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Chronological Expression of PITX2 and SIX1 Genes and the Association between Their Polymorphisms and Chicken Meat Quality Traits. Animals (Basel) 2021; 11:ani11020445. [PMID: 33567786 PMCID: PMC7916052 DOI: 10.3390/ani11020445] [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: 12/31/2020] [Revised: 01/29/2021] [Accepted: 02/03/2021] [Indexed: 12/19/2022] Open
Abstract
Meat quality is closely related to the development of skeletal muscle, in which PITX2 and SIX1 genes play important regulatory roles. The present study firstly provided the data of chronological expression files of PITX2 and SIX1 genes in the post-hatching pectoral muscle and analyzed the association of their polymorphisms with the meat quality traits of Wuliang Mountain Black-bone (WLMB) chickens. The results showed that both PITX2 and SIX1 genes were weakly expressed in the second and third weeks, and then increased significantly from the third week to the fourth week. Furthermore, there was a significant positive correlation between the expression levels of the two genes. Twelve and one SNPs were detected in the chicken PITX2 and SIX1 genes, respectively, of which four SNPs (g.9830C > T, g.10073C > T, g.13335G > A, g.13726A > G) of the PITX2 gene and one SNP (g.564G > A) of the SIX1 gene were significantly associated with chicken meat quality traits. For the PITX2 gene, chickens with the CT genotype of g.9830C > T showed the highest meat color L*, shear force (SF), pH, and the lowest electrical conductivity (EC), and drip loss (DL) (p < 0.05 or p < 0.01); chickens with the CC genotype of g.10073C > T had the lowest L*, pH, and the highest DL (p < 0.01). For the SIX1 gene, chickens with the GG genotype of g.564G > A had the highest (p < 0.05) SF and pH. Furthermore, pH had a significant correlation with all the other meat quality traits. The current study could contribute to the research of regulatory mechanisms of meat quality and lay the foundation for improving meat quality based on marker-assisted selection in chickens.
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2
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Turner DC, Gorski PP, Maasar MF, Seaborne RA, Baumert P, Brown AD, Kitchen MO, Erskine RM, Dos-Remedios I, Voisin S, Eynon N, Sultanov RI, Borisov OV, Larin AK, Semenova EA, Popov DV, Generozov EV, Stewart CE, Drust B, Owens DJ, Ahmetov II, Sharples AP. DNA methylation across the genome in aged human skeletal muscle tissue and muscle-derived cells: the role of HOX genes and physical activity. Sci Rep 2020; 10:15360. [PMID: 32958812 PMCID: PMC7506549 DOI: 10.1038/s41598-020-72730-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/04/2020] [Indexed: 12/15/2022] Open
Abstract
Skeletal muscle tissue demonstrates global hypermethylation with age. However, methylome changes across the time-course of differentiation in aged human muscle derived cells, and larger coverage arrays in aged muscle tissue have not been undertaken. Using 850K DNA methylation arrays we compared the methylomes of young (27 ± 4.4 years) and aged (83 ± 4 years) human skeletal muscle and that of young/aged heterogenous muscle-derived human primary cells (HDMCs) over several time points of differentiation (0, 72 h, 7, 10 days). Aged muscle tissue was hypermethylated compared with young tissue, enriched for; pathways-in-cancer (including; focal adhesion, MAPK signaling, PI3K-Akt-mTOR signaling, p53 signaling, Jak-STAT signaling, TGF-beta and notch signaling), rap1-signaling, axon-guidance and hippo-signalling. Aged cells also demonstrated a hypermethylated profile in pathways; axon-guidance, adherens-junction and calcium-signaling, particularly at later timepoints of myotube formation, corresponding with reduced morphological differentiation and reductions in MyoD/Myogenin gene expression compared with young cells. While young cells showed little alterations in DNA methylation during differentiation, aged cells demonstrated extensive and significantly altered DNA methylation, particularly at 7 days of differentiation and most notably in focal adhesion and PI3K-AKT signalling pathways. While the methylomes were vastly different between muscle tissue and HDMCs, we identified a small number of CpG sites showing a hypermethylated state with age, in both muscle tissue and cells on genes KIF15, DYRK2, FHL2, MRPS33, ABCA17P. Most notably, differential methylation analysis of chromosomal regions identified three locations containing enrichment of 6–8 CpGs in the HOX family of genes altered with age. With HOXD10, HOXD9, HOXD8, HOXA3, HOXC9, HOXB1, HOXB3, HOXC-AS2 and HOXC10 all hypermethylated in aged tissue. In aged cells the same HOX genes (and additionally HOXC-AS3) displayed the most variable methylation at 7 days of differentiation versus young cells, with HOXD8, HOXC9, HOXB1 and HOXC-AS3 hypermethylated and HOXC10 and HOXC-AS2 hypomethylated. We also determined that there was an inverse relationship between DNA methylation and gene expression for HOXB1, HOXA3 and HOXC-AS3. Finally, increased physical activity in young adults was associated with oppositely regulating HOXB1 and HOXA3 methylation compared with age. Overall, we demonstrate that a considerable number of HOX genes are differentially epigenetically regulated in aged human skeletal muscle and HDMCs and increased physical activity may help prevent age-related epigenetic changes in these HOX genes.
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Affiliation(s)
- D C Turner
- Institute for Physical Performance, Norwegian School of Sport Sciences (NiH), Oslo, Norway.,Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK.,Institute for Science and Technology in Medicine (ISTM), School of Pharmacy & Bioengineering, Keele University, Staffordshire, UK
| | - P P Gorski
- Institute for Physical Performance, Norwegian School of Sport Sciences (NiH), Oslo, Norway.,Institute for Science and Technology in Medicine (ISTM), School of Pharmacy & Bioengineering, Keele University, Staffordshire, UK
| | - M F Maasar
- Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
| | - R A Seaborne
- Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK.,Institute for Science and Technology in Medicine (ISTM), School of Pharmacy & Bioengineering, Keele University, Staffordshire, UK.,Centre for Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - P Baumert
- Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK.,Exercise Biology Group, Faculty of Sport and Health Sciences, Technical University of Munich, Munich, Germany
| | - A D Brown
- Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
| | - M O Kitchen
- Institute for Science and Technology in Medicine (ISTM), School of Pharmacy & Bioengineering, Keele University, Staffordshire, UK
| | - R M Erskine
- Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK.,Institute of Sport, Exercise and Health, University College London, London, UK
| | - I Dos-Remedios
- Orthopedics Department, University Hospitals of the North Midlands, Keele University, Staffordshire, UK
| | - S Voisin
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC, Australia
| | - N Eynon
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC, Australia
| | - R I Sultanov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - O V Borisov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia.,Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn, Germany
| | - A K Larin
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - E A Semenova
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - D V Popov
- Laboratory of Exercise Physiology, Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | - E V Generozov
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - C E Stewart
- Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
| | - B Drust
- School of Sport, Exercise and Rehabilitation Sciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - D J Owens
- Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK.,Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
| | - I I Ahmetov
- Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK. .,Laboratory of Molecular Genetics, Kazan State Medical University, Kazan, Russia. .,Department of Physical Education, Plekhanov Russian University of Economics, Moscow, Russia.
| | - A P Sharples
- Institute for Physical Performance, Norwegian School of Sport Sciences (NiH), Oslo, Norway. .,Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK. .,Institute for Science and Technology in Medicine (ISTM), School of Pharmacy & Bioengineering, Keele University, Staffordshire, UK.
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3
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Min B, Jeon K, Park JS, Kang Y. Demethylation and derepression of genomic retroelements in the skeletal muscles of aged mice. Aging Cell 2019; 18:e13042. [PMID: 31560164 PMCID: PMC6826136 DOI: 10.1111/acel.13042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/07/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Changes in DNA methylation influence the aging process and contribute to aging phenotypes, but few studies have been conducted on DNA methylation changes in conjunction with skeletal muscle aging. We explored the DNA methylation changes in a variety of retroelement families throughout aging (at 2, 20, and 28 months of age) in murine skeletal muscles by methyl‐binding domain sequencing (MBD‐seq). The two following contrasting patterns were observed among the members of each repeat family in superaged mice: (a) hypermethylation in weakly methylated retroelement copies and (b) hypomethylation in copies with relatively stronger methylation levels, representing a pattern of “regression toward the mean” within a single retroelement family. Interestingly, these patterns depended on the sizes of the copies. While the majority of the elements showed a slight increase in methylation, the larger copies (>5 kb) displayed evident demethylation. All these changes were not observed in T cells. RNA sequencing revealed a global derepression of retroelements during the late phase of aging (between 20 and 28 months of age), which temporally coincided with retroelement demethylation. Following this methylation drift trend of “regression toward the mean,” aging tended to progressively lose the preexisting methylation differences and local patterns in the genomic regions that had been elaborately established during the early period of development.
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Affiliation(s)
- Byungkuk Min
- Development and Differentiation Research Center Korea Research Institute of Bioscience Biotechnology (KRIBB) Daejeon Korea
| | - Kyuheum Jeon
- Development and Differentiation Research Center Korea Research Institute of Bioscience Biotechnology (KRIBB) Daejeon Korea
- Department of Functional Genomics University of Science and Technology (UST) Daejeon Korea
| | - Jung Sun Park
- Development and Differentiation Research Center Korea Research Institute of Bioscience Biotechnology (KRIBB) Daejeon Korea
| | - Yong‐Kook Kang
- Development and Differentiation Research Center Korea Research Institute of Bioscience Biotechnology (KRIBB) Daejeon Korea
- Department of Functional Genomics University of Science and Technology (UST) Daejeon Korea
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4
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Wu WJ, Liu KQ, Li BJ, Dong C, Zhang ZK, Li PH, Huang RH, Wei W, Chen J, Liu HL. Identification of an (AC)n microsatellite in the Six1 gene promoter and its effect on production traits in Pietrain × Duroc × Landrace × Yorkshire pigs. J Anim Sci 2018; 96:17-26. [PMID: 29432614 DOI: 10.1093/jas/skx024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 02/05/2018] [Indexed: 12/22/2022] Open
Abstract
The Sine oculis homeobox 1 (Six1) gene is important for skeletal muscle growth and fiber specification; therefore, it is considered as a promising candidate gene that may influence porcine growth and meat quality traits. Nevertheless, the association of Six1 with these processes and the mechanisms regulating its expression remain unclear. The objectives of this study were to identify variant sites of Six1 in different pig breeds, conduct association analysis to evaluate the relationship between polymorphisms of these variants and porcine production traits in Pietrain × Duroc × Landrace × Yorkshire commercial pigs, and explore the potential regulatory mechanisms of Six1 affecting production traits. A total of 12 variants were identified, including 10 single- nucleotide variations (SNVs), 1 insertion- deletion (Indel), and 1 (AC)n microsatellite. Association analysis demonstrated that the SNV, g.1595A>G, was significantly associated with meat color (redness, a*); individuals with the G allele had greater a* values (P < 0.05). Moreover, our results demonstrated that the (AC)n polymorphism in the Six1 promoter was significantly associated with weaning weight (P < 0.05), carcass weight (P < 0.05), and thoracic and lumbar back fat (P < 0.01).In addition, we found that the (AC)n variant was closely related with Six1 expression levels and demonstrated this polymorphism on promoter activity by in vitro experiments. Overall, this study provides novel evidence for elucidating the effects of Six1 on porcine production traits as promising candidate and describes two variants with these traits, which are potential reference markers for pig molecular breeding. In addition, our data on the relationship between porcine Six1 expression and the polymorphic (AC)n microsatellite in its promoter may facilitate similar studies in other species.
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Affiliation(s)
- W J Wu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - K Q Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - B J Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - C Dong
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Z K Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - P H Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - R H Huang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - W Wei
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - J Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - H L Liu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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5
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Wei D, Raza SHA, Zhang J, Gui L, Rahman SU, Khan R, Hosseini SM, Kaleri HA, Zan L. Polymorphism in promoter of SIX4 gene shows association with its transcription and body measurement traits in Qinchuan cattle. Gene 2018; 656:9-16. [DOI: 10.1016/j.gene.2018.02.059] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 02/14/2018] [Accepted: 02/23/2018] [Indexed: 12/30/2022]
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6
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Wei DW, Ma XY, Zhang S, Hong JY, Gui LS, Mei CG, Guo HF, Wang L, Ning Y, Zan LS. Characterization of the promoter region of the bovine SIX1 gene: Roles of MyoD, PAX7, CREB and MyoG. Sci Rep 2017; 7:12599. [PMID: 28974698 PMCID: PMC5626756 DOI: 10.1038/s41598-017-12787-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/15/2017] [Indexed: 12/20/2022] Open
Abstract
The SIX1 gene belongs to the family of six homeodomain transcription factors (TFs), that regulates the extracellular signal-regulated kinase 1/2 (ERK1/2) pathway and mediate skeletal muscle growth and regeneration. Previous studies have demonstrated that SIX1 is positively correlated with body measurement traits (BMTs). However, the transcriptional regulation of SIX1 remains unclear. In the present study, we determined that bovine SIX1 was highly expressed in the longissimus thoracis. To elucidate the molecular mechanisms involved in bovine SIX1 regulation, 2-kb of the 5' regulatory region were obtained. Sequence analysis identified neither a consensus TATA box nor a CCAAT box in the 5' flanking region of bovine SIX1. However, a CpG island was predicted in the region -235 to +658 relative to the transcriptional start site (TSS). An electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) assay in combination with serial deletion constructs of the 5' flanking region, site-directed mutation and siRNA interference demonstrated that MyoD, PAX7 and CREB binding occur in region -689/-40 and play important roles in bovine SIX1 transcription. In addition, MyoG drives SIX1 transcription indirectly via the MEF3 motif. Taken together these interactions suggest a key functional role for SIX1 in mediating skeletal muscle growth in cattle.
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Affiliation(s)
- Da-Wei Wei
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xue-Yao Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Song- Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jie-Yun Hong
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Lin-Sheng Gui
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.,Modern Cattle Biotechnology and Application of National-Local Engineering Research Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Chu-Gang Mei
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.,Modern Cattle Biotechnology and Application of National-Local Engineering Research Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Hong-Fang Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Li- Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yue- Ning
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Lin-Sen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China. .,National Beef Cattle Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China. .,Shaanxi Beef Cattle Engineering Research Center, Yangling, 712100, Shaanxi, People's Republic of China.
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7
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Wei DW, Gui LS, Raza SHA, Zhang S, Khan R, Wang L, Guo HF, Zan LS. NRF1 and ZSCAN10 bind to the promoter region of the SIX1 gene and their effects body measurements in Qinchuan cattle. Sci Rep 2017; 7:7867. [PMID: 28801681 PMCID: PMC5554236 DOI: 10.1038/s41598-017-08384-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 07/10/2017] [Indexed: 12/19/2022] Open
Abstract
The SIX1 homeobox gene belongs to the six homeodomain family and is widely thought to play a principal role in mediating of skeletal muscle development. In the present study, we determined that the bovine SIX1 gene was highly expressed in the longissimus thoracis and physiologically immature individuals. DNA sequencing of 428 individual Qinchuan cattle identified nine single nucleotide polymorphisms (SNPs) in the promoter region of the SIX1 gene. Using a series of 5′ deletion promoter plasmid luciferase reporter assays and 5′-rapid amplification of cDNA end analysis (RACE), two of these SNPs were found to be located in the proximal minimal promoter region −216/−28 relative to the transcriptional start site (TSS). Correlation analysis showed the combined haplotypes H1-H2 (-GG-GA-) was significantly greater in the body measurement traits (BMTs) than the others, which was consistent with the results showing that the transcriptional activity of Hap2 was higher than the others in Qinchuan cattle myoblast cells. Furthermore, the electrophoretic mobility shift assays (EMSA) and chromatin immunoprecipitation assay (ChIP) demonstrated that NRF1 and ZSCAN10 binding occurred in the promoter region of diplotypes H1-H2 to regulate SIX1 transcriptional activity. This information may be useful for molecular marker-assisted selection (MAS) in cattle breeding.
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Affiliation(s)
- Da-Wei Wei
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.,Shaanxi Beef Cattle Engineering Research Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Lin-Sheng Gui
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.,Shaanxi Beef Cattle Engineering Research Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Song Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.,Shaanxi Beef Cattle Engineering Research Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Li Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.,Shaanxi Beef Cattle Engineering Research Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Hong-Fang Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.,Shaanxi Beef Cattle Engineering Research Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Lin-Sen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China. .,National Beef Cattle Improvement Center, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China. .,Modern Cattle Biotechnology and Application of National-Local Engineering Research Center, Yangling, 712100, Shaanxi, People's Republic of China.
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Cai B, Li Z, Ma M, Wang Z, Han P, Abdalla BA, Nie Q, Zhang X. LncRNA-Six1 Encodes a Micropeptide to Activate Six1 in Cis and Is Involved in Cell Proliferation and Muscle Growth. Front Physiol 2017; 8:230. [PMID: 28473774 PMCID: PMC5397475 DOI: 10.3389/fphys.2017.00230] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/31/2017] [Indexed: 12/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play important roles in epigenetic regulation of skeletal muscle development. In our previous RNA-seq study (accession number GSE58755), we found that lncRNA-Six1 is an lncRNA that is differentially expressed between White Recessive Rock (WRR) and Xinghua (XH) chicken. In this study, we have further demonstrated that lncRNA-Six1 is located 432 bp upstream of the gene encoding the protein Six homeobox 1 (Six1). A dual-luciferase reporter assay identified that lncRNA-Six1 overlaps the Six1 proximal promoter. In lncRNA-Six1, a micropeptide of about 7.26 kDa was found to play an important role in the lncRNA-Six1 in cis activity. Overexpression of lncRNA-Six1 promoted the mRNA and protein expression level of the Six1 gene, while knockdown of lncRNA-Six1 inhibited Six1 expression. Moreover, tissue expression profiles showed that both the lncRNA-Six1 and the Six1 mRNA were highly expressed in chicken breast tissue. LncRNA-Six1 overexpression promoted cell proliferation and induced cell division. Conversely, its loss of function inhibited cell proliferation and reduced cell viability. Similar effects were observed after overexpression or knockdown of the Six1 gene. In addition, overexpression or knockdown of Six1 promoted or inhibited, respectively, the expression levels of muscle-growth-related genes, such as MYOG, MYHC, MYOD, IGF1R, and INSR. Taken together, these data demonstrate that lncRNA-Six1 carries out cis-acting regulation of the protein-encoding Six1 gene, and encodes a micropeptide to activate Six1 gene, thus promoting cell proliferation and being involved in muscle growth.
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Affiliation(s)
- Bolin Cai
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.,National-Local Joint Engineering Research Center for Livestock BreedingGuangzhou, China
| | - Zhenhui Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.,National-Local Joint Engineering Research Center for Livestock BreedingGuangzhou, China
| | - Manting Ma
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.,National-Local Joint Engineering Research Center for Livestock BreedingGuangzhou, China
| | - Zhijun Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.,National-Local Joint Engineering Research Center for Livestock BreedingGuangzhou, China
| | - Peigong Han
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.,National-Local Joint Engineering Research Center for Livestock BreedingGuangzhou, China
| | - Bahareldin A Abdalla
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.,National-Local Joint Engineering Research Center for Livestock BreedingGuangzhou, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.,National-Local Joint Engineering Research Center for Livestock BreedingGuangzhou, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural UniversityGuangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhou, China.,National-Local Joint Engineering Research Center for Livestock BreedingGuangzhou, China
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9
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Carrió E, Suelves M. DNA methylation dynamics in muscle development and disease. Front Aging Neurosci 2015; 7:19. [PMID: 25798107 PMCID: PMC4350440 DOI: 10.3389/fnagi.2015.00019] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/15/2015] [Indexed: 12/12/2022] Open
Abstract
DNA methylation is an essential epigenetic modification for mammalian development and is crucial for the establishment and maintenance of cellular identity. Traditionally, DNA methylation has been considered as a permanent repressive epigenetic mark. However, the application of genome-wide approaches has allowed the analysis of DNA methylation in different genomic contexts revealing a more dynamic regulation than originally thought, since active DNA methylation and demethylation occur during cellular differentiation and tissue specification. Satellite cells are the primary stem cells in adult skeletal muscle and are responsible for postnatal muscle growth, hypertrophy, and muscle regeneration. This review outlines the published data regarding DNA methylation changes along the skeletal muscle program, in both physiological and pathological conditions, to better understand the epigenetic mechanisms that control myogenesis.
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Affiliation(s)
- Elvira Carrió
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) and Health Sciences Research Institute Germans Trias I Pujol (IGTP) Badalona, Spain
| | - Mònica Suelves
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) and Health Sciences Research Institute Germans Trias I Pujol (IGTP) Badalona, Spain
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Wu W, Huang R, Wu Q, Li P, Chen J, Li B, Liu H. The role of Six1 in the genesis of muscle cell and skeletal muscle development. Int J Biol Sci 2014; 10:983-9. [PMID: 25210496 PMCID: PMC4159689 DOI: 10.7150/ijbs.9442] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 06/06/2014] [Indexed: 02/06/2023] Open
Abstract
The sine oculis homeobox 1 (Six1) gene encodes an evolutionarily conserved transcription factor. In the past two decades, much research has indicated that Six1 is a powerful regulator participating in skeletal muscle development. In this review, we summarized the discovery and structural characteristics of Six1 gene, and discussed the functional roles and molecular mechanisms of Six1 in myogenesis and in the formation of skeletal muscle fibers. Finally, we proposed areas of future interest for understanding Six1 gene function.
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Affiliation(s)
- Wangjun Wu
- 1. Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China; ; 2. Huaian Academy of Nanjing Agricultural University, Huaian, Jiangsu, 223001, China
| | - Ruihua Huang
- 1. Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China; ; 2. Huaian Academy of Nanjing Agricultural University, Huaian, Jiangsu, 223001, China
| | - Qinghua Wu
- 3. College of Life Science, Yangtze University, Jingzhou, Hubei, 434023, China. ; 4. Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kradec Kralove, Hradec Kralove, Czech Republic
| | - Pinghua Li
- 1. Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China; ; 2. Huaian Academy of Nanjing Agricultural University, Huaian, Jiangsu, 223001, China
| | - Jie Chen
- 1. Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bojiang Li
- 1. Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Honglin Liu
- 1. Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
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Wu W, Ren Z, Li P, Yu D, Chen J, Huang R, Liu H. Six1: A critical transcription factor in tumorigenesis. Int J Cancer 2014; 136:1245-53. [DOI: 10.1002/ijc.28755] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/15/2014] [Accepted: 01/20/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Wangjun Wu
- Department of Animal Genetics; Breeding and Reproduction; College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
- Huaian Academy of Nanjing Agricultural University; Huaian Jiangsu China
| | - Zhuqing Ren
- Key Laboratory of Swine Genetics and Breeding; Ministry of Agriculture; Key Lab of Agriculture Animal Genetics; Breeding and Reproduction; Ministry of Education; College of Animal Science; Huazhong Agricultural University; Wuhan Hubei China
| | - Pinghua Li
- Department of Animal Genetics; Breeding and Reproduction; College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - Debing Yu
- Department of Animal Genetics; Breeding and Reproduction; College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - Jie Chen
- Department of Animal Genetics; Breeding and Reproduction; College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - Ruihua Huang
- Department of Animal Genetics; Breeding and Reproduction; College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - Honglin Liu
- Department of Animal Genetics; Breeding and Reproduction; College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
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Core promoter analysis of porcine Six1 gene and its regulation of the promoter activity by CpG methylation. Gene 2013; 529:238-44. [DOI: 10.1016/j.gene.2013.07.102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 07/23/2013] [Accepted: 07/27/2013] [Indexed: 11/22/2022]
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13
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Wu W, Ren Z, Zhang L, Liu Y, Li H, Xiong Y. Overexpression of Six1 gene suppresses proliferation and enhances expression of fast-type muscle genes in C2C12 myoblasts. Mol Cell Biochem 2013; 380:23-32. [PMID: 23613228 DOI: 10.1007/s11010-013-1653-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 04/12/2013] [Indexed: 12/15/2022]
Abstract
Sine oculis homeobox 1 (Six1) homeodomain transcription factor is implicated in the genesis of muscle fiber type diversity, but its regulatory mechanisms on the formation of muscle fiber type are still poorly understood. To elucidate the biological roles of Six1 gene in muscle fiber formation, we established C2C12 cell line overexpressing Six1 and determined the effects of forced Six1 expression on muscle-specific genes expression, cell proliferation, and cell cycles. Our results indicated that Six1 overexpression could significantly promote the expression of fast-type muscle genes Atp2a1, Srl, and Mylpf. Furthermore, Six1 overexpressing C2C12 cells displayed a relative lower proliferative potential, and cell cycle analysis showed that Six1 exerted its role in cell cycle primarily through the regulation of G1/S and G2/M phases. In conclusion, Six1 plays an essential role in modulation of the fast-twitch muscle fiber phenotype through up-regulating fast-type muscle genes expression, and it could suppress the proliferation of muscle cells.
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Affiliation(s)
- Wangjun Wu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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Subcellular localization of different regions of porcine Six1 gene and its expression analysis in C2C12 myoblasts. Mol Biol Rep 2012; 39:9995-10002. [DOI: 10.1007/s11033-012-1868-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 06/19/2012] [Indexed: 11/25/2022]
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15
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Selection of reference genes for quantitative real-time RT-PCR analysis in citrus. Mol Biol Rep 2011; 39:1831-8. [PMID: 21633888 DOI: 10.1007/s11033-011-0925-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 05/24/2011] [Indexed: 10/18/2022]
Abstract
Quantitative real-time reverse transcription polymerase chain reaction (qPCR) has become the preferred method for studying low-abundant mRNA expression. Appropriate application of qPCR in such studies requires the use of reference gene(s) as an internal control in order to normalize the mRNA levels between different samples for an exact comparison of gene expression levels. Expression of the reference gene should be independent from development stage, cell/tissue types, treatments and environmental conditions. Recognizing the importance of reference gene(s) in normalization of qPCR data, various reference genes have been evaluated for stable expression under specific conditions in various organisms. In plants, only a few of them have been investigated, and very few reports about such reference genes in citrus. In the present study, seven candidate reference genes (18SrRNA, ACTB, rpII, UBQI, UBQ10, GAPDH and TUB) were tested, and three of them (18SrRNA, ACTB and rpII) proved to be the most stable ones among six leaf samples of different citrus genotypes. The three candidate reference genes were further analyzed for their stability of expression in five different tissues, and the results indicated that they were not completely stable. It is commonly accepted that gene expression studies should be normalized using more than one reference gene. Based on our results, we propose the use of the mean result rendered by18SrRNA, ACTB and rpII as reference genes to normalize mRNA levels in qPCR analysis of diverse cultivars and tissues of citrus. These results may provide a guideline for future works on gene expression in citrus by using qPCR.
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