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Cui Y, Ru M, Wang Y, Weng L, Haji RA, Liang H, Zeng Q, Wei Q, Xie X, Yin C, Huang J. Epigenetic regulation of H3K27me3 in laying hens with fatty liver hemorrhagic syndrome induced by high-energy and low-protein diets. BMC Genomics 2024; 25:374. [PMID: 38627644 PMCID: PMC11022457 DOI: 10.1186/s12864-024-10270-w] [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: 02/20/2024] [Accepted: 03/29/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Fatty liver hemorrhagic syndrome (FLHS) in the modern poultry industry is primarily caused by nutrition. Despite encouraging progress on FLHS, the mechanism through which nutrition influences susceptibility to FLHS is still lacking in terms of epigenetics. RESULTS In this study, we analyzed the genome-wide patterns of trimethylated lysine residue 27 of histone H3 (H3K27me3) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes in healthy and FLHS hens. The study results indicated that H3K27me3 levels were increased in the FLHS hens on a genome-wide scale. Additionally, H3K27me3 was found to occupy the entire gene and the distant intergenic region, which may function as silencer-like regulatory elements. The analysis of transcription factor (TF) motifs in hypermethylated peaks has demonstrated that 23 TFs are involved in the regulation of liver metabolism and development. Transcriptomic analysis indicated that differentially expressed genes (DEGs) were enriched in fatty acid metabolism, amino acid, and carbohydrate metabolism. The hub gene identified from PPI network is fatty acid synthase (FASN). Combined ChIP-seq and transcriptome analysis revealed that the increased H3K27me3 and down-regulated genes have significant enrichment in the ECM-receptor interaction, tight junction, cell adhesion molecules, adherens junction, and TGF-beta signaling pathways. CONCLUSIONS Overall, the trimethylation modification of H3K27 has been shown to have significant regulatory function in FLHS, mediating the expression of crucial genes associated with the ECM-receptor interaction pathway. This highlights the epigenetic mechanisms of H3K27me3 and provides insights into exploring core regulatory targets and nutritional regulation strategies in FLHS.
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Affiliation(s)
- Yong Cui
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Meng Ru
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yujie Wang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Linjian Weng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ramlat Ali Haji
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Haiping Liang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qingjie Zeng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qing Wei
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xianhua Xie
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chao Yin
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jianzhen Huang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
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Liu L, Wang W, Liu W, Li X, Yi G, Adetula AA, Huang H, Tang Z. Comprehensive Atlas of Alternative Splicing Reveals NSRP1 Promoting Adipogenesis through CCDC18. Int J Mol Sci 2024; 25:2874. [PMID: 38474122 DOI: 10.3390/ijms25052874] [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: 01/17/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Alternative splicing (AS) plays a crucial role in regulating gene expression, function, and diversity. However, limited reports exist on the identification and comparison of AS in Eastern and Western pigs. Here, we analyzed 243 transcriptome data from eight tissues, integrating information on transcription factors (TFs), selection signals, splicing factors (SFs), and quantitative trait loci (QTL) to comprehensively study alternative splicing events (ASEs) in pigs. Five ASE types were identified, with Mutually Exclusive Exon (MXE) and Skipped Exon (SE) ASEs being the most prevalent. A significant portion of genes with ASEs (ASGs) showed conservation across all eight tissues (63.21-76.13% per tissue). Differentially alternative splicing genes (DASGs) and differentially expressed genes (DEGs) exhibited tissue specificity, with blood and adipose tissues having more DASGs. Functional enrichment analysis revealed coDASG_DEGs in adipose were enriched in pathways associated with adipose deposition and immune inflammation, while coDASG_DEGs in blood were enriched in pathways related to immune inflammation and metabolism. Adipose deposition in Eastern pigs might be linked to the down-regulation of immune-inflammation-related pathways and reduced insulin resistance. The TFs, selection signals, and SFs appeared to regulate ASEs. Notably, ARID4A (TF), NSRP1 (SF), ANKRD12, IFT74, KIAA2026, CCDC18, NEXN, PPIG, and ROCK1 genes in adipose tissue showed potential regulatory effects on adipose-deposition traits. NSRP1 could promote adipogenesis by regulating alternative splicing and expression of CCDC18. Conducting an in-depth investigation into AS, this study has successfully identified key marker genes essential for pig genetic breeding and the enhancement of meat quality, which will play important roles in promoting the diversity of pork quality and meeting market demand.
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Affiliation(s)
- Lei Liu
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Wei Wang
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Weiwei Liu
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xingzheng Li
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Guoqiang Yi
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China
| | - Adeyinka Abiola Adetula
- Reproductive Biotechnology, Department of Molecular Life Sciences, TUM School of Life Sciences, Technical University Munich, 85354 Freising, Germany
| | - Haibo Huang
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Zhonglin Tang
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China
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Sun C, Lan F, Zhou Q, Guo X, Jin J, Wen C, Guo Y, Hou Z, Zheng J, Wu G, Li G, Yan Y, Li J, Ma Q, Yang N. Mechanisms of hepatic steatosis in chickens: integrated analysis of the host genome, molecular phenomics and gut microbiome. Gigascience 2024; 13:giae023. [PMID: 38837944 DOI: 10.1093/gigascience/giae023] [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: 05/14/2023] [Revised: 01/14/2024] [Accepted: 04/22/2024] [Indexed: 06/07/2024] Open
Abstract
Hepatic steatosis is the initial manifestation of abnormal liver functions and often leads to liver diseases such as nonalcoholic fatty liver disease in humans and fatty liver syndrome in animals. In this study, we conducted a comprehensive analysis of a large chicken population consisting of 705 adult hens by combining host genome resequencing; liver transcriptome, proteome, and metabolome analysis; and microbial 16S ribosomal RNA gene sequencing of each gut segment. The results showed the heritability (h2 = 0.25) and duodenal microbiability (m2 = 0.26) of hepatic steatosis were relatively high, indicating a large effect of host genetics and duodenal microbiota on chicken hepatic steatosis. Individuals with hepatic steatosis had low microbiota diversity and a decreased genetic potential to process triglyceride output from hepatocytes, fatty acid β-oxidation activity, and resistance to fatty acid peroxidation. Furthermore, we revealed a molecular network linking host genomic variants (GGA6: 5.59-5.69 Mb), hepatic gene/protein expression (PEMT, phosphatidyl-ethanolamine N-methyltransferase), metabolite abundances (folate, S-adenosylmethionine, homocysteine, phosphatidyl-ethanolamine, and phosphatidylcholine), and duodenal microbes (genus Lactobacillus) to hepatic steatosis, which could provide new insights into the regulatory mechanism of fatty liver development.
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Affiliation(s)
- Congjiao Sun
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Fangren Lan
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Qianqian Zhou
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaoli Guo
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jiaming Jin
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chaoliang Wen
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yanxin Guo
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhuocheng Hou
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jiangxia Zheng
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Guiqin Wu
- Beijing Engineering Research Centre of Layer, Beijing 101206, China
| | - Guangqi Li
- Beijing Engineering Research Centre of Layer, Beijing 101206, China
| | - Yiyuan Yan
- Beijing Engineering Research Centre of Layer, Beijing 101206, China
| | - Junying Li
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Qiugang Ma
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ning Yang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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Chokeshaiusaha K, Sananmuang T, Puthier D, Nguyen C. Cross-species analysis of differential transcript usage in humans and chickens with fatty liver disease. Vet World 2023; 16:1964-1973. [PMID: 37859957 PMCID: PMC10583885 DOI: 10.14202/vetworld.2023.1964-1973] [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: 05/23/2023] [Accepted: 08/30/2023] [Indexed: 10/21/2023] Open
Abstract
Background and Aim Fatty liver disease is a common condition, characterized by excess fat accumulation in the liver. It can contribute to more severe liver-related health issues, making it a critical concern in avian and human medicine. Apart from modifying the gene expression of liver cells, the disease also alters the expression of specific transcript isoforms, which might serve as new biological markers for both species. This study aimed to identify cross-species genes displaying differential expressions in their transcript isoforms in humans and chickens with fatty liver disease. Materials and Methods We performed differential gene expression and differential transcript usage (DTU) analyses on messenger RNA datasets from the livers of both chickens and humans with fatty liver disease. Using appropriate cross-species gene identification methods, we reviewed the acquired candidate genes and their transcript isoforms to determine their potential role in fatty liver disease's pathogenesis. Results We identified seven genes - ALG5, BRD7, DIABLO, RSU1, SFXN5, STIMATE, TJP3, and VDAC2 - and their corresponding transcript isoforms as potential candidates (false discovery rate ≤0.05). Our findings showed that these genes most likely contribute to fatty disease development and progression. Conclusion This study successfully identified novel human-chicken DTU genes in fatty liver disease. Further research is encouraged to verify the functions and regulations of these transcript isoforms as potential diagnostic markers for fatty liver disease in humans and chickens.
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Affiliation(s)
- Kaj Chokeshaiusaha
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chonburi, Thailand
| | - Thanida Sananmuang
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chonburi, Thailand
| | - Denis Puthier
- Aix-Marseille Université, INSERM, UMR 1090, TAGC, Marseille, France
| | - Catherine Nguyen
- Aix-Marseille Université, INSERM, UMR 1090, TAGC, Marseille, France
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5
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Guo X, Zhou Q, Jin J, Lan F, Wen C, Li J, Yang N, Sun C. Hepatic steatosis is associated with dysregulated cholesterol metabolism and altered protein acetylation dynamics in chickens. J Anim Sci Biotechnol 2023; 14:108. [PMID: 37568219 PMCID: PMC10422840 DOI: 10.1186/s40104-023-00910-8] [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: 04/23/2023] [Accepted: 06/28/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND Hepatic steatosis is a prevalent manifestation of fatty liver, that has detrimental effect on the health and productivity of laying hens, resulting in economic losses to the poultry industry. Here, we aimed to systematically investigate the genetic regulatory mechanisms of hepatic steatosis in laying hens. METHODS Ninety individuals with the most prominent characteristics were selected from 686 laying hens according to the accumulation of lipid droplets in the liver, and were graded into three groups, including the control, mild hepatic steatosis and severe hepatic steatosis groups. A combination of transcriptome, proteome, acetylome and lipidome analyses, along with bioinformatics analysis were used to screen the key biological processes, modifications and lipids associated with hepatic steatosis. RESULTS The rationality of the hepatic steatosis grouping was verified through liver biochemical assays and RNA-seq. Hepatic steatosis was characterized by increased lipid deposition and multiple metabolic abnormalities. Integration of proteome and acetylome revealed that differentially expressed proteins (DEPs) interacted with differentially acetylated proteins (DAPs) and were involved in maintaining the metabolic balance in the liver. Acetylation alterations mainly occurred in the progression from mild to severe hepatic steatosis, i.e., the enzymes in the fatty acid oxidation and bile acid synthesis pathways were significantly less acetylated in severe hepatic steatosis group than that in mild group (P < 0.05). Lipidomics detected a variety of sphingolipids (SPs) and glycerophospholipids (GPs) were negatively correlated with hepatic steatosis (r ≤ -0.5, P < 0.05). Furthermore, the severity of hepatic steatosis was associated with a decrease in cholesterol and bile acid synthesis and an increase in exogenous cholesterol transport. CONCLUSIONS In addition to acquiring a global and thorough picture of hepatic steatosis in laying hens, we were able to reveal the role of acetylation in hepatic steatosis and depict the changes in hepatic cholesterol metabolism. The findings provides a wealth of information to facilitate a deeper understanding of the pathophysiology of fatty liver and contributes to the development of therapeutic strategies.
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Affiliation(s)
- Xiaoli Guo
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193 China
| | - Qianqian Zhou
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193 China
| | - Jiaming Jin
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193 China
| | - Fangren Lan
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193 China
| | - Chaoliang Wen
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193 China
| | - Junying Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193 China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193 China
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, 100193 China
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Cheng X, Li X, Liu Y, Ma Y, Zhang R, Zhang Y, Fan C, Qu L, Ning Z. DNA methylome and transcriptome identified Key genes and pathways involved in Speckled Eggshell formation in aged laying hens. BMC Genomics 2023; 24:31. [PMID: 36658492 PMCID: PMC9854222 DOI: 10.1186/s12864-022-09100-8] [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: 08/07/2022] [Accepted: 12/26/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND The quality of poultry eggshells is closely related to the profitability of egg production. Eggshell speckles reflect an important quality trait that influences egg appearance and customer preference. However, the mechanism of speckle formation remains poorly understood. In this study, we systematically compared serum immune and antioxidant indices of hens laying speckled and normal eggs. Transcriptome and methylome analyses were used to elucidate the mechanism of eggshell speckle formation. RESULTS The results showed that seven differentially expressed genes (DEGs) were identified between the normal and speckle groups. Gene set enrichment analysis (GSEA) revealed that the expressed genes were mainly enriched in the calcium signaling pathway, focal adhesion, and MAPK signaling pathway. Additionally, 282 differentially methylated genes (DMGs) were detected, of which 15 genes were associated with aging, including ARNTL, CAV1, and GCLC. Pathway analysis showed that the DMGs were associated with T cell-mediated immunity, response to oxidative stress, and cellular response to DNA damage stimulus. Integrative analysis of transcriptome and DNA methylation data identified BFSP2 as the only overlapping gene, which was expressed at low levels and hypomethylated in the speckle group. CONCLUSIONS Overall, these results indicate that aging- and immune-related genes and pathways play a crucial role in the formation of speckled eggshells, providing useful information for improving eggshell quality.
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Affiliation(s)
- Xue Cheng
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Xinghua Li
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Yuchen Liu
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Ying Ma
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Ruiqi Zhang
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Yalan Zhang
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Cuidie Fan
- Rongde Breeding Company Limited, Hebei, 053000 China
| | - Lujiang Qu
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Zhonghua Ning
- grid.22935.3f0000 0004 0530 8290National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
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Song H, Yang R, Zhang J, Sun P, Xing X, Wang L, Sairijima T, Hu Y, Liu Y, Cheng H, Zhang Q, Li L. Oleic acid-induced steatosis model establishment in LMH cells and its effect on lipid metabolism. Poult Sci 2023; 102:102297. [PMID: 36446267 PMCID: PMC9709224 DOI: 10.1016/j.psj.2022.102297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 11/24/2022] Open
Abstract
Hepatic steatosis is a highly prevalent liver disease, yet research on it is hampered by the lack of tractable cellular models in poultry. To examine the possibility of using organoids to model steatosis and detect it efficiently in leghorn male hepatocellular (LMH) cells, we first established steatosis using different concentrations of oleic acid (OA) (0.05-0.75 mmol/L) for 12 or 24 h. The subsequent detections found that the treatment of LMH cells with OA resulted in a dramatic increase in intracellular triglyceride (TG) concentrations, which was positively associated with the concentration of the inducing OA (R2 > 0.9). Then, the modeled steatosis was detected by flow cytometry after NileRed staining and it was found that the intensity of NileRed-A was positively correlated with the TG concentration (R2 > 0.93), which demonstrates that the flow cytometry is suitable for the detection of steatosis in LMH cells. According to the detection results of the different steatosis models, we confirmed that the optimal induction condition for the establishment of the steatosis model in LMH cells is OA (0.375 mmol/L) incubation for 12 h. Finally, the transcription and protein content of fat metabolism-related genes in steatosis model cells were detected. It was found that OA-induced steatosis could significantly decrease the expression of nuclear receptor PPAR-γ and the synthesis of fatty acids (SREBP-1C, ACC1, FASN), increasing the oxidative decomposition of triglycerides (CPT1A) and the assembly of low-density lipoproteins (MTTP, ApoB). Sterol metabolism in model cells was also significantly enhanced (HMGR, ABCA1, L-BABP). This study established, detected, and analyzed an OA-induced steatosis model in LMH cells, which provides a stable model and detection method for the study of poultry steatosis-related diseases.
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Affiliation(s)
- Huiqi Song
- College of life science and technology, Tarim University, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang ,China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang ,China
| | - Ruizhi Yang
- College of life science and technology, Tarim University, Alar 843300, Xinjiang, China; College of animal science and technology, Alar 843300, Xinjiang, China; Engineering Laboratory of Tarim Animal Diseases Diagnosis and Control, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang, China
| | - Jiahao Zhang
- College of animal science and technology, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang ,China; Engineering Laboratory of Tarim Animal Diseases Diagnosis and Control, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang, China
| | - Pengliang Sun
- College of animal science and technology, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang ,China; Engineering Laboratory of Tarim Animal Diseases Diagnosis and Control, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang, China
| | - Xiaoyue Xing
- College of animal science and technology, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang ,China; Engineering Laboratory of Tarim Animal Diseases Diagnosis and Control, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang, China
| | - Lan Wang
- College of animal science and technology, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang ,China; Engineering Laboratory of Tarim Animal Diseases Diagnosis and Control, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang, China
| | - Ta Sairijima
- College of animal science and technology, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang ,China; Engineering Laboratory of Tarim Animal Diseases Diagnosis and Control, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang, China
| | - Yahui Hu
- College of animal science and technology, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang ,China; Engineering Laboratory of Tarim Animal Diseases Diagnosis and Control, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang, China
| | - Yang Liu
- College of animal science and technology, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang ,China; Engineering Laboratory of Tarim Animal Diseases Diagnosis and Control, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang, China
| | - Huixu Cheng
- College of animal science and technology, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang ,China; Engineering Laboratory of Tarim Animal Diseases Diagnosis and Control, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang, China
| | - Qiulin Zhang
- College of animal science and technology, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang ,China; Engineering Laboratory of Tarim Animal Diseases Diagnosis and Control, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang, China
| | - Lianrui Li
- College of life science and technology, Tarim University, Alar 843300, Xinjiang, China; College of animal science and technology, Alar 843300, Xinjiang, China; Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang ,China; Engineering Laboratory of Tarim Animal Diseases Diagnosis and Control, Xinjiang Production and Construction Corps, Alar 843300, Xinjiang, China.
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Cui X, Abouelezz K, Jiang Z, Gou Z, Wang Y, Jiang S. Effects of metabolic energy intervention on lipid content and liver transcriptome in finisher yellow-feathered chickens. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2022.2116607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Xiaoyan Cui
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou, China
| | - Khaled Abouelezz
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou, China
- Department of Poultry Production, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Zongyong Jiang
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou, China
| | - Zhongyong Gou
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou, China
| | - Yibing Wang
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou, China
| | - Shouqun Jiang
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou, China
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9
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Xiao C, Sun T, Yang Z, Zou L, Deng J, Yang X. Whole transcriptome RNA Sequencing Reveals the Global Molecular Responses and circRNA/lncRNA-miRNA-mRNA ceRNA Regulatory Network in Chicken Fat Deposition. Poult Sci 2022; 101:102121. [PMID: 36116349 PMCID: PMC9485216 DOI: 10.1016/j.psj.2022.102121] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/21/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022] Open
Abstract
Fat deposition is a vital factor affecting the economics of poultry production. Numerous studies on fat deposition have been done. However, the molecular regulatory mechanism is still unclear. In the present study, the whole-transcriptome RNA sequencing in abdominal fat, back skin, and liver both high- and low-abdominal fat groups was used to uncover the competitive endogenous RNA (ceRNA) regulation network related to chicken fat deposition. The results showed that differentially expressed (DE) genes in abdominal fat, back skin, liver were 1207(784 mRNAs, 330 lncRNAs, 41 circRNAs, 52 miRNAs), 860 (607 mRNAs, 166 lncRNAs, 26 circRNAs, 61 miRNAs), and 923 (501 mRNAs, 262 lncRNAs, 15 circRNAs, 145 miRNAs), respectively. The ceRNA regulatory network analysis indicated that the fatty acid metabolic process, monocarboxylic acid metabolic process, carboxylic acid metabolic process, glycerolipid metabolism, fatty acid metabolism, and peroxisome proliferator-activated receptor (PPAR) signaling pathway took part in chicken fat deposition. Meanwhile, we scan the important genes, FADS2, HSD17B12, ELOVL5, AKR1E2, DGKQ, GPAM, PLIN2, which were regulated by gga-miR-460b-5p, gga-miR-199-5p, gga-miR-7470-3p, gga-miR-6595-5p, gga-miR-101-2-5p. While these miRNAs were competitive combined by lncRNAs including MSTRG.18043, MSTRG.7738, MSTRG.21310, MSTRG.19577, and circRNAs including novel_circ_PTPN2, novel_circ_CTNNA1, novel_circ_PTPRD. This finding provides new insights into the regulatory mechanism of mRNA, miRNA, lncRNA, and circRNA in chicken fat deposition.
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Affiliation(s)
- Cong Xiao
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Tiantian Sun
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Zhuliang Yang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Leqin Zou
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jixian Deng
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Xiurong Yang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
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10
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Jin Y, Yuan X, Liu J, Wen J, Cui H, Zhao G. Inhibition of cholesterol biosynthesis promotes the production of 1-octen-3-ol through mevalonic acid. Food Res Int 2022; 158:111392. [DOI: 10.1016/j.foodres.2022.111392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/08/2022] [Accepted: 05/19/2022] [Indexed: 12/22/2022]
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11
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Shi L, Bai H, Li Y, Yuan J, Wang P, Wang Y, Ni A, Jiang L, Ge P, Bian S, Zong Y, Isa AM, Tesfay HH, Yang F, Ma H, Sun Y, Chen J. Analysis of DNA Methylation Profiles in Mandibular Condyle of Chicks With Crossed Beaks Using Whole-Genome Bisulfite Sequencing. Front Genet 2021; 12:680115. [PMID: 34306022 PMCID: PMC8298039 DOI: 10.3389/fgene.2021.680115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 06/03/2021] [Indexed: 01/17/2023] Open
Abstract
Crossed beaks have been observed in at least 12 chicken strains around the world, which severely impairs their growth and welfare. To explore the intrinsic factor causing crossed beaks, this study measured the length of bilateral mandibular ramus of affected birds, and investigated the genome-wide DNA methylation profiles of normal and affected sides of mandibular condyle. Results showed that the trait was caused by impaired development of unilateral mandibular ramus, which is extended through calcification of mandibular condyle. The methylation levels in the CG contexts were higher than that of CHG and CHH, with the highest methylation level of gene body region, followed by transcription termination sites and downstream. Subsequently, we identified 1,568 differentially methylated regions and 1,317 differentially methylated genes in CG contexts. Functional annotation analysis of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes showed that these genes were involved in bone mineralization and bone morphogenesis. Furthermore, by combining the WGBS and previous RNA-Seq data, 11 overlapped genes were regulated by both long non-coding RNA and DNA methylation. Among them, FIGNL1 is an important gene in calcification of mandibular condyle. Generally, because the affected genes play key roles in maintaining mandibular calcification, these changes may be pivotal factors of crossed beaks.
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Affiliation(s)
- Lei Shi
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Yunlei Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingwei Yuan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Panlin Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanmei Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Aixin Ni
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Linlin Jiang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pingzhuang Ge
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shixiong Bian
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunhe Zong
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Adamu Mani Isa
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hailai Hagos Tesfay
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fujian Yang
- Guangxi Shenhuang Group Co., Ltd., Yulin, China
| | - Hui Ma
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanyan Sun
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jilan Chen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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12
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Tan X, Liu R, Zhang Y, Wang X, Wang J, Wang H, Zhao G, Zheng M, Wen J. Integrated analysis of the methylome and transcriptome of chickens with fatty liver hemorrhagic syndrome. BMC Genomics 2021; 22:8. [PMID: 33407101 PMCID: PMC7789526 DOI: 10.1186/s12864-020-07305-3] [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: 08/19/2020] [Accepted: 12/06/2020] [Indexed: 12/22/2022] Open
Abstract
Background DNA methylation, a biochemical modification of cytosine, has an important role in lipid metabolism. Fatty liver hemorrhagic syndrome (FLHS) is a serious disease and is tightly linked to lipid homeostasis. Herein, we compared the methylome and transcriptome of chickens with and without FLHS. Results We found genome-wide dysregulated DNA methylation pattern in which regions up- and down-stream of gene body were hypo-methylated in chickens with FLHS. A total of 4155 differentially methylated genes and 1389 differentially expressed genes were identified. Genes were focused when a negative relationship between mRNA expression and DNA methylation in promoter and gene body were detected. Based on pathway enrichment analysis, we found expression of genes related to lipogenesis and oxygenolysis (e.g., PPAR signaling pathway, fatty acid biosynthesis, and fatty acid elongation) to be up-regulated with associated down-regulated DNA methylation. In contrast, genes related to cellular junction and communication pathways (e.g., vascular smooth muscle contraction, phosphatidylinositol signaling system, and gap junction) were inhibited and with associated up-regulation of DNA methylation. Conclusions In the current study, we provide a genome-wide scale landscape of DNA methylation and gene expression. The hepatic hypo-methylation feature has been identified with FLHS chickens. By integrated analysis, the results strongly suggest that increased lipid accumulation and hepatocyte rupture are central pathways that are regulated by DNA methylation in chickens with FLHS. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07305-3.
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Affiliation(s)
- Xiaodong Tan
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ranran Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yonghong Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Animal Science, Jilin University, Changchun, 130062, China
| | - Xicai Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jie Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hailong Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guiping Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Maiqing Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Jie Wen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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13
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Cai J, Xu Y, Zhang W, Ding S, Sun Y, Lyu J, Duan M, Liu S, Huang L, Zhou F. A comprehensive comparison of residue-level methylation levels with the regression-based gene-level methylation estimations by ReGear. Brief Bioinform 2020; 22:5921981. [PMID: 33048108 DOI: 10.1093/bib/bbaa253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/10/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION DNA methylation is a biological process impacting the gene functions without changing the underlying DNA sequence. The DNA methylation machinery usually attaches methyl groups to some specific cytosine residues, which modify the chromatin architectures. Such modifications in the promoter regions will inactivate some tumor-suppressor genes. DNA methylation within the coding region may significantly reduce the transcription elongation efficiency. The gene function may be tuned through some cytosines are methylated. METHODS This study hypothesizes that the overall methylation level across a gene may have a better association with the sample labels like diseases than the methylations of individual cytosines. The gene methylation level is formulated as a regression model using the methylation levels of all the cytosines within this gene. A comprehensive evaluation of various feature selection algorithms and classification algorithms is carried out between the gene-level and residue-level methylation levels. RESULTS A comprehensive evaluation was conducted to compare the gene and cytosine methylation levels for their associations with the sample labels and classification performances. The unsupervised clustering was also improved using the gene methylation levels. Some genes demonstrated statistically significant associations with the class label, even when no residue-level methylation features have statistically significant associations with the class label. So in summary, the trained gene methylation levels improved various methylome-based machine learning models. Both methodology development of regression algorithms and experimental validation of the gene-level methylation biomarkers are worth of further investigations in the future studies. The source code, example data files and manual are available at http://www.healthinformaticslab.org/supp/.
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