Genome-wide analysis of DNA methylation patterns in horse
详细信息 查看全文
- 作者：Ja-Rang Lee (41)
Chang Pyo Hong (42)
Jae-Woo Moon (42)
Yi-Deun Jung (41)
Dae-Soo Kim (43)
Tae-Hyung Kim (42)
Jeong-An Gim (41)
Jin-Han Bae (41)
Yuri Choi (41)
Jungwoo Eo (41)
Yun-Jeong Kwon (41)
Sanghoon Song (42)
Junsu Ko (42)
Young Mok Yang (44)
Hak-Kyo Lee (45)
Kyung-Do Park (45)
Kung Ahn (42)
Kyoung-Tag Do (45)
Hong-Seok Ha (46)
Kyudong Han (47)
Joo Mi Yi (48)
Hee-Jae Cha (49)
Byung-Wook Cho (41)
Jong Bhak (42)
Heui-Soo Kim (41)
41. Department of Biological Sciences ; College of Natural Sciences ; Pusan National University ; Busan ; 609-735 ; Republic of Korea
42. TBI ; Theragen BiO Institute ; TheragenEtex ; Suwon ; 443-270 ; Republic of Korea
43. Genome Resource Center ; Korea Research Institute of Bioscience and Biotechnology (KRIBB) ; 111 Gwahangno ; Yuseong-gu ; Daejeon ; 305-806 ; Republic of Korea
44. Department of Pathology ; School of Medicine ; Institute of Biomedical Science and Technology ; Konkuk University ; Seoul ; 143-701 ; Republic of Korea
45. Department of Biotechnology ; Hankyong National University ; Anseong ; 456-749 ; Republic of Korea
46. Department of Genetics ; Human Genetics Institute of New Jersey ; Rutgers ; the State University of New Jersey ; 145 Bevier Rd ; Piscataway ; NJ ; 08854 ; USA
47. Department of Nanobiomedical Science and WCU Research Center ; Dankook University ; Cheonan ; 330-714 ; Republic of Korea
48. Research Center ; Dongnam Institute of Radiological & Medical Sciences (DIRAMS) ; Jwadong-gil 40 ; Jangan-eup ; Gijang-gun ; Busan ; 619-950 ; Republic of Korea
49. Department of Parasitology and Genetics ; Kosin University College of Medicine ; Busan ; 602-703 ; Republic of Korea - 关键词：Thoroughbred horse ; Jeju horse ; Genome ; wide DNA methylation ; Differential methylated region (DMR) ; MeDIP ; seq
- 刊名：BMC Genomics
- 出版年：2014
- 出版时间：December 2014
- 年：2014
- 卷：15
- 期：1
- 全文大小：2,132 KB
- 参考文献：1. Sasaki, H, Allen, ND, Surani, MA (1993) DNA methylation and genomic imprinting in mammals. EXS 64: pp. 469-486
2. 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: pp. 3531-3535 CrossRef
3. Siegfried, Z, Eden, S, Mendelsohn, M, Feng, X, Tsuberi, BZ, Cedar, H (1999) DNA methylation represses transcription in vivo. Nat Genet 22: pp. 203-206 CrossRef
4. Bird, A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16: pp. 6-21 CrossRef
5. Robertson, KD (2005) DNA methylation and human disease. Nat Rev Genet 6: pp. 597-610 CrossRef
6. Conerly, M, Grady, WM (2010) Insights into the role of DNA methylation in disease through the use of mouse models. Dis Model Mech 3: pp. 290-297 CrossRef
7. Kulis, M, Esteller, M (2010) DNA methylation and cancer. Adv Genet 70: pp. 27-56 CrossRef
8. Illingworth, R, Kerr, A, Desousa, D, Jorgensen, H, Ellis, P, Stalker, J, Jackson, D, Clee, C, Plumb, R, Rogers, J, Humphray, S, Cox, T, Langford, C, Bird, A (2008) A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol 6: pp. e22 CrossRef
9. Jaenisch, R, Bird, A (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33: pp. 245-254 CrossRef
10. Li, E, Bestor, TH, Jaenisch, R (1992) Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69: pp. 915-926 CrossRef
11. Okano, M, Bell, DW, Haber, DA, Li, E (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99: pp. 247-257 CrossRef
12. Weber, M, Davies, JJ, Wittig, D, Oakeley, EJ, Haase, M, Lam, WL, Schubeler, D (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37: pp. 853-862 CrossRef
13. Zhang, X, Yazaki, J, Sundaresan, A, Cokus, S, Chan, SW, Chen, H, Henderson, IR, Shinn, P, Pellegrini, M, Jacobsen, SE, Ecker, JR (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 126: pp. 1189-1201 CrossRef
14. Zilberman, D, Gehring, M, Tran, RK, Ballinger, T, Henikoff, S (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39: pp. 61-69 CrossRef
15. Gehring, M, Bubb, KL, Henikoff, S (2009) Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324: pp. 1447-1451 CrossRef
16. 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: pp. 137 CrossRef
17. Sati, S, Tanwar, VS, Kumar, KA, Patowary, A, Jain, V, Ghosh, S, Ahmad, S, Singh, M, Reddy, SU, Chandak, GR, Raghunath, M, Sivasubbu, S, Chakraborty, K, Scaria, V, Sengupta, S (2012) High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region. PLoS One 7: pp. e31621 CrossRef
18. Irizarry, RA, Ladd-Acosta, C, Wen, B, Wu, Z, Montano, C, Onyango, P, Cui, H, Gabo, K, Rongione, M, Webster, M, Ji, H, Potash, JB, Sabunciyan, S, Feinberg, AP (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41: pp. 178-186 CrossRef
19. Feng, S, Cokus, SJ, Zhang, X, Chen, PY, Bostick, M, Goll, MG, Hetzel, J, Jain, J, Strauss, SH, Halpern, ME, Ukomadu, C, Sadler, KC, Pradhan, S, Pellegrini, M, Jacobsen, SE (2010) Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A 107: pp. 8689-8694 CrossRef
20. Enard, W, Fassbender, A, Model, F, Adorjan, P, Paabo, S, Olek, A (2004) Differences in DNA methylation patterns between humans and chimpanzees. Curr Biol 14: pp. R148-R149 CrossRef
21. Gama-Sosa, MA, Midgett, RM, Slagel, VA, Githens, S, Kuo, KC, Gehrke, CW, Ehrlich, M (1983) Tissue-specific differences in DNA methylation in various mammals. Biochim Biophys Acta 740: pp. 212-219 CrossRef
22. Zemach, A, McDaniel, IE, Silva, P, Zilberman, D (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328: pp. 916-919 CrossRef
23. Igarashi, J, Muroi, S, Kawashima, H, Wang, X, Shinojima, Y, Kitamura, E, Oinuma, T, Nemoto, N, Song, F, Ghosh, S, Held, WA, Nagase, H (2008) Quantitative analysis of human tissue-specific differences in methylation. Biochem Biophys Res Commun 376: pp. 658-664 CrossRef
24. Weber, M, Hellmann, I, Stadler, MB, Ramos, L, Paabo, S, Rebhan, M, Schubeler, D (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39: pp. 457-466 CrossRef
25. Rakyan, VK, Down, TA, Thorne, NP, Flicek, P, Kulesha, E, Gr盲f, S, Tomazou, EM, Backdahl, L, Johnson, N, Herberth, M, Howe, KL, Jackson, DK, Miretti, MM, Fiegler, H, Marioni, JC, Birney, E, Hubbard, TJ, Carter, NP, Tavar茅, S, Beck, S (2008) An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res 18: pp. 1518-1529 CrossRef
26. Eckhardt, F, Lewin, J, Cortese, R, Rakyan, VK, Attwood, J, Burger, M, Burton, J, Cox, TV, Davies, R, Down, TA, Haefliger, C, Horton, R, Howe, K, Jackson, DK, Kunde, J, Koenig, C, Liddle, J, Niblett, D, Otto, T, Pettett, R, Seemann, S, Thompson, C, West, T, Rogers, J, Olek, A, Berlin, K, Beck, S (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38: pp. 1378-1385 CrossRef
27. Kitamura, E, Igarashi, J, Morohashi, A, Hida, N, Oinuma, T, Nemoto, N, Song, F, Ghosh, S, Held, WA, Yoshida-Noro, C, Nagase, H (2007) Analysis of tissue-specific differentially methylated regions (TDMs) in humans. Genomics 89: pp. 326-337 CrossRef
28. Gibbs, JR, van der Brug, MP, Hernandez, DG, Traynor, BJ, Nalls, MA, Lai, SL, Arepalli, S, Dillman, A, Rafferty, IP, Troncoso, J, Johnson, R, Zielke, HR, Ferrucci, L, Longo, DL, Cookson, MR, Singleton, AB (2010) Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet 6: pp. e1000952 CrossRef
29. Hill, EW, Gu, J, Eivers, SS, Fonseca, RG, McGivney, BA, Govindarajan, P, Orr, N, Katz, LM, MacHugh, DE (2010) A sequence polymorphism in MSTN predicts sprinting ability and racing stamina in thoroughbred horses. PLoS One 5: pp. e8645 CrossRef
30. McGivney, BA, Browne, JA, Fonseca, RG, Katz, LM, Machugh, DE, Whiston, R, Hill, EW (2012) MSTN genotypes in Thoroughbred horses influence skeletal muscle gene expression and racetrack performance. Anim Genet 43: pp. 810-812 CrossRef
31. Bower, MA, McGivney, BA, Campana, MG, Gu, J, Andersson, LS, Barrett, E, Davis, CR, Mikko, S, Stock, F, Voronkova, V, Bradley, DG, Fahey, AG, Lindgren, G, MacHugh, DE, Sulimova, G, Hill, EW (2012) The genetic origin and history of speed in the Thoroughbred racehorse. Nat Commun 3: pp. 643 CrossRef
32. Webbon, P (2012) Harnessing the genetic toolbox for the benefit of the racing Thoroughbred. Equine Vet J 44: pp. 8-12 CrossRef
33. Hill, EW, Gu, J, McGivney, BA, MacHugh, DE (2010) Targets of selection in the Thoroughbred genome contain exercise-relevant gene SNPs associated with elite racecourse performance. Anim Genet 41: pp. 56-63 CrossRef
34. Hill, EW, McGivney, BA, Gu, J, Whiston, R, Machugh, DE (2010) A genome-wide SNP-association study confirms a sequence variant (g.66493737C鈥?鈥塗) in the equine myostatin (MSTN) gene as the most powerful predictor of optimum racing distance for Thoroughbred racehorses. BMC Genomics 11: pp. 552 CrossRef
35. Park, KD, Park, J, Ko, J, Kim, BC, Kim, HS, Ahn, K, Do, KT, Choi, H, Kim, HM, Song, S, Lee, S, Jho, S, Kong, HS, Yang, YM, Jhun, BH, Kim, C, Kim, TH, Hwang, S, Bhak, J, Lee, HK, Cho, BW (2012) Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq. BMC Genomics 13: pp. 473 CrossRef
36. Cho, BW, Lee, KW, Kang, HS, Kim, SK, Shin, TS, Kim, YG (2001) Application of polymerase chain reaction with short oligonucletide primers of arbitrary sequence for the genetic analysis of Cheju native horse. J Agr Tech Dev Inst 5: pp. 109-114
37. Cho, GJ (2007) Genetic Relationship and Characteristics Using microsatellite. J Life Sci 17: pp. 699-705 CrossRef
38. Kim, KI, Yang, YH, Lee, SS, Park, C, Ma, R, Bouzat, JL, Lewin, HA (1999) Phylogenetic relationships of Cheju horses to other horse breeds as determined by mtDNA D-loop sequence polymorphism. Anim Genet 30: pp. 102-108 CrossRef
39. Shin, JA, Yang, YH, Kim, HS, Yun, YM, Lee, KK (2002) Genetic polymorphism of the serum proteins of horses in Jeju. J Vet Sci 3: pp. 255-263
40. Schroder, W, Klostermann, A, Stock, KF, Distl, O (2012) A genome-wide association study for quantitative trait loci of show-jumping in Hanoverian warmblood horses. Anim Genet 43: pp. 392-400 CrossRef
41. Corbin, LJ, Blott, SC, Swinburne, JE, Sibbons, C, Fox-Clipsham, LY, Helwegen, M, Parkin, TD, Newton, JR, Bramlage, LR, McIlwraith, CW, Bishop, SC, Woolliams, JA, Vaudin, M (2012) A genome-wide association study of osteochondritis dissecans in the Thoroughbred. Mamm Genome 23: pp. 294-303 CrossRef
42. Barres, R, Yan, J, Egan, B, Treebak, JT, Rasmussen, M, Fritz, T, Caidahl, K, Krook, A, O'Gorman, DJ, Zierath, JR (2012) Acute exercise remodels promoter methylation in human skeletal muscle. Cell Metab 15: pp. 405-411 CrossRef
43. Gomez-Pinilla, F, Zhuang, Y, Feng, J, Ying, Z, Fan, G (2011) Exercise impacts brain-derived neurotrophic factor plasticity by engaging mechanisms of epigenetic regulation. Eur J Neurosci 33: pp. 383-390 CrossRef
44. Brutsaert, TD, Parra, EJ (2006) What makes a champion? Explaining variation in human athletic performance. Respir Physiol Neurobiol 151: pp. 109-123 CrossRef
45. Terruzzi, I, Senesi, P, Montesano, A, La Torre, A, Alberti, G, Benedini, S, Caumo, A, Fermo, I, Luzi, L (2011) Genetic polymorphisms of the enzymes involved in DNA methylation and synthesis in elite athletes. Physiol Genomics 43: pp. 965-973 CrossRef
46. Hu, Y, Xu, H, Li, Z, Zheng, X, Jia, X, Nie, Q, Zhang, X (2013) Comparison of the genome-wide DNA methylation profiles between fast-growing and slow-growing broilers. PLoS One 8: pp. e56411 CrossRef
47. Jones, PA (2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 13: pp. 484-492 CrossRef
48. da Huang, W, Sherman, BT, Lempicki, RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: pp. 44-57 CrossRef
49. Booth, FW, Chakravarthy, MV, Spangenburg, EE (2002) Exercise and gene expression: physiological regulation of the human genome through physical activity. J Physiol 543: pp. 399-411 CrossRef
50. Li, Q, Li, N, Hu, X, Li, J, Du, Z, Chen, L, Yin, G, Duan, J, Zhang, H, Zhao, Y, Wang, J, Li, N (2011) Genome-wide mapping of DNA methylation in chicken. PLoS One 6: pp. e19428 CrossRef
51. Klose, RJ, Bird, AP (2006) Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 31: pp. 89-97 CrossRef
52. 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: pp. 1068-1075 CrossRef
53. Adelson, DL, Raison, JM, Garber, M, Edgar, RC (2010) Interspersed repeats in the horse (Equus caballus); spatial correlations highlight conserved chromosomal domains. Anim Genet 41: pp. 91-99 CrossRef
54. Portela, A, Esteller, M (2010) Epigenetic modifications and human disease. Nat Biotechnol 28: pp. 1057-1068 CrossRef
55. Gordenin, DA, Lobachev, KS, Degtyareva, NP, Malkova, AL, Perkins, E, Resnick, MA (1993) Inverted DNA repeats: a source of eukaryotic genomic instability. Mol Cell Biol 13: pp. 5315-5322
56. Walsh, CP, Chaillet, JR, Bestor, TH (1998) Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat Genet 20: pp. 116-117 CrossRef
57. Gao, F, Luo, Y, Li, S, Li, J, Lin, L, Nielsen, AL, S酶rensen, CB, Vajta, G, Wang, J, Zhang, X, Du, Y, Yang, H, Bolund, L (2011) Comparison of gene expression and genome-wide DNA methylation profiling between phenotypically normal cloned pigs and conventionally bred controls. PLoS One 6: pp. e25901 CrossRef
58. Grunau, C, Hindermann, W, Rosenthal, A (2000) Large-scale methylation analysis of human genomic DNA reveals tissue-specific differences between the methylation profiles of genes and pseudogenes. Hum Mol Genet 9: pp. 2651-2663 CrossRef
59. Bang, WY, Kim, SW, Kwon, SG, Hwang, JH, Kim, TW, Ko, MS, Cho, IC, Joo, YK, Cho, KK, Jeong, JY, Kim, CW (2013) Swine liver methylomes of Berkshire, Duroc and Landrace breeds by MeDIPS. Anim Genet 44: pp. 463-466 CrossRef
60. Yang, C, Zhang, M, Niu, W, Yang, R, Zhang, Y, Qiu, Z, Sun, B, Zhao, Z (2011) Analysis of DNA methylation in various swine tissues. PLoS One 6: pp. e16229 CrossRef
61. Shukla, S, Kavak, E, Gregory, M, Imashimizu, M, Shutinoski, B, Kashlev, M, Oberdoerffer, P, Sandberg, R, Oberdoerffer, S (2011) CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 479: pp. 74-79 CrossRef
62. Hirano, M, Anderson, DE, Erickson, HP, Hirano, T (2001) Bimodal activation of SMC ATPase by intra- and inter-molecular interactions. EMBO J 20: pp. 3238-3250 CrossRef
63. Karki, S, Holzbaur, EL (1999) Cytoplasmic dynein and dynactin in cell division and intracellular transport. Curr Opin Cell Biol 11: pp. 45-53 CrossRef
64. Fletcher, DA, Mullins, RD (2010) Cell mechanics and the cytoskeleton. Nature 463: pp. 485-492 CrossRef
65. Li, R, Yu, C, Li, Y, Lam, TW, Yiu, SM, Kristiansen, K, Wang, J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: pp. 1966-1967 CrossRef
66. Zhang, Y, Liu, T, Meyer, CA, Eeckhoute, J, Johnson, DS, Bernstein, BE, Nusbaum, C, Myers, RM, Brown, M, Li, W, Liu, XS (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: pp. R137 CrossRef
67. Ye, T, Krebs, AR, Choukrallah, MA, Keime, C, Plewniak, F, Davidson, I, Tora, L (2011) seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res 39: pp. e35 CrossRef - 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
- 出版者：BioMed Central
- ISSN：1471-2164
文摘
Background DNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms. Although the horse reference genome and whole transcriptome data are publically available the global DNA methylation data are yet to be known. Results We report the first genome-wide DNA methylation characteristics data from skeletal muscle, heart, lung, and cerebrum tissues of thoroughbred (TH) and Jeju (JH) horses, an indigenous Korea breed, respectively by methyl-DNA immunoprecipitation sequencing. The analysis of the DNA methylation patterns indicated that the average methylation density was the lowest in the promoter region, while the density in the coding DNA sequence region was the highest. Among repeat elements, a relatively high density of methylation was observed in long interspersed nuclear elements compared to short interspersed nuclear elements or long terminal repeat elements. We also successfully identified differential methylated regions through a comparative analysis of corresponding tissues from TH and JH, indicating that the gene body regions showed a high methylation density. Conclusions We provide report the first DNA methylation landscape and differentially methylated genomic regions (DMRs) of thoroughbred and Jeju horses, providing comprehensive DMRs maps of the DNA methylome. These data are invaluable resource to better understanding of epigenetics in the horse providing information for the further biological function analyses.