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Chen Z, Hua G, Shu X, Zhuang W, Zhang J, Zhu R, Zheng X, Chen J. Screening of reliable reference genes for the normalization of RT-qPCR in chicken liver tissues and LMH cells. Sci Rep 2024; 14:17828. [PMID: 39090210 PMCID: PMC11294616 DOI: 10.1038/s41598-024-68752-6] [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: 03/07/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
The liver plays a vital role in lipid synthesis and metabolism in poultry. To study the functional genes more effectively, it is essential to screen of reliable reference genes in the chicken liver, including females, males, embryos, as well as the Leghorn Male Hepatoma (LMH) cell line. Traditional reference gene screening involves selecting commonly used housekeeping genes (HKGs) for RT-qPCR experiments and using different algorithms to identify the most stable ones. However, this approach is limited in selecting the best reference gene from a small pool of HKGs. High-throughput sequencing technology may offer a solution to this limitation. This study aimed to identify the most consistently expressed genes by utilizing multiple published RNA-seq data of chicken liver and LMH cells. Subsequently, the stability of the newly identified reference genes was assessed in comparison to previously validated stable poultry liver expressed reference genes and the commonly employed HKGs using RT-qPCR. The findings indicated that there is a higher degree of similarity in stable expression genes between female and male liver (such as LSM14A and CDC40). In embryonic liver, the optimal new reference genes were SUDS3, TRIM33, and ERAL1. For LMH cells, the optimal new reference genes were ALDH9A1, UGGT1, and C21H1orf174. However, it is noteworthy that most HKGs did not exhibit stable expression across multiple samples, indicating potential instability under diverse conditions. Furthermore, RT-qPCR experiments proved that the stable expression genes identified from RNA-seq data outperformed commonly used HKGs and certain validated reference genes specific to poultry liver. Over all, this study successfully identified new stable reference genes in chicken liver and LMH cells using RNA-seq data, offering researchers a wider range of reference gene options for RT-qPCR in diverse situations.
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Affiliation(s)
- Ziwei Chen
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, China
| | - Guoying Hua
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xin Shu
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, China
| | - Wuchao Zhuang
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Jilong Zhang
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Runbang Zhu
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Xiaotong Zheng
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, China
| | - Jianfei Chen
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China.
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, China.
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Du X, Wang Y, Amevor FK, Ning Z, Deng X, Wu Y, Wei S, Cao X, Xu D, Tian Y, Ye L, Shu G, Zhao X. Effect of High Energy Low Protein Diet on Lipid Metabolism and Inflammation in the Liver and Abdominal Adipose Tissue of Laying Hens. Animals (Basel) 2024; 14:1199. [PMID: 38672347 PMCID: PMC11047412 DOI: 10.3390/ani14081199] [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: 02/21/2024] [Revised: 04/06/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The aim of this study was to evaluate the effects of a high-energy low-protein (HELP) diet on lipid metabolism and inflammation in the liver and abdominal adipose tissue (AAT) of laying hens. A total of 200 Roman laying hens (120 days old) were randomly divided into two experimental groups: negative control group (NC group) and HELP group, with 100 hens per group. The chickens in the NC group were fed with a basic diet, whereas those in the HELP group were given a HELP diet. Blood, liver, and AAT samples were collected from 20 chickens per group at each experimental time point (30, 60, and 90 d). The morphological and histological changes in the liver and AAT were observed, and the level of serum biochemical indicators and the relative expression abundance of key related genes were determined. The results showed that on day 90, the chickens in the HELP group developed hepatic steatosis and inflammation. However, the diameter of the adipocytes of AAT in the HELP group was significantly larger than that of the NC group. Furthermore, the results showed that the extension of the feeding time significantly increased the lipid contents, lipid deposition, inflammatory parameters, and peroxide levels in the HELP group compared with the NC group, whereas the antioxidant parameters decreased significantly. The mRNA expression levels of genes related to lipid synthesis such as fatty acid synthase (FASN), stearoyl-coA desaturase (SCD), fatty acid binding protein 4 (FABP4), and peroxisome proliferator-activated receptor gamma (PPARγ) increased significantly in the liver and AAT of the HELP group, whereas genes related to lipid catabolism decreased significantly in the liver. In addition, the expression of genes related to lipid transport and adipokine synthesis decreased significantly in the AAT, whereas in the HELP group, the expression levels of pro-inflammatory parameters such as tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), and interleukin-1 beta (IL-1β) increased significantly in the liver and AAT. Conversely, the expression level of the anti-inflammatory parameter interleukin-10 (IL-10) decreased significantly in the liver. The results indicated that the HELP diet induced lipid peroxidation and inflammation in the liver and AAT of the laying hens. Hence, these results suggest that chicken AAT may be involved in the development of fatty liver.
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Affiliation(s)
- Xiaxia Du
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.D.); (Y.W.); (F.K.A.); (Z.N.); (X.D.); (Y.W.); (S.W.); (X.C.); (D.X.); (Y.T.); (L.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, Sichuan Agricultural University, Chengdu 611130, China
| | - Yinuo Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.D.); (Y.W.); (F.K.A.); (Z.N.); (X.D.); (Y.W.); (S.W.); (X.C.); (D.X.); (Y.T.); (L.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, Sichuan Agricultural University, Chengdu 611130, China
| | - Felix Kwame Amevor
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.D.); (Y.W.); (F.K.A.); (Z.N.); (X.D.); (Y.W.); (S.W.); (X.C.); (D.X.); (Y.T.); (L.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, Sichuan Agricultural University, Chengdu 611130, China
| | - Zifan Ning
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.D.); (Y.W.); (F.K.A.); (Z.N.); (X.D.); (Y.W.); (S.W.); (X.C.); (D.X.); (Y.T.); (L.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, Sichuan Agricultural University, Chengdu 611130, China
| | - Xun Deng
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.D.); (Y.W.); (F.K.A.); (Z.N.); (X.D.); (Y.W.); (S.W.); (X.C.); (D.X.); (Y.T.); (L.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, Sichuan Agricultural University, Chengdu 611130, China
| | - Youhao Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.D.); (Y.W.); (F.K.A.); (Z.N.); (X.D.); (Y.W.); (S.W.); (X.C.); (D.X.); (Y.T.); (L.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, Sichuan Agricultural University, Chengdu 611130, China
| | - Shuo Wei
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.D.); (Y.W.); (F.K.A.); (Z.N.); (X.D.); (Y.W.); (S.W.); (X.C.); (D.X.); (Y.T.); (L.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, Sichuan Agricultural University, Chengdu 611130, China
| | - Xueqing Cao
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.D.); (Y.W.); (F.K.A.); (Z.N.); (X.D.); (Y.W.); (S.W.); (X.C.); (D.X.); (Y.T.); (L.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, Sichuan Agricultural University, Chengdu 611130, China
| | - Dan Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.D.); (Y.W.); (F.K.A.); (Z.N.); (X.D.); (Y.W.); (S.W.); (X.C.); (D.X.); (Y.T.); (L.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, Sichuan Agricultural University, Chengdu 611130, China
| | - Yaofu Tian
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.D.); (Y.W.); (F.K.A.); (Z.N.); (X.D.); (Y.W.); (S.W.); (X.C.); (D.X.); (Y.T.); (L.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, Sichuan Agricultural University, Chengdu 611130, China
| | - Lin Ye
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.D.); (Y.W.); (F.K.A.); (Z.N.); (X.D.); (Y.W.); (S.W.); (X.C.); (D.X.); (Y.T.); (L.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, Sichuan Agricultural University, Chengdu 611130, China
| | - Gang Shu
- Department of Basic Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China;
| | - Xiaoling Zhao
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.D.); (Y.W.); (F.K.A.); (Z.N.); (X.D.); (Y.W.); (S.W.); (X.C.); (D.X.); (Y.T.); (L.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, Sichuan Agricultural University, Chengdu 611130, China
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Chen H, Zhou S, Wang Y, Zhang Q, Leng L, Cao Z, Luan P, Li Y, Wang S, Li H, Cheng B. HBP1 promotes chicken preadipocyte proliferation via directly repressing SOCS3 transcription. Int J Biol Macromol 2024; 256:128414. [PMID: 38029903 DOI: 10.1016/j.ijbiomac.2023.128414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/13/2023] [Accepted: 11/22/2023] [Indexed: 12/01/2023]
Abstract
Preadipocyte proliferation is an essential process in adipose development. During proliferation of preadipocytes, transcription factors play crucial roles. HMG-box protein 1 (HBP1) is an important transcription factor of cellular proliferation. However, the function and underlying mechanisms of HBP1 in the proliferation of preadipocytes remain unclear. Here, we found that the expression level of HBP1 decreased first and then increased during the proliferation of chicken preadipocytes. Knockout of HBP1 could inhibit the proliferation of preadipocytes, while overexpression of HBP1 could promote the proliferation of preadipocytes. ChIP-seq data showed that HBP1 had the unique DNA binding motif in chicken preadipocytes. By integrating ChIP-Seq and RNA-Seq, we revealed a total of 3 candidate target genes of HBP1. Furthermore, the results of ChIP-qPCR, RT-qPCR, luciferase reporter assay and EMSA showed that HBP1 could inhibit the transcription of suppressor of cytokine signaling 3 (SOCS3) by binding to its promoter. Moreover, we confirmed that SOCS3 can mediate the regulation of HBP1 on the proliferation of preadipocytes through RNAi and rescue experiments. Altogether, these data demonstrated that HBP1 directly targets SOCS3 to regulate chicken preadipocyte proliferation. Our findings expand the transcriptional regulatory network of preadipocyte proliferation, and they will be helpful in formulating a molecular breeding scheme to control excessive abdominal fat deposition and to improve meat quality in chickens.
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Affiliation(s)
- Hongyan Chen
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China; College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar 161006, Heilongjiang, China
| | - Sitong Zhou
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Youdong Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Qi Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Li Leng
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Zhiping Cao
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Peng Luan
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Yumao Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Shouzhi Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
| | - Bohan Cheng
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin 150030, Heilongjiang, China; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin 150030, Heilongjiang, China; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, Heilongjiang, China.
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Chen J, Chen Z, Zhang J, Zhuang W, Zheng X. Screening of reliable reference genes for the normalization of RT-qPCR in chicken gastrointestinal tract. Poult Sci 2023; 102:103169. [PMID: 37918133 PMCID: PMC10641542 DOI: 10.1016/j.psj.2023.103169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 11/04/2023] Open
Abstract
The application of reverse transcription quantitative real-time PCR technology for the production of gene tissue expression profiles is a widely employed approach in molecular biology research. It is imperative to ascertain internal reference genes that exhibit stable expression across diverse tissues to ensure the precision of tissue gene expression profiles. While there have been studies documenting the most suitable reference genes for various tissues in chickens, there is a dearth of research on the identification of reference genes in the gastrointestinal (GI) tract of chickens. This study utilized 4 different algorithms (Delta CT, BestKeeper, NormFinder, and Genorm) to assess the stability of 19 internal reference genes in various GI tract tissues, including individual GI tract tissues, the anterior and posterior GI tract, and the entire GI tissue. The RefFinder software was employed to comprehensively rank these genes. The research findings successfully identified the most appropriate internal reference genes for each type of GI tissue. Furthermore, TBP, DNAJC24, Polr2b, RPL13, andAp2m exhibited stable expression in the entire and posterior GI tract, whereas HMBS, TBP, Ap2m, GUSB, DNAJC24, and RPL13 demonstrated stable expression in the anterior GI tract. However, the internal reference genes commonly utilized, namely β-Actin, 18s RNA, and ALB, exhibit poor stability and are not advised for future investigations concerning gene expression in the GI region. Consequently, MUC2 and CDX1, 2 genes that specifically express in the gut, were chosen for examination to ascertain the stability of the aforementioned internal reference genes in this particular study. In summary, this study presents a relatively stable set of internal reference genes that can be employed to enhance the precision of quantifying mRNA expression levels in functional genes within the chicken GI tract.
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Affiliation(s)
- Jianfei Chen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Ziwei Chen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Jilong Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Wuchao Zhuang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Xiaotong Zheng
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China.
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Nishiura H, Nakajima T, Saito S, Kato A, Hatai H, Ochiai K. Assessing avian leukosis virus proviral load and lesion correlates in fowl glioma-inducing virus-infected Japanese bantam chickens. J Vet Diagn Invest 2023; 35:484-491. [PMID: 37452573 PMCID: PMC10467450 DOI: 10.1177/10406387231186954] [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] [Indexed: 07/18/2023] Open
Abstract
The fowl glioma-inducing virus prototype (FGVp) and its variants, which belong to avian leukosis virus subgroup A (ALV-A), induce cardiomyocyte abnormalities and gliomas in chickens. However, the molecular mechanisms underlying these myocardial changes remain unclear, and ALV-induced tumorigenesis, which is caused by proviral insertional mutagenesis, does not explain the early development of cardiac changes in infected chickens. We established a quantitative PCR (qPCR) assay to measure ALV-A proviral loads in the brains and hearts of FGV-infected Japanese bantam chickens and compared these results with morphologic lesions. Four of 22 bantams had both gliomas and cardiac lesions. Hearts with cardiac lesions had a higher proviral load (10.3 ± 2.7 proviral copies/nucleus) than those without cardiac lesions (0.4 ± 0.4), suggesting that the proviral load in hearts is correlated with the frequency of myocardial changes. Our qPCR method may be useful in the study of ALV-induced cardiomyocyte abnormalities.
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Affiliation(s)
- Hayate Nishiura
- Laboratory of Veterinary Pathology, Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | - Tomoe Nakajima
- Laboratory of Veterinary Pathology, Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | - Shun Saito
- Laboratory of Veterinary Pathology, Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | - Azusa Kato
- Laboratory of Veterinary Pathology, Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | - Hitoshi Hatai
- Farm Animal Clinical Skills and Disease Control Center, Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | - Kenji Ochiai
- Laboratory of Veterinary Pathology, Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
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Shui F, Qiu G, Pan S, Wang X, Jia F, Jiang T, Li Y, Geng Z, Jin S. Identification of stable reference genes for quantitative gene expression analysis in the duodenum of meat-type ducks. Front Vet Sci 2023; 10:1160384. [PMID: 37077952 PMCID: PMC10106614 DOI: 10.3389/fvets.2023.1160384] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
Quantitative polymerase chain reaction (qPCR) is an important method to detect gene expression at the molecular level. The selection of appropriate housekeeping genes is the key to accurately calculating the expression level of target genes and conducting gene function studies. In this study, the expression of eight candidate reference genes, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), beta-actin (β-actin), 18S ribosomal RNA (18S rRNA), hydroxymethylbilane synthase (HMBS), hypoxanthine phosphoribosyltransferase 1 (HPRT1), TATA box binding protein (TBP), ribosomal protein L13 (RPL13), and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein (YWHAZ), in the duodenal epithelial tissue of 42-day-old meat-type ducks were detected using qPCR. Furthermore, their expression stability was analyzed using the geNorm, NormFinder, and BestKeeper programs. The results indicated that HMBS and YWHAZ were the most stably expressed genes. All three programs indicated that the expression of 18S rRNA was the least stable, making it unsuitable for the study of gene expression in meat-type duck tissues. This study provides stable reference genes for gene expression analysis and contributes to further studies on the gene function of meat-type ducks.
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Affiliation(s)
- Fei Shui
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-Breeding, Hefei, China
| | - Guiru Qiu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Shenqiang Pan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xin Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-Breeding, Hefei, China
| | - Fumin Jia
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-Breeding, Hefei, China
| | - Tingting Jiang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yongsheng Li
- Extension Center for Animal Husbandry and Veterinary Medicine of Huangshan City, Huangshan, China
| | - Zhaoyu Geng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-Breeding, Hefei, China
| | - Sihua Jin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-Breeding, Hefei, China
- *Correspondence: Sihua Jin
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Study on the muscle transcriptome of two diverse Indian backyard poultry breeds acclimatized to different agro-ecological conditions. Mol Biol Rep 2023; 50:2453-2461. [PMID: 36598628 DOI: 10.1007/s11033-022-08223-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023]
Abstract
OBJECTIVE Free-range (FR) poultry production systems are associated with quality products and improved welfare. All the 19 diverse chicken breeds of India have evolved under the FR system and are adapted to different agro-climatic conditions. It is vital to explore indigenous germplasm with modern genomic tools to have insights into genomic characteristics of production traits and adaptation. METHODS In this study, breast tissue transcriptome profiles were generated and analyzed from four biological replicates of two indigenous backyard poultry breeds of India-Ankaleshwar, a breed of the mainland, and Nicobari, a breed adapted to islands. The read quality of sequences was checked by FASTQC and processed reads were aligned to the reference genome (bGalGal1). RESULTS More than 94% mapping to the reference genome was observed for all samples. A total of 12,790 transcripts were common across both groups, while 657 were expressed only in Ankaleshwar and 169 in Nicobari. The highest expressed genes across both groups were associated mainly with muscle structure, contraction, and energy metabolism. The highly expressed genes identified in Ankaleshwar were involved in fatty acid catabolism and oxidative stress mitigation. Functional terms, pathways, and hub genes in Nicobari participated in muscle fiber growth, adipogenesis, and fatty acid anabolism. A key hub gene (RAC1) in Nicobari is a potential candidate affecting the laying rate in chickens. The qRT-PCR results also substantiate the RNA-seq results. CONCLUSION The findings provide a precious molecular resource to advance understanding of the genetic basis of adaptation, meat quality, and egg production in backyard chickens.
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Sun Y, Xu H, Li J, Peng M, Jia Z, Kong L, Zhang X, Shao S, Zhang W, Wang W. Genome-wide survey identifies TNNI2 as a target of KLF7 that inhibits chicken adipogenesis via downregulating FABP4. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194899. [PMID: 36410687 DOI: 10.1016/j.bbagrm.2022.194899] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/26/2022] [Accepted: 11/12/2022] [Indexed: 11/19/2022]
Abstract
Krüppel-like factor 7 (KLF7) negatively regulates adipocyte differentiation; however, the mechanism underlying its activity in mammals and birds remains poorly understood. To identify genome-wide KLF7-binding motifs in preadipocytes, we conducted a chromatin immunoprecipitation-sequencing analysis of immortalized chicken preadipocytes (ICP2), which revealed 11,063 specific binding sites. Intergenic binding site analysis showed that KLF7 regulates several novel factors whose functions in chicken and mammal adipogenesis are underexplored. We identified a novel regulator, troponin I2 (TNNI2), which is positively regulated by KLF7. TNNI2 is downregulated during preadipocyte differentiation and acts as an adipogenic repressor at least in part by repressing FABP4 promoter activity. In conclusion, we demonstrated that KLF7 functions through cis-regulation of TNNI2, which inhibits adipogenesis. Our findings not only provide the first genome-wide picture of KLF7 associations in preadipocytes but also identify a novel function of TNNI2.
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Affiliation(s)
- Yingning Sun
- College of Life Science and Agriculture Forestry, Qiqihar University, Heilongjiang Provincial Key Laboratory of Resistance Gene Engineering and Protection of Biodiversity in Cold Areas, Qiqihar, Heilongjiang 161000, China.
| | - Hu Xu
- College of Life Science and Agriculture Forestry, Qiqihar University, Heilongjiang Provincial Key Laboratory of Resistance Gene Engineering and Protection of Biodiversity in Cold Areas, Qiqihar, Heilongjiang 161000, China
| | - Jinwei Li
- College of Life Science and Agriculture Forestry, Qiqihar University, Heilongjiang Provincial Key Laboratory of Resistance Gene Engineering and Protection of Biodiversity in Cold Areas, Qiqihar, Heilongjiang 161000, China
| | - Min Peng
- College of Life Science and Agriculture Forestry, Qiqihar University, Heilongjiang Provincial Key Laboratory of Resistance Gene Engineering and Protection of Biodiversity in Cold Areas, Qiqihar, Heilongjiang 161000, China
| | - Ziqiu Jia
- College of Life Science and Agriculture Forestry, Qiqihar University, Heilongjiang Provincial Key Laboratory of Resistance Gene Engineering and Protection of Biodiversity in Cold Areas, Qiqihar, Heilongjiang 161000, China
| | - Lingzhe Kong
- College of Life Science and Agriculture Forestry, Qiqihar University, Heilongjiang Provincial Key Laboratory of Resistance Gene Engineering and Protection of Biodiversity in Cold Areas, Qiqihar, Heilongjiang 161000, China
| | - Xin Zhang
- College of Life Science and Agriculture Forestry, Qiqihar University, Heilongjiang Provincial Key Laboratory of Resistance Gene Engineering and Protection of Biodiversity in Cold Areas, Qiqihar, Heilongjiang 161000, China
| | - Shuli Shao
- College of Life Science and Agriculture Forestry, Qiqihar University, Heilongjiang Provincial Key Laboratory of Resistance Gene Engineering and Protection of Biodiversity in Cold Areas, Qiqihar, Heilongjiang 161000, China
| | - Weiwei Zhang
- College of Life Science and Agriculture Forestry, Qiqihar University, Heilongjiang Provincial Key Laboratory of Resistance Gene Engineering and Protection of Biodiversity in Cold Areas, Qiqihar, Heilongjiang 161000, China
| | - Weiyu Wang
- College of Life Science and Agriculture Forestry, Qiqihar University, Heilongjiang Provincial Key Laboratory of Resistance Gene Engineering and Protection of Biodiversity in Cold Areas, Qiqihar, Heilongjiang 161000, China
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Hasanpur K, Hosseinzadeh S, Mirzaaghayi A, Alijani S. Investigation of chicken housekeeping genes using next-generation sequencing data. Front Genet 2022; 13:827538. [PMID: 36176302 PMCID: PMC9514876 DOI: 10.3389/fgene.2022.827538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
Accurate normalization of the gene expression assays, using housekeeping genes (HKGs), is critically necessary. To do so, selection of a proper set of HKGs for a specific experiment is of great importance. Despite many studies, there is no consensus about the suitable set of HKGs for implementing in the quantitative real-time PCR analyses of chicken tissues. A limited number of HKGs have been widely used. However, wide utilization of a little number of HKGs for all tissues is challenging. The emergence of high-throughput gene expression RNA-seq data has enabled the simultaneous comparison of the stability of multiple HKGs. Therefore, employing the average coefficient of variations of at least three datasets per tissue, we sorted all reliably expressed genes (REGs; with FPKM ≥ 1 in at least one sample) and introduced the top 10 most suitable and stable reference genes for each of the 16 chicken tissues. We evaluated the consistency of the results of five tissues using the same methodology on other datasets. Furthermore, we assessed 96 previously widely used HKGs (WU-HKGs) in order to challenge the accuracy of the previous studies. The New Tuxedo software suite was used for the main analyses. The results revealed novel, different sets of reference genes for each of the tissues with 17 common genes among the top 10 genes lists of 16 tissues. The results did disprove the suitability of WU-HKGs such as Actb, Ldha, Scd, B2m, and Hprt1 for any of the tissues examined. On the contrary, a total of 6, 13, 14, 23, and 32 validated housekeeping genes (V-HKGs) were discovered as the most stable and suitable reference genes for muscle, spleen, liver, heart, and kidney tissues, respectively. Although we identified a few new HKGs usable for multiple tissues, the selection of suitable HKGs is required to be tissue specific. The newly introduced reference genes from the present study, despite lacking experimental validation, will be able to contribute to the more accurate normalization for future expression analysis of chicken genes.
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Meng J, Zhang Q, Ma M, Shi H, He G. Persistence of avian influenza virus (H9N2) on plastic surface. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155355. [PMID: 35460779 DOI: 10.1016/j.scitotenv.2022.155355] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/13/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Plastics have been found to be colonized with pathogens and may become vectors for transmission of diseases. In this study, we evaluated the persistence of H9N2 avian influenza virus (AIV) on the surfaces of various plastics (PP, PE, PS, PET, PVC, PMMA) under different environmental conditions using glass and stainless steel for comparison. Our results showed that the RNA abundance of AIV on plastics was decreased over time but still detectable 14 days after AIV had been dropped on plastic surfaces. Low temperature (4 °C) was more favorable for AIV RNA preservation and infectivity maintenance. The abundance of AIV RNA was significantly greater on polyethylene terephthalate (PET) than that on glass and stainless steel at higher temperature (i.e., 25 °C and 37 °C) and lower humidity (<20% and 40-60%) (p < 0.05). Infectivity assay showed that AIV infectivity was only maintained at 4 °C after 24 h of incubation. Taken together, the persistence of AIV was more affected by environmental factors than material types. Plastics were able to preserve viral RNA more effectively in relatively high-temperature or low-humidity environments. Our study indicates that environmental factors should be taken into consideration when we evaluate the capacity of plastics to spread viruses.
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Affiliation(s)
- Jian Meng
- Institute of Eco-Chongming, East China Normal University, Shanghai 200162, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China.
| | - Qun Zhang
- Shanghai Key Laboratory for Urban Ecological Process and Eco-Restoration, School of Ecological and Environmental Sciences; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Min Ma
- Laboratory of Wildlife Epidemic Diseases, School of Life Sciences, East China Normal University, Shanghai 200062, China
| | - Huahong Shi
- Institute of Eco-Chongming, East China Normal University, Shanghai 200162, China; State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China.
| | - Guimei He
- Institute of Eco-Chongming, East China Normal University, Shanghai 200162, China; Laboratory of Wildlife Epidemic Diseases, School of Life Sciences, East China Normal University, Shanghai 200062, China.
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Yuan ZW, Zhang XH, Pang YZ, Qi YX, Wang QK, Ren SW, Hu YQ, Zhao YW, Wang T, Huo LK. Screening of Stably Expressed Internal Reference Genes for Quantitative Real-Time PCR Analysis in Quail. BIOL BULL+ 2022. [DOI: 10.1134/s1062359022050223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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