Enrichment of short interspersed transposable elements to embryonic stem cell-specific hypomethylated gene regions

Genes to Cells

Volumn 15, Issue 8, 2010, Pages 855-865

  Muramoto, Hiroki ^a   Yagi, Shintaro ^a   Hirabayashi, Keiji ^a   Sato, Shinya ^a   Ohgane, Jun ^a   Tanaka, Satoshi ^a   Shiota, Kunio ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; EMBRYONIC STEM CELL; GENE LOCUS; LONG INTERSPERSED REPEAT; LONG TERMINAL REPEAT; MOUSE; NONHUMAN; PRIORITY JOURNAL; SHORT INTERSPERSED REPEAT; SOMATIC CELL; TRANSPOSON;

ANIMALS; DNA METHYLATION; EMBRYONIC STEM CELLS; HOMEODOMAIN PROTEINS; MICE; MICE, INBRED C57BL; OCTAMER TRANSCRIPTION FACTOR-3; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS;

EID: 77954726621     PISSN: 13569597     EISSN: 13652443     Source Type: Journal    
DOI: 10.1111/j.1365-2443.2010.01423.x     Document Type: Article

References (41)

1. Allen E, Horvath S, Tong F, Kraft P, Spiteri E, Riggs A, Marahrens Y. High concentrations of long interspersed nuclear element sequence distinguish monoallelically expressed genes. Proc. Natl Acad. Sci. USA 2003, 100:9940-9945.
2. Arnaud P, Goubely C, Pélissier T, Deragon J. SINE retroposons can be used in vivo as nucleation centers for de novo methylation. Mol. Cell. Biol. 2000, 20:3434-3441.
3. Bernstein B, Mikkelsen T, Xie X, Kamal M, Huebert D, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber S, Lander E. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 2006, 125:315-326.
4. Chambers I, Colby D, Robertson M, Nichols J, Lee S, Tweedie S, Smith A. Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell 2003, 113:643-655.
5. Chapman V, Forrester L, Sanford J, Hastie N, Rossant J. Cell lineage-specific undermethylation of mouse repetitive DNA. Nature 1984, 307:284-286.
6. Chen X, Xu H, Yuan P. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008, 133:1106-1117.
7. Eckhardt F, Lewin J, Cortese R. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet. 2006, 38:1378-1385.
8. Giardine B, Riemer C, Hardison R, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent W, Nekrutenko A. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005, 15:1451-1455.
9. Goodier J, Kazazian HJ. Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell 2008, 135:23-35.
10. Greally J. Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome. Proc. Natl Acad. Sci. USA 2002, 99:327-332.
11. Hattori N, Imao Y, Nishino K, Hattori N, Ohgane J, Yagi S, Tanaka S, Shiota K. Epigenetic regulation of Nanog gene in embryonic stem and trophoblast stem cells. Genes Cells 2007, 12:387-396.
12. Hattori N, Nishino K, Ko Y, Hattori N, Ohgane J, Tanaka S, Shiota K. Epigenetic control of mouse Oct-4 gene expression in embryonic stem cells and trophoblast stem cells. J. Biol. Chem. 2004, 279:17063-17069.
13. Hellmann-Blumberg U, Hintz M, Gatewood J, Schmid C. Developmental differences in methylation of human Alu repeats. Mol. Cell. Biol. 1993, 13:4523-4530.
14. Ikegami K, Ohgane J, Tanaka S, Yagi S, Shiota K. Interplay between DNA methylation, histone modification and chromatin remodeling in stem cells and during development. Int. J. Dev. Biol. 2009, 53:203-214.
15. Imamura M, Miura K, Iwabuchi K, Ichisaka T, Nakagawa M, Lee J, Kanatsu-Shinohara M, Shinohara T, Yamanaka S. Transcriptional repression and DNA hypermethylation of a small set of ES cell marker genes in male germline stem cells. BMC Dev. Biol. 2006, 6:34.
16. Imamura T, Ohgane J, Ito S, Ogawa T, Hattori N, Tanaka S, Shiota K. CpG island of rat sphingosine kinase-1 gene: tissue-dependent DNA methylation status and multiple alternative first exons. Genomics 2001, 76:117-125.
17. Johnson W, Li W, Meyer C, Gottardo R, Carroll J, Brown M, Liu X. Model-based analysis of tiling-arrays for ChIP-chip. Proc. Natl Acad. Sci. USA 2006, 103:12457-12462.
18. Khulan B, Thompson R, Ye K. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res. 2006, 16:1046-1055.
19. Kramerov DA, Vassetzky NS. Short retroposons in eukaryotic genomes. Int. Rev. Cytol. 2005, 247:165-221.
20. Lei H, Oh S, Okano M, Jüttermann R, Goss K, Jaenisch R, Li E. De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells. Development 1996, 122:3195-3205.
21. Li E, Bestor TH, Jaenisch R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 1992, 69:915-926.
22. Liu W, Schmid C. Proposed roles for DNA methylation in Alu transcriptional repression and mutational inactivation. Nucleic Acids Res. 1993, 21:1351-1359.
23. Maeda C, Sato S, Hattori N, Tanaka S, Yagi S, Shiota K. DNA Hypomethylation Circuit of the Mouse Oocyte-Specific Histone H1foo Gene in Female Germ Cell Lineage. Biol. Reprod. 2008, 78:816-821.
24. Meissner A, Mikkelsen T, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein B, Nusbaum C, Jaffe D, Gnirke A, Jaenisch R, Lander E. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 2008, 454:766-770.
25. Mitsui K, Tokuzawa Y, Itoh H, Segawa K, Murakami M, Takahashi K, Maruyama M, Maeda M, Yamanaka S. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell 2003, 113:631-642.
26. Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562.
27. Niwa H, Miyazaki J, Smith AG. Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat. Genet. 2000, 24:372-376.
28. Ohshima K, Okada N. SINEs and LINEs: symbionts of eukaryotic genomes with a common tail. Cytogenet. Genome Res. 2005, 110:475-490.
29. Okano M, Bell D, Haber D, Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 1999, 99:247-257.
30. Rollins R, Haghighi F, Edwards J, Das R, Zhang M, Ju J, Bestor T. Large-scale structure of genomic methylation patterns. Genome Res. 2006, 16:157-163.
31. Sakamoto H, Suzuki M, Abe T, Hosoyama T, Himeno E, Tanaka S, Greally J, Hattori N, Yagi S, Shiota K. Cell type-specific methylation profiles occurring disproportionately in CpG-less regions that delineate developmental similarity. Genes Cells 2007, 12:1123-1132.
32. Sato M, Kimura T, Kurokawa K, Fujita Y, Abe K, Masuhara M, Yasunaga T, Ryo A, Yamamoto M, Nakano T. Identification of PGC7, a new gene expressed specifically in preimplantation embryos and germ cells. Mech. Dev. 2002, 113:91-94.
33. Sato S, Yagi S, Arai Y, Hirabayashi K, Hattori N, Iwatani M, Okita K, Ohgane J, Tanaka S, Wakayama T, Yamanaka S, Shiota K. Genome-wide DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) residing in mouse pluripotent stem cells. Genes Cells 2010, 15:607-618.
34. Shiota K, Kogo Y, Ohgane J, Imamura T, Urano A, Nishino K, Tanaka S, Hattori N. Epigenetic marks by DNA methylation specific to stem, germ and somatic cells in mice. Genes Cells 2002, 7:961-969.
35. Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 2006, 126:663-676.
36. Tomikawa J, Fukatsu K, Tanaka S, Shiota K. DNA methylation-dependent epigenetic regulation of dimethylarginine dimethylaminohydrolase 2 gene in trophoblast cell lineage. J. Biol. Chem. 2006, 281:12163-12169.
37. Walsh C, Chaillet J, Bestor T. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat. Genet. 1998, 20:116-117.
38. Xie H, Wang M, Bonaldo MF, Smith C, Rajaram V, Goldman S, Tomita T, Soares M. High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum. Nucleic Acids Res. 2009, 37:4331-4340.
39. Yagi S, Hirabayashi K, Sato S, Li W, Takahashi Y, Hirakawa T, Wu G, Hattori N, Hattori N, Ohgane J, Tanaka S, Liu X, Shiota K. DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression. Genome Res. 2008, 18:1969-1978.
40. Yates P, Burman R, Mummaneni P, Krussel S, Turker M. Tandem B1 elements located in a mouse methylation center provide a target for de novo DNA methylation. J. Biol. Chem. 1999, 274:36357-36361.
41. Yoder J, Walsh C, Bestor T. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet. 1997, 13:335-340.