메뉴 건너뛰기




Volumn 6, Issue 1, 2013, Pages

Identical sets of methylated and nonmethylated genes in Ciona intestinalis sperm and muscle cells

Author keywords

[No Author keywords available]

Indexed keywords

5 METHYLCYTOSINE; BISULFITE; GENOMIC DNA;

EID: 84887359411     PISSN: None     EISSN: 17568935     Source Type: Journal    
DOI: 10.1186/1756-8935-6-38     Document Type: Article
Times cited : (26)

References (47)
  • 1
    • 43749098985 scopus 로고    scopus 로고
    • DNA methylation landscapes: Provocative insights from epigenomics
    • DOI 10.1038/nrg2341, PII NRG2341
    • DNA methylation landscapes: provocative insights from epigenomics. Suzuki MM, Bird A, Nat Rev Genet 2008 9 465 476 18463664 (Pubitemid 351693975)
    • (2008) Nature Reviews Genetics , vol.9 , Issue.6 , pp. 465-476
    • Suzuki, M.M.1    Bird, A.2
  • 2
    • 0036144048 scopus 로고    scopus 로고
    • DNA methylation patterns and epigenetic memory
    • DOI 10.1101/gad.947102
    • DNA methylation patterns and epigenetic memory. Bird A, Genes Dev 2002 16 6 21 10.1101/gad.947102 11782440 (Pubitemid 34049633)
    • (2002) Genes and Development , vol.16 , Issue.1 , pp. 6-21
    • Bird, A.1
  • 3
    • 0037372003 scopus 로고    scopus 로고
    • Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals
    • DOI 10.1038/ng1089
    • Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Jaenisch R, Bird A, Nat Genet 2003 33 Suppl 245 254 12610534 (Pubitemid 36278835)
    • (2003) Nature Genetics , vol.33 , Issue.SUPPL. , pp. 245-254
    • Jaenisch, R.1    Bird, A.2
  • 4
    • 84859910536 scopus 로고    scopus 로고
    • A unique regulatory phase of DNA methylation in the early mammalian embryo
    • 10.1038/nature10960 22456710
    • A unique regulatory phase of DNA methylation in the early mammalian embryo. Smith ZD, Chan MM, Mikkelsen TS, Gu H, Gnirke A, Regev A, Meissner A, Nature 2012 484 339 344 10.1038/nature10960 22456710
    • (2012) Nature , vol.484 , pp. 339-344
    • Smith, Z.D.1    Chan, M.M.2    Mikkelsen, T.S.3    Gu, H.4    Gnirke, A.5    Regev, A.6    Meissner, A.7
  • 5
  • 6
    • 0009832780 scopus 로고
    • In vitro methylation of the hamster adenine phosphoribosyltransferase gene inhibits its expression in mouse L cells
    • DOI 10.1073/pnas.79.11.3418
    • In vitro methylation of the hamster adenine phosphoribosyltransferase gene inhibits its expression in mouse L cells. Stein R, Razin A, Cedar H, Proc Natl Acad Sci USA 1982 79 3418 3422 10.1073/pnas.79.11.3418 6954487 (Pubitemid 12011375)
    • (1982) Proceedings of the National Academy of Sciences of the United States of America , vol.79 , Issue.11 I , pp. 3418-3422
    • Stein, R.1    Razin, A.2    Cedar, H.3
  • 7
    • 51649129596 scopus 로고    scopus 로고
    • Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors
    • 10.1016/j.molcel.2008.05.007 18514006
    • Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mohn F, Weber M, Rebhan M, Roloff TC, Richter J, Stadler MB, Bibel M, Schübeler D, Mol Cell 2008 30 755 766 10.1016/j.molcel.2008.05.007 18514006
    • (2008) Mol Cell , vol.30 , pp. 755-766
    • Mohn, F.1    Weber, M.2    Rebhan, M.3    Roloff, T.C.4    Richter, J.5    Stadler, M.B.6    Bibel, M.7    Schübeler, D.8
  • 8
    • 58549109636 scopus 로고    scopus 로고
    • X chromosome dosage compensation: How mammals keep the balance
    • 10.1146/annurev.genet.42.110807.091711 18729722
    • X chromosome dosage compensation: how mammals keep the balance. Payer B, Lee JT, Annu Rev Genet 2008 42 733 772 10.1146/annurev.genet.42.110807.091711 18729722
    • (2008) Annu Rev Genet , vol.42 , pp. 733-772
    • Payer, B.1    Lee, J.T.2
  • 10
    • 33845880624 scopus 로고    scopus 로고
    • Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription
    • DOI 10.1038/ng1929, PII NG1929
    • Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S, Nat Genet 2007 39 61 69 10.1038/ng1929 17128275 (Pubitemid 46026502)
    • (2007) Nature Genetics , vol.39 , Issue.1 , pp. 61-69
    • Zilberman, D.1    Gehring, M.2    Tran, R.K.3    Ballinger, T.4    Henikoff, S.5
  • 11
    • 34248195006 scopus 로고    scopus 로고
    • CpG methylation is targeted to transcription units in an invertebrate genome
    • DOI 10.1101/gr.6163007
    • CpG methylation is targeted to transcription units in an invertebrate genome. Suzuki MM, Kerr ARW, De Sousa D, Bird A, Genome Res 2007 17 625 631 10.1101/gr.6163007 17420183 (Pubitemid 46715513)
    • (2007) Genome Research , vol.17 , Issue.5 , pp. 625-631
    • Suzuki, M.M.1    Kerr, A.R.W.2    De Sousa, D.3    Bird, A.4
  • 13
    • 77952355762 scopus 로고    scopus 로고
    • Genome-wide evolutionary analysis of eukaryotic DNA methylation
    • 10.1126/science.1186366 20395474
    • Genome-wide evolutionary analysis of eukaryotic DNA methylation. Zemach A, McDaniel IE, Silva P, Zilberman D, Science 2010 328 916 919 10.1126/science.1186366 20395474
    • (2010) Science , vol.328 , pp. 916-919
    • Zemach, A.1    McDaniel, I.E.2    Silva, P.3    Zilberman, D.4
  • 15
    • 78751693154 scopus 로고    scopus 로고
    • Replication timing-related and gene body-specific methylation of active human genes
    • 10.1093/hmg/ddq513 21112978
    • Replication timing-related and gene body-specific methylation of active human genes. Aran D, Toperoff G, Rosenberg M, Hellman A, Hum Mol Genet 2011 20 670 680 10.1093/hmg/ddq513 21112978
    • (2011) Hum Mol Genet , vol.20 , pp. 670-680
    • Aran, D.1    Toperoff, G.2    Rosenberg, M.3    Hellman, A.4
  • 16
    • 84863986133 scopus 로고    scopus 로고
    • Functions of DNA methylation: Islands, start sites, gene bodies and beyond
    • 10.1038/nrg3230 22641018
    • Functions of DNA methylation: islands, start sites, gene bodies and beyond. Jones PA, Nat Rev Genet 2012 13 484 492 10.1038/nrg3230 22641018
    • (2012) Nat Rev Genet , vol.13 , pp. 484-492
    • Jones, P.A.1
  • 18
    • 80555125018 scopus 로고    scopus 로고
    • Comparative methylomics reveals gene-body H3K36me3 in Drosophila predicts DNA methylation and CpG landscapes in other invertebrates
    • 10.1101/gr.121640.111 21940836
    • Comparative methylomics reveals gene-body H3K36me3 in Drosophila predicts DNA methylation and CpG landscapes in other invertebrates. Nanty L, Carbajosa G, Heap GA, Ratnieks F, van Heel DA, Down TA, Rakyan VK, Genome Res 2011 21 1841 1850 10.1101/gr.121640.111 21940836
    • (2011) Genome Res , vol.21 , pp. 1841-1850
    • Nanty, L.1    Carbajosa, G.2    Heap, G.A.3    Ratnieks, F.4    Van Heel, D.A.5    Down, T.A.6    Rakyan, V.K.7
  • 19
    • 84864659030 scopus 로고    scopus 로고
    • The evolution of invertebrate gene body methylation
    • 10.1093/molbev/mss062 22328716
    • The evolution of invertebrate gene body methylation. Sarda S, Zeng J, Hunt BG, Yi SV, Mol Biol Evol 2012 29 1907 1916 10.1093/molbev/mss062 22328716
    • (2012) Mol Biol Evol , vol.29 , pp. 1907-1916
    • Sarda, S.1    Zeng, J.2    Hunt, B.G.3    Yi, S.V.4
  • 20
    • 84861062626 scopus 로고    scopus 로고
    • Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly
    • 10.1093/molbev/msr188 21813466
    • Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly. Takuno S, Gaut BS, Mol Biol Evol 2012 29 219 227 10.1093/molbev/msr188 21813466
    • (2012) Mol Biol Evol , vol.29 , pp. 219-227
    • Takuno, S.1    Gaut, B.S.2
  • 21
    • 78649955848 scopus 로고    scopus 로고
    • The honey bee epigenomes: Differential methylation of brain DNA in queens and workers
    • 10.1371/journal.pbio.1000506 21072239
    • The honey bee epigenomes: differential methylation of brain DNA in queens and workers. Lyko F, Foret S, Kucharski R, Wolf S, Falckenhayn C, Maleszka R, PLoS Biol 2010 8 1000506 10.1371/journal.pbio.1000506 21072239
    • (2010) PLoS Biol , vol.8 , pp. 51000506
    • Lyko, F.1    Foret, S.2    Kucharski, R.3    Wolf, S.4    Falckenhayn, C.5    Maleszka, R.6
  • 22
    • 84859465140 scopus 로고    scopus 로고
    • DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees
    • 10.1073/pnas.1202392109 22416128
    • DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees. Foret S, Kucharski R, Pellegrini M, Feng S, Jacobsen SE, Robinson GE, Maleszka R, Proc Natl Acad Sci USA 2012 109 4968 4973 10.1073/pnas.1202392109 22416128
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. 4968-4973
    • Foret, S.1    Kucharski, R.2    Pellegrini, M.3    Feng, S.4    Jacobsen, S.E.5    Robinson, G.E.6    Maleszka, R.7
  • 23
    • 0031027468 scopus 로고    scopus 로고
    • Methylation of genomes and genes at the invertebrate-vertebrate boundary
    • Methylation of genomes and genes at the invertebrate-vertebrate boundary. Tweedie S, Charlton J, Clark V, Bird A, Mol Cell Biol 1997 17 1469 1475 9032274 (Pubitemid 27097376)
    • (1997) Molecular and Cellular Biology , vol.17 , Issue.3 , pp. 1469-1475
    • Tweedie, S.1    Charlton, J.2    Clark, V.3    Bird, A.4
  • 24
    • 0033582623 scopus 로고    scopus 로고
    • Nonmethylated transposable elements and methylated genes in a chordate genome
    • DOI 10.1126/science.283.5405.1164
    • Nonmethylated transposable elements and methylated genes in a chordate genome. Simmen MW, Leitgeb S, Charlton J, Jones SJ, Harris BR, Clark VH, Bird A, Science 1999 283 1164 1167 10.1126/science.283.5405.1164 10024242 (Pubitemid 29102218)
    • (1999) Science , vol.283 , Issue.5405 , pp. 1164-1167
    • Simmen, M.W.1    Leitgeb, S.2    Charlton, J.3    Jones, S.J.M.4    Harris, B.R.5    Clark, V.H.6    Bird, A.7
  • 25
    • 0035839126 scopus 로고    scopus 로고
    • Epigenetic reprogramming in mammalian development
    • DOI 10.1126/science.1063443
    • Epigenetic reprogramming in mammalian development. Reik W, Dean W, Walter J, Science 2001 293 1089 1093 10.1126/science.1063443 11498579 (Pubitemid 32758081)
    • (2001) Science , vol.293 , Issue.5532 , pp. 1089-1093
    • Reik, W.1    Dean, W.2    Walter, J.3
  • 27
    • 80051575124 scopus 로고    scopus 로고
    • Direct examination of chromosomal clustering of organ-specific genes in the chordate Ciona intestinalis
    • 10.1002/dvg.20730 21328518
    • Direct examination of chromosomal clustering of organ-specific genes in the chordate Ciona intestinalis. Shoguchi E, Hamada M, Fujie M, Satoh N, Genesis 2011 49 662 672 10.1002/dvg.20730 21328518
    • (2011) Genesis , vol.49 , pp. 662-672
    • Shoguchi, E.1    Hamada, M.2    Fujie, M.3    Satoh, N.4
  • 29
    • 33744458441 scopus 로고    scopus 로고
    • Regulatory blueprint for a chordate embryo
    • DOI 10.1126/science.1123404
    • Regulatory blueprint for a chordate embryo. Imai KS, Levine M, Satoh N, Satou Y, Science 2006 312 1183 1187 10.1126/science.1123404 16728634 (Pubitemid 43801138)
    • (2006) Science , vol.312 , Issue.5777 , pp. 1183-1187
    • Imai, K.S.1    Levine, M.2    Satoh, N.3    Satou, Y.4
  • 33
    • 26944480299 scopus 로고    scopus 로고
    • Transposon-mediated insertional mutagenesis revealed the functions of animal cellulose synthase in the ascidian Ciona intestinalis
    • Transposon-mediated insertional mutagenesis revealed the functions of animal cellulose synthase in the ascidian Ciona intestinalis. Sasakura Y, Nakashima K, Awazu S, Matsuoka T, Nakayama A, Azuma J, Satoh N, Proc Natl Acad Sci USA 2005 102 151134 151139
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 151134-151139
    • Sasakura, Y.1    Nakashima, K.2    Awazu, S.3    Matsuoka, T.4    Nakayama, A.5    Azuma, J.6    Satoh, N.7
  • 34
    • 38149064451 scopus 로고    scopus 로고
    • Enhancer detection in the ascidian Ciona intestinalis with transposase-expressing lines of Minos
    • 10.1002/dvdy.21333 17948255
    • Enhancer detection in the ascidian Ciona intestinalis with transposase-expressing lines of Minos. Sasakura Y, Konno A, Mizuno K, Satoh N, Inaba K, Dev Dyn 2008 237 39 50 10.1002/dvdy.21333 17948255
    • (2008) Dev Dyn , vol.237 , pp. 39-50
    • Sasakura, Y.1    Konno, A.2    Mizuno, K.3    Satoh, N.4    Inaba, K.5
  • 35
    • 75649117804 scopus 로고    scopus 로고
    • Maternal factor-mediated epigenetic gene silencing in the ascidian Ciona intestinalis
    • 10.1007/s00438-009-0500-4 19946786
    • Maternal factor-mediated epigenetic gene silencing in the ascidian Ciona intestinalis. Sasakura Y, Suzuki MM, Hozumi A, Inaba K, Satoh N, Mol Genet Genomics 2010 283 99 110 10.1007/s00438-009-0500-4 19946786
    • (2010) Mol Genet Genomics , vol.283 , pp. 99-110
    • Sasakura, Y.1    Suzuki, M.M.2    Hozumi, A.3    Inaba, K.4    Satoh, N.5
  • 36
    • 0032130696 scopus 로고    scopus 로고
    • Regulation of gene expression during spermatogenesis
    • Regulation of gene expression during spermatogenesis. Eddy EM, Semin Cell Dev Biol 1998 9 451 457 10.1006/scdb.1998.0201 9813192 (Pubitemid 128350672)
    • (1998) Seminars in Cell and Developmental Biology , vol.9 , Issue.4 , pp. 451-457
    • Eddy, E.M.1
  • 37
    • 0018289345 scopus 로고
    • Methylated and unmethylated DNA compartments in the sea urchin genome
    • Methylated and unmethylated the sea urchin genome DNA compartments in the sea urchin genome. Bird AP, Taggart MH, Smith BA, Cell 1979 17 889 901 10.1016/0092-8674(79)90329-5 487434 (Pubitemid 9252298)
    • (1979) Cell , vol.17 , Issue.4 , pp. 889-901
    • Bird, A.P.1    Taggart, M.H.2    Smith, B.A.3
  • 38
    • 18744414795 scopus 로고    scopus 로고
    • Dynamic changes in developmental gene expression in the basal chordate Ciona intestinalis
    • DOI 10.1111/j.1440-169X.2005.00794.x
    • Dynamic changes in developmental gene expression in the basal chordate Ciona intestinalis. Kawashima T, Satou Y, Murakami SD, Satoh N, Dev Growth Differ 2005 47 187 199 10.1111/j.1440-169X.2005.00794.x 15840003 (Pubitemid 40676940)
    • (2005) Development Growth and Differentiation , vol.47 , Issue.3 , pp. 187-199
    • Kawashima, T.1    Satou, Y.2    Murakami, S.D.3    Satoh, N.4
  • 39
    • 80054790080 scopus 로고    scopus 로고
    • DNA methylation: Superior or subordinate in the epigenetic hierarchy?
    • 10.1177/1947601910393957 21941617
    • DNA methylation: superior or subordinate in the epigenetic hierarchy? Jin B, Li Y, Robertson KD, Genes Cancer 2011 2 607 617 10.1177/1947601910393957 21941617
    • (2011) Genes Cancer , vol.2 , pp. 607-617
    • Jin, B.1    Li, Y.2    Robertson, K.D.3
  • 41
    • 25444448272 scopus 로고    scopus 로고
    • An integrated database of the ascidian, Ciona intestinalis: Towards functional genomics
    • DOI 10.2108/zsj.22.837
    • An integrated database of the ascidian, Ciona intestinalis: towards functional genomics. Satou Y, Kawashima T, Shoguchi E, Nakayama A, Satoh N, Zoolog Sci 2005 22 837 843 10.2108/zsj.22.837 16141696 (Pubitemid 41360613)
    • (2005) Zoological Science , vol.22 , Issue.8 , pp. 837-843
    • Satou, Y.1    Kawashima, T.2    Shoguchi, E.3    Nakayama, A.4    Satoh, N.5
  • 44
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • 10.1093/bioinformatics/btq033 20110278
    • BEDTools: a flexible suite of utilities for comparing genomic features. Quinlan AR, Hall IM, Bioinformatics 2010 26 841 842 10.1093/bioinformatics/ btq033 20110278
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 45
    • 79957868920 scopus 로고    scopus 로고
    • Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications
    • 10.1093/bioinformatics/btr167 21493656
    • Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Krueger F, Andrews SR, Bioinformatics 2011 27 1571 1572 10.1093/bioinformatics/btr167 21493656
    • (2011) Bioinformatics , vol.27 , pp. 1571-1572
    • Krueger, F.1    Andrews, S.R.2
  • 46
    • 79952749156 scopus 로고    scopus 로고
    • DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria
    • 10.1073/pnas.1012311108 21321201
    • DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria. Shock LS, Thakkar PV, Peterson EJ, Moran RG, Taylor SM, Proc Natl Acad Sci USA 2011 108 3630 3635 10.1073/pnas.1012311108 21321201
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 3630-3635
    • Shock, L.S.1    Thakkar, P.V.2    Peterson, E.J.3    Moran, R.G.4    Taylor, S.M.5
  • 47
    • 42749087226 scopus 로고    scopus 로고
    • Highly integrated single-base resolution maps of the epigenome in Arabidopsis
    • 10.1016/j.cell.2008.03.029 18423832
    • Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR, Cell 2008 133 523 536 10.1016/j.cell.2008.03.029 18423832
    • (2008) Cell , vol.133 , pp. 523-536
    • Lister, R.1    O'Malley, R.C.2    Tonti-Filippini, J.3    Gregory, B.D.4    Berry, C.C.5    Millar, A.H.6    Ecker, J.R.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.