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Ren T, Xu M, Lin W, Luo W, Zhang X. Transcriptome sequencing reveals the potential mechanisms of dietary lutein regulation on chicken leg muscle development. Poult Sci 2024; 103:104265. [PMID: 39293263 PMCID: PMC11426042 DOI: 10.1016/j.psj.2024.104265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 08/03/2024] [Accepted: 08/21/2024] [Indexed: 09/20/2024] Open
Abstract
Lutein is an antioxidant that can indicate the oxidative status of organisms through its coloration and may be involved in the development process of chicken skeletal muscle. In this study, after feeding Nanhai Yellow Chickens with lutein-containing feed for 21 d, the lutein group significantly increased the muscle fiber diameter and decreased the fiber density in the chicken's leg muscles compared to the control group. To elucidate the potential regulatory mechanisms by which lutein is involved in muscle development, RNA-seq was used to detect changes in gene expression in chicken leg muscle tissue. After data analysis, a total of 249 significantly differentially expressed genes (DEG) were identified, including TGF-β superfamily (MSTN and TGFB1) and nonreceptor tyrosine kinase c-Src (SRC). Results from GO and KEGG analysis showed that the DEGs were enriched in GO terms such as positive regulation of the ERK1/ERK2 cascade and negative regulation of myoblast differentiation, as well as signaling pathways including the Toll-like receptor signaling pathway and the MAPK signaling pathway. These significantly enriched GO terms and pathways are closely related to muscle development, suggesting that lutein may play an important role in the process of chicken muscle development. This study provides insights into the regulatory mechanisms of dietary lutein on chicken muscle development.
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Affiliation(s)
- Tuanhui Ren
- Department of Animal Genetics, College of Animal Science, Breeding and Reproduction, South China Agricultural University, Guangzhou, 510642, China; Guangdong Key Laboratory of Genome and Molecular Breeding of Agricultural Animals and Key Laboratory of Chicken Genetic Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Meng Xu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Wujian Lin
- Department of Animal Genetics, College of Animal Science, Breeding and Reproduction, South China Agricultural University, Guangzhou, 510642, China; Guangdong Key Laboratory of Genome and Molecular Breeding of Agricultural Animals and Key Laboratory of Chicken Genetic Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Wen Luo
- Department of Animal Genetics, College of Animal Science, Breeding and Reproduction, South China Agricultural University, Guangzhou, 510642, China; Guangdong Key Laboratory of Genome and Molecular Breeding of Agricultural Animals and Key Laboratory of Chicken Genetic Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xiquan Zhang
- Department of Animal Genetics, College of Animal Science, Breeding and Reproduction, South China Agricultural University, Guangzhou, 510642, China; Guangdong Key Laboratory of Genome and Molecular Breeding of Agricultural Animals and Key Laboratory of Chicken Genetic Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China.
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Luo J, Yang Z, Li X, Xiao C, Yuan H, Yang X, Zhou B, Zheng Y, Zhang J, Yang X. High Muscle Expression of IGF2BP1 Gene Promotes Proliferation and Differentiation of Chicken Primary Myoblasts: Results of Transcriptome Analysis. Animals (Basel) 2024; 14:2024. [PMID: 39061491 PMCID: PMC11274093 DOI: 10.3390/ani14142024] [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: 06/11/2024] [Revised: 07/06/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
Muscle development is a multifaceted process influenced by numerous genes and regulatory networks. Currently, the regulatory network of chicken muscle development remains incompletely elucidated, and its molecular genetic mechanisms require further investigation. The Longsheng-Feng chicken, one of the elite local breeds in Guangxi, serves as an excellent resource for the selection and breeding of high-quality broiler chickens. In this study, we conducted transcriptome sequencing of the pectoral muscles of Longsheng-Feng chickens and AA broiler chickens with different growth rates. Through comprehensive bioinformatics analysis, we identified differentially expressed genes that affect muscle growth and showed that IGF2BP1 is a key participant in chicken muscle development. Subsequently, we employed QRT-PCR, EdU staining, and flow cytometry to further investigate the role of IGF2BP1 in the proliferation and differentiation of chicken myogenic cells. We identified 1143 differentially expressed genes, among which IGF2BP1 is intimately related to the muscle development process and is highly expressed in muscle tissues. Overexpression of IGF2BP1 significantly promotes the proliferation and differentiation of chicken primary myoblasts, while knockdown of IGF2BP1 significantly inhibits these processes. In summary, these results provide valuable preliminary insights into the regulatory roles of IGF2BP1 in chicken growth and development.
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Affiliation(s)
- Jintang Luo
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.L.); (Z.Y.); (X.L.); (C.X.); (H.Y.); (X.Y.); (B.Z.); (Y.Z.); (J.Z.)
| | - Zhuliang Yang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.L.); (Z.Y.); (X.L.); (C.X.); (H.Y.); (X.Y.); (B.Z.); (Y.Z.); (J.Z.)
| | - Xianchao Li
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.L.); (Z.Y.); (X.L.); (C.X.); (H.Y.); (X.Y.); (B.Z.); (Y.Z.); (J.Z.)
| | - Cong Xiao
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.L.); (Z.Y.); (X.L.); (C.X.); (H.Y.); (X.Y.); (B.Z.); (Y.Z.); (J.Z.)
| | - Hong Yuan
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.L.); (Z.Y.); (X.L.); (C.X.); (H.Y.); (X.Y.); (B.Z.); (Y.Z.); (J.Z.)
| | - Xueqin Yang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.L.); (Z.Y.); (X.L.); (C.X.); (H.Y.); (X.Y.); (B.Z.); (Y.Z.); (J.Z.)
| | - Biyan Zhou
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.L.); (Z.Y.); (X.L.); (C.X.); (H.Y.); (X.Y.); (B.Z.); (Y.Z.); (J.Z.)
| | - Yan Zheng
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.L.); (Z.Y.); (X.L.); (C.X.); (H.Y.); (X.Y.); (B.Z.); (Y.Z.); (J.Z.)
| | - Jiayi Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.L.); (Z.Y.); (X.L.); (C.X.); (H.Y.); (X.Y.); (B.Z.); (Y.Z.); (J.Z.)
| | - Xiurong Yang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (J.L.); (Z.Y.); (X.L.); (C.X.); (H.Y.); (X.Y.); (B.Z.); (Y.Z.); (J.Z.)
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning 530004, China
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Chen B, Zhang Y, Niu Y, Wang Y, Liu Y, Ji H, Han R, Tian Y, Liu X, Kang X, Li Z. RRM2 promotes the proliferation of chicken myoblasts, inhibits their differentiation and muscle regeneration. Poult Sci 2024; 103:103407. [PMID: 38198913 PMCID: PMC10825555 DOI: 10.1016/j.psj.2023.103407] [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: 10/10/2023] [Revised: 12/10/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
During myogenesis and regeneration, the proliferation and differentiation of myoblasts play key regulatory roles and may be regulated by many genes. In this study, we analyzed the transcriptomic data of chicken primary myoblasts at different periods of proliferation and differentiation with protein‒protein interaction network, and the results indicated that there was an interaction between cyclin-dependent kinase 1 (CDK1) and ribonucleotide reductase regulatory subunit M2 (RRM2). Previous studies in mammals have a role for RRM2 in skeletal muscle development as well as cell growth, but the role of RRM2 in chicken is unclear. In this study, we investigated the effects of RRM2 on skeletal muscle development and regeneration in chickens in vitro and in vivo. The interaction between RRM2 and CDK1 was initially identified by co-immunoprecipitation and mass spectrometry. Through a dual luciferase reporter assay and quantitative real-time PCR, we identified the core promoter region of RRM2, which is regulated by the SP1 transcription factor. In this study, through cell counting kit-8 assays, 5-ethynyl-2'-deoxyuridine incorporation assays, flow cytometry, immunofluorescence staining, and Western blot analysis, we demonstrated that RRM2 promoted the proliferation and inhibited the differentiation of myoblasts. In vivo studies showed that RRM2 reduced the diameter of muscle fibers and slowed skeletal muscle regeneration. In conclusion, these data provide preliminary insights into the biological functions of RRM2 in chicken muscle development and skeletal muscle regeneration.
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Affiliation(s)
- Bingjie Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yushi Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yufang Niu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yanxing Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yang Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Haigang Ji
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China.
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Zhao W, Cai Z, Jiang Q, Zhang J, Yu B, Feng X, Fu X, Zhang T, Hu J, Gu Y. Transcriptome analysis reveals the role of long noncoding RNAs in specific deposition of inosine monphosphate in Jingyuan chickens. J Anim Sci 2024; 102:skae136. [PMID: 38738625 PMCID: PMC11249926 DOI: 10.1093/jas/skae136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 05/10/2024] [Indexed: 05/14/2024] Open
Abstract
Inosine monphosphate (IMP) is one of the important indicators for evaluating meat flavor, and long noncoding RNAs (lncRNAs) play an important role in its transcription and post-transcriptional regulation. Currently, there is little information about how lncRNA regulates the specific deposition of IMP in chicken muscle. In this study, we used transcriptome sequencing to analyze the lncRNAs of the breast and leg muscles of the Jingyuan chicken and identified a total of 357 differentially expressed lncRNAs (DELs), of which 158 were up-regulated and 199 were down-regulated. There were 2,203 and 7,377 cis- and trans-regulated target genes of lncRNAs, respectively, and we identified the lncRNA target genes that are involved in NEGF signaling pathway, glycolysis/glucoseogenesis, and biosynthesis of amino acids pathways. Meanwhile, 621 pairs of lncRNA-miRNA-mRNA interaction networks were constructed with target genes involved in purine metabolism, fatty acid metabolism, and biosynthesis of amino acids. Next, three interacting meso-networks gga-miR-1603-LNC_000324-PGM1, gga-miR-1768-LNC_000324-PGM1, and gga-miR-21-LNC_011339-AMPD1 were identified as closely associated with IMP-specific deposition. Both differentially expressed genes (DEGs) PGM1 and AMPD1 were significantly enriched in IMP synthesis and metabolism-related pathways, and participated in the anabolic process of IMP in the form of organic matter synthesis and energy metabolism. This study obtained lncRNAs and target genes affecting IMP-specific deposition in Jingyuan chickens based on transcriptome analysis, which deepened our insight into the role of lncRNAs in chicken meat quality.
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Affiliation(s)
- Wei Zhao
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Zhengyun Cai
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Qiufei Jiang
- Animal Husbandry Extension Station, Yinchuan750021, China
| | - Juan Zhang
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Baojun Yu
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Xiaofang Feng
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Xi Fu
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Tong Zhang
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Jiahuan Hu
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
| | - Yaling Gu
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, College of Animal Science and Technology, Ningxia University, Yinchuan, 750021, China
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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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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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Ren T, Lin W, Yang X, Zhang Z, He S, Li W, Li Z, Zhang X. QPCTL Affects the Daily Weight Gain of the F2 Population and Regulates Myogenic Cell Proliferation and Differentiation in Chickens. Animals (Basel) 2022; 12:ani12243535. [PMID: 36552455 PMCID: PMC9774964 DOI: 10.3390/ani12243535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/10/2022] [Accepted: 12/11/2022] [Indexed: 12/16/2022] Open
Abstract
Molecular breeding can accelerate the process of animal breeding and improve the breeding efficiency. To date, many Indel molecular markers have been identified in livestock and poultry, but how Indels affect economic traits is not well understood. For molecular breeding, it is crucial to reveal the mechanism of action of Indels and to provide more accurate information. The purpose of this study was to investigate how the 52/224-bp multiallelic Indels of the chicken QPCTL promoter area affect the daily weight gain of chickens and the potential regulatory mechanism of the QPCTL gene. The analysis was conducted by association analysis, qPCR, dual-fluorescence assay and Western blotting. The results showed that Indels in the QPCTL promoter region were significantly associated with the daily weight gain in chickens and that QPCTL expression showed a decreasing trend in embryonic breast muscle tissues. Furthermore, QPCTL expression was significantly higher in breast muscle tissues of the AC genotype than in those of the AB and BB genotypes. Based on the transcriptional activity results, the pGL3-C vector produced more luciferase activity than pGL3-A and pGL3-B. In addition, overexpression of QPCTL promoted chicken primary myoblast (CPM) proliferation and inhibited differentiation. The results of this study suggest that Indels in the promoter region of the QPCTL gene may regulate the proliferation and differentiation of CPMs by affecting the expression of QPCTL, which ultimately affects the growth rate of chickens. These Indels have important value for the molecular breeding of chickens, and QPCTL can be used as a candidate gene to regulate and improve chicken growth and development.
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Affiliation(s)
- Tuanhui Ren
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Wujian Lin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Xiuxian Yang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Zihao Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Shizi He
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Wangyu Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Correspondence: (Z.L.); (X.Z.)
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- Correspondence: (Z.L.); (X.Z.)
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Wu P, He M, Zhang X, Zhou K, Zhang T, Xie K, Dai G, Wang J, Wang X, Zhang G. miRNA-seq analysis in skeletal muscle of chicken and function exploration of miR-24-3p. Poult Sci 2022; 101:102120. [PMID: 36113166 PMCID: PMC9483787 DOI: 10.1016/j.psj.2022.102120] [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: 03/12/2021] [Revised: 06/16/2022] [Accepted: 08/03/2022] [Indexed: 10/31/2022] Open
Abstract
The regulation of skeletal muscle growth and development in chicken is complex. MicroRNAs (miRNAs) have been found to play an important role in the process, and more research is needed to further understand the regulatory mechanism of miRNAs. In this study, leg muscles of Jinghai yellow chickens at 300 d with low body weight (slow-growing group) and high body weight (fast-growing group) were collected for miRNA sequencing (miRNA-seq) and Bioinformatics analysis revealed 12 differentially expressed miRNAs (DEMs) between the two groups. We predicted 150 target genes for the DEMs, and GO and KEGG pathway analysis showed the target genes of miR-24-3p and novel_miR_133 were most enriched in the terms related to growth and development. Moreover, networks of DEMs and target genes showed that miR-24-3p and novel_miR_133 were the 2 core miRNAs. Hence, miR-24-3p was selected for further functional exploration in chicken primary myoblasts (CPMs) with molecular biology technologies including qPCR, cell counting kit-8 (CCK-8), 5-ethynyl-2'-deoxyuridine (EdU) and immunofluorescence. When proliferating CPMs were transfected with miR-24-3p mimic, the expression of cyclin dependent kinase inhibitor 1A (P21) was up-regulated and both CCK-8 and EdU assays showed that the proliferation of CPMs was inhibited. However, when the inhibitor was transfected into the proliferating CPMs, the opposite results were found. In differentiated CPMs, transfection with miR-24-3p mimic resulted in up regulation of MYOD, MYOG and MYHC after 48 h. Myotube areas also increased significantly compared to the mimic negative control (NC) group. When treated with inhibitor, differentiation CPMs produced the opposite effects. Overall, we revealed 2 miRNAs (novel_miR_133 and miR-24-3p) significantly related with growth and development and further proved that miR-24-3p could suppress the proliferation and promote differentiation of CPMs. The results would facilitate understanding the effects of miRNAs on the growth and development of chickens at the post-transcriptional level and could also have an important guiding role in yellow-feathered chicken breeding.
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Affiliation(s)
- Pengfei Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Mingliang He
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Xinchao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Kaizhi Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Tao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Kaizhou Xie
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Guojun Dai
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Jinyu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Xinglong Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China.
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Shi X, Li P, Wu X, Wang Z, Zhao G, Shu J. RNA-Seq Comprehensive Analysis Reveals the Long Noncoding RNA Expression Profile and Coexpressed mRNA in Adult Degenerative Scoliosis. Front Genet 2022; 13:902943. [PMID: 36035195 PMCID: PMC9403536 DOI: 10.3389/fgene.2022.902943] [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: 03/23/2022] [Accepted: 06/23/2022] [Indexed: 11/23/2022] Open
Abstract
Objective: Owing to the intensification of the aging process worldwide, the prevalence of adult degenerative scoliosis (ADS) is increasing at an alarming rate. However, genomic research related to the etiology of ADS is rarely reported worldwide. Since long noncoding RNAs (lncRNAs) play a pivotal role in the progression of human diseases, this study aimed to investigate ADS-associated messenger RNAs (mRNAs) and lncRNAs by RNA sequencing (RNA-seq), as well as performed comprehensive bioinformatics analysis based on the lncRNA–mRNA coexpression network and protein–protein interaction (PPI) network. Methods: Initially, six whole blood (WB) samples were obtained from three ADS and three nondegenerative lumbar trauma patients who underwent surgical operation for RNA-seq exploration to construct differential mRNA and lncRNA expression profiles. Subsequently, quantitative RT-PCR (qRT-PCR) was performed to validate three randomly selected differentially expressed mRNAs and lncRNAs derived from the nucleus pulposus (NP) tissue of 14 other subjects (seven ADS patients and seven nondegenerative lumbar trauma patients), respectively. Results: A total of 1,651 upregulated and 1,524 downregulated mRNAs and 147 upregulated and 83 downregulated lncRNAs were screened out from the RNA-Seq data, which constructed coexpression networks to investigate their regulatory interactions further. GO gene function prediction revealed that lncRNA-targeted genes might play a vital role in ADS via participation in multiple biological processes such as the AMPK signaling pathway, lysosomes, and ubiquitin-mediated proteolysis, as well as cellular metabolic processes. Moreover, the expression levels of three selected lncRNAs and mRNAs were validated by qRT-PCR, respectively, demonstrating that the relative expression levels were consistent with the RNA-seq data. Notably, the dysregulated RNAs, AKT1, UBA52, PTPN12, and CLEC16A, were significantly differentially expressed in ADS WB samples and might serve as potentially regulated genes for research in the future. Conclusions: This study provides the first insight into the altered transcriptome profile of long-stranded noncoding RNAs associated with ADS, which paves the way for further exploration of the clinical biomarkers and molecular regulatory mechanisms for this poorly understood degenerative disease. However, the detailed biological mechanisms underlying these candidate lncRNAs in ADS necessitate further elucidation in future studies.
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Affiliation(s)
- Xin Shi
- The Second Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China
- Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
| | - Panpan Li
- The Second Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China
- Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany
- *Correspondence: Panpan Li, , Jun Shu,
| | - Xiang Wu
- The Second Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China
| | - Zhihua Wang
- The Second Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China
| | - Gang Zhao
- The Second Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China
| | - Jun Shu
- The Second Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China
- *Correspondence: Panpan Li, , Jun Shu,
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10
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Shao M, Shi K, Zhao Q, Duan Y, Shen Y, Tian J, He K, Li D, Yu M, Lu Y, Tang Y, Feng C. Transcriptome Analysis Reveals the Differentially Expressed Genes Associated with Growth in Guangxi Partridge Chickens. Genes (Basel) 2022; 13:genes13050798. [PMID: 35627183 PMCID: PMC9140345 DOI: 10.3390/genes13050798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
The Guangxi Partridge chicken is a well-known chicken breed in southern China with good meat quality, which has been bred as a meat breed to satisfy the increased demand of consumers. Compared with line D whose body weight is maintained at the average of the unselected group, the growth rate and weight of the selected chicken group (line S) increased significantly after breeding for four generations. Herein, transcriptome analysis was performed to identify pivotal genes and signal pathways of selective breeding that contributed to potential mechanisms of growth and development under artificial selection pressure. The average body weight of line S chickens was 1.724 kg at 90 d of age, which showed a significant increase at 90 d of age than line D chickens (1.509 kg), although only the internal organ ratios of lung and kidney changed after standardizing by body weight. The myofiber area and myofiber density of thigh muscles were affected by selection to a greater extent than that of breast muscle. We identified 51, 210, 31, 388, and 100 differentially expressed genes (DEGs) in the hypothalamus, pituitary, breast muscle, thigh muscle, and liver between the two lines, respectively. Several key genes were identified in the hypothalamus-pituitary-muscle axis, such as FST, THSB, PTPRJ, CD36, PITX1, PITX2, AMPD1, PRKAB1, PRKAB2, and related genes for muscle development, which were attached to the cytokine–cytokine receptor interaction signaling pathway, the PPAR signaling pathway, and lipid metabolism. However, signaling molecular pathways and the cell community showed that elevated activity in the liver of line S fowl was mainly involved in focal adhesion, ECM-receptor interaction, cell adhesion molecules, and signal transduction. Collectively, muscle development, lipid metabolism, and several signaling pathways played crucial roles in the improving growth performance of Guangxi Partridge chickens under artificial selection for growth rate. These results support further study of the adaptation of birds under selective pressure.
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Affiliation(s)
- Minghui Shao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Kai Shi
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Qian Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Ying Duan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Yangyang Shen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Jinjie Tian
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Kun He
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Dongfeng Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Minli Yu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Yangqing Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China;
| | - Yanfei Tang
- Guangxi Fufeng Agricultural and Animal Husbandry Group Co., Ltd., Nanning 530024, China;
| | - Chungang Feng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
- Correspondence:
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11
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Karimi P, Bakhtiarizadeh MR, Salehi A, Izadnia HR. Transcriptome analysis reveals the potential roles of long non-coding RNAs in feed efficiency of chicken. Sci Rep 2022; 12:2558. [PMID: 35169237 PMCID: PMC8847365 DOI: 10.1038/s41598-022-06528-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/02/2022] [Indexed: 12/13/2022] Open
Abstract
Feed efficiency is an important economic trait and reduces the production costs per unit of animal product. Up to now, few studies have conducted transcriptome profiling of liver tissue in feed efficiency-divergent chickens (Ross vs native breeds). Also, molecular mechanisms contributing to differences in feed efficiency are not fully understood, especially in terms of long non-coding RNAs (lncRNAs). Hence, transcriptome profiles of liver tissue in commercial and native chicken breeds were analyzed. RNA-Seq data along with bioinformatics approaches were applied and a series of lncRNAs and target genes were identified. Furthermore, protein-protein interaction network construction, co-expression analysis, co-localization analysis of QTLs and functional enrichment analysis were used to functionally annotate the identified lncRNAs. In total, 2,290 lncRNAs were found (including 1,110 annotated, 593 known and 587 novel), of which 53 (including 39 known and 14 novel), were identified as differentially expressed genes between two breeds. The expression profile of lncRNAs was validated by RT-qPCR. The identified novel lncRNAs showed a number of characteristics similar to those of known lncRNAs. Target prediction analysis showed that these lncRNAs have the potential to act in cis or trans mode. Functional enrichment analysis of the predicted target genes revealed that they might affect the differences in feed efficiency of chicken by modulating genes associated with lipid metabolism, carbohydrate metabolism, growth, energy homeostasis and glucose metabolism. Some gene members of significant modules in the constructed co-expression networks were reported as important genes related to feed efficiency. Co-localization analysis of QTLs related to feed efficiency and the identified lncRNAs suggested several candidates to be involved in residual feed intake. The findings of this study provided valuable resources to further clarify the genetic basis of regulation of feed efficiency in chicken from the perspective of lncRNAs.
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Affiliation(s)
- Parastoo Karimi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | | | - Abdolreza Salehi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Hamid Reza Izadnia
- Animal Science Improvement Research Department, Agricultural and Natural Resources Research and Education Center, Safiabad AREEO, Dezful, Iran
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12
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Emerging Roles of Non-Coding RNAs in the Feed Efficiency of Livestock Species. Genes (Basel) 2022; 13:genes13020297. [PMID: 35205343 PMCID: PMC8872339 DOI: 10.3390/genes13020297] [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: 12/15/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 01/27/2023] Open
Abstract
A global population of already more than seven billion people has led to an increased demand for food and water, and especially the demand for meat. Moreover, the cost of feed used in animal production has also increased dramatically, which requires animal breeders to find alternatives to reduce feed consumption. Understanding the biology underlying feed efficiency (FE) allows for a better selection of feed-efficient animals. Non-coding RNAs (ncRNAs), especially micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), play important roles in the regulation of bio-logical processes and disease development. The functions of ncRNAs in the biology of FE have emerged as they participate in the regulation of many genes and pathways related to the major FE indicators, such as residual feed intake and feed conversion ratio. This review provides the state of the art studies related to the ncRNAs associated with FE in livestock species. The contribution of ncRNAs to FE in the liver, muscle, and adipose tissues were summarized. The research gap of the function of ncRNAs in key processes for improved FE, such as the nutrition, heat stress, and gut–brain axis, was examined. Finally, the potential uses of ncRNAs for the improvement of FE were discussed.
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13
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Lagarrigue S, Lorthiois M, Degalez F, Gilot D, Derrien T. LncRNAs in domesticated animals: from dog to livestock species. Mamm Genome 2021; 33:248-270. [PMID: 34773482 PMCID: PMC9114084 DOI: 10.1007/s00335-021-09928-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022]
Abstract
Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.
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Affiliation(s)
| | - Matthias Lorthiois
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France
| | - Fabien Degalez
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, 35590, Saint-Gilles, France
| | - David Gilot
- CLCC Eugène Marquis, INSERM, Université Rennes, UMR_S 1242, 35000, Rennes, France
| | - Thomas Derrien
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France.
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14
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Wu P, Zhou K, Zhang L, Li P, He M, Zhang X, Ye H, Zhang Q, Wei Q, Zhang G. High-throughput sequencing reveals crucial miRNAs in skeletal muscle development of Bian chicken. Br Poult Sci 2021; 62:658-665. [PMID: 33874802 DOI: 10.1080/00071668.2021.1919994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
1. Growth performance is significant for chickens. MicroRNAs (miRNAs) have been found to play important roles in the post-transcriptional regulation of skeletal muscle growth. However, the mechanism of miRNAs in this process has not been elucidated.2. This study involved collecting leg muscle from slow- and fast-growing groups of Bian chicken at 16 weeks of age for high-throughput sequencing. A total of 42 differentially expressed miRNAs (DEMs) were identified. Among them, 22 DEMs were up-regulated and 20 DEMs were down-regulated.3. Biological process terms, relating to growth, were found by GO enrichment for target genes of DEMs and KEGG pathway analysis of target genes. This revealed some significantly enriched pathways closely related to skeletal muscle development, such as the calcium signalling pathway, ECM-receptor interaction, lysine degradation, apoptosis and tight junctions. Network interaction analysis of DEMs and target genes showed that the top fifty hub genes were targeted by thirteen DEMs.4. Four important miRNAs (novel_miR_158, novel_miR_144, novel_miR_291, and miR-205a) as well as some other valuable miRNAs, such as gga-miR-214 and gga-miR-3525 were identified. The qPCR results of five DEMs were highly consistent with that of sequencing between the two groups, which proved the reliability of miRNA-seq.5. The study will help to improve the molecular mechanism of miRNAs in chickens and guide future experiments concerning miRNA function in chicken growth.
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Affiliation(s)
- P Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - K Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - L Zhang
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - P Li
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - M He
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - X Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - H Ye
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - Q Zhang
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - Q Wei
- College of Animal Science, Shanxi Agricultural University, Taiyuan, China
| | - G Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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15
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Liu J, Zhou Y, Hu X, Yang J, Lei Q, Liu W, Han H, Li F, Cao D. Transcriptome Analysis Reveals the Profile of Long Non-coding RNAs During Chicken Muscle Development. Front Physiol 2021; 12:660370. [PMID: 34040544 PMCID: PMC8141850 DOI: 10.3389/fphys.2021.660370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/26/2021] [Indexed: 12/19/2022] Open
Abstract
The developmental complexity of muscle arises from elaborate gene regulation. Long non-coding RNAs (lncRNAs) play critical roles in muscle development through the regulation of transcription and post-transcriptional gene expression. In chickens, previous studies have focused on the lncRNA profile during the embryonic periods, but there are no studies that explore the profile from the embryonic to post-hatching period. Here, we reconstructed 14,793 lncRNA transcripts and identified 2,858 differentially expressed lncRNA transcripts and 4,282 mRNAs from 12-day embryos (E12), 17-day embryos (E17), 1-day post-hatch chicks (D1), 14-day post-hatch chicks (D14), 56-day post-hatch chicks (D56), and 98-day post-hatch chicks (D98), based on our published RNA-seq datasets. We performed co-expression analysis for the differentially expressed lncRNAs and mRNAs, using STEM, and identified two profiles with opposite expression trends: profile 4 with a downregulated pattern and profile 21 with an upregulated pattern. The cis- and trans-regulatory interactions between the lncRNAs and mRNAs were predicted within each profile. Functional analysis of the lncRNA targets showed that lncRNAs in profile 4 contributed to the cell proliferation process, while lncRNAs in profile 21 were mainly involved in metabolism. Our work highlights the lncRNA profiles involved in the development of chicken breast muscle and provides a foundation for further experiments on the role of lncRNAs in the regulation of muscle development.
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Affiliation(s)
- Jie Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, China
| | - Yan Zhou
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xin Hu
- Molecular and Cellular Biology, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Jingchao Yang
- Shandong Animal Husbandry General Station, Jinan, China
| | - Qiuxia Lei
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, China
| | - Wei Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, China
| | - Haixia Han
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Fuwei Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Dingguo Cao
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, China
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16
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Zhang G, Wu P, Zhou K, He M, Zhang X, Qiu C, Li T, Zhang T, Xie K, Dai G, Wang J. Study on the transcriptome for breast muscle of chickens and the function of key gene RAC2 on fibroblasts proliferation. BMC Genomics 2021; 22:157. [PMID: 33676413 PMCID: PMC7937270 DOI: 10.1186/s12864-021-07453-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 02/19/2021] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Growth performance is significant in broiler production. In the growth process of broilers, gene expression varies at different growth stages. However, limited research has been conducted on the molecular mechanisms of muscle growth and development in yellow-feathered male chickens. RESULTS In the study, we used RNA-seq to study the transcriptome of the breast muscle of male Jinghai yellow chickens at 4 (M4F), 8 (M8F) and 12 weeks (M12F) of age. The results showed that 4608 differentially expressed genes (DEGs) were obtained by comparison in pairs of the three groups with Fold Change (FC) ≥ 2 and False Discovery Rate (FDR) ≤ 0.05, and 83, 3445 and 3903 DEGs were obtained separately from M4FvsM8F, M4FvsM12F and M8FvsM12F. Six genes were found as co-differentially expressed in the three age groups, namely SNCG, MYH1A, ARHGDIB, ENSGALG00000031598, ENSGALG00000035660 and ENSGALG00000030559. The GO analysis showed that 0, 304 and 408 biological process (BP) were significantly enriched in M4FvsM8F, M4FvsM12F and M8FvsM12F groups, respectively. KEGG pathway enrichment showed that 1, 2, 4 and 4 pathways were significantly enriched in M4FvsM8F, M4FvsM12F, M8FvsM12F and all DEGs, respectively. They were steroid biosynthesis, carbon metabolism, focal adhesion, cytokine-cytokine receptor interaction, biosynthesis of amino acids and salmonella infection. We constructed short hairpin RNA (shRNA) to interfere the differentially expressed gene RAC2 in DF-1 cells and detected mRNA and protein expression of the downstream genes PAK1 and MAPK8. Results of qPCR showed that RAC2, PAK1 and MAPK8 mRNA expression significantly decreased in the shRAC2-2 group compared with the negative control (NC) group. Western Blot (WB) results showed that the proteins of RAC2, PAK1 and MAPK8 also decreased in the shRAC2-2 group. Cell Counting Kit-8 (CCK-8) and 5-Ethynyl-2'-deoxyuridine (EdU) assay both showed that the proliferation of DF-1 cells was significantly inhibited after transfection of shRAC2-2. CONCLUSIONS The results of RNA-seq revealed genes, BP terms and KEGG pathways related to growth and development of male Jinghai yellow chickens, and they would have important guiding significance to our production practice. Further research suggested that RAC2 might regulate cell proliferation by regulating PAKs/MAPK8 pathway and affect growth of chickens.
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Affiliation(s)
- Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Pengfei Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China.
| | - Kaizhi Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Mingliang He
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Xinchao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Cong Qiu
- Jiangsu Jinghai Poultry Group Co. Ltd., Nantong, 226100, China
| | - Tingting Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Tao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Kaizhou Xie
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Guojun Dai
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Jinyu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
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17
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Ren T, Yang Y, Lin W, Li W, Xian M, Fu R, Zhang Z, Mo G, Luo W, Zhang X. A 31-bp indel in the 5' UTR region of GNB1L is significantly associated with chicken body weight and carcass traits. BMC Genet 2020; 21:91. [PMID: 32847500 PMCID: PMC7450547 DOI: 10.1186/s12863-020-00900-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/16/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND G-protein subunit beta 1 like (GNB1L) encodes a G-protein beta-subunit-like polypeptide. Chicken GNB1L is upregulated in the breast muscle of high feed efficiency chickens, and its expression is 1.52-fold that in low feed efficiency chickens. However, no report has described the effects of GNB1L indels on the chicken carcass and growth traits. RESULTS This study identified a 31-bp indel in the 5' untranslated region (UTR) of GNB1L and elucidated the effect of this gene mutation on the carcass and growth traits in chickens. The 31-bp indel showed a highly significant association with the body weight at 8 different stages and was significantly correlated with daily gains at 0 to 4 weeks and 4 to 8 weeks. Similarly, the mutation was significantly associated with small intestine length, breast width, breast depth and breast muscle weight. Moreover, DD and ID were superior genotypes for chicken growth and carcass traits. CONCLUSIONS These results show that the 31-bp indel of GNB1L significantly affects chicken body weight and carcass traits and can serve as a candidate molecular marker for chicken genetics and breeding programs.
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Affiliation(s)
- Tuanhui Ren
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China.,College of Life Science, Foshan University, Foshan, 528231, Guangdong, China
| | - Ying Yang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Wujian Lin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Wangyu Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Mingjian Xian
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Rong Fu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Zihao Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Guodong Mo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Wen Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China. .,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China.
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18
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Ren T, Zhang Z, Fu R, Yang Y, Li W, Liang J, Mo G, Luo W, Zhang X. A 51 bp indel polymorphism within the PTH1R gene is significantly associated with chicken growth and carcass traits. Anim Genet 2020; 51:568-578. [PMID: 32400914 DOI: 10.1111/age.12942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2020] [Indexed: 01/04/2023]
Abstract
Parathyroid hormone (PTH) is a crucial regulator of calcium homeostasis and bone remodeling, and the parathyroid hormone 1 receptor (PTH1R) belongs to a class II G-protein-coupled receptor. PTH activates PTH1R, which mediates catabolic and anabolic processes in the skeleton. However, the functional mechanism of PTH1R has not been thoroughly elucidated in organisms. This study identified a 51 bp indel mutation in the first intron of the PTH1R gene and elucidated the effect of this gene mutation on the growth and carcass traits in chickens. The results indicated that the 51 bp indel was significantly associated with subcutaneous fat thickness, abdominal fat weight, body weight and daily gain over 4-8 weeks. Furthermore, we found that PTH1R gene expression was highest in the kidney and liver tissues, and it showed a trend of decreasing in leg and breast muscle tissues at different embryonic stages. In addition, we examined the expression of the three genotypes of the PTH1R gene in the liver, breast muscle and abdominal fat and found that the II genotype was significantly higher than the DD and ID genotypes. In summary, these findings suggest that the PTH1R gene can serve as a potential molecular marker for chicken breeding.
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Affiliation(s)
- T Ren
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Z Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - R Fu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - Y Yang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - W Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - J Liang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - G Mo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - W Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
| | - X Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642, Guangdong, China
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19
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Abstract
Less than 2% of mammalian genomes code for proteins, but 'the majority of its bases can be found in primary transcripts' - a phenomenon termed the pervasive transcription, which was first reported in 2007. Even though most of the transcripts do not code for proteins, they play a variety of biological functions, with regulation of gene expression appearing as the most common one. Those transcripts are divided into two groups based on their length: small non-coding RNAs, which are maximally 200 bp long, and long non-coding RNAs (lncRNAs), which are longer than 200 nucleotides. The advances in next-generation sequencing methods provided a new possibility of investigating the full set of RNA molecules in the cell. In this review, we summarized the current state of knowledge on lncRNAs in three major livestock species - Sus scrofa, Bos taurus and Gallus gallus, based on the literature and the content of biological databases. In the NONCODE database, the largest number of identified lncRNA transcripts is available for pigs, but cattle have the largest number of lncRNA genes. Poultry is represented by less than a half of records. Genomic annotation of lncRNAs showed that the majority of them are assigned to introns (pig, poultry) or intergenic (cattle). The comparison with well-annotated human and mouse genomes indicates that such annotation is a result of lack of proper lncRNA annotation data. Since lncRNAs play an important role in genomic studies, their characterization in farm animals' genomes is critical in bridging the gap between genotype and phenotype.
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20
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Wu P, Zhang X, Zhang G, Chen F, He M, Zhang T, Wang J, Xie K, Dai G. Transcriptome for the breast muscle of Jinghai yellow chicken at early growth stages. PeerJ 2020; 8:e8950. [PMID: 32328350 PMCID: PMC7166044 DOI: 10.7717/peerj.8950] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/20/2020] [Indexed: 12/31/2022] Open
Abstract
Background The meat quality of yellow feathered broilers is better than the quality of its production. Growth traits are important in the broiler industry. The exploration of regulation mechanisms for the skeletal muscle would help to increase the growth performance of chickens. At present, some progress has been made by researchers, but the molecular mechanisms of the skeletal muscle still remain unclear and need to be improved. Methods In this study, the breast muscles of fast- and slow-growing female Jinghai yellow chickens (F4F, F8F, F4S, F8S) and slow-growing male Jinghai yellow chickens (M4S, M8S) aged four and eight weeks were selected for transcriptome sequencing (RNA-seq). All analyses of differentially expressed genes (DEGs) and functional enrichment were performed. Finally, we selected nine DEGs to verify the accuracy of the sequencing by qPCR. Results The differential gene expression analysis resulted in 364, 219 and 111 DEGs (adjusted P-value ≤ 0.05) for the three comparison groups, F8FvsF4F, F8SvsF4S, and M8SvsM4S, respectively. Three common DEGs (ADAMTS20, ARHGAP19, and Novel00254) were found, and they were all highly expressed at four weeks of age. In addition, some other genes related to growth and development, such as ANXA1, COL1A1, MYH15, TGFB3 and ACTC1, were obtained. The most common DEGs (n = 58) were found between the two comparison groups F8FvsF4F and F8SvsF4S, and they might play important roles in the growth of female chickens. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway also showed some significant enrichment pathways, for instance, extracellular matrix (ECM)-receptor interaction, focal adhesion, cell cycle, and DNA replication. The two pathways that were significantly enriched in the F8FvsF4F group were all contained in that of F8SvsF4S. The same two pathways were ECM–receptor interaction and focal adhesion, and they had great influence on the growth of chickens. However, many differences existed between male and female chickens in regards to common DEGs and KEGG pathways. The results would help to reveal the regulation mechanism of the growth and development of chickens and serve as a guideline to propose an experimental design on gene function with the DEGs and pathways.
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Affiliation(s)
- Pengfei Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xinchao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Fuxiang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Mingliang He
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Tao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jinyu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Kaizhou Xie
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guojun Dai
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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21
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Guo Y, Tang H, Li Z, Zhang Y, Li D, Li W, Sun G, Kang X, Han R. High-throughput transcriptome analysis reveals potentially important relationships between lncRNAs and genes in broilers affected by Valgus-varus Deformity (Gallus gallus). Gene 2020; 743:144511. [PMID: 32112984 DOI: 10.1016/j.gene.2020.144511] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 02/06/2023]
Abstract
Valgus-varus Deformity (VVD) is an outward or inward deviation of the tibiotarsus or tarsometatarsus, which results in physical distress of chickens and economic loss in poultry industry. While the etiology and pathogenesis of VVD at the molecular level are still not fully understood so far. Here, based on a case/control design with VVD birds and normal birds, we identified genes and lncRNAs which associated with VVD using RNA sequencing. Transcriptome analysis revealed 231 differentially expressed mRNAs and 23 differentially expressed lncRNAs between case and control of leg cartilage. We identified the cis- and trans-regulatory targets of the differentially expressed lncRNAs, and we constructed a functional lncRNA-mRNA co-expression network. Analysis of the network showed that the differentially expressed mRNAs and the target genes of the differentially expressed lncRNAs were enriched in the signaling pathways associated with bone development, including p53, MAPK, Toll-like receptor, Jak-STAT, Hedgehog, and PPAR. The expression levels of DENND4A, FGF10, FGF12 and BMP3 were also determined in cartilage and other six tissues. Overall, our study predicted the mRNAs and lncRNAs related with leg diseases by transcriptome analyses, which might contribute to understand the etiology and pathogenesis of VVD. It established the foundation for the further research on the function of -mRNAs and lncRNAs in skeleton development.
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Affiliation(s)
- Yaping Guo
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Hehe Tang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yanhua Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Donghua Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Wenting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China.
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China.
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22
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Functions and Regulatory Mechanisms of lncRNAs in Skeletal Myogenesis, Muscle Disease and Meat Production. Cells 2019; 8:cells8091107. [PMID: 31546877 PMCID: PMC6769631 DOI: 10.3390/cells8091107] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/04/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022] Open
Abstract
Myogenesis is a complex biological process, and understanding the regulatory network of skeletal myogenesis will contribute to the treatment of human muscle related diseases and improvement of agricultural animal meat production. Long noncoding RNAs (lncRNAs) serve as regulators in gene expression networks, and participate in various biological processes. Recent studies have identified functional lncRNAs involved in skeletal muscle development and disease. These lncRNAs regulate the proliferation, differentiation, and fusion of myoblasts through multiple mechanisms, such as chromatin modification, transcription regulation, and microRNA sponge activity. In this review, we presented the latest advances regarding the functions and regulatory activities of lncRNAs involved in muscle development, muscle disease, and meat production. Moreover, challenges and future perspectives related to the identification of functional lncRNAs were also discussed.
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23
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Li Z, Ren T, Li W, Zhou Y, Han R, Li H, Jiang R, Yan F, Sun G, Liu X, Tian Y, Kang X. Association Between the Methylation Statuses at CpG Sites in the Promoter Region of the SLCO1B3, RNA Expression and Color Change in Blue Eggshells in Lushi Chickens. Front Genet 2019; 10:161. [PMID: 30863430 PMCID: PMC6399514 DOI: 10.3389/fgene.2019.00161] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/14/2019] [Indexed: 12/31/2022] Open
Abstract
The formation mechanism underlying the blue eggshell characteristic has been discovered in birds, and SLCO1B3 is the key gene that regulates the blue eggshell color. Insertion of an endogenous retrovirus, EAV-HP, in the SLCO1B3 5′ flanking region promotes SLCO1B3 expression in the chicken shell gland, and this expression causes bile salts to enter the shell gland, where biliverdin is secreted into the eggshell, forming a blue shell. However, at different laying stages of the same group of chickens, the color of the eggshell can vary widely, and the molecular mechanism underlying the eggshell color change remains unknown. Therefore, to reveal the molecular mechanism of the blue eggshell color variations, we analyzed the change in the eggshell color during the laying period. The results indicated that the eggshell color in Lushi chickens can be divided into three stages: 20–25 weeks for dark blue, 26–45 weeks for medium blue, and 46–60 weeks for light blue. We further investigated the expression and methylation levels of the SLCO1B3 gene at eight different weeks, finding that the relative expression of SLCO1B3 was significantly higher at 25 and 30 weeks than at other laying weeks. Furthermore, the overall methylation rate of the SLCO1B3 gene in Lushi chickens increased gradually with increasing weeks of egg production, as shown by bisulfite sequencing PCR. Pearson correlation analysis showed that methylation of the promoter region of SLCO1B3 was significantly negatively correlated with both SLCO1B3 expression in the shell gland tissue and eggshell color. In addition, we predicted that CpG5 and CpG8 may be key sites for regulating SLCO1B3 gene transcription. Our findings show that as the level of methylation increases, methylation of the CpG5 and CpG8 sites hinders the binding of transcription factors to the promoter, reducing SLCO1B3 expression during the late period and resulting in a lighter eggshell color.
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Affiliation(s)
- Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Tuanhui Ren
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Wenya Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yu Zhou
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Hong Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Ruirui Jiang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Fengbin Yan
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Xiaojun Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China
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24
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lncRNA-Six1 Is a Target of miR-1611 that Functions as a ceRNA to Regulate Six1 Protein Expression and Fiber Type Switching in Chicken Myogenesis. Cells 2018; 7:cells7120243. [PMID: 30518151 PMCID: PMC6315877 DOI: 10.3390/cells7120243] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 11/23/2018] [Accepted: 12/04/2018] [Indexed: 12/18/2022] Open
Abstract
Emerging studies indicate important roles for non-coding RNAs (ncRNAs) as essential regulators in myogenesis, but relatively less is known about their function. In our previous study, we found that lncRNA-Six1 can regulate Six1 in cis to participate in myogenesis. Here, we studied a microRNA (miRNA) that is specifically expressed in chickens (miR-1611). Interestingly, miR-1611 was found to contain potential binding sites for both lncRNA-Six1 and Six1, and it can interact with lncRNA-Six1 to regulate Six1 expression. Overexpression of miR-1611 represses the proliferation and differentiation of myoblasts. Moreover, miR-1611 is highly expressed in slow-twitch fibers, and it drives the transformation of fast-twitch muscle fibers to slow-twitch muscle fibers. Together, these data demonstrate that miR-1611 can mediate the regulation of Six1 by lncRNA-Six1, thereby affecting proliferation and differentiation of myoblasts and transformation of muscle fiber types.
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25
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Lin X, Gao Q, Zhu L, Zhou G, Ni S, Han H, Yue Z. Long noncoding RNAs regulate Wnt signaling during feather regeneration. Development 2018; 145:dev.162388. [DOI: 10.1242/dev.162388] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 10/04/2018] [Indexed: 02/01/2023]
Abstract
Long noncoding RNAs (lncRNAs) are non-protein coding transcripts that are involved in a broad range of biological processes. Here, we examined the functional roles of lncRNAs in feather regeneration. RNA-seq profiling of the regenerating feather blastema revealed that the Wnt signaling is among the most active pathways during feather regeneration, with the Wnt ligands and their inhibitors showing distinct expression patterns. Co-expression analysis identified hundreds of lncRNAs with similar expression patterns to either the Wnt ligands (the Lwnt group) or their downstream target genes (the Twnt group). Among these, we randomly picked two lncRNAs in the Lwnt group, and three lncRNAs in the Twnt group to validate their expression and function. Members in the Twnt group regulated feather regeneration and axis formation, whereas members in the Lwnt group showed no obvious phenotype. Further analysis confirmed that the three Twnt group members inhibit Wnt signal transduction and at the same time are down-stream target genes of this pathway. Our results suggested that the feather regeneration model can be utilized to systematically annotate the functions of lncRNAs in the chicken genome.
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Affiliation(s)
- Xiang Lin
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, China
| | - QingXiang Gao
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, China
| | - LiYan Zhu
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, China
| | - GuiXuan Zhou
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, China
| | - ShiWei Ni
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, China
| | - Hao Han
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - ZhiCao Yue
- Institute of Life Sciences, Fuzhou University, Fuzhou, Fujian, China
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