Comparison of gene expression and Genome-Wide DNA methylation profiling between phenotypically normal cloned pigs and conventionally bred controls

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  Gao, Fei ^a   Luo, Yonglun ^a   Li, Shengting ^a   Li, Jian ^a   Lin, Lin ^a   Nielsen, Anders Lade ^a   Sørensen, Charlotte Brandt ^a   Vajta, Gábor ^a   Wang, Jun ^b,c   Zhang, Xiuqing ^c   Du, Yutao ^c   Yang, Huanming ^c   Bolund, Lars ^a,c  

^a AARHUS UNIVERSITY   (Denmark)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c BGI SHENZHEN   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL TISSUE; ARTICLE; BREEDING; CLONING; CLUSTER ANALYSIS; CONTROLLED STUDY; DNA METHYLATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE LOCUS; GENOME; HIERARCHICAL CLUSTERING; KARYOTYPING; LIVER; MODIFIED METHYLATION SPECIFIC DIGITAL KARYOTYPING; MUSCLE; NONHUMAN; SEQUENCE ANALYSIS; ANIMAL; COMPARATIVE STUDY; DNA MICROARRAY; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENE LIBRARY; GENE REGULATORY NETWORK; GENETICS; METABOLISM; PHENOTYPE; POLYMERASE CHAIN REACTION; REPRODUCIBILITY; SWINE;

ANIMALIA; SUIDAE; SUS;

ANIMALS; BREEDING; CLONING, ORGANISM; CLUSTER ANALYSIS; DNA METHYLATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENE REGULATORY NETWORKS; GENETIC LOCI; GENOME; LIVER; MUSCLES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; SUS SCROFA;

EID: 80053991872     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0025901     Document Type: Article

References (41)

1. Prokhortchouk E, Defossez PA, (2008) The cell biology of DNA methylation in mammals. Biochim Biophys Acta 1783: 2167-2173.
2. Morgan HD, Santos F, Green K, Dean W, Reik W, (2005) Epigenetic reprogramming in mammals. Hum Mol Genet 14 Spec No 1: R47-58.
3. Arney KL, Fisher AG, (2004) Epigenetic aspects of differentiation. J Cell Sci 117: 4355-4363.
4. Wilmut I, Beaujean N, de Sousa PA, Dinnyes A, King TJ, et al. (2002) Somatic cell nuclear transfer. Nature 419: 583-586.
5. Yang X, Smith SL, Tian XC, Lewin HA, Renard JP, et al. (2007) Nuclear reprogramming of cloned embryos and its implications for therapeutic cloning. Nat Genet 39: 295-302.
6. Kragh PM, Vajta G, Corydon TJ, Purup S, Bolund L, et al. (2004) Production of transgenic porcine blastocysts by hand-made cloning. Reprod Fertil Dev 16: 315-318.
7. Du Y, Li J, Kragh PM, Zhang Y, Schmidt M, et al. (2007) Piglets born from vitrified cloned blastocysts produced with a simplified method of delipation and nuclear transfer. Cloning Stem Cells 9: 469-476.
8. Du Y, Lin L, Schmidt M, Bogh IB, Kragh PM, et al. (2008) High hydrostatic pressure treatment of porcine oocytes before handmade cloning improves developmental competence and cryosurvival. Cloning Stem Cells 10: 325-330.
9. Cibelli JB, Campbell KH, Seidel GE, West MD, Lanza RP, (2002) The health profile of cloned animals. Nat Biotechnol 20: 13-14.
10. Farin PW, Piedrahita JA, Farin CE, (2006) Errors in development of fetuses and placentas from in vitro-produced bovine embryos. Theriogenology 65: 178-191.
11. Ohgane J, Wakayama T, Kogo Y, Senda S, Hattori N, et al. (2001) DNA methylation variation in cloned mice. Genesis 30: 45-50.
12. Li J, Gao F, Li N, Li S, Yin G, et al. (2009) An improved method for genome wide DNA methylation profiling correlated to transcription and genomic instability in two breast cancer cell lines. BMC Genomics 10: 223.
13. Schmidt M, Kragh PM, Li J, Du Y, Lin L, et al. (2010) Pregnancies and piglets from large white sow recipients after two transfer methods of cloned and transgenic embryos of different pig breeds. Theriogenology 74: 1233-1240.
14. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, et al. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31: e15.
15. Suzuki R, Shimodaira H, (2006) Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22: 1540-1542.
16. Smyth GK, (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3.
17. Smyth GK, Michaud J, Scott HS, (2005) Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21: 2067-2075.
18. Quilter CR, Gilbert CL, Oliver GL, Jafer O, Furlong RA, et al. (2008) Gene expression profiling in porcine maternal infanticide: A model for puerperal psychosis. Am J Med Genet B Neuropsychiatr Genet.
19. Flori L, Rogel-Gaillard C, Cochet M, Lemonnier G, Hugot K, et al. (2008) Transcriptomic analysis of the dialogue between Pseudorabies virus and porcine epithelial cells during infection. BMC Genomics 9: 123.
20. Smit A, Hubley R, Green P, (1996) RepeatMasker Open-3.0.
21. Wilcoxon F, (1945) Individual comparisons by ranking methods. Biometrics Bulletin 1: 80-83.
22. Cai L, Huang H, Blackshaw S, Liu JS, Cepko C, et al. (2004) Clustering analysis of SAGE data using a Poisson approach. Genome Biol 5: R51.
23. Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I, (2001) Controlling the false discovery rate in behavior genetics research. Behav Brain Res 125: 279-284.
24. Ponger L, Mouchiroud D, (2002) CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. Bioinformatics 18: 631-633.
25. Hollborn M, Francke M, Iandiev I, Buhner E, Foja C, et al. (2008) Early activation of inflammation- and immune response-related genes after experimental detachment of the porcine retina. Invest Ophthalmol Vis Sci 49: 1262-1273.
26. Jiang L, Jobst P, Lai L, Samuel M, Ayares D, et al. (2007) Expression levels of growth-regulating imprinted genes in cloned piglets. Cloning Stem Cells 9: 97-106.
27. Smith SL, Everts RE, Tian XC, Du F, Sung LY, et al. (2005) Global gene expression profiles reveal significant nuclear reprogramming by the blastocyst stage after cloning. Proc Natl Acad Sci U S A 102: 17582-17587.
28. Beyhan Z, Ross PJ, Iager AE, Kocabas AM, Cunniff K, et al. (2007) Transcriptional reprogramming of somatic cell nuclei during preimplantation development of cloned bovine embryos. Dev Biol 305: 637-649.
29. Vassena R, Han Z, Gao S, Baldwin DA, Schultz RM, et al. (2007) Tough beginnings: alterations in the transcriptome of cloned embryos during the first two cell cycles. Dev Biol 304: 75-89.
30. Park SH, Park SB, Kim NH, (2003) Expression of early development-related genes in bovine nuclear transferred and fertilized embryos. Zygote 11: 355-360.
31. Hall VJ, Ruddock NT, French AJ, (2005) Expression profiling of genes crucial for placental and preimplantation development in bovine in vivo, in vitro, and nuclear transfer blastocysts. Mol Reprod Dev 72: 16-24.
32. Everts RE, Chavatte-Palmer P, Razzak A, Hue I, Green CA, et al. (2008) Aberrant gene expression patterns in placentomes are associated with phenotypically normal and abnormal cattle cloned by somatic cell nuclear transfer. Physiol Genomics 33: 65-77.
33. Tsai S, Mir B, Martin AC, Estrada JL, Bischoff SR, et al. (2006) Detection of transcriptional difference of porcine imprinted genes using different microarray platforms. BMC Genomics 7: 328.
34. Cho SK, Kim JH, Park JY, Choi YJ, Bang JI, et al. (2007) Serial cloning of pigs by somatic cell nuclear transfer: restoration of phenotypic normality during serial cloning. Dev Dyn 236: 3369-3382.
35. Dinnyes A, Tian XC, Yang X, (2008) Epigenetic regulation of foetal development in nuclear transfer animal models. Reprod Domest Anim 43 (Suppl 2): 302-309.
36. Kang YK, Koo DB, Park JS, Choi YH, Kim HN, et al. (2001) Typical demethylation events in cloned pig embryos. Clues on species-specific differences in epigenetic reprogramming of a cloned donor genome. J Biol Chem 276: 39980-39984.
37. Bonk AJ, Li R, Lai L, Hao Y, Liu Z, et al. (2008) Aberrant DNA methylation in porcine in vitro-, parthenogenetic-, and somatic cell nuclear transfer-produced blastocysts. Mol Reprod Dev 75: 250-264.
38. Han DW, Im YB, Do JT, Gupta MK, Uhm SJ, et al. (2008) Methylation status of putative differentially methylated regions of porcine IGF2 and H19. Mol Reprod Dev 75: 777-784.
39. Kim SH, Kang YK, Koo DB, Kang MJ, Moon SJ, et al. (2004) Differential DNA methylation reprogramming of various repetitive sequences in mouse preimplantation embryos. Biochem Biophys Res Commun 324: 58-63.
40. Shiota K, Kogo Y, Ohgane J, Imamura T, Urano A, et al. (2002) Epigenetic marks by DNA methylation specific to stem, germ and somatic cells in mice. Genes Cells 7: 961-969.
41. Hemberger M, Dean W, Reik W, (2009) Epigenetic dynamics of stem cells and cell lineage commitment: digging Waddington's canal. Nat Rev Mol Cell Biol 10: 526-537.