Comparison of the Genome-Wide DNA Methylation Profiles between Fast-Growing and Slow-Growing Broilers

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Hu, Yongsheng ^a,b   Xu, Haiping ^a,b   Li, Zhenhui ^a,b   Zheng, Xuejuan ^a,b   Jia, Xinzheng ^a,b   Nie, Qinghua ^a,b   Zhang, Xiquan ^a,b  

^a SOUTH CHINA AGRICULTURAL UNIVERSITY   (China)

^b AGRO ENVIRONMENTAL PROTECTION INSTITUTE   (China)

Author keywords

[No Author keywords available]

Indexed keywords

FIBROBLAST GROWTH FACTOR; FIBROBLAST GROWTH FACTOR 12; FIBROBLAST GROWTH FACTOR 14; FIBROBLAST GROWTH FACTOR 18; FIBROBLAST GROWTH FACTOR RECEPTOR 2; FIBROBLAST GROWTH FACTOR RECEPTOR 3; SOMATOMEDIN C RECEPTOR; UNCLASSIFIED DRUG;

AGE; ANIMAL GENETICS; ARTICLE; BREED DIFFERENCE; BROILER; COMPARATIVE STUDY; CONTROLLED STUDY; DNA METABOLISM; DNA METHYLATION; DNA SEQUENCE; GENE FUNCTION; GENE IDENTIFICATION; GENOME ANALYSIS; GROWTH CURVE; IMMUNOPRECIPITATION; NONHUMAN; PROMOTER REGION; SEQUENCE ANALYSIS; UNTRANSLATED REGION;

ANIMALS; CHICKENS; COMPUTATIONAL BIOLOGY; CPG ISLANDS; DNA METHYLATION; EPIGENOMICS; FEMALE; GENE EXPRESSION REGULATION; GENOME; GENOME-WIDE ASSOCIATION STUDY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOLECULAR SEQUENCE ANNOTATION; QUANTITATIVE TRAIT, HERITABLE; REPRODUCIBILITY OF RESULTS;

EID: 84874144418     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0056411     Document Type: Article

References (56)

1. Scanes CG, Harvey S, Marsh JA, King DB, (1984) Hormones and growth in poultry. Poult Sci 63: 2062-2074.
2. Gu X, Feng C, Ma L, Song C, Wang Y, et al. (2011) Genome-wide association study of body weight in chicken F2 resource population. PLoS One 6: e21872.
3. Xie L, Luo C, Zhang C, Zhang R, Tang J, et al. (2012) Genome-wide association study identified a narrow chromosome 1 region associated with chicken growth traits. PLoS One 7: e30910.
4. Lei M, Peng X, Zhou M, Luo C, Nie Q, et al. (2008) Polymorphisms of the IGF1R gene and their genetic effects on chicken early growth and carcass traits. BMC Genet 9: 70.
5. Rubin CJ, Zody MC, Eriksson J, Meadows JR, Sherwood E, et al. (2010) Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464: 587-591.
6. Zhang H, Liu SH, Zhang Q, Zhang YD, Wang SZ, et al. (2011) Fine-mapping of quantitative trait loci for body weight and bone traits and positional cloning of the RB1 gene in chicken. J Anim Breed Genet 128: 366-375.
7. Abasht B, Dekkers JC, Lamont SJ, (2006) Review of quantitative trait loci identified in the chicken. Poult Sci 85: 2079-2096.
8. Zhou H, Deeb N, Evock-Clover CM, Ashwell CM, Lamont SJ, (2006) Genome-wide linkage analysis to identify chromosomal regions affecting phenotypic traits in the chicken. I. Growth and average daily gain. Poult Sci 85: 1700-1711.
9. Nadaf J, Pitel F, Gilbert H, Duclos MJ, Vignoles F, et al. (2009) QTL for several metabolic traits map to loci controlling growth and body composition in an F2 intercross between high- and low-growth chicken lines. Physiol Genomics 38: 241-249.
10. Uemoto Y, Sato S, Odawara S, Nokata H, Oyamada Y, et al. (2009) Genetic mapping of quantitative trait loci affecting growth and carcass traits in F2 intercross chickens. Poult Sci 88: 477-482.
11. Ankra-Badu GA, Le Bihan-Duval E, Mignon-Grasteau S, Pitel F, Beaumont C, et al. (2010) Mapping QTL for growth and shank traits in chickens divergently selected for high or low body weight. Anim Genet 41: 400-405.
12. Petronis A, (2010) Epigenetics as a unifying principle in the aetiology of complex traits and diseases. Nature 465: 721-727.
13. Sasaki H, Allen ND, Surani MA, (1993) DNA methylation and genomic imprinting in mammals. EXS 64: 469-486.
14. Courtier B, Heard E, Avner P, (1995) Xce haplotypes show modified methylation in a region of the active X chromosome lying 3′ to Xist. Proc Natl Acad Sci U S A 92: 3531-3535.
15. Siegfried Z, Eden S, Mendelsohn M, Feng X, Tsuberi BZ, et al. (1999) DNA methylation represses transcription in vivo. Nat Genet 22: 203-206.
16. Bird A, (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16: 6-21.
17. Robertson KD, (2005) DNA methylation and human disease. Nat Rev Genet 6: 597-610.
18. Conerly M, Grady WM, (2010) Insights into the role of DNA methylation in disease through the use of mouse models. Dis Model Mech 3: 290-297.
19. Kulis M, Esteller M, (2010) DNA methylation and cancer. Adv Genet 70: 27-56.
20. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, et al. (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126: 1189-1201.
21. Ruike Y, Imanaka Y, Sato F, Shimizu K, Tsujimoto G, (2010) Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing. BMC Genomics 11: 137.
22. Sati S, Tanwar VS, Kumar KA, Patowary A, Jain V, et al. (2012) High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region. PLoS One 7: e31621.
23. Li Q, Li N, Hu X, Li J, Du Z, et al. (2011) Genome-wide mapping of DNA methylation in chicken. PLoS One 6: e19428.
24. Li R, Li Y, Kristiansen K, Wang J, (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713-714.
25. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137.
26. Huang da W, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
27. Saxonov S, Berg P, Brutlag DL, (2006) A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A 103: 1412-1417.
28. Illingworth RS, Bird AP, (2009) CpG islands-'a rough guide'. FEBS Lett 583: 1713-1720.
29. Laurent L, Wong E, Li G, Huynh T, Tsirigos A, et al. (2010) Dynamic changes in the human methylome during differentiation. Genome Res 20: 320-331.
30. Klose RJ, Bird AP, (2006) Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 31: 89-97.
31. Lorincz MC, Dickerson DR, Schmitt M, Groudine M, (2004) Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat Struct Mol Biol 11: 1068-1075.
32. Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, et al. (2010) Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A 107: 8689-8694.
33. Thomson JP, Skene PJ, Selfridge J, Clouaire T, Guy J, et al. (2010) CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 464: 1082-1086.
34. Deaton AM, Bird A, (2011) CpG islands and the regulation of transcription. Genes 25: 1010-1022.
35. Illingworth R, Kerr A, Desousa D, Jørgensen H, Ellis P, et al. (2008) A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol 6: e22.
36. Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, et al. (2010) Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466: 253-257.
37. Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr AR, James KD, et al. (2010) Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet 6. pii: e1001134.
38. International Chicken Genome Sequencing Consortium, (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.
39. Deeb N, Lamont SJ, (2002) Genetic architecture of growth and body composition in unique chicken populations. J Hered 93: 107-118.
40. Arbabi S, Maier RV, (2002) Mitogen-activated protein kinases. Crit Care Med 30: S74-S79.
41. Coolican SA, Samuel DS, Ewton DZ, McWade FJ, Florini JR, (1997) The mitogenic and myogenic actions of insulin-like growth factors utilize distinct signaling pathways. Biol Chem 272: 6653-6662.
42. Keren A, Tamir Y, Bengal E, (2006) The p38 MAPK signaling pathway: a major regulator of skeletal muscle development. Mol Cell Endocrinol 252: 224-230.
43. Holbro T, Hynes NE, (2004) ErbB receptors: directing key signaling networks throughout life. Annu Rev Pharmacol Toxicol 44: 195-217.
44. Lu Y, Chen SR, Liu WB, Hou ZC, Xu GY, et al. (2012) Polymorphisms in Wnt signaling pathway genes are significantly associated with chicken carcass traits. Poult Sci 91: 1299-1307.
45. Sastry SK, Burridge K, (2000) Focal adhesions: a nexus for intracellular signaling and cytoskeletal dynamics. Exp Cell Res 261: 25-36.
46. Balda MS, Matter K, (1998) Tight junctions. J Cell Sci 111: 541-547.
47. Pötter E, Bergwitz C, Brabant G, (1999) The cadherin-catenin system: implications for growth and differentiation of endocrine tissues. Endocr Rev 20: 207-239.
48. Bazzoni G, Dejana E, (2004) Endothelial cell-to-cell junctions: molecular organization and role in vascular homeostasis. Physiol Rev 84: 869-901.
49. Liu JP, Baker J, Perkins AS, Robertson EJ, Efstratiadis A, (1993) Mice carrying null mutations of the genes encoding insulin-like growth factor I (Igf-1) and type 1 IGF receptor (Igf1r). Cell 75: 59-72.
50. Huang MB, Xu H, Xie SJ, Zhou H, Qu LH, (2011) Insulin-like growth factor-1 receptor is regulated by microRNA-133 during skeletal myogenesis. PLoS One 6: e29173.
51. Itoh N, (2007) The Fgf families in humans, mice, and zebrafish: their evolutional processes and roles in development, metabolism, and disease. Biol Pharm Bull 30: 1819-1825.
52. Ohuchi H, Kimura S, Watamoto M, Itoh N, (2000) Involvement of fibroblast growth factor (FGF)18-FGF8 signaling in specification of left-right asymmetry and brain and limb development of the chick embryo. Mech Dev 95: 55-66.
53. Cormier S, Leroy C, Delezoide AL, Silve C, (2005) Expression of fibroblast growth factors 18 and 23 during human embryonic and fetal development. Gene Expr Patterns 5: 569-573.
54. Florini JR, Ewton DZ, Magri KA, (1991) Hormones, growth factors, and myogenic differentiation. Annu Rev Physiol 53: 201-216.
55. Loeys BL, Chen J, Neptune ER, Judge DP, Podowski M, et al. (2005) A syndrome of altered cardiovascular, craniofacial, neurocognitive and skeletal development caused by mutations in TGFBR1 or TGFBR2. Nat Genet 37: 275-281.
56. Chen K, Hawken R, Flickinger GH, Rodriguez-Zas SL, Rund LA, et al. (2012) Association of the porcine transforming growth factor beta type I receptor (TGFBR1) gene with growth and carcass traits. Anim Biotechnol 23: 43-63.