha Kwan
- Carol & Richard Yu Peritoneal Dialysis Research Centre, Department of Medicine & Therapeutics, The Chinese University of Hong Kong
| | - Ka-Bik Lai
- Carol & Richard Yu Peritoneal Dialysis Research Centre, Department of Medicine & Therapeutics, The Chinese University of Hong Kong
| | - Ronald Cheong-Kin Chan
- Department of Anatomical & Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Jack Kit-Chung Ng
- Carol & Richard Yu Peritoneal Dialysis Research Centre, Department of Medicine & Therapeutics, The Chinese University of Hong Kong
| | - Kai-Ming Chow
- Carol & Richard Yu Peritoneal Dialysis Research Centre, Department of Medicine & Therapeutics, The Chinese University of Hong Kong
| | - Phyllis Mei-Shan Cheng
- Carol & Richard Yu Peritoneal Dialysis Research Centre, Department of Medicine & Therapeutics, The Chinese University of Hong Kong
| | - Man-Ching Law
- Carol & Richard Yu Peritoneal Dialysis Research Centre, Department of Medicine & Therapeutics, The Chinese University of Hong Kong
| | - Chi-Bon Leung
- Carol & Richard Yu Peritoneal Dialysis Research Centre, Department of Medicine & Therapeutics, The Chinese University of Hong Kong
| | - Philip Kam-Tao Li
- Carol & Richard Yu Peritoneal Dialysis Research Centre, Department of Medicine & Therapeutics, The Chinese University of Hong Kong
| | - Cheuk-Chun Szeto
- Carol & Richard Yu Peritoneal Dialysis Research Centre, Department of Medicine & Therapeutics, The Chinese University of Hong Kong
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11
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Xie Y, Liu Z, Guo J, Su X, Zhao C, Zhang C, Qin Q, Dai D, Zhao Y, Wang Z, Wang R, Zhang Y, Su R, Wang Z, Li J. MicroRNA-mRNA Regulatory Networking Fine-Tunes Polyunsaturated Fatty Acid Synthesis and Metabolism in the Inner Mongolia Cashmere Goat. Front Genet 2021; 12:649015. [PMID: 34149800 PMCID: PMC8206643 DOI: 10.3389/fgene.2021.649015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Fatty acid composition is an important aspect of meat quality in ruminants. Improving the beneficial fatty acid level in cashmere goat meat is important to its economic value. To investigate microRNAs (miRNAs) and mRNAs that regulate or coregulate polyunsaturated fatty acid (PUFA) synthesis and metabolism in the Inner Mongolia cashmere goat, we used longissimus dorsi muscle (WLM) and biceps femoris muscle (WBM) for transcript-level sequencing. RT-qPCR was used to evaluate the expression of mRNAs and miRNAs associated with PUFA synthesis and metabolism. The total PUFA content in the WBM was significantly higher than that in the WLM (P < 0.05). Our study is the first to systematically report miRNAs in cashmere goat meat. At the mRNA level, 20,375 genes were identified. ACSL1, CD36 and TECRL were at the center of a gene regulatory network and contributed significantly to the accumulation and metabolic regulation of fatty acids. At the miRNA level, 426 known miRNAs and 30 novel miRNAs were identified. KEGG analysis revealed that the miRNA target genes were involved mainly in the PPAR signaling pathway. The mRNA-miRNA coregulation analysis showed that ACSL1 was negatively targeted by nine miRNAs: chi-miR-10a-5p, chi-miR-10b-5p, chi-miR-130b-5p, chi-miR-15a-5p_R-1, chi-miR-15b-5p, chi-miR-16a-5p, chi-miR-16b-5p, chi-miR-181c-5p_R+1, and chi-miR-26b-5p. Finally, we speculated that the simultaneous silencing of ACSL1 by one or more of these nine miRNAs through PPAR signaling led to low ACSL1 expression in the WLM and, ultimately to high PUFA content in the WBM. Our study helps elucidate the metabolic regulation of fatty acids in Inner Mongolia cashmere goats.
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Affiliation(s)
- Yuchun Xie
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Juntao Guo
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Xin Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Cun Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Chongyan Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Qing Qin
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Dongliang Dai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Yanhong Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Zhixin Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Engineering Research Center for Goat Genetics and Breeding, Hohhot, China
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12
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Lin W, Tang Y, Zhao Y, Zhao J, Zhang L, Wei W, Chen J. MiR-144-3p Targets FoxO1 to Reduce Its Regulation of Adiponectin and Promote Adipogenesis. Front Genet 2021; 11:603144. [PMID: 33381152 PMCID: PMC7767994 DOI: 10.3389/fgene.2020.603144] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/23/2020] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs), as a series of important short-chain non-coding RNAs, play an important post-transcriptional role in many biological activities, including adipogenesis. miR-144 is significantly upregulated in type II diabetes (T2D), and is considered to be an important biomarker for T2D. However, although the occurrence of T2D is inextricably linked to adipogenesis, whether miR-144 directly regulates adipogenesis remains to be further explored. In this paper, we demonstrate that miR-144 has a higher expression level in a porcine high backfat group, and it has a significant positive effect on promoting the differentiation of pre-adipocytes. FoxO1 is a target gene of miR-144, and inhibits the differentiation of pre-adipocytes. On the other hand, we demonstrate that FoxO1 can bind to the AdipoQ gene promoter, then regulate the AdipoQ expression by binding to the FoxO1 binding site in the AdipoQ promoter -1,499 to -1,489 bp and -1,238 to -1,228 bp regions, especially the -1,499 to -1,489 bp region. Meanwhile, miR-144 and FoxO1 co-expressional research has also shown that both factors regulate adipogenesis. To sum up, our research indicates that miR-144 targets FoxO1, thus reducing its expression and inhibiting its promotional effect on adiponectin, thereby alleviating the inhibitory effect of adiponectin on adipogenesis.
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Affiliation(s)
- Weimin Lin
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yonghang Tang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yuelei Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jindi Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Lifan Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Wei Wei
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jie Chen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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13
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Zhang M, Han Y, Zhai Y, Ma X, An X, Zhang S, Li Z. Integrative analysis of circRNAs, miRNAs, and mRNAs profiles to reveal ceRNAs networks in chicken intramuscular and abdominal adipogenesis. BMC Genomics 2020; 21:594. [PMID: 32847498 PMCID: PMC7450580 DOI: 10.1186/s12864-020-07000-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/17/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Tissue-specific fat deposition is regulated by a series of complex regulatory mechanisms. Reports indicate that epigenetic regulators, such as circular RNAs (circRNAs), are crucial in diseases progression, animal development, metabolism, and adipogenesis. In this study, to assess the functional roles of circRNAs in adipogenesis and tissue-specific fat deposition, we comprehensively analyzed the Ribo-Zero RNA-Seq and miRNAs data during chicken intramuscular and abdominal adipogenic differentiation. RESULTS circRNAs and miRNAs profiles during chicken adipogenic differentiation were found in adipocytes derived from various adipose tissues. It was also discovered that high levels of downregulated miRNAs potentially promote adipogenesis by activating their target genes which are associated with fatty acid metabolism and adipogenic differentiation. Through analysis of the correlation between the expression levels of circRNAs and adipogenic genes, as well as the dynamic expression patterns of circRNAs during adipogenic differentiation, several candidate circRNAs were identified. Moreover, competing endogenous RNA (ceRNAs) networks were constructed during chicken intramuscular and abdominal adipogenesis by combining miRNAs with mRNAs data. Several candidate circRNAs potentially influence adipogenesis by regulating miRNAs via PPAR and fatty acid metabolism-related pathways were identified, such as circLCLAT1, circFNDC3AL, circCLEC19A and circARMH1. CONCLUSION In conclusion, our findings reveal that circRNAs and the circRNA-miRNAs-mRNAs-ceRNAs network may play important roles in chicken adipocytes differentiation and tissue-specific fat deposition.
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Affiliation(s)
- Meng Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021, Jilin, China
| | - Yu Han
- College of Veterinary Medicine, Jilin University, Changchun, 130021, Jilin, China
| | - Yanhui Zhai
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021, Jilin, China
| | - Xiangfei Ma
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Xinglan An
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021, Jilin, China
| | - Sheng Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021, Jilin, China.
| | - Ziyi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, 130021, Jilin, China.
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14
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Wang L, Zhang S, Zhang W, Cheng G, Khan R, Junjvlieke Z, Li S, Zan L. miR-424 Promotes Bovine Adipogenesis Through an Unconventional Post-Transcriptional Regulation of STK11. Front Genet 2020; 11:145. [PMID: 32194625 PMCID: PMC7064614 DOI: 10.3389/fgene.2020.00145] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/07/2020] [Indexed: 11/26/2022] Open
Abstract
Adipose tissue is the largest energy reservoir and secretory organ in the animal body, and is essential for maintaining normal physiological functions and metabolic balance. MicroRNAs regulate the process of adipogenic differentiation through post-transcriptional regulatory mechanisms. In the present study, miR-424 was upregulated during bovine adipocyte differentiation both in vivo and in vitro. The overexpression and interference of miR-424 exhibited the positive regulatory role in the differentiation of bovine adipocytes. Furthermore, miR-424 directly binds to the three prime untranslated region (3' UTR) of serine/threonine kinase 11 (STK11, also called LKB1), a master upstream gene in the AMP-activated protein kinase (AMPK) cascade, and up-regulates its expression. Functional studies showed that the knockdown of STK11 attenuated the pro-adipogenic effect of miR-424. Post-transcriptional regulation of STK11 by miR-424 was mediated potentially in an RNA binding protein (RBP) binding site-dependent manner. In conclusion, our study shows that miR-424 promotes bovine adipogenesis through an unconventional post-transcriptional regulation of STK11, which may serve as a potential target for the regulation of bovine adipogenesis and the improvement of livestock breeding efficiency.
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Affiliation(s)
- Li Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Song Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wenzhen Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zainaguli Junjvlieke
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shijun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,National Beef Cattle Improvement Center, Northwest A&F University, Yangling, China
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15
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Zhang L, Huang Y, Wang M, Guo Y, Liang J, Yang X, Qi W, Wu Y, Si J, Zhu S, Li Z, Li R, Shi C, Wang S, Zhang Q, Tang Z, Wang L, Li K, Fei JF, Lan G. Development and Genome Sequencing of a Laboratory-Inbred Miniature Pig Facilitates Study of Human Diabetic Disease. iScience 2019; 19:162-176. [PMID: 31376679 PMCID: PMC6677790 DOI: 10.1016/j.isci.2019.07.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/11/2019] [Accepted: 07/13/2019] [Indexed: 01/10/2023] Open
Abstract
Pig has been proved to be a valuable large animal model used for research on diabetic disease. However, their translational value is limited given their distinct anatomy and physiology. For the last 30 years, we have been developing a laboratory Asian miniature pig inbred line (Bama miniature pig [BM]) from the primitive Bama xiang pig via long-term selective inbreeding. Here, we assembled a BM reference genome at full chromosome-scale resolution with a total length of 2.49 Gb. Comparative and evolutionary genomic analyses identified numerous variations between the BM and commercial pig (Duroc), particularly those in the genetic loci associated with the features advantageous to diabetes studies. Resequencing analyses revealed many differentiated gene loci associated with inbreeding and other selective forces. These together with transcriptome analyses of diabetic pig models provide a comprehensive genetic basis for resistance to diabetogenic environment, especially related to energy metabolism. Bama miniature pig (BM) is one of the pig lines with the highest inbreeding coefficient This atlas is a report on the chromosome-level genome assembly of miniature pig Genomic analyses revealed genetic basis underlying BM's advantages to study diabetes Some lncRNAs and mRNAs may be linked to resistance to diabetogenic environment
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Affiliation(s)
- Li Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuemeng Huang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Meng Wang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Yafen Guo
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jing Liang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
| | - Xiurong Yang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Wenjing Qi
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Yanjun Wu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jinglei Si
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Siran Zhu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Zhe Li
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Chao Shi
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Shuo Wang
- Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Qunjie Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Zhonglin Tang
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Kui Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ji-Feng Fei
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Ganqiu Lan
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
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16
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Comprehensive Analysis of Differentially Expressed mRNA, lncRNA and circRNA and Their ceRNA Networks in the Longissimus Dorsi Muscle of Two Different Pig Breeds. Int J Mol Sci 2019; 20:ijms20051107. [PMID: 30836719 PMCID: PMC6429497 DOI: 10.3390/ijms20051107] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 12/22/2022] Open
Abstract
Circular RNA (circRNA) and long non-coding RNA (lncRNA) are known to participate in adipogenesis and myogenic differentiation, but their impact on porcine muscle traits is not well understood. We compared their expressional profiles in the longissimus dorsi muscle of Chinese Huainan pigs (HN, the fat type) and Western commercial Duroc×(Landrace×Yorkshire) (DLY, the thin type) pigs, and 854 mRNAs, 233 lncRNAs, and 66 circRNAs (p < 0.05 and |log₂FoldChange|>1) were found to be differentially expressed. The differentially expressed mRNA and circRNA parental genes were enriched in the Wnt signaling pathway (adipogenesis), the transition between fast and slow fibers (myogenic differentiation), and alanine, aspartate and glutamate metabolism (pork flavor). The potential lncRNAs/circRNAs-miRNAs-mRNAs regulatory networks shared MYOD1, PPARD, miR-423-5p and miR-874, which were associated with skeletal muscle muscular proliferation, differentiation/regeneration and adipogenesis. Taken together, these differentially expressed non-coding RNAs may be involved in the molecular basis of muscle traits, acting as the competing endogenous RNA (ceRNA) for miRNAs.
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17
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Wang S, Zhang Y, Yuan X, Pan R, Yao W, Zhong L, Song Q, Zheng S, Wang Z, Xu Q, Chang G, Chen G. Identification of differentially expressed microRNAs during preadipocyte differentiation in Chinese crested duck. Gene 2018; 661:126-132. [PMID: 29604463 DOI: 10.1016/j.gene.2018.03.085] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/04/2018] [Accepted: 03/26/2018] [Indexed: 01/19/2023]
Abstract
MicroRNAs (miRNAs) are considered key players in the regulation of a broad range of biological processes. Specifically, miRNAs have been reported to play an important role in the process of adipogenesis. In this study, we constructed a model of adipogenesis by isolating preadipocytes (WCC) derived from adipose tissue and preadipocytes after 72 h differentiation (WCT) in vitro. Deep sequencing of miRNAs expressed in WCT and WCC cells was conducted; we identified 105 differentially expressed miRNA candidates (fifty up-regulated and fifty-five down-regulated). Among them, twelve were novel miRNAs, and ninety-three were previously known miRNAs. Furthermore, seven miRNAs were selected for expression confirmation by reverse transcription quantitative PCR (RT-qPCR); the results showed that the differential expression of miRNAs between the two groups was consistent with our sequencing results. Of them, miR-223, miR-184-3p, and miR-10b-5 showed a strong correlation to adipogenesis. Using target prediction, we predicted that the 105 differentially expressed miRNAs targeted 4155 unique mRNAs. The prediction of targets of differentially expressed miRNAs revealed that the miRNAs participated in the regulation of multiple adipogenesis-related signalling pathways, including the peroxisome proliferator-activated receptor (PPAR) signalling pathway, insulin signalling pathway, fatty acid biosynthesis, and fatty acid degradation. Overall, our findings provide a background for further research into miRNAs and lay a foundation for the prediction and analysis of miRNAs related to adipogenesis.
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Affiliation(s)
- Shasha Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yang Zhang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xiaoya Yuan
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Rui Pan
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Wencheng Yao
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Li Zhong
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | | | - Shenghan Zheng
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhixiu Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Qi Xu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Guobin Chang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Guohong Chen
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China.
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