메뉴 건너뛰기




Volumn 13, Issue 1, 2012, Pages

A histone arginine methylation localizes to nucleosomes in satellite II and III DNA sequences in the human genome

Author keywords

ChIP Seq; Classification; Data pre processing; Epigenomics; Histone modifications

Indexed keywords

ARGININE; DNA METHYLTRANSFERASE 3A; HISTONE; HISTONE H2A; HISTONE H3; HISTONE H4; SATELLITE DNA; SATELLITE II DNA; SATELLITE III DNA; UNCLASSIFIED DRUG;

EID: 84868689206     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-630     Document Type: Article
Times cited : (9)

References (56)
  • 1
    • 79960563344 scopus 로고    scopus 로고
    • Determinants and dynamics of genome accessibility
    • 10.1038/nrg3017, 21747402
    • Bell O, Tiwari VK, Thomä NH, Schübeler D. Determinants and dynamics of genome accessibility. Nat Rev Genet 2011, 12:554-564. 10.1038/nrg3017, 21747402.
    • (2011) Nat Rev Genet , vol.12 , pp. 554-564
    • Bell, O.1    Tiwari, V.K.2    Thomä, N.H.3    Schübeler, D.4
  • 2
    • 39549083972 scopus 로고    scopus 로고
    • Chromatin modifications and their mechanism of action
    • Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, Allis C, Jenuwein T, Reinberg D, 1
    • Kouzarides T, Berger S. Chromatin modifications and their mechanism of action. Epigenetics 2007, 191-209. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, Allis C, Jenuwein T, Reinberg D, 1.
    • (2007) Epigenetics , pp. 191-209
    • Kouzarides, T.1    Berger, S.2
  • 3
    • 77954766475 scopus 로고    scopus 로고
    • Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression
    • Xu X, Hoang S, Mayo MW, Bekiranov S. Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression. BMC Bioinforma 2010, 11:396.
    • (2010) BMC Bioinforma , vol.11 , pp. 396
    • Xu, X.1    Hoang, S.2    Mayo, M.W.3    Bekiranov, S.4
  • 4
    • 34047274419 scopus 로고    scopus 로고
    • Global patterns of histone modifications
    • 10.1016/j.gde.2007.02.006, 17317148
    • Rando OJ. Global patterns of histone modifications. Curr Opin Genet Dev 2007, 17:94-99. 10.1016/j.gde.2007.02.006, 17317148.
    • (2007) Curr Opin Genet Dev , vol.17 , pp. 94-99
    • Rando, O.J.1
  • 5
    • 36248982297 scopus 로고    scopus 로고
    • edited by Allis C, Jenuwein T, Reinberg D, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, In Epigenetics. 1st edition
    • Allis C, Jenuwein T, Reinberg D, In Epigenetics. 1st edition Overview and concepts 2007, 23-61. edited by Allis C, Jenuwein T, Reinberg D, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, In Epigenetics. 1st edition.
    • (2007) Overview and concepts , pp. 23-61
    • Allis, C.1    Jenuwein, T.2    Reinberg, D.3
  • 6
    • 80052805267 scopus 로고    scopus 로고
    • Histone modification: cause or cog?
    • 10.1016/j.tig.2011.06.006, 21764166
    • Henikoff S, Shilatifard A. Histone modification: cause or cog?. Trends Genet 2011, 27:389-396. 10.1016/j.tig.2011.06.006, 21764166.
    • (2011) Trends Genet , vol.27 , pp. 389-396
    • Henikoff, S.1    Shilatifard, A.2
  • 7
    • 34748826166 scopus 로고    scopus 로고
    • A high-resolution atlas of nucleosome occupancy in yeast
    • 10.1038/ng2117, 17873876
    • Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C. A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 2007, 39:1235-1244. 10.1038/ng2117, 17873876.
    • (2007) Nat Genet , vol.39 , pp. 1235-1244
    • Lee, W.1    Tillo, D.2    Bray, N.3    Morse, R.H.4    Davis, R.W.5    Hughes, T.R.6    Nislow, C.7
  • 8
    • 43149114926 scopus 로고    scopus 로고
    • Re-cracking the nucleosome positioning code
    • Segal MR. Re-cracking the nucleosome positioning code. Stat Appl Genet Mol Biol 2008, 7:14.
    • (2008) Stat Appl Genet Mol Biol , vol.7 , pp. 14
    • Segal, M.R.1
  • 9
    • 46349097649 scopus 로고    scopus 로고
    • DNA physical properties determine nucleosome occupancy from yeast to fly
    • 10.1093/nar/gkn262, 2441789, 18487627
    • Miele V, Vaillant C, D'Aubenton-Carafa Y, Thermes C, Grange T. DNA physical properties determine nucleosome occupancy from yeast to fly. Nucleic Acids Res 2008, 36:3746-3756. 10.1093/nar/gkn262, 2441789, 18487627.
    • (2008) Nucleic Acids Res , vol.36 , pp. 3746-3756
    • Miele, V.1    Vaillant, C.2    D'Aubenton-Carafa, Y.3    Thermes, C.4    Grange, T.5
  • 10
    • 75149135277 scopus 로고    scopus 로고
    • G+C content dominates intrinsic nucleosome occupancy
    • Tillo D, Hughes TR. G+C content dominates intrinsic nucleosome occupancy. BMC Bioinforma 2009, 10:442.
    • (2009) BMC Bioinforma , vol.10 , pp. 442
    • Tillo, D.1    Hughes, T.R.2
  • 11
    • 34249026300 scopus 로고    scopus 로고
    • High-resolution profiling of histone methylations in the human genome
    • 10.1016/j.cell.2007.05.009, 17512414
    • Barski A, Cuddapah S, Cui K, Roh T-Y, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129:823-837. 10.1016/j.cell.2007.05.009, 17512414.
    • (2007) Cell , vol.129 , pp. 823-837
    • Barski, A.1    Cuddapah, S.2    Cui, K.3    Roh, T.-Y.4    Schones, D.E.5    Wang, Z.6    Wei, G.7    Chepelev, I.8    Zhao, K.9
  • 13
    • 63349106258 scopus 로고    scopus 로고
    • Discriminating nucleosomes containing histone H2A.Z or H2A based on genetic and epigenetic information
    • 10.1186/1471-2199-10-18, 2660331, 19261190
    • Gervais AL, Gaudreau L. Discriminating nucleosomes containing histone H2A.Z or H2A based on genetic and epigenetic information. BMC Mol Biol 2009, 10:18. 10.1186/1471-2199-10-18, 2660331, 19261190.
    • (2009) BMC Mol Biol , vol.10 , pp. 18
    • Gervais, A.L.1    Gaudreau, L.2
  • 14
  • 15
    • 70449711243 scopus 로고    scopus 로고
    • Computation for ChIP-seq and RNA-seq studies
    • 10.1038/nmeth.1371, 19844228
    • Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nat Methods 2009, 6:S22-S32. 10.1038/nmeth.1371, 19844228.
    • (2009) Nat Methods , vol.6
    • Pepke, S.1    Wold, B.2    Mortazavi, A.3
  • 16
    • 84873308621 scopus 로고    scopus 로고
    • edited by Appasani K Cambridge, Cambridge University Press, In Epigenomics: from chromatin biology to therapeutics. 1st edition
    • Song J, Fisher D, In Epigenomics: from chromatin biology to therapeutics. 1st edition Nucleosome positioning in promoters: significance and open questions 2012, edited by Appasani K Cambridge, Cambridge University Press, In Epigenomics: from chromatin biology to therapeutics. 1st edition.
    • (2012) Nucleosome positioning in promoters: significance and open questions
    • Song, J.1    Fisher, D.2
  • 17
    • 57449095143 scopus 로고    scopus 로고
    • Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq
    • 10.1186/1471-2164-9-537, 2596141, 19014516
    • Zhang Y, Shin H, Song JS, Lei Y, Liu XS. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics 2008, 9:537. 10.1186/1471-2164-9-537, 2596141, 19014516.
    • (2008) BMC Genomics , vol.9 , pp. 537
    • Zhang, Y.1    Shin, H.2    Song, J.S.3    Lei, Y.4    Liu, X.S.5
  • 19
    • 79953788666 scopus 로고    scopus 로고
    • Impact of chromatin structure on sequence variability in the human genome
    • 10.1038/nsmb.2012, 3188321, 21399641
    • Tolstorukov MY, Volfovsky N, Stephens RM, Park PJ. Impact of chromatin structure on sequence variability in the human genome. Nat Struct Mol Biol 2011, 18:510-515. 10.1038/nsmb.2012, 3188321, 21399641.
    • (2011) Nat Struct Mol Biol , vol.18 , pp. 510-515
    • Tolstorukov, M.Y.1    Volfovsky, N.2    Stephens, R.M.3    Park, P.J.4
  • 20
    • 60349089645 scopus 로고    scopus 로고
    • Nucleosome positioning and gene regulation: advances through genomics
    • Jiang C, Pugh BF. Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 2009, 10:161-172.
    • (2009) Nat Rev Genet , vol.10 , pp. 161-172
    • Jiang, C.1    Pugh, B.F.2
  • 21
    • 84873313333 scopus 로고    scopus 로고
    • Normalization of ChIP-Seq data with control
    • Liang K, Keles S. Normalization of ChIP-Seq data with control. Submitted 2012,
    • (2012) Submitted
    • Liang, K.1    Keles, S.2
  • 22
    • 80755126015 scopus 로고    scopus 로고
    • Sequence-based classification using discriminatory motif feature selection
    • 10.1371/journal.pone.0027382, 3213122, 22102890
    • Xiong H, Capurso D, Sen T, Segal MR. Sequence-based classification using discriminatory motif feature selection. PLoS One 2011, 6:e27382. 10.1371/journal.pone.0027382, 3213122, 22102890.
    • (2011) PLoS One , vol.6
    • Xiong, H.1    Capurso, D.2    Sen, T.3    Segal, M.R.4
  • 23
    • 69949162927 scopus 로고    scopus 로고
    • SOLpro: accurate sequence-based prediction of protein solubility
    • 10.1093/bioinformatics/btp386, 19549632
    • Magnan CN, Randall A, Baldi P. SOLpro: accurate sequence-based prediction of protein solubility. Bioinformatics 2009, 25:2200-2207. 10.1093/bioinformatics/btp386, 19549632.
    • (2009) Bioinformatics , vol.25 , pp. 2200-2207
    • Magnan, C.N.1    Randall, A.2    Baldi, P.3
  • 24
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L. Random forests. Mach Learn 2001, 45:5-32.
    • (2001) Mach Learn , vol.45 , pp. 5-32
    • Breiman, L.1
  • 27
    • 77957988489 scopus 로고    scopus 로고
    • Class prediction for high-dimensional class-imbalanced data
    • Blagus R, Lusa L. Class prediction for high-dimensional class-imbalanced data. BMC Bioinforma 2010, 11:523.
    • (2010) BMC Bioinforma , vol.11 , pp. 523
    • Blagus, R.1    Lusa, L.2
  • 29
    • 78049402859 scopus 로고    scopus 로고
    • Molecular signals of epigenetic states
    • 10.1126/science.1191078, 21030644
    • Bonasio R, Tu S, Reinberg D. Molecular signals of epigenetic states. Science 2010, 330:612-616. 10.1126/science.1191078, 21030644.
    • (2010) Science , vol.330 , pp. 612-616
    • Bonasio, R.1    Tu, S.2    Reinberg, D.3
  • 30
    • 70349303348 scopus 로고    scopus 로고
    • The secret message of heterochromatin: new insights into the mechanisms and function of centromeric and pericentric repeat sequence transcription
    • 10.1387/ijdb.082673ae, 19412885
    • Eymery A, Callanan M, Vourc'h C. The secret message of heterochromatin: new insights into the mechanisms and function of centromeric and pericentric repeat sequence transcription. Int J Dev Biol 2009, 53:259-268. 10.1387/ijdb.082673ae, 19412885.
    • (2009) Int J Dev Biol , vol.53 , pp. 259-268
    • Eymery, A.1    Callanan, M.2    Vourc'h, C.3
  • 31
    • 0022512703 scopus 로고
    • Sequence relationships of three human satellite DNAs
    • 10.1016/0022-2836(86)90224-X, 3701863
    • Prosser J, Frommer M, Paul C, Vincent PC. Sequence relationships of three human satellite DNAs. J Mol Biol 1986, 187:145-155. 10.1016/0022-2836(86)90224-X, 3701863.
    • (1986) J Mol Biol , vol.187 , pp. 145-155
    • Prosser, J.1    Frommer, M.2    Paul, C.3    Vincent, P.C.4
  • 32
    • 78650576256 scopus 로고    scopus 로고
    • Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology
    • 10.1186/gb-2010-11-11-140, 3156944, 21118582
    • Kaplan N, Hughes TR, Lieb JD, Widom J, Segal E. Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology. Genome Biol 2010, 11:140. 10.1186/gb-2010-11-11-140, 3156944, 21118582.
    • (2010) Genome Biol , vol.11 , pp. 140
    • Kaplan, N.1    Hughes, T.R.2    Lieb, J.D.3    Widom, J.4    Segal, E.5
  • 33
    • 84872495357 scopus 로고    scopus 로고
    • Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines [published online ahead of print 10 Feb 2012]
    • Fernández M, Miranda-Saavedra D. Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines [published online ahead of print 10 Feb 2012]. Nucleic Acids Res 2012, .
    • (2012) Nucleic Acids Res
    • Fernández, M.1    Miranda-Saavedra, D.2
  • 34
    • 84873310132 scopus 로고    scopus 로고
    • Signal analysis for genome wide maps of histone modifications measured by ChIP-seq [published online ahead of print 27 Feb 2012]
    • Beck D, Brandl MB, Boelen L, Unnikrishnan A, Pimanda JE, Wong JWH. Signal analysis for genome wide maps of histone modifications measured by ChIP-seq [published online ahead of print 27 Feb 2012]. Bioinformatics 2012, .
    • (2012) Bioinformatics
    • Beck, D.1    Brandl, M.B.2    Boelen, L.3    Unnikrishnan, A.4    Pimanda, J.E.5    Wong, J.W.H.6
  • 35
    • 33846983276 scopus 로고    scopus 로고
    • Polycomb/Trithorax response elements and epigenetic memory of cell identity
    • 10.1242/dev.02723, 17185323
    • Ringrose L, Paro R. Polycomb/Trithorax response elements and epigenetic memory of cell identity. Development 2007, 134:223-232. 10.1242/dev.02723, 17185323.
    • (2007) Development , vol.134 , pp. 223-232
    • Ringrose, L.1    Paro, R.2
  • 36
    • 0036358995 scopus 로고    scopus 로고
    • The spectrum kernel: a string kernel for SVM protein classification
    • Leslie C, Eskin E, Noble WS. The spectrum kernel: a string kernel for SVM protein classification. Pac Symp Biocomput 2002, 564-575.
    • (2002) Pac Symp Biocomput , pp. 564-575
    • Leslie, C.1    Eskin, E.2    Noble, W.S.3
  • 37
    • 84883575579 scopus 로고    scopus 로고
    • Fast string kernels using inexact matching for protein sequences
    • Leslie C, Kuang R. Fast string kernels using inexact matching for protein sequences. 2004, 5:1435-1455.
    • (2004) , vol.5 , pp. 1435-1455
    • Leslie, C.1    Kuang, R.2
  • 38
    • 29144512262 scopus 로고    scopus 로고
    • RASE: recognition of alternatively spliced exons in C. elegans
    • Ratsch G, Sonnenburg S, Scholkopf B. RASE: recognition of alternatively spliced exons in C. elegans. Bioinformatics 2005, 21(1):369-377.
    • (2005) Bioinformatics , vol.21 , Issue.1 , pp. 369-377
    • Ratsch, G.1    Sonnenburg, S.2    Scholkopf, B.3
  • 39
    • 46249106500 scopus 로고    scopus 로고
    • POIMs: positional oligomer importance matrices-understanding support vector machine-based signal detectors
    • 10.1093/bioinformatics/btn170, 2718648, 18586746
    • Sonnenburg S, Zien A, Philips P, Rätsch G. POIMs: positional oligomer importance matrices-understanding support vector machine-based signal detectors. Bioinformatics 2008, 24:i6-i14. 10.1093/bioinformatics/btn170, 2718648, 18586746.
    • (2008) Bioinformatics , vol.24
    • Sonnenburg, S.1    Zien, A.2    Philips, P.3    Rätsch, G.4
  • 41
    • 67650711619 scopus 로고    scopus 로고
    • A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
    • 10.1093/bioinformatics/btp340, 2732366, 19505939
    • Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 2009, 25:1952-1958. 10.1093/bioinformatics/btp340, 2732366, 19505939.
    • (2009) Bioinformatics , vol.25 , pp. 1952-1958
    • Zang, C.1    Schones, D.E.2    Zeng, C.3    Cui, K.4    Zhao, K.5    Peng, W.6
  • 42
    • 4744366752 scopus 로고    scopus 로고
    • The PWWP Domain of Dnmt3a and Dnmt3b Is Required for Directing DNA Methylation to the Major Satellite Repeats at Pericentric Heterochromatin
    • 10.1128/MCB.24.20.9048-9058.2004, 517890, 15456878
    • Chen T, Tsujimoto N, Li E. The PWWP Domain of Dnmt3a and Dnmt3b Is Required for Directing DNA Methylation to the Major Satellite Repeats at Pericentric Heterochromatin. Mol Cell Biol 2004, 24:9048-9058. 10.1128/MCB.24.20.9048-9058.2004, 517890, 15456878.
    • (2004) Mol Cell Biol , vol.24 , pp. 9048-9058
    • Chen, T.1    Tsujimoto, N.2    Li, E.3
  • 43
    • 33744552284 scopus 로고    scopus 로고
    • CpG sites preferentially methylated by Dnmt3a in vivo
    • 10.1074/jbc.M511100200, 16439359
    • Oka M, Rodić N, Graddy J, Chang L-J, Terada N. CpG sites preferentially methylated by Dnmt3a in vivo. J Biol Chem 2006, 281:9901-9908. 10.1074/jbc.M511100200, 16439359.
    • (2006) J Biol Chem , vol.281 , pp. 9901-9908
    • Oka, M.1    Rodić, N.2    Graddy, J.3    Chang, L.-J.4    Terada, N.5
  • 45
    • 78751470921 scopus 로고    scopus 로고
    • Structure and function of mammalian DNA methyltransferases
    • 10.1002/cbic.201000195, 21243710
    • Jurkowska RZ, Jurkowski TP, Jeltsch A. Structure and function of mammalian DNA methyltransferases. ChemBioChem 2011, 12:206-222. 10.1002/cbic.201000195, 21243710.
    • (2011) ChemBioChem , vol.12 , pp. 206-222
    • Jurkowska, R.Z.1    Jurkowski, T.P.2    Jeltsch, A.3
  • 46
    • 77956601372 scopus 로고    scopus 로고
    • Identification of a PRMT5-dependent repressor complex linked to silencing of human fetal globin gene expression
    • 10.1182/blood-2009-10-251116, 2938845, 20495075
    • Rank G, Cerruti L, Simpson RJ, Moritz RL, Jane SM, Zhao Q. Identification of a PRMT5-dependent repressor complex linked to silencing of human fetal globin gene expression. Blood 2010, 116:1585-1592. 10.1182/blood-2009-10-251116, 2938845, 20495075.
    • (2010) Blood , vol.116 , pp. 1585-1592
    • Rank, G.1    Cerruti, L.2    Simpson, R.J.3    Moritz, R.L.4    Jane, S.M.5    Zhao, Q.6
  • 47
    • 34848878368 scopus 로고    scopus 로고
    • Human chromosome 1 satellite 3 DNA is decondensed, demethylated and transcribed in senescent cells and in A431 epithelial carcinoma cells
    • 10.1159/000106440, 17901699
    • Enukashvily NI, Donev R, Waisertreiger ISR, Podgornaya OI. Human chromosome 1 satellite 3 DNA is decondensed, demethylated and transcribed in senescent cells and in A431 epithelial carcinoma cells. Cytogenet. Genome Res. 2007, 118:42-54. 10.1159/000106440, 17901699.
    • (2007) Cytogenet. Genome Res. , vol.118 , pp. 42-54
    • Enukashvily, N.I.1    Donev, R.2    Waisertreiger, I.S.R.3    Podgornaya, O.I.4
  • 49
    • 0036731869 scopus 로고    scopus 로고
    • Correlation of DNA hypomethylation at pericentromeric heterochromatin regions of chromosomes 16 and 1 with histological features and chromosomal abnormalities of human breast carcinomas
    • 10.1016/S0002-9440(10)64246-0, 3277345, 12213714
    • Tsuda H, Takarabe T, Kanai Y, Fukutomi T, Hirohashi S. Correlation of DNA hypomethylation at pericentromeric heterochromatin regions of chromosomes 16 and 1 with histological features and chromosomal abnormalities of human breast carcinomas. Am J Pathol 2002, 161:859-866. 10.1016/S0002-9440(10)64246-0, 3277345, 12213714.
    • (2002) Am J Pathol , vol.161 , pp. 859-866
    • Tsuda, H.1    Takarabe, T.2    Kanai, Y.3    Fukutomi, T.4    Hirohashi, S.5
  • 50
    • 0345040873 scopus 로고    scopus 로고
    • Classification and regression by randomForest
    • Liaw A, Wiener M. Classification and regression by randomForest. R news 2002, 2:18-22.
    • (2002) R news , vol.2 , pp. 18-22
    • Liaw, A.1    Wiener, M.2
  • 53
    • 23144460837 scopus 로고    scopus 로고
    • WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar
    • 10.1093/nar/gki492, 1160252, 15980501
    • Wang G, Yu T, Zhang W. WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar. Nucleic Acids Res 2005, 33:W412-W416. 10.1093/nar/gki492, 1160252, 15980501.
    • (2005) Nucleic Acids Res , vol.33
    • Wang, G.1    Yu, T.2    Zhang, W.3
  • 54
    • 33745631199 scopus 로고    scopus 로고
    • A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements
    • 10.1186/gb-2006-7-6-r49, 1779545, 16787547
    • Wang G, Zhang W. A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements. Genome Biol 2006, 7:R49. 10.1186/gb-2006-7-6-r49, 1779545, 16787547.
    • (2006) Genome Biol , vol.7
    • Wang, G.1    Zhang, W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.