1
|
Yu B, Cai Z, Liu J, Zhang T, Feng X, Wang C, Li J, Gu Y, Zhang J. Identification of key differentially methylated genes in regulating muscle development and intramuscular fat deposition in chickens. Int J Biol Macromol 2024; 264:130737. [PMID: 38460642 DOI: 10.1016/j.ijbiomac.2024.130737] [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: 12/20/2023] [Revised: 02/26/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Muscle development and intramuscular fat (IMF) deposition are intricate physiological processes characterized by multiple gene expressions and interactions. In this research, the phenotypic variations in the breast muscle of Jingyuan chickens were examined at three different time points: 42, 126, and 180 days old. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were performed to identify differentially methylated genes (DMGs) responsible for regulating muscle development and IMF deposition. The findings indicate a significant increase in breast muscle weight (BMW), myofiber diameter, and cross-sectional area, as well as IMF content, in correlation with the progressive number of growing days in Jingyuan chickens. The findings also revealed that 380 hypo-methylated and 253 hyper-methylated DMGs were identified between the three groups of breast muscle. Module gene and DMG association analysis identified m6A methylation-mediated multiple DMGs associated with muscle development and fat metabolism. In vitro cell modeling analysis reveals stage-specific differences in the expression of CUBN, MEGF10, BOP1, and BMPR2 during the differentiation of myoblasts and intramuscular preadipocytes. Cycloleucine treatment significantly inhibited the expression levels of CUBN, BOP1, and BMPR2, and promoted the expression of MEGF10. These results suggest that m6A methylation-mediated CUBN, MEGF10, BOP1, and BMPR2 can serve as potential candidate genes for regulating muscle development and IMF deposition, and provide an important theoretical basis for further investigation of the functional mechanism of m6A modification involved in adipogenesis.
Collapse
Affiliation(s)
- Baojun Yu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Zhengyun Cai
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Jiamin Liu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Tong Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Xiaofang Feng
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Chuanchuan Wang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Jiwei Li
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Yaling Gu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Juan Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China.
| |
Collapse
|
2
|
Zhao W, Cai Z, Jiang Q, Zhang J, Yu B, Feng X, Fu X, Zhang T, Hu J, Gu Y. Transcriptome analysis reveals the role of long noncoding RNAs in specific deposition of inosine monphosphate in Jingyuan chickens. J Anim Sci 2024; 102:skae136. [PMID: 38738625 PMCID: PMC11249926 DOI: 10.1093/jas/skae136] [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: 01/26/2024] [Accepted: 05/10/2024] [Indexed: 05/14/2024] Open
Abstract
Inosine monphosphate (IMP) is one of the important indicators for evaluating meat flavor, and long noncoding RNAs (lncRNAs) play an important role in its transcription and post-transcriptional regulation. Currently, there is little information about how lncRNA regulates the specific deposition of IMP in chicken muscle. In this study, we used transcriptome sequencing to analyze the lncRNAs of the breast and leg muscles of the Jingyuan chicken and identified a total of 357 differentially expressed lncRNAs (DELs), of which 158 were up-regulated and 199 were down-regulated. There were 2,203 and 7,377 cis- and trans-regulated target genes of lncRNAs, respectively, and we identified the lncRNA target genes that are involved in NEGF signaling pathway, glycolysis/glucoseogenesis, and biosynthesis of amino acids pathways. Meanwhile, 621 pairs of lncRNA-miRNA-mRNA interaction networks were constructed with target genes involved in purine metabolism, fatty acid metabolism, and biosynthesis of amino acids. Next, three interacting meso-networks gga-miR-1603-LNC_000324-PGM1, gga-miR-1768-LNC_000324-PGM1, and gga-miR-21-LNC_011339-AMPD1 were identified as closely associated with IMP-specific deposition. Both differentially expressed genes (DEGs) PGM1 and AMPD1 were significantly enriched in IMP synthesis and metabolism-related pathways, and participated in the anabolic process of IMP in the form of organic matter synthesis and energy metabolism. This study obtained lncRNAs and target genes affecting IMP-specific deposition in Jingyuan chickens based on transcriptome analysis, which deepened our insight into the role of lncRNAs in chicken meat quality.
Collapse
Affiliation(s)
- Wei Zhao
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Zhengyun Cai
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Qiufei Jiang
- Animal Husbandry Extension Station, Yinchuan750021, China
| | - Juan Zhang
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Baojun Yu
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Xiaofang Feng
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Xi Fu
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Tong Zhang
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Jiahuan Hu
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Yaling Gu
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| |
Collapse
|
3
|
Zhao W, Cai Z, Wei C, Ma X, Yu B, Fu X, Zhang T, Gu Y, Zhang J. Functional identification of PGM1 in the regulating development and depositing of inosine monophosphate specific for myoblasts. Front Vet Sci 2023; 10:1276582. [PMID: 38164393 PMCID: PMC10758172 DOI: 10.3389/fvets.2023.1276582] [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: 08/23/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024] Open
Abstract
Background Inosine monophosphate (IMP) is naturally present in poultry muscle and plays a key role in improving meat flavour. However, IMP deposition is regulated by numerous genes and complex molecular networks. In order to excavate key candidate genes that may regulate IMP synthesis, we performed proteome and metabolome analyses on the leg muscle, compared to the breast muscle control of 180-day-old Jingyuan chickens (hens), which had different IMP content. The key candidate genes identified by a differential analysis were verified to be associated with regulation of IMP-specific deposition. Results The results showed that the differentially expressed (DE) proteins and metabolites jointly involve 14 metabolic pathways, among which the purine metabolic pathway closely related to IMP synthesis and metabolism is enriched with four DE proteins downregulated (with higher expression in breast muscles than in leg muscles), including adenylate kinase 1 (AK1), adenosine monophosphate deaminase 1 (AMPD1), pyruvate kinase muscle isoenzyme 2 (PKM2) and phosphoglucomutase 1 (PGM1), six DE metabolites, Hypoxanthine, Guanosine, L-Glutamine, AICAR, AMP and Adenylsuccinic acid. Analysis of PGM1 gene showed that the high expression of PGM1 promoted the proliferation and differentiation of myoblasts and inhibited the apoptosis of myoblasts. ELISA tests have shown that PGM1 reduced adenosine triphosphate (ATP) and IMP and uric acid (UA), while enhancing the biosynthesis of hypoxanthine (HX). In addition, up-regulation of PGM1 inhibited the expression of purine metabolism pathway related genes, and promoted the IMP de novo and salvage synthesis pathways. Conclusion This study preliminarily explored the mechanism of action of PGM1 in regulating the growth and development of myoblasts and specific IMP deposition in Jingyuan chickens, which provided certain theoretical basis for the development and utilization of excellent traits in Jingyuan chickens.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Juan Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
| |
Collapse
|
4
|
Huang Z, Cai Z, Zhang J, Gu Y, Wang J, Yang J, Lv G, Yang C, Zhang Y, Ji C, Jiang S. Integrating proteomics and metabolomics to elucidate the molecular network regulating of inosine monophosphate-specific deposition in Jingyuan chicken. Poult Sci 2023; 102:103118. [PMID: 37862870 PMCID: PMC10590753 DOI: 10.1016/j.psj.2023.103118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 10/22/2023] Open
Abstract
Inosine monophosphate (IMP) plays a significant role in meat taste, yet the molecular mechanisms controlling IMP deposition in muscle tissues still require elucidation. The present study systematically and comprehensively explores the molecular network governing IMP deposition in different regions of Jingyuan chicken muscle. Two muscle groups, the breast and leg, were examined as test materials. Using nontargeted metabolomic sequencing, we screened and identified 20 metabolites that regulate IMP-specific deposition. We maintained regular author and institution formatting, used clear, objective, and value-neutral language, and avoided biased or emotional language. We followed a consistent footnote style and formatting features and used precise word choice with technical terms where appropriate. Out of these, 5 were identified as significant contributors to the regulation of IMP deposition. We explained technical term abbreviations when first used and ensured a logical flow of information with causal connections between statements. The results indicate that PGM1, a key enzyme involved in synthesis, is higher in the breast muscle compared to the leg muscle, which may provide an explanation for the increased deposition of IMP in the breast muscle. We aimed for a clear structure with logical progression, avoided filler words, and ensured grammatical correctness. The activity of key enzymes (PKM2, AK1, AMPD1) involved in this process was higher in the breast muscle than in the leg muscle. In the case of IMP degradation metabolism, the activity of its participating enzyme (PurH) was lower in the breast muscle than in the leg muscle. These findings suggest that the increased deposition of IMP in Jingyuan chickens' breast muscle may result from elevated metabolism and reduced catabolism of key metabolites. In summary, a metaomic strategy was utilized to assess the molecular network regulation mechanism of IMP-specific deposition in various segments of Jingyuan chicken. These findings provide insight into genetic improvement and molecular breeding of meat quality traits for top-notch broilers.
Collapse
Affiliation(s)
- Zengwen Huang
- Agriculture College, Ningxia University, Ningxia, Yinchuan 750021, China; College of Animal Science, Xichang University, Sichuan, Xichang 615012, China; Xinjiang Taikun Group Co., Ltd., Xinjiang, Changji 831100, China
| | - Zhengyun Cai
- Agriculture College, Ningxia University, Ningxia, Yinchuan 750021, China
| | - Juan Zhang
- Agriculture College, Ningxia University, Ningxia, Yinchuan 750021, China.
| | - Yaling Gu
- Agriculture College, Ningxia University, Ningxia, Yinchuan 750021, China
| | - Jing Wang
- College of Animal Science, Xichang University, Sichuan, Xichang 615012, China
| | - Jinzeng Yang
- Department of Human Nutrition, Food & Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Manoa, HI 96822
| | - Gang Lv
- Xinjiang Taikun Group Co., Ltd., Xinjiang, Changji 831100, China
| | - Chaoyun Yang
- College of Animal Science, Xichang University, Sichuan, Xichang 615012, China
| | - Yi Zhang
- College of Animal Science, Xichang University, Sichuan, Xichang 615012, China
| | - Chen Ji
- College of Animal Science, Xichang University, Sichuan, Xichang 615012, China
| | - Shengwang Jiang
- College of Animal Science, Xichang University, Sichuan, Xichang 615012, China
| |
Collapse
|
5
|
Zhang T, Yu B, Cai Z, Jiang Q, Fu X, Zhao W, Wang H, Gu Y, Zhang J. Regulatory role of N 6-methyladenosine in intramuscular fat deposition in chicken. Poult Sci 2023; 102:102972. [PMID: 37573849 PMCID: PMC10448335 DOI: 10.1016/j.psj.2023.102972] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/15/2023] Open
Abstract
Intramuscular fat (IMF) has a pivotal influence on meat quality, with its deposition being a multifaceted physiological interaction of several regulatory factors. N6-methyladenosine (m6A), the preeminent epigenetic alteration among eukaryotic RNA modifications, holds a crucial role in moderating post-transcriptional gene expression. However, there is a dearth of comprehensive understanding regarding the functional machinery of m6A modification in the context of IMF deposition in poultry. Our current study entails an analysis of the disparities in IMF within the breast and leg of 180-day-old Jingyuan chickens. We implemented methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) to delve into the distribution of m6A and its putative regulatory frameworks on IMF deposition in chickens. The findings demonstrated a markedly higher IMF content in leg relative to breast (P < 0.01). Furthermore, the expression of METTL14, WTAP, FTO, and ALKBH5 was significantly diminished in comparison to that of breast (P < 0.01). The m6A peaks in the breast and leg primarily populated 3'untranslated regions (3'UTR) and coding sequence (CDS) regions. The leg, when juxtaposed with the breast, manifested 176 differentially methylated genes (DMGs), including 151 hyper-methylated DMGs and 25 hypo-methylated DMGs. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed a pronounced enrichment of DMGs in the biosynthesis of amino acids, peroxisome, Fatty acid biosynthesis, fatty acid elongation, and cell adhesion molecules (CAMs) pathways. Key DMGs, namely ECH1, BCAT1, and CYP1B1 were implicated in the regulation of muscle lipid anabolism. Our study offers substantial insight and forms a robust foundation for further exploration of the functional mechanisms of m6A modification in modulating IMF deposition. This holds profound theoretical importance for improving and leveraging meat quality in indigenous chicken breeds.
Collapse
Affiliation(s)
- Tong Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Baojun Yu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Zhengyun Cai
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Qiufei Jiang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Xi Fu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Wei Zhao
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Haorui Wang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Yaling Gu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Juan Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China.
| |
Collapse
|
6
|
Yu B, Cai Z, Liu J, Zhao W, Fu X, Gu Y, Zhang J. Transcriptome and co-expression network analysis reveals the molecular mechanism of inosine monophosphate-specific deposition in chicken muscle. Front Physiol 2023; 14:1199311. [PMID: 37265843 PMCID: PMC10229883 DOI: 10.3389/fphys.2023.1199311] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/05/2023] [Indexed: 06/03/2023] Open
Abstract
The inosine monophosphate (IMP) content in chicken meat is closely related to muscle quality and is an important factor affecting meat flavor. However, the molecular regulatory mechanisms underlying the IMP-specific deposition in muscle remain unclear. This study performed transcriptome analysis of muscle tissues from different parts, feeding methods, sexes, and breeds of 180-day-old Jingyuan chickens, combined with differential expression and weighted gene co-expression network analysis (WGCNA), to identify the functional genes that regulate IMP deposition. Out of the four comparison groups, 1,775, 409, 102, and 60 differentially expressed genes (DEGs) were identified, of which PDHA2, ACSS2, PGAM1, GAPDH, PGM1, GPI, and TPI1 may be involved in the anabolic process of muscle IMP in the form of energy metabolism or amino acid metabolism. WGCNA identified 11 biofunctional modules associated with IMP deposition. The brown, midnight blue, red, and yellow modules were strongly correlated with IMP and cooking loss (p < 0.05). Functional enrichment analysis showed that glycolysis/gluconeogenesis, arginine and proline metabolism, and pyruvate metabolism, regulated by PYCR1, SMOX, and ACSS2, were necessary for muscle IMP-specific deposition. In addition, combined analyses of DEGs and four WGCNA modules identified TGIF1 and THBS1 as potential candidate genes affecting IMP deposition in muscle. This study explored the functional genes that regulate muscle development and IMP synthesis from multiple perspectives, providing an important theoretical basis for improving the meat quality and molecular breeding of Jingyuan chickens.
Collapse
|