Co-expression analysis of fetal weight-related genes in ovine skeletal muscle during mid and late fetal development stages

International Journal of Biological Sciences

Volumn 10, Issue 9, 2014, Pages 1039-1050

  Xu, Lingyang ^a,d,e   Zhao, Fuping ^a   Ren, Hangxing ^a,b   Li, L ^a,c   Lu, Jian ^a   Liu, Jiasen ^a   Zhang, Shifang ^a   Liu, George E ^d   Song, Jiuzhou ^e   Zhang, L ^a   Wei, Caihong ^a   Du, Lixin ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b Chongqing Academy of Animal Science   (China)

^c SICHUAN AGRICULTURAL UNIVERSITY   (China)

^d AGRICULTURAL RESEARCH SERVICE   (United States)

^e UNIVERSITY OF MARYLAND   (United States)

Author keywords

Fetal development stages; Fetal weight; Serial expression analysis; WGCNA

Indexed keywords

OVIS; OVIS ARIES;

TRANSCRIPTOME;

ANIMAL; EMBRYOLOGY; FEMALE; FETUS DEVELOPMENT; FETUS WEIGHT; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGY; PREGNANCY; PROTEIN MICROARRAY; SHEEP; SKELETAL MUSCLE; VETERINARY MEDICINE;

ANIMALS; FEMALE; FETAL DEVELOPMENT; FETAL WEIGHT; GENE EXPRESSION REGULATION, DEVELOPMENTAL; MUSCLE, SKELETAL; PREGNANCY; PROTEIN ARRAY ANALYSIS; SHEEP; TRANSCRIPTOME;

EID: 84928103853     PISSN: 14492288     EISSN: None     Source Type: Journal    
DOI: 10.7150/ijbs.9737     Document Type: Article

References (75)

1. Hocquette JF. Endocrine and metabolic regulation of muscle growth and body composition in cattle. Animal: an international journal of animal bioscience. 2010; 4: 1797-809. doi: 10.1017/S1751731110001448.
2. Hickford JG, Forrest RH, Zhou H. Association between a g.+6723G-A SNP in the myostatin gene (MSTN) and carcass traits in New Zealand Texel sheep. J Anim Sci. 2009; 87: 1853. doi:10.2527/jas.2009-1960.
3. Clop A, Marcq F, Takeda H, Pirottin D, Tordoir X, Bibe B, et al. A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat Genet. 2006; 38: 813-8. doi:10.1038/ng1810.
4. Kambadur R, Sharma M, Smith TP, Bass JJ. Mutations in myostatin (GDF8) in double-muscled Belgian Blue and Piedmontese cattle. Genome Res. 1997; 7: 910-6.
5. Grobet L, Martin LJ, Poncelet D, Pirottin D, Brouwers B, Riquet J, et al. A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle. Nat Genet. 1997; 17: 71-4. doi: 10.1038/ng0997-71.
6. Mosher DS, Quignon P, Bustamante CD, Sutter NB, Mellersh CS, Parker HG, et al. A mutation in the myostatin gene increases muscle mass and enhances racing performance in heterozygote dogs. PLoS Genet. 2007; 3: e79. doi:10.1371/journal.pgen.0030079.
7. Lee SJ, McPherron AC. Regulation of myostatin activity and muscle growth. Proc Natl Acad Sci U S A. 2001; 98: 9306-11. doi: 10.1073/pnas.151270098.
8. Schuelke M, Wagner KR, Stolz LE, Hubner C, Riebel T, Komen W, et al. Myostatin mutation associated with gross muscle hypertrophy in a child. The New England journal of medicine. 2004; 350: 2682-8. doi: 10.1056/NEJMoa040933.
9. Johnson PL, McEwan JC, Dodds KG, Purchas RW, Blair HT. Meat quality traits were unaffected by a quantitative trait locus affecting leg composition traits in Texel sheep. Journal of Animal Science. 2005; 83: 2729-35.
10. Meng XR, Guo J, Zhao Q, Ma YH, Guan WJ, Liu D, et al. Variation of MSTN gene UTR in eleven sheep breeds. Yi Chuan. 2008; 30: 1585-90
11. Picard B, Lefaucheur L, Berri C, Duclos MJ. Muscle fibre ontogenesis in farm animal species. Reproduction, nutrition, development. 2002; 42: 415-31.
12. Byrne K, Vuocolo T, Gondro C, White J, Cockett N, Hadfield T, et al. A gene network switch enhances the oxidative capacity of ovine skeletal muscle during late fetal development. BMC Genomics. 2010; 11: 378.
13. Cassar-Malek I, Passelaigue F, Bernard C, Leger J, Hocquette JF. Target genes of myostatin loss-of-function in muscles of late bovine fetuses. BMC Genomics. 2007; 8:63. doi: 10.1186/1471-2164-8-63.
14. Lehnert SA, Reverter A, Byrne KA, Wang Y, Nattrass GS, Hudson NJ, et al. Gene expression studies of developing bovine longissimus muscle from two different beef cattle breeds. BMC developmental biology. 2007; 7: 95. doi: 10.1186/1471-213X-7-95.
15. Hudson NJ, Reverter A, Dalrymple BP. A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation. PLoS Comput Biol. 2009; 5: e1000382. doi: 10.1371/journal.pcbi.1000382.
16. Hudson NJ, Reverter A, Wang Y, Greenwood PL, Dalrymple BP. Inferring the transcriptional landscape of bovine skeletal muscle by integrating co-expression networks. PloS one. 2009; 4: e7249. doi:10.1371/journal.pone.0007249.
17. Ren H, Li L, Su H, Xu L, Wei C, Zhang L, et al. Histological and transcriptome- wide level characteristics of fetal myofiber hyperplasia during the second half of gestation in Texel and Ujumqin sheep. BMC Genomics. 2011; 12: 411.
18. Bai Q, McGillivray C, da Costa N, Dornan S, Evans G, Stear MJ, et al. Development of a porcine skeletal muscle cDNA microarray: analysis of differential transcript expression in phenotypically distinct muscles. BMC Genomics. 2003; 4: 8.
19. Li Y, Xu Z, Li H, Xiong Y, Zuo B. Differential transcriptional analysis between red and white skeletal muscle of Chinese Meishan pigs. International journal of biological sciences. 2010; 6: 350.
20. Campbell WG, Gordon SE, Carlson CJ, Pattison JS, Hamilton MT, Booth FW. Differential global gene expression in red and white skeletal muscle. American journal of physiology Cell physiology. 2001; 280: C763-8.
21. Cui HX, Liu RR, Zhao GP, Zheng MQ, Chen JL, Wen J. Identification of differentially expressed genes and pathways for intramuscular fat deposition in pectoralis major tissues of fast-and slow-growing chickens. BMC Genomics. 2012; 13: 213. doi: 10.1186/1471-2164-13-213.
22. Moreno-Sanchez N, Rueda J, Carabano MJ, Reverter A, McWilliam S, Gonzalez C, et al. Skeletal muscle specific genes networks in cattle. Functional & integrative genomics. 2010; 10: 609-18. doi: 10.1007/s10142-010-0175-2.
23. Sudre K, Cassar-Malek I, Listrat A, Ueda Y, Leroux C, Jurie C, et al. Biochemical and transcriptomic analyses of two bovine skeletal muscles in Charolais bulls divergently selected for muscle growth. Meat science. 2005; 70: 267-77. doi: 10.1016/j.meatsci.2005.01.012.
24. Nueda MJ, Carbonell J, Medina I, Dopazo J, Conesa A. Serial Expression Analysis: a web tool for the analysis of serial gene expression data. Nucleic Acids Res. 2010; 38: W239-45.
25. Conesa A, Nueda MJ, Ferrer A, Talon M. maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics. 2006; 22: 1096-102.
26. Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nature reviews Genetics. 2004; 5: 101-13. doi: 10.1038/nrg1272.
27. Mitra K, Carvunis AR, Ramesh SK, Ideker T. Integrative approaches for finding modular structure in biological networks. Nature reviews Genetics. 2013; 14: 719-32. doi:10.1038/nrg3552.
28. Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature. 2004; 431: 308-12. doi:10.1038/nature02782.
29. Schadt EE, Friend SH, Shaywitz DA. A network view of disease and compound screening. Nature reviews Drug discovery. 2009; 8: 286-95. doi: 10.1038/nrd2826.
30. Stuart JM, Segal E, Koller D, Kim SK. A gene-coexpression network for global discovery of conserved genetic modules. Science. 2003; 302: 249-55. doi: 10.1126/science.1087447.
31. Jordan IK, Marino-Ramirez L, Wolf YI, Koonin EV. Conservation and coevolution in the scale-free human gene coexpression network. Molecular biology and evolution. 2004; 21: 2058-70. doi: 10.1093/molbev/msh222.
32. Fuller TF, Ghazalpour A, Aten JE, Drake TA, Lusis AJ, Horvath S. Weighted gene coexpression network analysis strategies applied to mouse weight. Mamm Genome. 2007; 18: 463-72.
33. Stanley D, Watson-Haigh N., Cowled CJ, Moore RJ. Genetic architecture of gene expression in the chicken. BMC Genomics. 2013; 14: 13. doi: 10.1186/1471-2164-14-13.
34. Kogelman L, Byrne K, Vuocolo T, Watson-Haigh N, Kadarmideen H, Kijas J, et al. Genetic architecture of gene expression in ovine skeletal muscle. BMC Genomics. 2011; 12: 607.
35. Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Statistical applications in genetics and molecular biology. 2005; 4.
36. Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008; 9: 559.
37. Mason M, Fan G, Plath K, Zhou Q, Horvath S. Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells. BMC Genomics. 2009; 10.
38. Gustin MP, Paultre CZ, Randon J, Bricca G, Cerutti C. Functional meta- analysis of double connectivity in gene coexpression networks in mammals. Physiol Genomics. 2008; 34: 34-41.
39. Saris CG, Horvath S, van Vught PW, van Es MA, Blauw HM, Fuller TF, et al. Weighted gene co-expression network analysis of the peripheral blood from Amyotrophic Lateral Sclerosis patients. BMC Genomics. 2009; 10: 405.
40. Kadarmideen H, Watson-Haigh N, Andronicos N. Systems biology of ovine intestinal parasite resistance: disease gene modules and biomarkers. Molecular Biosystems. 2011; 7: 235-46.
41. Kadarmideen HN, von Rohr P, Janss LL. From genetical genomics to systems genetics: potential applications in quantitative genomics and animal breeding. Mamm Genome. 2006; 17: 548-64.
42. Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol. 2005; 4 Article17.
43. Langfelder P, Zhang B, Horvath S. Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics. 2008; 24: 719-20.
44. Langfelder P, Horvath S. Eigengene networks for studying the relationships between co-expression modules. BMC Syst Biol. 2007; 1: 54.
45. Ghazalpour A, Doss S, Zhang B, Wang S, Plaisier C, Castellanos R, et al. Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet. 2006; 2: e130.
46. Kadarmideen HN, Watson-Haigh N., Andronicos NM. Systems biology of ovine intestinal parasite resistance: disease gene modules and biomarkers. Mol Biosyst. 2011; 7: 235-46.
47. Huang da W, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, et al. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 2007; 35: W169-75.
48. Hu Z, Hung JH, Wang Y, Chang YC, Huang CL, Huyck M, et al. VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res. 2009; 37: W115-21.
49. Gargalovic PS, Imura M, Zhang B, Gharavi NM, Clark MJ, Pagnon J, et al. Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids. Proc Natl Acad Sci U S A. 2006; 103: 12741-6.
50. Kadarmideen H, Watson-Haigh N. Building gene co-expression networks using transcriptomics data for systems biology investigations: Comparison of methods using microarray data. Bioinformation. 2012; 8: 855-61.
51. Maier A, McEwan JC, Dodds KG, Fischman DA, Fitzsimons RB, Harris AJ. Myosin heavy chain composition of single fibres and their origins and distribution in developing fascicles of sheep tibialis cranialis muscles. Journal of Muscle Research & Cell Motility. 1992; 13: 551-72.
52. Wilson S, McEwan J, Sheard P, Harris A. Early stages of myogenesis in a large mammal: formation of successive generations of myotubes in sheep tibialis cranialis muscle. Journal of Muscle Research & Cell Motility. 1992; 13: 534-50.
53. Andersson L, Georges M. Domestic-animal genomics: deciphering the genetics of complex traits. Nat Rev Genet. 2004; 5: 202-12.
54. Womack JE. Advances in livestock genomics: opening the barn door. Genome Res. 2005; 15: 1699-705.
55. Wang T, Kobayashi T, Takimoto R, Denes AE, Snyder EL, el-Deiry WS, et al. hADA3 is required for p53 activity. Embo J. 2001; 20: 6404-13.
56. Sekaric P, Shamanin VA, Luo J, Androphy EJ. hAda3 regulates p14ARF-induced p53 acetylation and senescence. Oncogene. 2007; 26: 6261-8.
57. Nag A, Germaniuk-Kurowska A, Dimri M, Sassack MA, Gurumurthy CB, Gao Q, et al. An essential role of human Ada3 in p53 acetylation. J Biol Chem. 2007; 282: 8812-20.
58. Mohibi S, Gurumurthy CB, Nag A, Wang J, Mirza S, Mian Y, et al. Mammalian alteration/deficiency in activation 3 (Ada3) is essential for embryonic development and cell cycle progression. J Biol Chem. 2012; 287: 29442-56. doi: 10.1074/jbc.M112.378901.
59. Mirza S, Katafiasz BJ, Kumar R, Wang J, Mohibi S, Jain S, et al. Alteration/ deficiency in activation-3 (Ada3) plays a critical role in maintaining genomic stability. Cell Cycle. 2012; 11: 4266-74. doi: 10.4161/cc.22613.
60. Buendia B, Santa-Maria A, Courvalin JC. Caspase-dependent proteolysis of integral and peripheral proteins of nuclear membranes and nuclear pore complex proteins during apoptosis. J Cell Sci. 1999; 112 (Pt 11): 1743-53.
61. Maske CP, Hollinshead MS, Higbee NC, Bergo MO, Young SG, Vaux DJ. A carboxyl-terminal interaction of lamin B1 is dependent on the CAAX endoprotease Rce1 and carboxymethylation. J Cell Biol. 2003; 162: 1223-32.
62. Kaufmann SH, Mabry M, Jasti R, Shaper JH. Differential expression of nuclear envelope lamins A and C in human lung cancer cell lines. Cancer Res. 1991; 51: 581-6.
63. Takamori Y, Tamura Y, Kataoka Y, Cui Y, Seo S, Kanazawa T, et al. Differential expression of nuclear lamin, the major component of nuclear lamina, during neurogenesis in two germinal regions of adult rat brain. Eur J Neurosci. 2007; 25: 1653-62.
64. Derynck R, Akhurst RJ. Differentiation plasticity regulated by TGF-beta family proteins in development and disease. Nature cell biology. 2007; 9: 1000-4. doi:10.1038/ncb434.
65. Campbell W, Kelly D, Rizzino A. Expression of transforming growth factor-β3 by embryonal carcinoma cells, parietal endoderm-like cells and early mouse embryos. In Vitro Cell Dev Biol. 1990; 26: 1181-5. doi: 10.1007/bf02623696.
66. Kaartinen V, Voncken JW, Shuler C, Warburton D, Bu D, Heisterkamp N, et al. Abnormal lung development and cleft palate in mice lacking TGF-beta 3 indicates defects of epithelial-mesenchymal interaction. Nat Genet. 1995; 11: 415-21. doi: 10.1038/ng1295-415.
67. Newbery HJ, Loh DH, O'Donoghue JE, Tomlinson VA, Chau YY, Boyd JA, et al. Translation elongation factor eEF1A2 is essential for post-weaning survival in mice. J Biol Chem. 2007; 282: 28951-9. doi: 10.1074/jbc.M703962200.
68. Griffiths LA, Doig J, Churchhouse AM, Davies FC, Squires CE, Newbery HJ, et al. Haploinsufficiency for translation elongation factor eEF1A2 in aged mouse muscle and neurons is compatible with normal function. PloS one. 2012; 7: e41917. doi: 10.1371/journal.pone.0041917.
69. Eash J, Olsen A, Breur G, Gerrard D, Hannon K. FGFR1 inhibits skeletal muscle atrophy associated with hindlimb suspension. BMC musculoskeletal disorders. 2007; 8: 32. doi: 10.1186/1471-2474-8-32.
70. Scholpp S, Groth C, Lohs C, Lardelli M, Brand M. Zebrafish fgfr1 is a member of the fgf8 synexpression group and is required for fgf8 signalling at the midbrain- hindbrain boundary. Dev Genes Evol. 2004; 214: 285-95.
71. Guasch G, Popovici C, Mugneret F, Chaffanet M, Pontarotti P, Birnbaum D, et al. Endogenous retroviral sequence is fused to FGFR1 kinase in the 8p12 stem-cell myeloproliferative disorder with t(8;19)(p12;q13.3). Blood. 2003; 101: 286-8.
72. Frey N, Richardson JA, Olson EN. Calsarcins, a novel family of sarcomeric calcineurin-binding proteins. Proc Natl Acad Sci U S A. 2000; 97: 14632-7. doi: 10.1073/pnas.260501097.
73. Wang H, Zhu Z, Yang S, Mo D, Li K. Characterization of different expression patterns of calsarcin-1 and calsarcin-2 in porcine muscle. Gene. 2006; 374: 104-11. doi: 10.1016/j.gene.2006.01.035.
74. Frey N, Frank D, Lippl S, Kuhn C, Kögler H, Barrientos T, et al. Calsarcin-2 deficiency increases exercise capacity in mice through calcineurin/NFAT activation. The Journal of clinical investigation. 2008; 118: 3598.
75. Reverter A, Hudson NJ, Wang Y, Tan SH, Barris W, Byrne KA, et al. A gene coexpression network for bovine skeletal muscle inferred from microarray data. Physiol Genomics. 2006; 28: 76-83. doi: 10.1152/physiolgenomics.00105.2006.