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Lau LY, Nguyen LT, Reverter A, Moore SS, Lynn A, McBride‐Kelly L, Phillips‐Rose L, Plath M, Macfarlane R, Vasudivan V, Morton L, Ardley R, Ye Y, Fortes MRS. Gene regulation could be attributed to TCF3 and other key transcription factors in the muscle of pubertal heifers. Vet Med Sci 2020; 6:695-710. [PMID: 32432381 PMCID: PMC7738712 DOI: 10.1002/vms3.278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 03/13/2020] [Accepted: 04/09/2020] [Indexed: 01/17/2023] Open
Abstract
Puberty is a whole-body event, driven by the hypothalamic integration of peripheral signals such as leptin or IGF-1. In the process of puberty, reproductive development is simultaneous to growth, including muscle growth. To enhance our understanding of muscle function related to puberty, we performed transcriptome analyses of muscle samples from six pre- and six post-pubertal Brahman heifers (Bos indicus). Our aims were to perform differential expression analyses and co-expression analyses to derive a regulatory gene network associate with puberty. As a result, we identified 431 differentially expressed (DEx) transcripts (genes and non-coding RNAs) when comparing pre- to post-pubertal average gene expression. The DEx transcripts were compared with all expressed transcripts in our samples (over 14,000 transcripts) for functional enrichment analyses. The DEx transcripts were associated with "extracellular region," "inflammatory response" and "hormone activity" (adjusted p < .05). Inflammatory response for muscle regeneration is a necessary aspect of muscle growth, which is accelerated during puberty. The term "hormone activity" may signal genes that respond to progesterone signalling in the muscle, as the presence of this hormone is an important difference between pre- and post-pubertal heifers in our experimental design. The DEx transcript with the highest average expression difference was a mitochondrial gene, ENSBTAG00000043574 that might be another important link between energy metabolism and puberty. In the derived co-expression gene network, we identified six hub genes: CDC5L, MYC, TCF3, RUNX2, ATF2 and CREB1. In the same network, 48 key regulators of DEx transcripts were identified, using a regulatory impact factor metric. The hub gene TCF3 was also a key regulator. The majority of the key regulators (22 genes) are members of the zinc finger family, which has been implicated in bovine puberty in other tissues. In conclusion, we described how puberty may affect muscle gene expression in cattle.
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Affiliation(s)
- Li Yieng Lau
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Loan T. Nguyen
- Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandBrisbaneQLDAustralia
| | - Antonio Reverter
- CSIRO Agriculture and FoodQueensland Biosciences PrecinctBrisbaneQLDAustralia
| | - Stephen S. Moore
- Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandBrisbaneQLDAustralia
| | - Aaron Lynn
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Liam McBride‐Kelly
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Louis Phillips‐Rose
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Mackenzie Plath
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Rhys Macfarlane
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Vanisha Vasudivan
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Lachlan Morton
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Ryan Ardley
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Yunan Ye
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
| | - Marina R. S. Fortes
- School of Chemistry and Molecular BiologyThe University of QueenslandBrisbaneQLDAustralia
- Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandBrisbaneQLDAustralia
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Guo X, Wang J, Chen H, Su H, Wang Z, Wan Y, Huang Y, Jiang R. Effects of exercise on carcass composition, meat quality, and mRNA expression profiles in breast muscle of a Chinese indigenous chicken breed. Poult Sci 2019; 98:5241-5246. [PMID: 31309226 DOI: 10.3382/ps/pez415] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 07/03/2019] [Indexed: 11/20/2022] Open
Abstract
In this study, we evaluated the effects of exercise on the growth performance, carcass composition, meat quality, and mRNA expression profile of breast muscle in a Chinese indigenous chicken breed. Briefly, 300 female Huainan chickens (60-day-old) with similar BW were selected and raised in a free-range environment. Daily steps were counted by pedometer for all birds from 61 to 140 D of age. At 140 D of age, based on the average counts of steps per day, 15 birds with the highest number of steps (HS), 15 birds with a medium number of steps (MS), and 15 birds with low numbers of steps (LS) were selected for use in subsequent experiments. The HS group had heavier BW than the other two groups (P < 0.05). Compared with the LS group, the HS group displayed higher meat redness and lower shear force, drip loss, cooking loss values, and the percentage of breast muscle weight (P < 0.05). Moreover, a total of 150 differentially expressed genes were identified from the pectoralis major muscles of the HS and LS group. Therefore, enhanced exercise increased BW, improved meat quality by increasing WHC and decreasing shear force values, and decreased percentage of breast muscle weight but had no effect on others carcass parameters. Additionally, the differentially expressed genes in breast muscle between the HS and LS groups were mainly associated with skeletal muscle tissue development and meat quality traits.
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Affiliation(s)
- Xing Guo
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Jiangxian Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Hong Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Hu Su
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Zhicheng Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Yi Wan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Yuanyuan Huang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
| | - Runshen Jiang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China
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Horodyska J, Wimmers K, Reyer H, Trakooljul N, Mullen AM, Lawlor PG, Hamill RM. RNA-seq of muscle from pigs divergent in feed efficiency and product quality identifies differences in immune response, growth, and macronutrient and connective tissue metabolism. BMC Genomics 2018; 19:791. [PMID: 30384851 PMCID: PMC6211475 DOI: 10.1186/s12864-018-5175-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 10/16/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Feed efficiency (FE) is an indicator of efficiency in converting energy and nutrients from feed into a tissue that is of major environmental and economic significance. The molecular mechanisms contributing to differences in FE are not fully elucidated, therefore the objective of this study was to profile the porcine Longissimus thoracis et lumborum (LTL) muscle transcriptome, examine the product quality from pigs divergent in FE and investigate the functional networks underpinning the potential relationship between product quality and FE. RESULTS RNA-Seq (n = 16) and product quality (n = 40) analysis were carried out in the LTL of pigs differing in FE status. A total of 272 annotated genes were differentially expressed with a P < 0.01. Functional annotation revealed a number of biological events related to immune response, growth, carbohydrate & lipid metabolism and connective tissue indicating that these might be the key mechanisms governing differences in FE. Five most significant bio-functions altered in FE groups were 'haematological system development & function', 'lymphoid tissue structure & development', 'tissue morphology', 'cellular movement' and 'immune cell trafficking'. Top significant canonical pathways represented among the differentially expressed genes included 'IL-8 signalling', 'leukocyte extravasation signalling, 'sphingosine-1-phosphate signalling', 'PKCθ signalling in T lymphocytes' and 'fMLP signalling in neutrophils'. A minor impairment in the quality of meat, in relation to texture and water-holding capacity, produced by high-FE pigs was observed. High-FE pigs also had reduced intramuscular fat content and improved nutritional profile in terms of fatty acid composition. CONCLUSIONS Ontology analysis revealed enhanced activity of adaptive immunity and phagocytes in high-FE pigs suggesting more efficient conserving of resources, which can be utilised for other important biological processes. Shifts in carbohydrate conversion into glucose in FE-divergent muscle may underpin the divergent evolution of pH profile in meat from the FE-groups. Moreover, altered amino acid metabolism and increased mobilisation & flux of calcium may influence growth in FE-divergent muscle. Furthermore, decreased degradation of fibroblasts in FE-divergent muscle could impact on collagen turnover and alter tenderness of meat, whilst enhanced lipid degradation in high-FE pigs may potentially underlie a more efficient fat metabolism in these animals.
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Affiliation(s)
- Justyna Horodyska
- Teagasc, Food Research Centre, Ashtown, Dublin, 15, Ireland.,Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Dummerstorf, Germany
| | - Klaus Wimmers
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Dummerstorf, Germany.,Faculty of Agricultural and Environmental Sciences, University Rostock, Rostock, Germany
| | - Henry Reyer
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Dummerstorf, Germany
| | - Nares Trakooljul
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Dummerstorf, Germany
| | | | - Peadar G Lawlor
- Teagasc, Pig Development Department, AGRIC, Moorepark, Fermoy, Co. Cork, Ireland
| | - Ruth M Hamill
- Teagasc, Food Research Centre, Ashtown, Dublin, 15, Ireland.
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Fonseca PADS, Id-Lahoucine S, Reverter A, Medrano JF, Fortes MS, Casellas J, Miglior F, Brito L, Carvalho MRS, Schenkel FS, Nguyen LT, Porto-Neto LR, Thomas MG, Cánovas A. Combining multi-OMICs information to identify key-regulator genes for pleiotropic effect on fertility and production traits in beef cattle. PLoS One 2018; 13:e0205295. [PMID: 30335783 PMCID: PMC6193631 DOI: 10.1371/journal.pone.0205295] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/21/2018] [Indexed: 12/21/2022] Open
Abstract
The identification of biological processes related to the regulation of complex traits is a difficult task. Commonly, complex traits are regulated through a multitude of genes contributing each to a small part of the total genetic variance. Additionally, some loci can simultaneously regulate several complex traits, a phenomenon defined as pleiotropy. The lack of understanding on the biological processes responsible for the regulation of these traits results in the decrease of selection efficiency and the selection of undesirable hitchhiking effects. The identification of pleiotropic key-regulator genes can assist in developing important tools for investigating biological processes underlying complex traits. A multi-breed and multi-OMICs approach was applied to study the pleiotropic effects of key-regulator genes using three independent beef cattle populations evaluated for fertility traits. A pleiotropic map for 32 traits related to growth, feed efficiency, carcass and meat quality, and reproduction was used to identify genes shared among the different populations and breeds in pleiotropic regions. Furthermore, data-mining analyses were performed using the Cattle QTL database (CattleQTLdb) to identify the QTL category annotated in the regions around the genes shared among breeds. This approach allowed the identification of a main gene network (composed of 38 genes) shared among breeds. This gene network was significantly associated with thyroid activity, among other biological processes, and displayed a high regulatory potential. In addition, it was possible to identify genes with pleiotropic effects related to crucial biological processes that regulate economically relevant traits associated with fertility, production and health, such as MYC, PPARG, GSK3B, TG and IYD genes. These genes will be further investigated to better understand the biological processes involved in the expression of complex traits and assist in the identification of functional variants associated with undesirable phenotypes, such as decreased fertility, poor feed efficiency and negative energetic balance.
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Affiliation(s)
- Pablo Augusto de Souza Fonseca
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
- Universidade Federal de Minas Gerais, Departamento de Biologia Geral, Belo Horizonte, Minas Gerais, Brazil
| | - Samir Id-Lahoucine
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
| | - Antonio Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Juan F. Medrano
- University of California-Davis, Department of Animal Science, Davis, California, United States of America
| | - Marina S. Fortes
- The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia
| | - Joaquim Casellas
- Universitat Autònoma de Barcelona, Departament de Ciència Animal i dels Aliments, Barcelona, Bellaterra, Barcelona, Spain
| | - Filippo Miglior
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
- Canadian Dairy Network, Guelph, Ontario, Canada
| | - Luiz Brito
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
| | - Maria Raquel S. Carvalho
- Universidade Federal de Minas Gerais, Departamento de Biologia Geral, Belo Horizonte, Minas Gerais, Brazil
| | - Flávio S. Schenkel
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
| | - Loan T. Nguyen
- The University of Queensland, School of Chemistry and Molecular Biosciences, Brisbane, Queensland, Australia
| | - Laercio R. Porto-Neto
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Milton G. Thomas
- Colorado State University, Department of Animal Science, Fort-Colins, Colorado, United States of America
| | - Angela Cánovas
- University of Guelph, Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, Guelph, Ontario, Canada
- * E-mail:
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Koutb F, Abdel-Rahman S, Hassona E, Haggag A. Association of C-myc and p53 Gene Expression and Polymorphisms with Hepatitis C (HCV) Chronic Infection, Cirrhosis and Hepatocellular Carcinoma (HCC) Stages in
Egypt. Asian Pac J Cancer Prev 2017; 18:2049-2057. [PMID: 28843220 PMCID: PMC5697458 DOI: 10.22034/apjcp.2017.18.8.2049] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The aim of this study is to investigate c-myc and p53 gene expression and polymorphisms in different stages of HCV infection,. Expression levels of c-myc and p53 were evaluated by RT-PCR and polymorphisms were determined by PCR-RFLP in 60 HCV patients classified into chronic infection, cirrhosis and HCC groups along with 30 controls. c-myc gene expression significant increased through the stages as compared to the control level (1.17, 1.82, 3.33 and 0.32, respectively), whereas p53 significantly declined (4,375, 3,842, 525 and 5,498, respectively). The C-myc CC genotype was predominant in the HCC group (90%) to a greater extent than in the cirrhosis, chronic infection and control cases (80%, 20% and 10%, respectively), while the GG genotype was predominant in controls (83%, as compared to 65%, 10% and 10%). The CG genotype was most common in chronic infection (15%). The p53 PP genotype predominated in controls (87%, with 15%, 10% and 20%, respectively, for the three stages) while the AA genotype demonstrated only slight increase to HCC (13%, 25% and 30%, respectively) and PA genotype was predominant in cirrhosis cases (90%). These findings reveal that c-myc and p53 gene expression and polymorphisms may be considered as promising sensitive genetic biomarkers for progression of HCV infection.
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Affiliation(s)
- Fayed Koutb
- Department of Nucleic Acid Research, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, Egypt.
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