메뉴 건너뛰기




Volumn 7, Issue 4, 2012, Pages

Spatial proximity and similarity of the epigenetic state of genome domains

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; HISTONE; RNA;

EID: 84859355664     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0033947     Document Type: Article
Times cited : (16)

References (43)
  • 1
    • 0020041622 scopus 로고
    • Rabl's model of the interphase chromosome arrangement tested in Chinese hamster cells by premature chromosome condensation and laser-UV-microbeam experiments
    • Cremer T, Cremer C, Baumann H, Luedtke EK, Sperling K, et al. (1982) Rabl's model of the interphase chromosome arrangement tested in Chinese hamster cells by premature chromosome condensation and laser-UV-microbeam experiments. Hum Genet 60: 46-56.
    • (1982) Hum Genet , vol.60 , pp. 46-56
    • Cremer, T.1    Cremer, C.2    Baumann, H.3    Luedtke, E.K.4    Sperling, K.5
  • 2
    • 77949919093 scopus 로고    scopus 로고
    • Interchromosomal association and gene regulation in trans
    • Williams A, Spilianakis CG, Flavell RA, (2010) Interchromosomal association and gene regulation in trans. Trends Genet 26: 188-197.
    • (2010) Trends Genet , vol.26 , pp. 188-197
    • Williams, A.1    Spilianakis, C.G.2    Flavell, R.A.3
  • 4
    • 70349873824 scopus 로고    scopus 로고
    • Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    • Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293.
    • (2009) Science , vol.326 , pp. 289-293
    • Lieberman-Aiden, E.1    van Berkum, N.L.2    Williams, L.3    Imakaev, M.4    Ragoczy, T.5
  • 6
    • 33847076849 scopus 로고    scopus 로고
    • Chromatin modifications and their function
    • Kouzarides T, (2007) Chromatin modifications and their function. Cell 128: 693-705.
    • (2007) Cell , vol.128 , pp. 693-705
    • Kouzarides, T.1
  • 7
    • 39449088572 scopus 로고    scopus 로고
    • Genome-wide approaches to studying chromatin modifications
    • Schones DE, Zhao K, (2008) Genome-wide approaches to studying chromatin modifications. Nat Rev Genet 9: 179-191.
    • (2008) Nat Rev Genet , vol.9 , pp. 179-191
    • Schones, D.E.1    Zhao, K.2
  • 8
    • 37548999369 scopus 로고    scopus 로고
    • Computational epigenetics
    • Bock C, Lengauer T, (2008) Computational epigenetics. Bioinformatics 24: 1-10.
    • (2008) Bioinformatics , vol.24 , pp. 1-10
    • Bock, C.1    Lengauer, T.2
  • 9
    • 48949099045 scopus 로고    scopus 로고
    • Inferring causal relationships among different histone modifications and gene expression
    • Yu H, Zhu S, Zhou B, Xue H, Han JD, (2008) Inferring causal relationships among different histone modifications and gene expression. Genome Res 18: 1314-1324.
    • (2008) Genome Res , vol.18 , pp. 1314-1324
    • Yu, H.1    Zhu, S.2    Zhou, B.3    Xue, H.4    Han, J.D.5
  • 10
    • 78650331647 scopus 로고    scopus 로고
    • Identification of functional elements and regulatory circuits by Drosophila modENCODE
    • modENCODE Consortium
    • Roy S, Ernst J, Kharchenko PV, Kheradpour P, et al. modENCODE Consortium (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330: 1787-1797.
    • (2010) Science , vol.330 , pp. 1787-1797
    • Roy, S.1    Ernst, J.2    Kharchenko, P.V.3    Kheradpour, P.4
  • 11
    • 78650410139 scopus 로고    scopus 로고
    • Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
    • Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, et al. (2010) Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330: 1775-1787.
    • (2010) Science , vol.330 , pp. 1775-1787
    • Gerstein, M.B.1    Lu, Z.J.2    Van Nostrand, E.L.3    Cheng, C.4    Arshinoff, B.I.5
  • 12
    • 78650747491 scopus 로고    scopus 로고
    • Discovery and characterization of chromatin states for systematic annotation of the human genome
    • Ernst J, Kellis M, (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28: 817-825.
    • (2010) Nat Biotechnol , vol.28 , pp. 817-825
    • Ernst, J.1    Kellis, M.2
  • 14
    • 70249129382 scopus 로고    scopus 로고
    • Implications of chimaeric non-co-linear transcripts
    • Gingeras TR, (2009) Implications of chimaeric non-co-linear transcripts. Nature 461: 206-211.
    • (2009) Nature , vol.461 , pp. 206-211
    • Gingeras, T.R.1
  • 16
    • 33746683274 scopus 로고    scopus 로고
    • Reverse transcriptase template switching and false alternative transcripts
    • Cocquet J, Chong A, Zhang G, Veitia RA, (2006) Reverse transcriptase template switching and false alternative transcripts. Genomics 88: 127-131.
    • (2006) Genomics , vol.88 , pp. 127-131
    • Cocquet, J.1    Chong, A.2    Zhang, G.3    Veitia, R.A.4
  • 19
    • 34249937354 scopus 로고    scopus 로고
    • Thousands of human mobile element fragments undergo strong purifying selection near developmental genes
    • Lowe CB, Bejerano G, Haussler D, (2007) Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci U S A 104: 8005-8010.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 8005-8010
    • Lowe, C.B.1    Bejerano, G.2    Haussler, D.3
  • 20
    • 80054984337 scopus 로고    scopus 로고
    • Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture
    • Yaffe E, Tanay A, (2011) Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet 43: 1059-1065.
    • (2011) Nat Genet , vol.43 , pp. 1059-1065
    • Yaffe, E.1    Tanay, A.2
  • 21
    • 77951942707 scopus 로고    scopus 로고
    • GOSemSim: an R package for measuring semantic similarity among GO terms and gene products
    • Yu G, Li F, Qin Y, Bo X, Wu Y, et al. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics 26: 976-978.
    • (2010) Bioinformatics , vol.26 , pp. 976-978
    • Yu, G.1    Li, F.2    Qin, Y.3    Bo, X.4    Wu, Y.5
  • 22
  • 23
    • 78651280402 scopus 로고    scopus 로고
    • COXPRESdb: a database to compare gene coexpression in seven model animals
    • Obayashi T, Kinoshita K, (2011) COXPRESdb: a database to compare gene coexpression in seven model animals. Nucleic Acids Res 39: 1016-1022.
    • (2011) Nucleic Acids Res , vol.39 , pp. 1016-1022
    • Obayashi, T.1    Kinoshita, K.2
  • 24
    • 84944178665 scopus 로고
    • Hierarchical grouping to optimize an objective function
    • Ward J, (1963) Hierarchical grouping to optimize an objective function. Journal of the American Statistical Association 58: 236-244.
    • (1963) Journal of the American Statistical Association , vol.58 , pp. 236-244
    • Ward, J.1
  • 25
    • 79951480123 scopus 로고    scopus 로고
    • R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria
    • R Development Core Team, URL. ISBN 3-900051-07-0
    • R Development Core Team (2010) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org. ISBN 3-900051-07-0.
    • (2010)
  • 26
    • 77957929225 scopus 로고    scopus 로고
    • Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq
    • Xu AG, He L, Li Z, Xu Y, Li M, et al. (2010) Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq. PLoS Comput Biol 6.
    • (2010) PLoS Comput Biol , vol.6
    • Xu, A.G.1    He, L.2    Li, Z.3    Xu, Y.4    Li, M.5
  • 27
    • 7444260846 scopus 로고    scopus 로고
    • The ENCODE (ENCyclopedia Of DNA Elements) project
    • ENCODE Project Consortium
    • ENCODE Project Consortium (2004) The ENCODE (ENCyclopedia Of DNA Elements) project. Science 306: 636-640.
    • (2004) Science , vol.306 , pp. 636-640
  • 29
    • 43049143055 scopus 로고    scopus 로고
    • Mapping and sequencing of structural variation from eight human genomes
    • Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56-64.
    • (2008) Nature , vol.453 , pp. 56-64
    • Kidd, J.M.1    Cooper, G.M.2    Donahue, W.F.3    Hayden, H.S.4    Sampas, N.5
  • 30
    • 75549092352 scopus 로고    scopus 로고
    • ChimerDB 2.0-a knowledgebase for fusion genes updated
    • Kim P, Yoon S, Kim N, Lee S, Ko M, et al. (2010) ChimerDB 2.0-a knowledgebase for fusion genes updated. Nucleic Acids Res 38: 81-85.
    • (2010) Nucleic Acids Res , vol.38 , pp. 81-85
    • Kim, P.1    Yoon, S.2    Kim, N.3    Lee, S.4    Ko, M.5
  • 32
    • 48749102722 scopus 로고    scopus 로고
    • A chromatin-wide transition to H4K20 monomethylation impairs genome integrity and programmed DNA rearrangements in the mouse
    • Schotta G, Sengupta R, Kubicek S, Malin S, Kauer M, et al. (2008) A chromatin-wide transition to H4K20 monomethylation impairs genome integrity and programmed DNA rearrangements in the mouse. Genes Dev 22: 2048-2061.
    • (2008) Genes Dev , vol.22 , pp. 2048-2061
    • Schotta, G.1    Sengupta, R.2    Kubicek, S.3    Malin, S.4    Kauer, M.5
  • 33
    • 0037436410 scopus 로고    scopus 로고
    • Chromatin fiber folding: requirement for the histone H4 N-terminal tail
    • Dorigo B, Schalch T, Bystricky K, Richmond TJ, (2003) Chromatin fiber folding: requirement for the histone H4 N-terminal tail. J Mol Biol 327: 85-96.
    • (2003) J Mol Biol , vol.327 , pp. 85-96
    • Dorigo, B.1    Schalch, T.2    Bystricky, K.3    Richmond, T.J.4
  • 34
    • 79952762476 scopus 로고    scopus 로고
    • Histone H4 Lys 20 monomethylation by histone methylase SET8 mediates Wnt target gene activation
    • Li Z, Nie F, Wang S, Li L, (2011) Histone H4 Lys 20 monomethylation by histone methylase SET8 mediates Wnt target gene activation. Proc Natl Acad Sci U S A 108: 3116-3123.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 3116-3123
    • Li, Z.1    Nie, F.2    Wang, S.3    Li, L.4
  • 35
    • 33644701666 scopus 로고    scopus 로고
    • Histone H4-lysine 20 monomethylation is increased in promoter and coding regions of active genes and correlates with hyperacetylation
    • Talasz H, Lindner HH, Sarg B, Helliger W, (2005) Histone H4-lysine 20 monomethylation is increased in promoter and coding regions of active genes and correlates with hyperacetylation. J Biol Chem 280: 38814-38822.
    • (2005) J Biol Chem , vol.280 , pp. 38814-38822
    • Talasz, H.1    Lindner, H.H.2    Sarg, B.3    Helliger, W.4
  • 36
    • 33845451555 scopus 로고    scopus 로고
    • Profile of histone lysine methylation across transcribed mammalian chromatin
    • Vakoc CR, Sachdeva MM, Wang H, Blobel GA, (2006) Profile of histone lysine methylation across transcribed mammalian chromatin. Mol Cell Biol 26: 9185-9195.
    • (2006) Mol Cell Biol , vol.26 , pp. 9185-9195
    • Vakoc, C.R.1    Sachdeva, M.M.2    Wang, H.3    Blobel, G.A.4
  • 37
    • 50349085791 scopus 로고    scopus 로고
    • Catalytic function of the PR-Set7 histone H4 lysine 20 monomethyltransferase is essential for mitotic entry and genomic stability
    • Houston SI, McManus KJ, Adams MM, Sims JK, Carpenter PB, et al. (2008) Catalytic function of the PR-Set7 histone H4 lysine 20 monomethyltransferase is essential for mitotic entry and genomic stability. J Biol Chem 283: 19478-19488.
    • (2008) J Biol Chem , vol.283 , pp. 19478-19488
    • Houston, S.I.1    McManus, K.J.2    Adams, M.M.3    Sims, J.K.4    Carpenter, P.B.5
  • 38
    • 77954954200 scopus 로고    scopus 로고
    • PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression
    • Liu W, Tanasa B, Tyurina OV, Zhou TY, Gassmann R, et al. (2010) PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression. Nature 466: 508-512.
    • (2010) Nature , vol.466 , pp. 508-512
    • Liu, W.1    Tanasa, B.2    Tyurina, O.V.3    Zhou, T.Y.4    Gassmann, R.5
  • 40
    • 34250369629 scopus 로고    scopus 로고
    • Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions
    • Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, et al. (2007) Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res 17: 746-759.
    • (2007) Genome Res , vol.17 , pp. 746-759
    • Denoeud, F.1    Kapranov, P.2    Ucla, C.3    Frankish, A.4    Castelo, R.5
  • 41
    • 59849091728 scopus 로고    scopus 로고
    • Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes
    • Li X, Zhao L, Jiang H, Wang W, (2009) Short homologous sequences are strongly associated with the generation of chimeric RNAs in eukaryotes. J Mol Evol 68: 56-65.
    • (2009) J Mol Evol , vol.68 , pp. 56-65
    • Li, X.1    Zhao, L.2    Jiang, H.3    Wang, W.4
  • 42
    • 40049104732 scopus 로고    scopus 로고
    • SOAP: short oligonucleotide alignment program
    • Li R, Li Y, Kristiansen K, Wang J, (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713-714.
    • (2008) Bioinformatics , vol.24 , pp. 713-714
    • Li, R.1    Li, Y.2    Kristiansen, K.3    Wang, J.4
  • 43
    • 0000418073 scopus 로고
    • On the stability of inverse problems
    • Tychonoff AN, (1943) On the stability of inverse problems. Doklady Akademii Nauk SSSR 39: 195-198.
    • (1943) Doklady Akademii Nauk SSSR , vol.39 , pp. 195-198
    • Tychonoff, A.N.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.