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Wang J, Hua G, Chen J, Cui K, Yang Z, Han D, Yang X, Dong X, Ma Y, Cai G, Zhang Y, Li J, Tai Y, Da L, Li X, Ma L, Ma Q, Li R, Liu J, Darwish HYA, Wu K, Rong W, Liu W, Zhao Y, Deng X. Epigenetic mechanism of Gtl2-miRNAs causes the primitive sheep characteristics found in purebred Merino sheep. Cell Biosci 2023; 13:190. [PMID: 37828606 PMCID: PMC10571318 DOI: 10.1186/s13578-023-01142-z] [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: 05/21/2023] [Accepted: 10/05/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND It is not uncommon for some individuals to retain certain primitive characteristics even after domestication or long-term intensive selection. Wild ancestors or original varieties of animals typically possess strong adaptability to environmental preservation, a trait that is often lacking in highly artificially selected populations. In the case of the Merino population, a world-renowned fine wool sheep breed, a phenotype with primitive coarse wool characteristic has re-emerged. It is currently unclear whether this characteristic is detrimental to the production of fine wool or whether it is linked to the adaptability of sheep. The underlying genetic/epigenetic mechanisms behind this trait are also poorly understood. RESULTS This study identified lambs with an ancestral-like coarse (ALC) wool type that emerged during the purebred breeding of Merino fine wool sheep. The presence of this primitive sheep characteristic resulted in better environmental adaptability in lambs, as well as improved fine wool yield in adulthood. Reciprocal cross experiments revealed that the ALC phenotype exhibited maternal genetic characteristics. Transcriptomic SNP analysis indicated that the ALC phenotype was localized to the imprinted Gtl2-miRNAs locus, and a significant correlation was found between the ALC wool type and a newly identified short Interstitial Telomeric Sequences (s-ITSs) at this locus. We further confirmed that a novel 38-nt small RNA transcribed from these s-ITSs, in combination with the previously reported 22-nt small RNAs cluster from the Gtl2-miRNAs locus, synergistically inhibited PI3K/AKT/Metabolic/Oxidative stress and subsequent apoptotic pathways in wool follicle stem cells, resulting in the ALC wool type. The necessity of Gtl2-miRNAs in controlling primary hair follicle morphogenesis, as well as the wool follicle type for ALC wool lambs, was verified using intergenic differentially methylated region-knockout mice. CONCLUSION The ALC wool type of Merino sheep, which does not reduce wool quality but increases yield and adaptability, is regulated by epigenetic mechanisms in the imprinted Gtl2-miRNAs region on sheep chromosome 18, with the maternally expressed imprinted gene responsible for the ALC phenotype. This study highlights the significance of epigenetic regulation during embryonic and juvenile stages and emphasizes the advantages of early adaptation breeding for maternal parents in enhancing the overall performance of their offspring.
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Affiliation(s)
- Jiankui Wang
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Guoying Hua
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Jianfei Chen
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Kai Cui
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100086, China
| | - Zu Yang
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Deping Han
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Xue Yang
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Xianggui Dong
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Yuhao Ma
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Ganxian Cai
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Yuanyuan Zhang
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Jinnan Li
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Yurong Tai
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Lai Da
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Huhhot, 010031, China
| | - Xinhai Li
- College of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Lina Ma
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Qing Ma
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Rui Li
- Jinfeng Animal Husbandry Group Co., Ltd., Chifeng, 024000, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Hesham Y A Darwish
- Department of Applied Biotechnology, Molecular Biology Researches & Studies Institute, Assiut University, Assiut, 71526, Egypt
| | - Keliang Wu
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Weiheng Rong
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Huhhot, 010031, China
| | - Wansheng Liu
- Department of Animal Science, Center for Reproductive Biology and Health, College of Agricultural Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yaofeng Zhao
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Xuemei Deng
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
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Shiura H, Kitazawa M, Ishino F, Kaneko-Ishino T. Roles of retrovirus-derived PEG10 and PEG11/RTL1 in mammalian development and evolution and their involvement in human disease. Front Cell Dev Biol 2023; 11:1273638. [PMID: 37842090 PMCID: PMC10570562 DOI: 10.3389/fcell.2023.1273638] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
PEG10 and PEG11/RTL1 are paternally expressed, imprinted genes that play essential roles in the current eutherian developmental system and are therefore associated with developmental abnormalities caused by aberrant genomic imprinting. They are also presumed to be retrovirus-derived genes with homology to the sushi-ichi retrotransposon GAG and POL, further expanding our comprehension of mammalian evolution via the domestication (exaptation) of retrovirus-derived acquired genes. In this manuscript, we review the importance of PEG10 and PEG11/RTL1 in genomic imprinting research via their functional roles in development and human disease, including neurodevelopmental disorders of genomic imprinting, Angelman, Kagami-Ogata and Temple syndromes, and the impact of newly inserted DNA on the emergence of newly imprinted regions. We also discuss their possible roles as ancestors of other retrovirus-derived RTL/SIRH genes that likewise play important roles in the current mammalian developmental system, such as in the placenta, brain and innate immune system.
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Affiliation(s)
- Hirosuke Shiura
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi, Japan
| | - Moe Kitazawa
- School of BioSciences, Faculty of Science, The University of Melbourne, Melbourne, VIC, Australia
| | - Fumitoshi Ishino
- Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Tomoko Kaneko-Ishino
- Faculty of Nursing, School of Medicine, Tokai University, Isehara, Kanagawa, Japan
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3
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Reichhardt CC, Cuthbert JM, Motsinger LA, Brady TJ, Briggs RK, Thomas AJ, Thornton KJ. Anabolic implants alter abundance of mRNA involved in muscle growth, metabolism, and inflammation in the longissimus of Angus steers in the feedlot. Domest Anim Endocrinol 2023; 82:106773. [PMID: 36375404 DOI: 10.1016/j.domaniend.2022.106773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/22/2022] [Accepted: 10/19/2022] [Indexed: 11/25/2022]
Abstract
The majority of beef cattle in the United States often receive at least one anabolic implant resulting in improved growth, feed efficiency, and environmental and economic sustainability. However, the physiological and molecular mechanisms through which anabolic implants increase skeletal muscle growth of beef cattle remain elusive. The objective of this study was to identify transcriptional changes occurring in skeletal muscle of steers receiving anabolic implants containing different steroid hormones. Forty-eight steers were stratified by weight into 1 of 4 (n = 12/treatment) implant treatment groups: (1) estradiol (ImpE2; 25.7 mg E2; Compudose, Elanco Animal Health, Greenfield, IN), (2) trenbolone acetate (ImpTBA; 200 mg TBA; Finaplix-H, Merck Animal Health, Madison, NJ), (3) combination (ImpETBA; 120 mg TBA + 24 mg E2; Revalor-S, Merck Animal Health), or (4) no implant (CON). Skeletal muscle biopsies were taken from the longissimus 2 and 10 d post-implantation. The mRNA abundance of 94 genes associated with skeletal muscle growth was examined. At 10 d post-implantation, steers receiving ImpETBA had greater (P = 0.02) myoblast differentiation factor 1 transcript abundance than CON. Citrate synthase abundance was increased (P = 0.04) in ImpETBA steers compared to CON steers. In ImpE2 steers 10 d post-implantation, muscle RING finger protein 1 decreased (P = 0.05) compared to CON steers, and forkhead box protein O4 decreased (P = 0.05) in ImpETBA steers compared to CON steers. Interleukin-6 abundance tended to be increased (P = 0.09) in ImpE2 steers compared to both ImpETBA and CON steers. Furthermore, interleukin-10 mRNA abundance tended to be increased (P = 0.06) in ImpTBA steers compared to ImpETBA steers. Leptin receptor abundance was reduced (P = 0.01) in both ImpE2 and ImpTBA steers when compared to CON steers. Abundance of phosphodiesterase 4B was increased (P = 0.04) in ImpTBA steers compared to CON steers 2 d post-implantation. Taken together, the results of this research demonstrate that estradiol increases skeletal muscle growth via pathways related to nutrient partitioning and mitochondria function, while trenbolone acetate improves steer skeletal muscle growth via pathways related to muscle growth.
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Affiliation(s)
- C C Reichhardt
- Department of Animal, Dairy and Veterinary Science, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA; Department of Human Nutrition, Food and Animal Sciences, University of Hawai`i at Mānoa, 1955 East-West Rd., Honolulu, HI, 96822, USA
| | - J M Cuthbert
- Department of Animal, Dairy and Veterinary Science, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA; Department of Biology, Westminster College, 1840 South 1300 East, Salt Lake City, UT, 84105, USA
| | - L A Motsinger
- Department of Animal, Dairy and Veterinary Science, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA; Department of Animal and Dairy Sciences, University of Georgia, 425 River Rd., Athens, GA, 30602, USA
| | - T J Brady
- Department of Animal, Dairy and Veterinary Science, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA
| | - R K Briggs
- Department of Animal, Dairy and Veterinary Science, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA
| | - A J Thomas
- Department of Animal, Dairy and Veterinary Science, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA
| | - K J Thornton
- Department of Animal, Dairy and Veterinary Science, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA.
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Ison EK, Hopf-Jannasch AS, Harding JCS, Alex Pasternak J. Effects of porcine reproductive and respiratory syndrome virus (PRRSV) on thyroid hormone metabolism in the late gestation fetus. Vet Res 2022; 53:74. [PMID: 36175938 PMCID: PMC9524047 DOI: 10.1186/s13567-022-01092-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/16/2022] [Indexed: 11/10/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) in late gestation causes a profound suppression of circulating maternal and fetal thyroid hormone during a critical window of development. To understand this relationship, we evaluated thyroid hormone metabolism at the maternal-fetal interface and within fetal tissues, along with hormone metabolite levels in serum. Fetuses were classified using an established model based on viral load in serum and thymus, and preservation status, including uninfected (UNIF), high-viral load viable (HV-VIA), and high-viral load meconium-stained (HV-MEC), with additional controls from sham-inoculated gilts (CON). Expression of three iodothyronine deiodinases, five sulfotransferases, sulfatase, and two solute carriers known to transport thyroid hormone were evaluated in maternal endometrium and fetal placenta, liver, and kidney. Serum thyroxin (T4), reverse triiodothyronine (rT3), and diiodothyronine (T2) were evaluated via liquid chromatography tandem mass spectrometry. Significant changes in gene expression were observed in all four tissues, with the liver being the most severely impacted. We observed local and fetal specific regulation of maternal tissues through significant upregulation of DIO2 and DIO3 expression in the endometrium corresponding to infected but viable fetuses relative to uninfected and control fetuses. Expression levels of DIO2 and DIO3 were significantly higher in the resilient (HV-VIA) fetuses relative to the susceptible (HV-MEC) fetuses. A substantial decrease in serum T4 was confirmed, with no corresponding increase in rT3 or T2. Collectively, these results show that thyroid hormone metabolism is altered at the maternal-fetal interface and within the PRRSV infected fetus and is associated with fetal viability.
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Affiliation(s)
- Erin K Ison
- Department of Animal Science, Purdue University, West Lafayette, IN, 47906, USA
| | | | - John C S Harding
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Dr., Saskatoon, SK, S7N 5B4, Canada
| | - J Alex Pasternak
- Department of Animal Science, Purdue University, West Lafayette, IN, 47906, USA.
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5
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Mészárosová M, Mészáros G, Moravčíková N, Pavlík I, Margetín M, Kasarda R. Within- and between-Breed Selection Signatures in the Original and Improved Valachian Sheep. Animals (Basel) 2022; 12:ani12111346. [PMID: 35681809 PMCID: PMC9179888 DOI: 10.3390/ani12111346] [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: 03/28/2022] [Revised: 05/13/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022] Open
Abstract
This study explored the genomic diversity and selection signatures in two Slovakian national breeds, the Original Valachian and the Improved Valachian sheep. As they are an important animal genetic resource within the country, but with decreasing population size, our aim is to identify potentially valuable genomic regions. A total of 97 sheep (18 male and 79 female) from the Original Valachian, and 69 sheep (25 male and 44 female) from the Improved Valachian populations were genotyped using the GeneSeek GGP Ovine 50 K chip. The inbreeding levels were assessed with runs of homozygosity (ROH). The selection signatures within breeds were identified based on the top 1% of most homozygous regions within the breed, the so-called ROH islands. The selection signatures between breeds were assessed based on variance in linkage disequilibrium. Overall, we have identified selection signatures with quantitative trait loci (QTL) and genes pointing towards all three production purposes of the Valachian sheep, milk, meat, and wool, including their quality characteristics. Another group with apparent large importance was the various traits related to health and resistance to parasites, which is well in line with the sturdy nature of this breed.
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Affiliation(s)
- Mária Mészárosová
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
| | - Gábor Mészáros
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, 1180 Vienna, Austria;
| | - Nina Moravčíková
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
- Correspondence:
| | - Ivan Pavlík
- Research Institute of Animal Production—NPPC Slovakia, Hlohovecká 2, 95141 Nitra—Lužianky, Slovakia;
| | - Milan Margetín
- Faculty of Agrobiology and Food Resources, Institute of Animal Science, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia;
| | - Radovan Kasarda
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
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6
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Role of MicroRNAs and Long Non-Coding RNAs in Sarcopenia. Cells 2022; 11:cells11020187. [PMID: 35053303 PMCID: PMC8773898 DOI: 10.3390/cells11020187] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/23/2021] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
Sarcopenia is an age-related pathological process characterized by loss of muscle mass and function, which consequently affects the quality of life of the elderly. There is growing evidence that non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), play a key role in skeletal muscle physiology. Alterations in the expression levels of miRNAs and lncRNAs contribute to muscle atrophy and sarcopenia by regulating various signaling pathways. This review summarizes the recent findings regarding non-coding RNAs associated with sarcopenia and provides an overview of sarcopenia pathogenesis promoted by multiple non-coding RNA-mediated signaling pathways. In addition, we discuss the impact of exercise on the expression patterns of non-coding RNAs involved in sarcopenia. Identifying non-coding RNAs associated with sarcopenia and understanding the molecular mechanisms that regulate skeletal muscle dysfunction during aging will provide new insights to develop potential treatment strategies.
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Vu Hong A, Sanson M, Richard I, Israeli D. A revised model for mitochondrial dysfunction in Duchenne muscular dystrophy. Eur J Transl Myol 2021; 31. [PMID: 34533019 PMCID: PMC8495359 DOI: 10.4081/ejtm.2021.10012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/12/2021] [Indexed: 12/27/2022] Open
Abstract
We recently identified a signaling pathway that links the upregulation of miR-379 with a mitochondrial response in dystrophic muscle. In the present commentary, we explain the significance that this pathway may have in mitochondrial dysfunction in Duchenne muscular dystrophy (DMD). We identified the upregulation of miR-379 in the serum and muscles of DMD animal models and patients. We found that miR-379 is one of very few miRNAs whose expression was normalized in DMD patients treated with glucocorticoid. We identified EIF4G2 as a miR-379 target, which may promote mitochondrial oxidative phosphorylation (OxPhos) in the skeletal muscle. We found enriched EIF4G2 expression in oxidative fibers, and identified the mitochondrial ATP synthase subunit DAPIT as a translational target of EIF4G2. The identified signaling cascade, which comprises miR-379, EIF4G2 and DAPIT, may link the glucocorticoid treatment in DMD to a recovered mitochondrial ATP synthesis rate. We propose an updated model of mitochondrial dysfunction in DMD.
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Affiliation(s)
- Ai Vu Hong
- Genethon, Evry, France; Université Paris-Saclay, Univ Evry, Inserm, Généthon, Integrare research unit UMR-S951, Evry.
| | - Mathilde Sanson
- Genethon, Evry, France; Université Paris-Saclay, Univ Evry, Inserm, Généthon, Integrare research unit UMR-S951, Evry.
| | - Isabelle Richard
- Genethon, Evry, France; Université Paris-Saclay, Univ Evry, Inserm, Généthon, Integrare research unit UMR-S951, Evry.
| | - David Israeli
- Genethon, Evry, France; Université Paris-Saclay, Univ Evry, Inserm, Généthon, Integrare research unit UMR-S951, Evry.
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Cortellari M, Barbato M, Talenti A, Bionda A, Carta A, Ciampolini R, Ciani E, Crisà A, Frattini S, Lasagna E, Marletta D, Mastrangelo S, Negro A, Randi E, Sarti FM, Sartore S, Soglia D, Liotta L, Stella A, Ajmone-Marsan P, Pilla F, Colli L, Crepaldi P. The climatic and genetic heritage of Italian goat breeds with genomic SNP data. Sci Rep 2021; 11:10986. [PMID: 34040003 PMCID: PMC8154919 DOI: 10.1038/s41598-021-89900-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/29/2021] [Indexed: 02/04/2023] Open
Abstract
Local adaptation of animals to the environment can abruptly become a burden when faced with rapid climatic changes such as those foreseen for the Italian peninsula over the next 70 years. Our study investigates the genetic structure of the Italian goat populations and links it with the environment and how genetics might evolve over the next 50 years. We used one of the largest national datasets including > 1000 goats from 33 populations across the Italian peninsula collected by the Italian Goat Consortium and genotyped with over 50 k markers. Our results showed that Italian goats can be discriminated in three groups reflective of the Italian geography and its geo-political situation preceding the country unification around two centuries ago. We leveraged the remarkable genetic and geographical diversity of the Italian goat populations and performed landscape genomics analysis to disentangle the relationship between genotype and environment, finding 64 SNPs intercepting genomic regions linked to growth, circadian rhythm, fertility, and inflammatory response. Lastly, we calculated the hypothetical future genotypic frequencies of the most relevant SNPs identified through landscape genomics to evaluate their long-term effect on the genetic structure of the Italian goat populations. Our results provide an insight into the past and the future of the Italian local goat populations, helping the institutions in defining new conservation strategy plans that could preserve their diversity and their link to local realities challenged by climate change.
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Affiliation(s)
- Matteo Cortellari
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy
| | - Mario Barbato
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti and BioDNA Centro di ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Andrea Talenti
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy.
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
| | - Arianna Bionda
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy
| | - Antonello Carta
- Unità di Ricerca di Genetica e Biotecnologie, Agris Sardegna, 07100, Sassari, Italy
| | - Roberta Ciampolini
- Dipartimento di Scienze Veterinarie, Università di Pisa, Viale delle Piagge 2, 56124, Pisa, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, Università degli Studi di Bari, Via Orabona 4, 70126, Bari, Italy
| | - Alessandra Crisà
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Research Centre for Animal Production and Acquaculture, 00015, Monterotondo, Rome, Italy
| | - Stefano Frattini
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Donata Marletta
- Department of Agriculture, Food and Environment, University of Catania, Via Valdisavoia 5, 95123, Catania, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy
| | - Alessio Negro
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy
| | - Ettore Randi
- Department of Chemistry and Bioscience, Faculty of Engineering and Science, University of Aalborg, Aalborg, Denmark
| | - Francesca M Sarti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Stefano Sartore
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, largo Braccini 2, 10095, Grugliasco, Italy
| | - Dominga Soglia
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, largo Braccini 2, 10095, Grugliasco, Italy
| | - Luigi Liotta
- Dipartimento di Scienze Veterinarie, University of Messina, Messina, Italy
| | - Alessandra Stella
- Institute of Biology and Biotechnology in Agriculture, National Research Council (CNR), Milan, Italy
| | - Paolo Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti and BioDNA Centro di ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Fabio Pilla
- Dipartimento Agricoltura, Ambiente e Alimenti Universitá degli Studi del Molise, 86100, Campobasso, Italy
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti and BioDNA Centro di ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Paola Crepaldi
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy
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9
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Masoudzadeh SH, Mohammadabadi M, Khezri A, Stavetska RV, Oleshko VP, Babenko OI, Yemets Z, Kalashnik OM. Effects of diets with different levels of fennel (Foeniculum vulgare) seed powder on DLK1 gene expression in brain, adipose tissue, femur muscle and rumen of Kermani lambs. Small Rumin Res 2020. [DOI: 10.1016/j.smallrumres.2020.106276] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Kitazawa M, Hayashi S, Imamura M, Takeda S, Oishi Y, Kaneko-Ishino T, Ishino F. Deficiency and overexpression of Rtl1 in the mouse cause distinct muscle abnormalities related to Temple and Kagami-Ogata syndromes. Development 2020; 147:147/21/dev185918. [PMID: 32878913 PMCID: PMC7490516 DOI: 10.1242/dev.185918] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 07/20/2020] [Indexed: 12/19/2022]
Abstract
Temple and Kagami-Ogata syndromes are genomic imprinting diseases caused by maternal and paternal duplication of human chromosome 14, respectively. They exhibit different postnatal muscle-related symptoms as well as prenatal placental problems. Using the mouse models for these syndromes, it has been demonstrated that retrotransposon gag like 1 [Rtl1, also known as paternally expressed 11 (Peg11)] located in the mouse orthologous imprinted region is responsible for the prenatal placental problems because it is an essential placental gene for maintenance of fetal capillary network during gestation. However, the causative imprinted gene for the postnatal muscle-related symptoms remains unknown. Here, we demonstrate that Rtl1 also plays an important role in fetal/neonatal skeletal muscle development: its deletion and overproduction in mice lead to neonatal lethality associated with severe but distinct skeletal muscle defects, similar to those of Temple and Kagami-Ogata syndromes, respectively. Thus, it is strongly suggested that RTL1 is the major gene responsible for the muscle defects in addition to the placental defects in these two genomic imprinting diseases. This is the first example of an LTR retrotransposon-derived gene specific to eutherians contributing to eutherian skeletal muscle development. Summary: Rtl1 plays an important role in fetal and neonatal skeletal muscle development. Abnormal expression of human RTL1 is the major cause of the muscle symptoms observed in Temple and Kagami-Ogata syndromes.
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Affiliation(s)
- Moe Kitazawa
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Shinichiro Hayashi
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan
| | - Michihiro Imamura
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan
| | - Shin'ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan
| | - Yumiko Oishi
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo 113-8602, Japan
| | - Tomoko Kaneko-Ishino
- Faculty of Nursing, School of Medicine, Tokai University, Kanagawa 259-1193, Japan
| | - Fumitoshi Ishino
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
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11
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Ma X, Fu D, Chu M, Ding X, Wu X, Guo X, Kalwar Q, Pei J, Bao P, Liang C, Yan P. Genome-Wide Analysis Reveals Changes in Polled Yak Long Non-coding RNAs in Skeletal Muscle Development. Front Genet 2020; 11:365. [PMID: 32351548 PMCID: PMC7176074 DOI: 10.3389/fgene.2020.00365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/25/2020] [Indexed: 11/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been extensively studied in recent years. Numerous lncRNAs have been identified in mice, rats, and humans, some of which play important roles in muscle formation and development. However, little is known about lncRNA regulators that affect muscle development in yak (Bos grunniens). LncRNA expression during skeletal muscle development in yak was analyzed by RNA sequencing at three development stages: 3 years (group A), 6 months (group M), and 90-day-old fetuses (group E). A total of 1180 lncRNAs were identified in the three development stages. Compared with group E, 154 were upregulated and 130 were downregulated in group A. Compared with group A, 31 were upregulated and 29 were downregulated in group M. Compared with group E, 147 were upregulated and 149 were downregulated in group M (padj < 0.001, |log2FC| > 1.2). In addition, functional annotation analysis based on gene ontology (GO) and the Kyoto protocol encyclopedia of genes and genomes (KEGG) database showed that differentially expressed lncRNAs (DElncRNAs) were cis–trans target genes. The results showed that DElncRNAs were mainly involved in PI3K-Akt signaling pathway, focal adhesion, MAPK signaling pathway, apoptosis, and p53 signaling pathway. Furthermore, RTL1, IGF2, MEF2C, Pax7, and other well-known muscle development regulators were included in a co-expression network of differentially expressed target genes and lncRNAs. These data will help to further clarify the function of lncRNAs in the different stages of skeletal muscle developmental in yak.
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Affiliation(s)
- Xiaoming Ma
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Donghai Fu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Min Chu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xuezhi Ding
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xian Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Qudratullah Kalwar
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jie Pei
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Pengjia Bao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chunnian Liang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Gansu Provincial Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Animal Husbandry and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Lanzhou, China
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12
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Ling Y, Zheng Q, Sui M, Zhu L, Xu L, Zhang Y, Liu Y, Fang F, Chu M, Ma Y, Zhang X. Comprehensive Analysis of LncRNA Reveals the Temporal-Specific Module of Goat Skeletal Muscle Development. Int J Mol Sci 2019; 20:ijms20163950. [PMID: 31416143 PMCID: PMC6719106 DOI: 10.3390/ijms20163950] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 12/12/2022] Open
Abstract
A series of complex processes regulate muscle development, and lncRNAs play essential roles in the regulation of skeletal myogenesis. Using RNA sequencing, we profiled the lncRNA expression during goat (Capra hircus) skeletal muscle development, which included seven stages across fetal 45 (F45), 65 (F65), 90 (F90), 120 (F120), 135 (F135) days, born for 24 h (B1) and 90 (B90) days. A total of 15,079 lncRNAs were identified in the seven stages, and they were less conservative with other species (human, cow, and mouse). Among them, 547 were differentially expressed, and they divided the seven stages into three functional transition periods. Following weighted gene co-expression network analysis (WGCNA), five lncRNA modules specific for developmental stages were defined as three types: 'Early modules', 'late modules', and 'individual-stage-specific modules'. The enrichment content showed that 'early modules' were related to muscle structure formation, 'late modules' participated in the 'p53 signaling pathway' and other pathways, the F90-highly related module was involved in the 'MAPK signaling pathway', and other pathways. Furthermore, we identified hub-lncRNA in three types of modules, and LNC_011371, LNC_ 007561, and LNC_001728 may play important roles in goat skeletal muscle. These data will facilitate further exploration of skeletal muscle lncRNA functions at different developmental stages in goats.
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Affiliation(s)
- Yinghui Ling
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China.
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
| | - Qi Zheng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei 230031, China
| | - Menghua Sui
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei 230031, China
| | - Lu Zhu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei 230031, China
| | - Lina Xu
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Institute of Plant Protection and Agro-Products Safety, Anhui Academy of Agricultural Sciences, Hefei 230036, China
| | - Yunhai Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei 230031, China
| | - Ya Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei 230031, China
| | - Fugui Fang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei 230031, China
| | - Mingxing Chu
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuehui Ma
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaorong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Local Animal Genetic Resources Conservation and Biobreeding Laboratory of Anhui Province, Hefei 230031, China
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13
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Wang C, Zhang B, Ratliff AC, Arrington J, Chen J, Xiong Y, Yue F, Nie Y, Hu K, Jin W, Tao WA, Hrycyna CA, Sun X, Kuang S. Methyltransferase-like 21e inhibits 26S proteasome activity to facilitate hypertrophy of type IIb myofibers. FASEB J 2019; 33:9672-9684. [PMID: 31162944 DOI: 10.1096/fj.201900582r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Skeletal muscles contain heterogeneous myofibers that are different in size and contractile speed, with type IIb myofiber being the largest and fastest. Here, we identify methyltransferase-like 21e (Mettl21e), a member of newly classified nonhistone methyltransferases, as a gene enriched in type IIb myofibers. The expression of Mettl21e was strikingly up-regulated in hypertrophic muscles and during myogenic differentiation in vitro and in vivo. Knockdown (KD) of Mettl21e led to atrophy of cultured myotubes, and targeted mutation of Mettl21e in mice reduced the size of IIb myofibers without affecting the composition of myofiber types. Mass spectrometry and methyltransferase assay revealed that Mettl21e methylated valosin-containing protein (Vcp/p97), a key component of the ubiquitin-proteasome system. KD or knockout of Mettl21e resulted in elevated 26S proteasome activity, and inhibition of proteasome activity prevented atrophy of Mettl21e KD myotubes. These results demonstrate that Mettl21e functions to maintain myofiber size through inhibiting proteasome-mediated protein degradation.-Wang, C., Zhang, B., Ratliff, A. C., Arrington, J., Chen, J., Xiong, Y., Yue, F., Nie, Y., Hu, K., Jin, W., Tao, W. A., Hrycyna, C. A., Sun, X., Kuang, S. Methyltransferase-like 21e inhibits 26S proteasome activity to facilitate hypertrophy of type IIb myofibers.
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Affiliation(s)
- Chao Wang
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Bin Zhang
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Anna C Ratliff
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Justine Arrington
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | - Jingjuan Chen
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Yan Xiong
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Feng Yue
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Yaohui Nie
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Keping Hu
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Wen Jin
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA.,Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Christine A Hrycyna
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA.,Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Xiaobo Sun
- Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Shihuan Kuang
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA.,Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
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14
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Yurchenko AA, Deniskova TE, Yudin NS, Dotsev AV, Khamiruev TN, Selionova MI, Egorov SV, Reyer H, Wimmers K, Brem G, Zinovieva NA, Larkin DM. High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia. BMC Genomics 2019; 20:294. [PMID: 32039702 PMCID: PMC7227232 DOI: 10.1186/s12864-019-5537-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. The genomes of local breeds, therefore, are valuable sources of genomic variants to be used to understand mechanisms of response to adaptation and artificial selection. As a step toward this we performed a high-density genotyping and comprehensive scans for signatures of selection in the genomes from 15 local sheep breeds reared across Russia. Results Results demonstrated that the genomes of Russian sheep breeds contain multiple regions under putative selection. More than 50% of these regions matched with intervals identified in previous scans for selective sweeps in sheep genomes. These regions contain well-known candidate genes related to morphology, adaptation, and domestication (e.g., KITLG, KIT, MITF, and MC1R), wool quality and quantity (e.g., DSG@, DSC@, and KRT@), growth and feed intake (e.g., HOXA@, HOXC@, LCORL, NCAPG, LAP3, and CCSER1), reproduction (e.g., CMTM6, HTRA1, GNAQ, UBQLN1, and IFT88), and milk-related traits (e.g., ABCG2, SPP1, ACSS1, and ACSS2). In addition, multiple genes that are putatively related to environmental adaptations were top-ranked in selected intervals (e.g., EGFR, HSPH1, NMUR1, EDNRB, PRL, TSHR, and ADAMTS5). Moreover, we observed that multiple key genes involved in human hereditary sensory and autonomic neuropathies, and genetic disorders accompanied with an inability to feel pain and environmental temperatures, were top-ranked in multiple or individual sheep breeds from Russia pointing to a possible mechanism of adaptation to harsh climatic conditions. Conclusions Our work represents the first comprehensive scan for signatures of selection in genomes of local sheep breeds from the Russian Federation of both European and Asian origins. We confirmed that the genomes of Russian sheep contain previously identified signatures of selection, demonstrating the robustness of our integrative approach. Multiple novel signatures of selection were found near genes which could be related to adaptation to the harsh environments of Russia. Our study forms a basis for future work on using Russian sheep genomes to spot specific genetic variants or haplotypes to be used in efforts on developing next-generation highly productive breeds, better suited to diverse Eurasian environments. Electronic supplementary material The online version of this article (10.1186/s12864-019-5537-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia
| | - Timur N Khamiruev
- Research Institute of Veterinary Medicine of Eastern Siberia, The Branch of the Siberian Federal Scientific Center for Agrobiotechnologies of the Russian Academy of Sciences, Chita, Russia
| | - Marina I Selionova
- All-Russian Research Institute of Sheep and Goat Breeding - branch of the Federal State Budgetary Scientific Institution North Caucasian Agrarian Center, Stavropol, 355017, Russia
| | - Sergey V Egorov
- Siberian Research Institute of Animal Husbandry, Krasnoobsk, Russia
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Gottfried Brem
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.,Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, 142132, Russia.
| | - Denis M Larkin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia. .,Royal Veterinary College, University of London, London, UK.
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15
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Yu X, Wang Z, Sun H, Yang Y, Li K, Tang Z. Long non-coding MEG3 is a marker for skeletal muscle development and meat production traits in pigs. Anim Genet 2018; 49:571-578. [PMID: 30294799 DOI: 10.1111/age.12712] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2018] [Indexed: 01/02/2023]
Abstract
Long non-coding RNAmaternally expressed gene 3 (lncRNAMEG3) plays an important role in mammalian muscle development. Our previous transcriptome study showed that lncRNAMEG3 is differentially expressed during postnatal skeletal muscle development in pigs. The objective of the present study was to analyse the role of lncRNAMEG3 in prenatal and postnatal skeletal muscle development and investigate the association of MEG3 with meat production traits in pigs. We investigated the sequence conservation and temporal-spatial expression of lncRNAMEG3 and identified its core promoter and single nucleotide polymorphisms (SNPs). Our results show that MEG3 is conserved among pig, human and mouse and is expressed in a tissue-specific manner with high expression levels in kidney and leg and dorsal muscles. In addition, MEG3 is more abundant in prenatal muscle compared to postnatal muscle, and its expression peaks at gestational day 60. Notably, we observed almost no expression 40 days after birth. The core promoter of MEG3 is located upstream of the transcription initiation site between -447 and -40 bp. In our SNP linkage disequilibrium and association analyses, four of the 10 potential polymorphism sites were found to be associated with corrected back fat thickness and age to reach 100 kg (rs325797437, rs344501106, rs81286029 and rs318656749). In addition, three haplotypes were found to be associated with differences in corrected age to reach 100 kg (AAAT, AAAT/GGGC, GAAT/GGGC). Our results indicate that MEG3 regulates skeletal muscle development and is a candidate gene for improving meat production traits in pigs.
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Affiliation(s)
- X Yu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,Group of Pig Genomic Design and Breeding, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Z Wang
- Department of Computer Science, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - H Sun
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Y Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - K Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Z Tang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,Group of Pig Genomic Design and Breeding, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
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16
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Armstrong E, Iriarte A, Nicolini P, De Los Santos J, Ithurralde J, Bielli A, Bianchi G, Peñagaricano F. Comparison of transcriptomic landscapes of different lamb muscles using RNA-Seq. PLoS One 2018; 13:e0200732. [PMID: 30040835 PMCID: PMC6057623 DOI: 10.1371/journal.pone.0200732] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 07/02/2018] [Indexed: 11/18/2022] Open
Abstract
Transcriptome deep sequencing is a powerful tool for exploring the genetic architecture of complex traits. Gene expression patterns may explain a high degree of the observed phenotypic differences in histochemical and metabolic parameters related to meat quality among different muscles. In this study, we sequenced by RNA-Seq the whole transcriptome of nine lamb muscles: Semimembranosus (SM), Semitendinosus (ST), Cranial gluteobiceps, Gluteus medius (GM), Rectus femoris, Supraspinatus (SS), Longissimus lumborum (LL), Adductor and Psoas major. Significant gene expression differences were detected between almost all pairwise comparisons, being more pronounced between SS and ST, SM and LL, and ST and GM. These differences can be explained in terms of ATPase and glycolytic activities, muscle fiber typing and oxidative score, clustering muscles as fast glycolytic, intermediate or slow oxidative. ST showed up-regulation of gene pathways related to carbohydrate metabolism, energy generation and protein turnover as expected from a fast white muscle. SS showed myosin isoforms typical of slow muscles and high expression of genes related to calcium homeostasis and vascularization. SM, LL and GM showed in general intermediate gene expression patterns. Several novel transcripts were detected, mostly related to muscle contraction and structure, oxidative metabolism, lipid metabolism and protein phosphorylation. Expression profiles were consistent with previous histochemical and metabolic characterization of these muscles. Up-regulation of ion transport genes may account for significant differences in water holding capacity. High expression of genes related to cell adhesion, cytoskeleton organization, extracellular matrix components and protein phosphorylation may be related to meat yellowness and lower tenderness scores. Differential expression of genes related to glycolytic activity and lactic acid generation among fast, intermediate and slow muscles may explain the detected final meat pH differences. These results reveal new candidate genes associated with lamb meat quality, and give a deeper insight into the genetic architecture of these complex traits.
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Affiliation(s)
- Eileen Armstrong
- Departamento de Genética y Mejora Animal, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
- * E-mail:
| | - Andres Iriarte
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Paula Nicolini
- Polo de Desarrollo Universitario Instituto Superior de la Carne, Centro Universitario de Tacuarembó, Universidad de la República, Tacuarembó, Uruguay
| | - Jorge De Los Santos
- Department of Animal Sciences, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Javier Ithurralde
- Departamento de Morfología y Desarrollo, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | - Alejandro Bielli
- Departamento de Morfología y Desarrollo, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | | | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
- University of Florida Genetics Institute, University of Florida, Gainesville, Florida, United States of America
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17
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Yu H, Waddell JN, Kuang S, Tellam RL, Cockett NE, Bidwell CA. Identification of genes directly responding to DLK1 signaling in Callipyge sheep. BMC Genomics 2018; 19:283. [PMID: 29690867 PMCID: PMC5937834 DOI: 10.1186/s12864-018-4682-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/16/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In food animal agriculture, there is a need to identify the mechanisms that can improve the efficiency of muscle growth and protein accretion. Callipyge sheep provide excellent machinery since the up-regulation of DLK1 and RTL1 results in extreme postnatal muscle hypertrophy in distinct muscles. The aim of this study is to distinguish the genes that directly respond to DLK1 and RTL1 signaling from the genes that change as the result of muscle specific effects. RESULTS The quantitative PCR results indicated that DLK1 expression was significantly increased in hypertrophied muscles but not in non-hypertrophied muscles. However, RTL1 was up-regulated in both hypertrophied and non-hypertrophied muscles. Five genes, including PARK7, DNTTIP1, SLC22A3, METTL21E and PDE4D, were consistently co-expressed with DLK1, and therefore were possible transcriptional target genes responding to DLK1 signaling. Treatment of myoblast and myotubes with DLK1 protein induced an average of 1.6-fold and 1.4-fold increase in Dnttip1 and Pde4d expression respectively. Myh4 expression was significantly elevated in DLK1-treated myotubes, whereas the expression of Mettl21e was significantly increased in the DLK1-treated myoblasts but reduced in DLK1-treated myotubes. DLK1 treatment had no impact on Park7 expression. In addition, Park7 and Dnttip1 increased Myh4 and decreased Myh7 promoter activity, resemble to the effects of Dlk1. In contrast, expression of Mettl21e increased Myh7 and decreased Myh4 luciferase activity. CONCLUSION The study provided additional supports that RTL1 alone was insufficient to induce muscle hypertrophy and concluded that DLK1 was likely the primary effector of the hypertrophy phenotype. The results also suggested that DNTTIP1 and PDE4D were secondary effector genes responding to DLK1 signaling resulting in muscle fiber switch and muscular hypertrophy in callipyge lamb.
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Affiliation(s)
- Hui Yu
- Department of Animal Sciences, Purdue University, 270 South Russell Street, West Lafayette, IN, 47907, USA. .,Department of Molecular and Integrative Physiology, University of Michigan, 1000 Wall Street, Ann Arbor, MI, 48105, USA.
| | - Jolena N Waddell
- Department of Animal Sciences, Purdue University, 270 South Russell Street, West Lafayette, IN, 47907, USA.,Department of Animal Science & Veterinary Technology, Tarleton State University, Stephenville, TX, USA
| | - Shihuan Kuang
- Department of Animal Sciences, Purdue University, 270 South Russell Street, West Lafayette, IN, 47907, USA.,Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Ross L Tellam
- CSIRO Animal, Food and Health Sciences, St. Lucia, QLD, Australia
| | - Noelle E Cockett
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UT, USA
| | - Christopher A Bidwell
- Department of Animal Sciences, Purdue University, 270 South Russell Street, West Lafayette, IN, 47907, USA.
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18
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Ren C, Deng M, Fan Y, Yang H, Zhang G, Feng X, Li F, Wang D, Wang F, Zhang Y. Genome-Wide Analysis Reveals Extensive Changes in LncRNAs during Skeletal Muscle Development in Hu Sheep. Genes (Basel) 2017; 8:genes8080191. [PMID: 28763026 PMCID: PMC5575655 DOI: 10.3390/genes8080191] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/21/2017] [Accepted: 07/24/2017] [Indexed: 12/14/2022] Open
Abstract
As an important type of noncoding RNA molecules, long non-coding RNAs (lncRNAs) act as versatile players in various biological processes. However, little is known about lncRNA regulators during sheep muscle growth. To explore functional lncRNAs during sheep muscle growth, we systematically investigated lncRNAs using strand-specific Ribo-Zero RNA sequencing at three key developmental stages in Hu sheep. A total of 6924 lncRNAs were obtained, and the differentially expressed lncRNAs and genes were screened from (control vs. experiment) fetus vs. lamb, lamb vs. adult, and fetus vs. adult comparisons, respectively. The quantitative real-time polymerase chain reaction (qRT-PCR) analysis results correlated well with the sequencing data. Moreover, functional annotation analysis based on the Gene Ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases showed that the target genes of the differentially expressed lncRNAs were significantly enriched in organ morphogenesis, skeletal system development as well as response to stimulus and some other terms related to muscle. Furthermore, a co-expression network of the differentially expressed target genes and lncRNAs was constructed and well-known muscle growth regulators such as retrotransposon-like 1 and Junctophilin-2 were included. Finally, we investigated the expression profiles of seven lncRNAs and their target genes, and found that they played vital roles in muscle growth. This study extends the sheep muscle lncRNA database and provides novel candidate regulators for future genetic and molecular studies on sheep muscle growth, which is helpful for optimizing the production of mutton.
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Affiliation(s)
- Caifang Ren
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Mingtian Deng
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yixuan Fan
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Hua Yang
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Guomin Zhang
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xu Feng
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Fengzhe Li
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Dan Wang
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Feng Wang
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yanli Zhang
- Jiangsu Engineering Technology Research Center of Mutton Sheep and Goat Industry, Nanjing Agricultural University, Nanjing 210095, China.
- Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing 210095, China.
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19
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Xie S, Chen L, Zhang X, Liu X, Chen Y, Mo D. An integrated analysis revealed different microRNA-mRNA profiles during skeletal muscle development between Landrace and Lantang pigs. Sci Rep 2017; 7:2516. [PMID: 28566753 PMCID: PMC5451474 DOI: 10.1038/s41598-017-02558-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 04/13/2017] [Indexed: 11/12/2022] Open
Abstract
Pigs supply vital dietary proteins for human consumption, and their economic value depends largely on muscle production. MicroRNAs are known to play important roles in skeletal muscle development. However, their relationship to distinct muscle production between pig breeds remains unknown. Here, we performed an integrated analysis of microRNA-mRNA expression profiles for Landrace (LR, lean) pigs and the Chinese indigenous Lantang pig (LT, lard-type) during 8 stages of skeletal muscle developmental, including at 35, 49, 63, 77 dpc (days post coitum) and 2, 28, 90, 180 dpn (days postnatal). As differentially expressed-miRNA expression profiles can be well classified into two clusters by PCA analysis, we grouped the embryonic stages as G1 and the postnatal stages as G2. A total of 203 genes were predicted miRNA targets, and a STEM analysis showed distinct expression patterns between G1 and G2 in both breeds based on their transcriptomic data. Furthermore, a STRING analysis predicted interactions between 22 genes and 35 miRNAs, including some crucial myogenic factors and myofibrillar genes. Thus, it can be reasonably speculated that myogenic miRNAs may regulate myofibrillar genes in myofiber formation during embryonic stages and muscle hypertrophy during postnatal stages, leading to distinct differences in muscle production between breeds.
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Affiliation(s)
- Shuihua Xie
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006, Guangdong, China
- General Station of Animal Husbandry Technology Extension, Department of Agriculture of Guangdong Province, Guangzhou, 510500, Guangdong, China
| | - Luxi Chen
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006, Guangdong, China
| | - Xumeng Zhang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006, Guangdong, China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006, Guangdong, China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006, Guangdong, China
| | - Delin Mo
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006, Guangdong, China.
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20
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Sudrajad P, Sharma A, Dang CG, Kim JJ, Kim KS, Lee JH, Kim S, Lee SH. Validation of Single Nucleotide Polymorphisms Associated with Carcass Traits in a Commercial Hanwoo Population. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:1541-1546. [PMID: 26954199 PMCID: PMC5088372 DOI: 10.5713/ajas.15.0836] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 01/12/2016] [Accepted: 02/23/2016] [Indexed: 12/25/2022]
Abstract
Four carcass traits, namely carcass weight (CW), eye muscle area (EMA), back fat thickness (BF), and marbling score (MS), are the main price decision parameters used for purchasing Hanwoo beef. The development of DNA markers for these carcass traits for use in a beef management system could result in substantial profit for beef producers in Korea. The objective of this study was to validate the association of highly significant single nucleotide polymorphisms (SNPs) identified in a previous genome-wide association study (GWAS) with the four carcass traits in a commercial Hanwoo population. We genotyped 83 SNPs distributed across all 29 autosomes in 867 steers from a Korean Hanwoo feedlot. Six SNPs, namely ARS-BFGL-NGS-22774 (Chr4, Pos:4889229), ARS-BFGL-NGS-100046 (Chr6, Pos:61917424), ARS-BFGL-NGS-39006 (Chr27, Pos:38059196), ARS-BFGL-NGS-18790 (Chr10, Pos:26489109), ARS-BFGL-NGS-43879 (Chr9, Pos:39964297), and BTB-00775794 (Chr20, Pos:20476265), were found to be associated with CW, EMA, BF, and MS. The ARS-BFGL-NGS-22774, BTB-00775794, and ARS-BFGL-NGS-39006 markers accounted for 1.80%, 1.72%, and 1.35% (p<0.01), respectively, of the phenotypic variance in the commercial Hanwoo population. Many genes located in close proximity to the significant SNPs identified in this study were previously reported to have roles in carcass traits. The results of this study could be useful for marker-assisted selection programs.
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Affiliation(s)
- Pita Sudrajad
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764, Korea.,Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Jakarta Selatan 12540, Indonesia
| | - Aditi Sharma
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Jeonju 565-851, Korea
| | - Chang Gwon Dang
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang 232-950, Korea
| | - Jong Joo Kim
- School of Biotechnology, Yeungnam University, Daegu 717-749, Korea
| | - Kwan Suk Kim
- Department of Animal Science, Chungbuk National University, Cheongju 361-763, Korea
| | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764, Korea
| | - Sidong Kim
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang 232-950, Korea
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764, Korea
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21
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Gao YQ, Chen X, Wang P, Lu L, Zhao W, Chen C, Chen CP, Tao T, Sun J, Zheng YY, Du J, Li CJ, Gan ZJ, Gao X, Chen HQ, Zhu MS. Regulation of DLK1 by the maternally expressed miR-379/miR-544 cluster may underlie callipyge polar overdominance inheritance. Proc Natl Acad Sci U S A 2015; 112:13627-32. [PMID: 26487685 PMCID: PMC4640741 DOI: 10.1073/pnas.1511448112] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Inheritance of the callipyge phenotype in sheep is an example of polar overdominance inheritance, an unusual mode of inheritance. To investigate the underlying molecular mechanism, we profiled the expression of the genes located in the Delta-like 1 homolog (Dlk1)-type III iodothyronine deiodinase (Dio3) imprinting region in mice. We found that the transcripts of the microRNA (miR) 379/miR-544 cluster were highly expressed in neonatal muscle and paralleled the expression of the Dlk1. We then determined the in vivo role of the miR-379/miR-544 cluster by establishing a mouse line in which the cluster was ablated. The maternal heterozygotes of young mutant mice displayed a hypertrophic tibialis anterior muscle, extensor digitorum longus muscle, gastrocnemius muscle, and gluteus maximus muscle and elevated expression of the DLK1 protein. Reduced expression of DLK1 was mediated by miR-329, a member of this cluster. Our results suggest that maternal expression of the imprinted miR-379/miR-544 cluster regulates paternal expression of the Dlk1 gene in mice. We therefore propose a miR-based molecular working model for polar overdominance inheritance.
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Affiliation(s)
- Yun-Qian Gao
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center and Ministry of Education (MOE) Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing 210061, China
| | - Xin Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center and Ministry of Education (MOE) Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing 210061, China
| | - Pei Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center and Ministry of Education (MOE) Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing 210061, China
| | - Lei Lu
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center and Ministry of Education (MOE) Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing 210061, China
| | - Wei Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center and Ministry of Education (MOE) Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing 210061, China
| | - Chen Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center and Ministry of Education (MOE) Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing 210061, China
| | - Cai-Ping Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center and Ministry of Education (MOE) Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing 210061, China
| | - Tao Tao
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center and Ministry of Education (MOE) Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing 210061, China
| | - Jie Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center and Ministry of Education (MOE) Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing 210061, China
| | - Yan-Yan Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center and Ministry of Education (MOE) Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing 210061, China
| | - Jie Du
- Innovation Center for Cardiovascular Disorders, Beijing Anzhen Hospital, Beijing 100029, China
| | - Chao-Jun Li
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center and Ministry of Education (MOE) Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing 210061, China
| | - Zhen-Ji Gan
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center and Ministry of Education (MOE) Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing 210061, China
| | - Xiang Gao
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center and Ministry of Education (MOE) Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing 210061, China
| | - Hua-Qun Chen
- School of Life Science, Nanjing Normal University, Nanjing 210009, China
| | - Min-Sheng Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center and Ministry of Education (MOE) Key Laboratory of Model Animal for Disease Study, Nanjing University, Nanjing 210061, China; Innovation Center for Cardiovascular Disorders, Beijing Anzhen Hospital, Beijing 100029, China;
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22
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Abstract
AbstractEnergy restriction (ER; also known as caloric restriction) is the only nutritional intervention that has repeatedly been shown to increase lifespan in model organisms and may delay ageing in humans. In the present review we discuss current scientific literature on ER and its molecular, metabolic and hormonal effects. Moreover, criteria for the classification of substances that might induce positive ER-like changes without having to reduce energy intake are summarised. Additionally, the putative ER mimetics (ERM) 2-deoxy-d-glucose, metformin, rapamycin, resveratrol, spermidine and lipoic acid and their suggested molecular targets are discussed. While there are reports on these ERM candidates that describe lifespan extension in model organisms, data on longevity-inducing effects in higher organisms such as mice remain controversial or are missing. Furthermore, some of these candidates produce detrimental side effects such as immunosuppression or lactic acidosis, or have not been tested for safety in long-term studies. Up to now, there are no known ERM that could be recommended without limitations for use in humans.
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23
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Kim JY, Park YK, Lee KP, Lee SM, Kang TW, Kim HJ, Dho SH, Kim SY, Kwon KS. Genome-wide profiling of the microRNA-mRNA regulatory network in skeletal muscle with aging. Aging (Albany NY) 2015; 6:524-44. [PMID: 25063768 PMCID: PMC4153621 DOI: 10.18632/aging.100677] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Skeletal muscle degenerates progressively, losing mass (sarcopenia) over time, which leads to reduced physical ability and often results in secondary diseases such as diabetes and obesity. The regulation of gene expression by microRNAs is a key event in muscle development and disease. To understand genome‐wide changes in microRNAs and mRNAs during muscle aging, we sequenced microRNAs and mRNAs from mouse gastrocnemius muscles at two different ages (6 and 24 months). Thirty‐four microRNAs (15 up‐regulated and 19 down‐regulated) were differentially expressed with age, including the microRNAs miR‐206 and ‐434, which were differentially expressed in aged muscle in previous studies. Interestingly, eight microRNAs in a microRNA cluster at the imprinted Dlk1‐Dio3 locus on chromosome 12 were coordinately down‐regulated. In addition, sixteen novel microRNAs were identified. Integrative analysis of microRNA and mRNA expression revealed that microRNAs may contribute to muscle aging through the positive regulation of transcription, metabolic processes, and kinase activity. Many of the age‐related microRNAs have been implicated in human muscular diseases. We suggest that genome‐wide microRNA profiling will expand our knowledge of microRNA function in the muscle aging process.
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24
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Tye CE, Gordon JAR, Martin-Buley LA, Stein JL, Lian JB, Stein GS. Could lncRNAs be the missing links in control of mesenchymal stem cell differentiation? J Cell Physiol 2015; 230:526-34. [PMID: 25258250 DOI: 10.1002/jcp.24834] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 09/18/2014] [Indexed: 12/31/2022]
Abstract
Long suspected, recently recognized, and increasingly studied, non protein-coding RNAs (ncRNAs) are emerging as key drivers of biological control and pathology. Since their discovery in 1993, microRNAs (miRNAs) have been the subject of intense research focus and investigations have revealed striking findings, establishing that these molecules can exert a substantial level of biological control in numerous tissues. More recently, long ncRNAs (lncRNAs), the lesser-studied siblings of miRNA, have been suggested to have a similar robust role in developmental and adult tissue regulation. Mesenchymal stem cells (MSCs) are an important source of multipotent cells for normal and therapeutic tissue repair. Much is known about the critical role of miRNAs in biogenesis and differentiation of MSCs however; recent studies have suggested lncRNAs may play an equally important role in the regulation of these cells. Here we highlight the role of lncRNAs in the regulation of mesenchymal stem cell lineages including adipocytes, chondrocytes, myoblasts, and osteoblasts. In addition, the potential for these noncoding RNAs to be used as biomarkers for disease or therapeutic targets is also discussed.
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Affiliation(s)
- Coralee E Tye
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, Vermont
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25
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Zhuang L, Hulin JA, Gromova A, Tran Nguyen TD, Yu RT, Liddle C, Downes M, Evans RM, Makarenkova HP, Meech R. Barx2 and Pax7 have antagonistic functions in regulation of wnt signaling and satellite cell differentiation. Stem Cells 2015; 32:1661-73. [PMID: 24753152 DOI: 10.1002/stem.1674] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Revised: 12/16/2013] [Accepted: 01/16/2012] [Indexed: 11/05/2022]
Abstract
The canonical Wnt signaling pathway is critical for myogenesis and can induce muscle progenitors to switch from proliferation to differentiation; how Wnt signals integrate with muscle-specific regulatory factors in this process is poorly understood. We previously demonstrated that the Barx2 homeobox protein promotes differentiation in cooperation with the muscle regulatory factor (MRF) MyoD. Pax7, another important muscle homeobox factor, represses differentiation. We now identify Barx2, MyoD, and Pax7 as novel components of the Wnt effector complex, providing a new molecular pathway for regulation of muscle progenitor differentiation. Canonical Wnt signaling induces Barx2 expression in muscle progenitors and perturbation of Barx2 leads to misregulation of Wnt target genes. Barx2 activates two endogenous Wnt target promoters as well as the Wnt reporter gene TOPflash, the latter synergistically with MyoD. Moreover, Barx2 interacts with the core Wnt effectors β-catenin and T cell-factor 4 (TCF4), is recruited to TCF/lymphoid enhancer factor sites, and promotes recruitment of β-catenin. In contrast, Pax7 represses the Wnt reporter gene and antagonizes the activating effect of Barx2. Pax7 also binds β-catenin suggesting that Barx2 and Pax7 may compete for interaction with the core Wnt effector complex. Overall, the data show for the first time that Barx2, Pax7, and MRFs can act as direct transcriptional effectors of Wnt signals in myoblasts and that Barx2 and Wnt signaling participate in a regulatory loop. We propose that antagonism between Barx2 and Pax7 in regulation of Wnt signaling may help mediate the switch from myoblast proliferation to differentiation.
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Affiliation(s)
- Lizhe Zhuang
- Department of Clinical Pharmacology, Flinders University, Bedford Park, Adelaide, South Australia, Australia
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26
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Jeanson-Leh L, Lameth J, Krimi S, Buisset J, Amor F, Le Guiner C, Barthélémy I, Servais L, Blot S, Voit T, Israeli D. Serum Profiling Identifies Novel Muscle miRNA and Cardiomyopathy-Related miRNA Biomarkers in Golden Retriever Muscular Dystrophy Dogs and Duchenne Muscular Dystrophy Patients. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:2885-98. [DOI: 10.1016/j.ajpath.2014.07.021] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 07/01/2014] [Accepted: 07/08/2014] [Indexed: 10/24/2022]
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27
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Fariello MI, Servin B, Tosser-Klopp G, Rupp R, Moreno C, Cristobal MS, Boitard S. Selection signatures in worldwide sheep populations. PLoS One 2014; 9:e103813. [PMID: 25126940 PMCID: PMC4134316 DOI: 10.1371/journal.pone.0103813] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 07/05/2014] [Indexed: 12/31/2022] Open
Abstract
The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populations, (ii) make use of linkage disequilibrium information and (iii) focus specifically on either recent or older selection signatures. We show that this allows pinpointing several new selection signatures in the sheep genome and distinguishing those related to modern breeding objectives and to earlier post-domestication constraints. The newly identified regions, together with the ones previously identified, reveal the extensive genome response to selection on morphology, color and adaptation to new environments.
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Affiliation(s)
- Maria-Ines Fariello
- Génétique, Physiologie et Systèmes d'Élevage, Institut National de la Recherche Agronomique & Ecole Nationale Vétérinaire de Toulouse & Ecole Nationale Supérieure Agronomique de Toulouse, Castanet-Tolosan, France
- Instituto de matemática y Estadística Prof. Ing. Rafael Laguardia, Facultad de Ingeniera, Universidad de la República, Montevideo, Uruguay
- Bioinformatics Unit, Institut Pasteur, Montevideo, Uruguay
| | - Bertrand Servin
- Génétique, Physiologie et Systèmes d'Élevage, Institut National de la Recherche Agronomique & Ecole Nationale Vétérinaire de Toulouse & Ecole Nationale Supérieure Agronomique de Toulouse, Castanet-Tolosan, France
| | - Gwenola Tosser-Klopp
- Génétique, Physiologie et Systèmes d'Élevage, Institut National de la Recherche Agronomique & Ecole Nationale Vétérinaire de Toulouse & Ecole Nationale Supérieure Agronomique de Toulouse, Castanet-Tolosan, France
| | - Rachel Rupp
- Génétique, Physiologie et Systèmes d'Élevage, Institut National de la Recherche Agronomique & Ecole Nationale Vétérinaire de Toulouse & Ecole Nationale Supérieure Agronomique de Toulouse, Castanet-Tolosan, France
| | - Carole Moreno
- Génétique, Physiologie et Systèmes d'Élevage, Institut National de la Recherche Agronomique & Ecole Nationale Vétérinaire de Toulouse & Ecole Nationale Supérieure Agronomique de Toulouse, Castanet-Tolosan, France
| | | | - Magali San Cristobal
- Génétique, Physiologie et Systèmes d'Élevage, Institut National de la Recherche Agronomique & Ecole Nationale Vétérinaire de Toulouse & Ecole Nationale Supérieure Agronomique de Toulouse, Castanet-Tolosan, France
| | - Simon Boitard
- Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique & AgroParisTech, Jouy-en-Josas, France
- Origine, Structure et Evolution de la Biodiversité, Museum National d'Histoire Naturelle & Ecole Pratique des Hautes Etudes & CNRS, Paris, France
- * E-mail:
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Bidwell CA, Waddell JN, Taxis TM, Yu H, Tellam RL, Neary MK, Cockett NE. New insights into polar overdominance in callipyge sheep. Anim Genet 2014; 45 Suppl 1:51-61. [PMID: 24990181 DOI: 10.1111/age.12132] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2013] [Indexed: 01/01/2023]
Abstract
The callipyge phenotype in sheep involves substantial postnatal muscle hypertrophy and other changes to carcass composition. A single nucleotide polymorphism in the DLK1-DIO3 imprinted gene cluster alters gene expression of the paternal allele-specific protein-coding genes and several maternal allele-specific long noncoding RNA and microRNA when the mutation is inherited in cis. The inheritance pattern of the callipyge phenotype is polar overdominant because muscle hypertrophy only occurs in heterozygous animals that inherit a normal maternal allele and the callipyge SNP on the paternal allele (+/C). We examined the changes of gene expression of four major transcripts from the DLK1-DIO3 cluster and four myosin isoforms during the development of muscle hypertrophy in the semimembranosus as well as in the supraspinatus that does not undergo hypertrophy. The homozygous (C/C) animals had an intermediate gene expression pattern for the paternal allele-specific genes and two myosin isoforms, indicating a biological activity that was insufficient to change muscle mass. Transcriptome analysis was conducted by RNA sequencing in the four callipyge genotypes. The data show that homozygous animals (C/C) have lower levels of gene expression at many loci relative to the other three genotypes. A number of the downregulated genes are putative targets of the maternal allele-specific microRNA with gene ontology, indicating regulatory and cell signaling functions. These results suggest that the trans-effect of the maternal noncoding RNA and associated miRNA is to stabilize the expression of a number of regulatory genes at a functional, but low level to make the myofibers of homozygous (C/C) lambs less responsive to hypertrophic stimuli of the paternal allele-specific genes.
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Affiliation(s)
- C A Bidwell
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
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29
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Magee DA, Spillane C, Berkowicz EW, Sikora KM, MacHugh DE. Imprinted loci in domestic livestock species as epigenomic targets for artificial selection of complex traits. Anim Genet 2014; 45 Suppl 1:25-39. [PMID: 24990393 DOI: 10.1111/age.12168] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2014] [Indexed: 12/30/2022]
Abstract
The phenomenon of genomic imprinting, whereby a subset of mammalian genes display parent-of-origin-specific monoallelic expression, is one of the most active areas of epigenetics research. Over the past two decades, more than 100 imprinted mammalian genes have been identified, while considerable advances have been made in elucidating the molecular mechanisms governing imprinting. These studies have helped to unravel the epigenome--a separate layer of regulatory information contained in eukaryotic chromosomes that influences gene expression and phenotypes without involving changes to the underlying DNA sequence. Although most studies of genomic imprinting in mammals have focussed on mouse models or human biomedical disorders, there is burgeoning interest in the phenotypic effects of imprinted genes in domestic livestock species. In particular, research has focused on imprinted genes influencing foetal growth and development, which are associated with economically important production traits in cattle, sheep and pigs. These findings, when coupled with the data emerging from the various different livestock genome projects, have major implications for the future of animal breeding, health and management. Here, we review current scientific knowledge regarding genomic imprinting in livestock species and evaluate how this information can be used in modern livestock improvement programmes.
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Affiliation(s)
- D A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, 4, Ireland
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30
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Li J, Greenwood PL, Cockett NE, Hadfield TS, Vuocolo T, Byrne K, White JD, Tellam RL, Schirra HJ. Impacts of the Callipyge mutation on ovine plasma metabolites and muscle fibre type. PLoS One 2014; 9:e99726. [PMID: 24937646 PMCID: PMC4061035 DOI: 10.1371/journal.pone.0099726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/17/2014] [Indexed: 12/02/2022] Open
Abstract
The ovine Callipyge mutation causes postnatal muscle hypertrophy localized to the pelvic limbs and torso, as well as body leanness. The mechanism underpinning enhanced muscle mass is unclear, as is the systemic impact of the mutation. Using muscle fibre typing immunohistochemistry, we confirmed muscle specific effects and demonstrated that affected muscles had greater prevalence and hypertrophy of type 2X fast twitch glycolytic fibres and decreased representation of types 1, 2C, 2A and/or 2AX fibres. To investigate potential systemic effects of the mutation, proton NMR spectra of plasma taken from lambs at 8 and 12 weeks of age were measured. Multivariate statistical analysis of plasma metabolite profiles demonstrated effects of development and genotype but not gender. Plasma from Callipyge lambs at 12 weeks of age, but not 8 weeks, was characterized by a metabolic profile consistent with contributions from the affected hypertrophic fast twitch glycolytic muscle fibres. Microarray analysis of the perirenal adipose tissue depot did not reveal a transcriptional effect of the mutation in this tissue. We conclude that there is an indirect systemic effect of the Callipyge mutation in skeletal muscle in the form of changes of blood metabolites, which may contribute to secondary phenotypes such as body leanness.
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Affiliation(s)
- Juan Li
- CSIRO Animal, Food and Health Sciences, St Lucia, Brisbane, Australia
| | - Paul L. Greenwood
- CSIRO Animal, Food and Health Sciences, FD McMaster Laboratory, Armidale, Australia
- New South Wales Department of Primary Industries, Beef Industry Centre of Excellence, University of New England, Armidale, Australia
| | - Noelle E. Cockett
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah, United States of America
| | - Tracy S. Hadfield
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, Utah, United States of America
| | - Tony Vuocolo
- CSIRO Animal, Food and Health Sciences, St Lucia, Brisbane, Australia
| | - Keren Byrne
- CSIRO Animal, Food and Health Sciences, St Lucia, Brisbane, Australia
| | - Jason D. White
- The University of Melbourne, School of Veterinary Science, Parkville, Australia
| | - Ross L. Tellam
- CSIRO Animal, Food and Health Sciences, St Lucia, Brisbane, Australia
- * E-mail: (RLT); (HJS)
| | - Horst Joachim Schirra
- The University of Queensland, Centre for Advanced Imaging, Brisbane, Australia
- * E-mail: (RLT); (HJS)
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31
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Yu H, Waddell JN, Kuang S, Bidwell CA. Park7 expression influences myotube size and myosin expression in muscle. PLoS One 2014; 9:e92030. [PMID: 24637782 PMCID: PMC3956870 DOI: 10.1371/journal.pone.0092030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 02/18/2014] [Indexed: 01/16/2023] Open
Abstract
Callipyge sheep exhibit postnatal muscle hypertrophy due to the up-regulation of DLK1 and/or RTL1. The up-regulation of PARK7 was identified in hypertrophied muscles by microarray analysis and further validated by quantitative PCR. The expression of PARK7 in hypertrophied muscle of callipyge lambs was confirmed to be up-regulated at the protein level. PARK7 was previously identified to positively regulate PI3K/AKT pathway by suppressing the phosphatase activity of PTEN in mouse fibroblasts. The purpose of this study was to investigate the effects of PARK7 in muscle growth and protein accretion in response to IGF1. Primary myoblasts isolated from Park7 (+/+) and Park7 (−/−) mice were used to examine the effect of differential expression of Park7. The Park7 (+/+) myotubes had significantly larger diameters and more total sarcomeric myosin expression than Park7 (−/−) myotubes. IGF1 treatment increased the mRNA abundance of Myh4, Myh7 and Myh8 between 20-40% in Park7 (+/+) myotubes relative to Park7 (−/−). The level of AKT phosphorylation was increased in Park7 (+/+) myotubes at all levels of IGF1 supplementation. After removal of IGF1, the Park7 (+/+) myotubes maintained higher AKT phosphorylation through 3 hours. PARK7 positively regulates the PI3K/AKT pathway by inhibition of PTEN phosphatase activity in skeletal muscle. The increased PARK7 expression can increase protein synthesis and result in myotube hypertrophy. These results support the hypothesis that elevated expression of PARK7 in callipyge muscle would increase levels of AKT activity to cause hypertrophy in response to the normal IGF1 signaling in rapidly growing lambs. Increasing expression of PARK7 could be a novel mechanism to increase protein accretion and muscle growth in livestock or help improve muscle mass with disease or aging.
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MESH Headings
- Animals
- Cell Size/drug effects
- Enzyme-Linked Immunosorbent Assay
- Genotype
- Hypertrophy
- Insulin-Like Growth Factor I/pharmacology
- Mice
- Mice, Inbred C57BL
- Muscle Fibers, Skeletal/drug effects
- Muscle Fibers, Skeletal/enzymology
- Muscle Fibers, Skeletal/metabolism
- Muscle Fibers, Skeletal/pathology
- Muscle, Skeletal/drug effects
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Myosins/genetics
- Myosins/metabolism
- Oncogene Proteins/deficiency
- Oncogene Proteins/genetics
- Oncogene Proteins/metabolism
- PTEN Phosphohydrolase/metabolism
- Peroxiredoxins
- Phosphorylation/drug effects
- Protein Deglycase DJ-1
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Proto-Oncogene Proteins c-akt/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Real-Time Polymerase Chain Reaction
- Sarcomeres/metabolism
- Sheep
- Up-Regulation/drug effects
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Affiliation(s)
- Hui Yu
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Jolena N. Waddell
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Shihuan Kuang
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
- Center for Cancer Research, Purdue University, West Lafayette, Indiana, United States of America
| | - Christopher A. Bidwell
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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Lan X, Cretney EC, Kropp J, Khateeb K, Berg MA, Peñagaricano F, Magness R, Radunz AE, Khatib H. Maternal Diet during Pregnancy Induces Gene Expression and DNA Methylation Changes in Fetal Tissues in Sheep. Front Genet 2013; 4:49. [PMID: 23577020 PMCID: PMC3617393 DOI: 10.3389/fgene.2013.00049] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 03/17/2013] [Indexed: 11/13/2022] Open
Abstract
Studies in rats and mice have established that maternal nutrition induces epigenetic modifications, sometimes permanently, that alter gene expression in the fetus, which in turn leads to phenotypic changes. However, limited data is available on the influence of maternal diet on epigenetic modifications and gene expression in sheep. Therefore, the objectives of this study were to investigate the impact of different maternal dietary energy sources on the expression of imprinted genes in fetuses in sheep. Ewes were naturally bred to a single sire and from days 67 ± 3 of gestation until necropsy (days 130 ± 1), they were fed one of three diets of alfalfa haylage (HY; fiber), corn (CN; starch), or dried corn distiller’s grains (DG; fiber plus protein plus fat). A total of 26 fetuses were removed from the dams and longissimus dorsi, semitendinosus, perirenal adipose depot, and subcutaneous adipose depot tissues were collected for expression and DNA methylation analyses. Expression analysis of nine imprinted genes and three DNA methyltransferase (DNMTs) genes showed significant effects of the different maternal diets on the expression of these genes. The methylation levels of CpG islands of both IGF2R and H19 were higher in HY and DG than CN fetuses in both males and females. This result is consistent with the low amino acid content of the CN diet, a source of methyl group donors, compared to HY and DG diets. Thus, results of this study provide evidence of association between maternal nutrition during pregnancy and transcriptomic and epigenomic alterations of imprinted genes and DNMTs in the fetal tissues.
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Affiliation(s)
- Xianyong Lan
- College of Animal Science and Technology, Northwest Agriculture and Forestry University Yangling, China ; Department of Animal Sciences, University of Wisconsin-Madison Madison, WI, USA
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33
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Tellam RL, Cockett NE, Vuocolo T, Bidwell CA. Genes contributing to genetic variation of muscling in sheep. Front Genet 2012; 3:164. [PMID: 22952470 PMCID: PMC3429854 DOI: 10.3389/fgene.2012.00164] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 08/10/2012] [Indexed: 12/24/2022] Open
Abstract
Selective breeding programs aiming to increase the productivity and profitability of the sheep meat industry use elite, progeny tested sires. The broad genetic traits of primary interest in the progeny of these sires include skeletal muscle yield, fat content, eating quality, and reproductive efficiency. Natural mutations in sheep that enhance muscling have been identified, while a number of genome scans have identified and confirmed quantitative trait loci (QTL) for skeletal muscle traits. The detailed phenotypic characteristics of sheep carrying these mutations or QTL affecting skeletal muscle show a number of common biological themes, particularly changes in developmental growth trajectories, alterations of whole animal morphology, and a shift toward fast twitch glycolytic fibers. The genetic, developmental, and biochemical mechanisms underpinning the actions of some of these genetic variants are described. This review critically assesses this research area, identifies gaps in knowledge, and highlights mechanistic linkages between genetic polymorphisms and skeletal muscle phenotypic changes. This knowledge may aid the discovery of new causal genetic variants and in some cases lead to the development of biochemical and immunological strategies aimed at enhancing skeletal muscle.
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Affiliation(s)
- Ross L Tellam
- Division of Animal, Food and Health Sciences, Commonwealth Scientific and Industrial Research Organisation St Lucia, QLD, Australia
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Poaty H, Coullin P, Peko JF, Dessen P, Diatta AL, Valent A, Leguern E, Prévot S, Gombé-Mbalawa C, Candelier JJ, Picard JY, Bernheim A. Genome-wide high-resolution aCGH analysis of gestational choriocarcinomas. PLoS One 2012; 7:e29426. [PMID: 22253721 PMCID: PMC3253784 DOI: 10.1371/journal.pone.0029426] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Accepted: 11/28/2011] [Indexed: 11/28/2022] Open
Abstract
Eleven samples of DNA from choriocarcinomas were studied by high resolution CGH-array 244 K. They were studied after histopathological confirmation of the diagnosis, of the androgenic etiology and after a microsatellite marker analysis confirming the absence of contamination of tumor DNA from maternal DNA. Three cell lines, BeWo, JAR, JEG were also studied by this high resolution pangenomic technique. According to aCGH analysis, the de novo choriocarcinomas exhibited simple chromosomal rearrangements or normal profiles. The cell lines showed various and complex chromosomal aberrations. 23 Minimal Critical Regions were defined that allowed us to list the genes that were potentially implicated. Among them, unusually high numbers of microRNA clusters and imprinted genes were observed.
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Affiliation(s)
- Henriette Poaty
- INSERM U985, Institut Gustave Roussy, Villejuif, France
- Université Paris XI, Paris Sud, Orsay, France
- INSERM U782, Endocrinologie et génétique de la reproduction et du développement, Clamart, France
| | - Philippe Coullin
- Université Paris XI, Paris Sud, Orsay, France
- INSERM U782, Endocrinologie et génétique de la reproduction et du développement, Clamart, France
| | - Jean Félix Peko
- Service de carcinologie, service d'anatomie et de pathologie, CHU Brazzaville, Congo
| | - Philippe Dessen
- INSERM U985, Institut Gustave Roussy, Villejuif, France
- Université Paris XI, Paris Sud, Orsay, France
| | - Ange Lucien Diatta
- Laboratoire de cytogénétique et de la reproduction, service d'obstétrique, Hôpital A. Le Dantec, Dakar, Sénégal
| | | | - Eric Leguern
- UF de neurogénétique moléculaire et cellulaire, Hôpital de la Salpêtrière, Paris, France
| | - Sophie Prévot
- Université Paris XI, Paris Sud, Orsay, France
- INSERM U782, Endocrinologie et génétique de la reproduction et du développement, Clamart, France
| | - Charles Gombé-Mbalawa
- Service de carcinologie, service d'anatomie et de pathologie, CHU Brazzaville, Congo
| | - Jean-Jacques Candelier
- Université Paris XI, Paris Sud, Orsay, France
- INSERM U782, Endocrinologie et génétique de la reproduction et du développement, Clamart, France
| | - Jean-Yves Picard
- Université Paris XI, Paris Sud, Orsay, France
- INSERM U782, Endocrinologie et génétique de la reproduction et du développement, Clamart, France
| | - Alain Bernheim
- INSERM U985, Institut Gustave Roussy, Villejuif, France
- Université Paris XI, Paris Sud, Orsay, France
- Molecular Pathology, Institut Gustave Roussy, Villejuif, France
- * E-mail:
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35
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Imumorin IG, Kim EH, Lee YM, De Koning DJ, van Arendonk JA, De Donato M, Taylor JF, Kim JJ. Genome Scan for Parent-of-Origin QTL Effects on Bovine Growth and Carcass Traits. Front Genet 2011; 2:44. [PMID: 22303340 PMCID: PMC3268597 DOI: 10.3389/fgene.2011.00044] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 06/25/2011] [Indexed: 11/13/2022] Open
Abstract
Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We identified 24 POE–QTL on 15 Bos taurus autosomes (BTAs) of which six were significant at 5% genome-wide (GW) level and 18 at the 5% chromosome-wide (CW) significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 (linkage region of 0–9 cM; genomic region of 5.0–10.8 Mb), for which only one imprinted ortholog is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4 ∼ 5.1% of each trait’s phenotypic variance. Comparative in silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologs map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only two (GNAS and PEG3) have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologs of imprinted genes so as to investigate their effects on quantitative traits.
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36
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Flisikowski K, Venhoranta H, Nowacka-Woszuk J, McKay SD, Flyckt A, Taponen J, Schnabel R, Schwarzenbacher H, Szczerbal I, Lohi H, Fries R, Taylor JF, Switonski M, Andersson M. A novel mutation in the maternally imprinted PEG3 domain results in a loss of MIMT1 expression and causes abortions and stillbirths in cattle (Bos taurus). PLoS One 2010; 5:e15116. [PMID: 21152099 PMCID: PMC2994898 DOI: 10.1371/journal.pone.0015116] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 10/21/2010] [Indexed: 12/27/2022] Open
Abstract
Congenital malformations resulting in late abortions and stillbirths affect the economic wellbeing of producers and the welfare of cattle in breeding programs. An extremely high incidence of stillbirths of “half-sized” calves of normal karyotype and uninflated lungs was diagnosed in the progeny of the Finnish Ayrshire (Bos taurus) bull - YN51. No other visible anatomical abnormalities were apparent in the stillborn calves. We herein describe the positional identification of a 110 kb microdeletion in the maternally imprinted PEG3 domain that results in a loss of paternal MIMT1 expression and causes late term abortion and stillbirth in cattle. Using the BovineSNP50 BeadChip we performed a genome-wide half-sib linkage analysis that identified a 13.3 Mb associated region on BTA18 containing the maternally imprinted PEG3 domain. Within this cluster we found a 110 kb microdeletion that removes a part of the non-protein coding MER1 repeat containing imprinted transcript 1 gene (MIMT1). To confirm the elimination of gene expression in calves inheriting this deletion, we examined the mRNA levels of the three maternally imprinted genes within the PEG3 domain, in brain and cotyledon tissue collected from eight fetuses sired by the proband. None of the fetuses that inherited the microdeletion expressed MIMT1 in either tissue. The mutation, when inherited from the sire, is semi-lethal for his progeny with an observed mortality rate of 85%. The survival of 15% is presumably due to the incomplete silencing of maternally inherited MIMT1 alleles. We designed a PCR-based assay to confirm the existence of the microdeletion in the MIMT1 region that can be used to assist cattle breeders in preventing the stillbirths.
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Waddell JN, Zhang P, Wen Y, Gupta SK, Yevtodiyenko A, Schmidt JV, Bidwell CA, Kumar A, Kuang S. Dlk1 is necessary for proper skeletal muscle development and regeneration. PLoS One 2010; 5:e15055. [PMID: 21124733 PMCID: PMC2993959 DOI: 10.1371/journal.pone.0015055] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 10/15/2010] [Indexed: 11/18/2022] Open
Abstract
Delta-like 1homolog (Dlk1) is an imprinted gene encoding a transmembrane protein whose increased expression has been associated with muscle hypertrophy in animal models. However, the mechanisms by which Dlk1 regulates skeletal muscle plasticity remain unknown. Here we combine conditional gene knockout and over-expression analyses to investigate the role of Dlk1 in mouse muscle development, regeneration and myogenic stem cells (satellite cells). Genetic ablation of Dlk1 in the myogenic lineage resulted in reduced body weight and skeletal muscle mass due to reductions in myofiber numbers and myosin heavy chain IIB gene expression. In addition, muscle-specific Dlk1 ablation led to postnatal growth retardation and impaired muscle regeneration, associated with augmented myogenic inhibitory signaling mediated by NF-κB and inflammatory cytokines. To examine the role of Dlk1 in satellite cells, we analyzed the proliferation, self-renewal and differentiation of satellite cells cultured on their native host myofibers. We showed that ablation of Dlk1 inhibits the expression of the myogenic regulatory transcription factor MyoD, and facilitated the self-renewal of activated satellite cells. Conversely, Dlk1 over-expression inhibited the proliferation and enhanced differentiation of cultured myoblasts. As Dlk1 is expressed at low levels in satellite cells but its expression rapidly increases upon myogenic differentiation in vitro and in regenerating muscles in vivo, our results suggest a model in which Dlk1 expressed by nascent or regenerating myofibers non-cell autonomously promotes the differentiation of their neighbor satellite cells and therefore leads to muscle hypertrophy.
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MESH Headings
- Animals
- Blotting, Western
- Calcium-Binding Proteins
- Cell Differentiation
- Cell Line
- Cell Proliferation
- Cells, Cultured
- Immunohistochemistry
- Intercellular Signaling Peptides and Proteins/genetics
- Intercellular Signaling Peptides and Proteins/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Muscle Fibers, Skeletal/cytology
- Muscle Fibers, Skeletal/metabolism
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/physiology
- MyoD Protein/genetics
- MyoD Protein/metabolism
- Myoblasts/cytology
- Myoblasts/metabolism
- Regeneration
- Reverse Transcriptase Polymerase Chain Reaction
- Satellite Cells, Skeletal Muscle/cytology
- Satellite Cells, Skeletal Muscle/metabolism
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Affiliation(s)
- Jolena N. Waddell
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Peijing Zhang
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Yefei Wen
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Sanjay K. Gupta
- Department of Anatomical Sciences and Neurobiology, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Aleksey Yevtodiyenko
- Division of Oncology, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Jennifer V. Schmidt
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Christopher A. Bidwell
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Ashok Kumar
- Department of Anatomical Sciences and Neurobiology, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Shihuan Kuang
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
- Center for Cancer Research, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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38
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Magee DA, Berry DP, Berkowicz EW, Sikora KM, Howard DJ, Mullen MP, Evans RD, Spillane C, MacHugh DE. Single nucleotide polymorphisms within the bovine DLK1-DIO3 imprinted domain are associated with economically important production traits in cattle. ACTA ACUST UNITED AC 2010; 102:94-101. [PMID: 20817761 DOI: 10.1093/jhered/esq097] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Previous studies show that DNA sequence variation within the mammalian DLK1-DIO3 imprinted domain influences production traits in domestic livestock, most notably the ovine callipyge phenotype. We assessed genotype-phenotype associations between 7 single nucleotide polymorphisms (SNPs) within the orthologous bovine DLK1-DIO3 domain and performance traits in 848 progeny-tested Holstein-Friesian dairy sires. One SNP (MEG3_01) located proximal to the maternally expressed 3 (MEG3/Gtl2) gene was associated with milk yield, subcutaneous fat levels, and progeny carcass conformation (P ≤ 0.01) and also tended to be associated with milk fat and protein yield (P ≤ 0.10). A single SNP (CLPG_01) within the putative CLPG1 locus was associated with progeny carcass fat (P ≤ 0.05), whereas a single SNP (PEG11_01) located proximal to the paternally expressed 11 (PEG11/Rtl) gene was associated with progeny carcass weight (P ≤ 0.05). The MEG3_01 SNP together with an additional 2 SNPs (MEG8_01 and MEG8_02) located proximal to the putative maternally expressed 8 (MEG8/Rian) ortholog were associated (P ≤ 0.05) with perinatal mortality. Finally, one SNP (MEG3_03) was associated (P ≤ 0.05) with gestation length, whereas both the CLPG_01 and MEG8_01 SNPs also tended to be associated with calving interval (P ≤ 0.10). Linkage disequilibrium analysis suggests that some phenotypic associations observed at these loci are independent. To our knowledge, this is one of the first studies demonstrating associations between the bovine DLK1-DIO3 domain and milk, carcass, fertility and, health traits in cattle. This imprinted domain may serve as a potential target for future genetic selection strategies.
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Affiliation(s)
- David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
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Byrne K, Colgrave ML, Vuocolo T, Pearson R, Bidwell CA, Cockett NE, Lynn DJ, Fleming-Waddell JN, Tellam RL. The imprinted retrotransposon-like gene PEG11 (RTL1) is expressed as a full-length protein in skeletal muscle from Callipyge sheep. PLoS One 2010; 5:e8638. [PMID: 20072617 PMCID: PMC2799525 DOI: 10.1371/journal.pone.0008638] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 12/15/2009] [Indexed: 01/22/2023] Open
Abstract
Members of the Ty3-Gypsy retrotransposon family are rare in mammalian genomes despite their abundance in invertebrates and some vertebrates. These elements contain a gag-pol-like structure characteristic of retroviruses but have lost their ability to retrotranspose into the mammalian genome and are thought to be inactive relics of ancient retrotransposition events. One of these retrotransposon-like elements, PEG11 (also called RTL1) is located at the distal end of ovine chromosome 18 within an imprinted gene cluster that is highly conserved in placental mammals. The region contains several conserved imprinted genes including BEGAIN, DLK1, DAT, GTL2 (MEG3), PEG11 (RTL1), PEG11as, MEG8, MIRG and DIO3. An intergenic point mutation between DLK1 and GTL2 causes muscle hypertrophy in callipyge sheep and is associated with large changes in expression of the genes linked in cis between DLK1 and MEG8. It has been suggested that over-expression of DLK1 is the effector of the callipyge phenotype; however, PEG11 gene expression is also strongly correlated with the emergence of the muscling phenotype as a function of genotype, muscle type and developmental stage. To date, there has been no direct evidence that PEG11 encodes a protein, especially as its anti-sense transcript (PEG11as) contains six miRNA that cause cleavage of the PEG11 transcript. Using immunological and mass spectrometry approaches we have directly identified the full-length PEG11 protein from postnatal nuclear preparations of callipyge skeletal muscle and conclude that its over-expression may be involved in inducing muscle hypertrophy. The developmental expression pattern of the PEG11 gene is consistent with the callipyge mutation causing recapitulation of the normal fetal-like gene expression program during postnatal development. Analysis of the PEG11 sequence indicates strong conservation of the regions encoding the antisense microRNA and in at least two cases these correspond with structural or functional domains of the protein suggesting co-evolution of the sense and antisense genes.
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Affiliation(s)
- Keren Byrne
- CSIRO Livestock Industries, St Lucia, Queensland, Australia
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