메뉴 건너뛰기




Volumn 26, Issue 1, 2014, Pages 102-120

In vivo mapping of Arabidopsis scaffold/matrix attachment regions reveals link to nucleosome-disfavoring poly(dA:dT) tracts

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS PROTEIN; CHROMATIN; NUCLEOSOME; POLY(DEOXYADENYLATE DEOXYTHYMIDYLATE); TRANSCRIPTION FACTOR;

EID: 84896818529     PISSN: 10404651     EISSN: 1532298X     Source Type: Journal    
DOI: 10.1105/tpc.113.121194     Document Type: Article
Times cited : (17)

References (95)
  • 1
    • 0024826968 scopus 로고
    • Preferential, cooperative binding of DNA topoisomerase II to scaffold-associated regions
    • Adachi, Y., Käs, E., and Laemmli, U.K. (1989). Preferential, cooperative binding of DNA topoisomerase II to scaffold-associated regions. EMBO J. 8: 3997-4006.
    • (1989) EMBO J. , vol.8 , pp. 3997-4006
    • Adachi, Y.1    Käs, E.2    Laemmli, U.K.3
  • 2
  • 3
    • 77956331782 scopus 로고    scopus 로고
    • Drosophila SAF-B links the nuclear matrix, chromosomes, and transcriptional activity
    • Alfonso-Parra, C., and Maggert, K.A. (2010). Drosophila SAF-B links the nuclear matrix, chromosomes, and transcriptional activity. PLoS ONE 5: e10248.
    • (2010) PLoS ONE , vol.5
    • Alfonso-Parra, C.1    Maggert, K.A.2
  • 4
    • 0030138749 scopus 로고    scopus 로고
    • High-level transgene expression in plant cells: Effects of a strong scaffold attachment region from tobacco
    • Allen, G.C., Hall, G., Jr., Michalowski, S., Newman, W., Spiker, S., Weissinger, A.K., and Thompson, W.F. (1996). High-level transgene expression in plant cells: effects of a strong scaffold attachment region from tobacco. Plant Cell 8: 899-913.
    • (1996) Plant Cell , vol.8 , pp. 899-913
    • Allen, G.C.1    Hall Jr., G.2    Michalowski, S.3    Newman, W.4    Spiker, S.5    Weissinger, A.K.6    Thompson, W.F.7
  • 5
    • 0033832638 scopus 로고    scopus 로고
    • Use of matrix attachment regions (MARs) to minimize transgene silencing
    • Allen, G.C., Spiker, S., and Thompson, W.F. (2000). Use of matrix attachment regions (MARs) to minimize transgene silencing. Plant Mol. Biol. 43: 361-376.
    • (2000) Plant Mol. Biol. , vol.43 , pp. 361-376
    • Allen, G.C.1    Spiker, S.2    Thompson, W.F.3
  • 6
    • 0034999881 scopus 로고    scopus 로고
    • Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites
    • Anderson, J.D., and Widom, J. (2001). Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites. Mol. Cell. Biol. 21: 3830-3839.
    • (2001) Mol. Cell. Biol. , vol.21 , pp. 3830-3839
    • Anderson, J.D.1    Widom, J.2
  • 7
    • 0029392459 scopus 로고
    • Matrix attachment regions and transcribed sequences within a long chromosomal continuum containing maize Adh1
    • Avramova, Z., SanMiguel, P., Georgieva, E., and Bennetzen, J.L. (1995). Matrix attachment regions and transcribed sequences within a long chromosomal continuum containing maize Adh1. Plant Cell 7: 1667-1680.
    • (1995) Plant Cell , vol.7 , pp. 1667-1680
    • Avramova, Z.1    SanMiguel, P.2    Georgieva, E.3    Bennetzen, J.L.4
  • 8
    • 0032004775 scopus 로고    scopus 로고
    • Matrix attachment regions and structural colinearity in the genomes of two grass species
    • Avramova, Z., Tikhonov, A., Chen, M., and Bennetzen, J.L. (1998). Matrix attachment regions and structural colinearity in the genomes of two grass species. Nucleic Acids Res. 26: 761-767.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 761-767
    • Avramova, Z.1    Tikhonov, A.2    Chen, M.3    Bennetzen, J.L.4
  • 9
    • 0033976643 scopus 로고    scopus 로고
    • Transposable element contributions to plant gene and genome evolution
    • Bennetzen, J.L. (2000). Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42: 251-269.
    • (2000) Plant Mol. Biol. , vol.42 , pp. 251-269
    • Bennetzen, J.L.1
  • 11
    • 1342282911 scopus 로고    scopus 로고
    • Formation of boundaries of transcriptionally silent chromatin by nucleosomeexcluding structures
    • Bi, X., Yu, Q., Sandmeier, J.J., and Zou, Y. (2004). Formation of boundaries of transcriptionally silent chromatin by nucleosomeexcluding structures. Mol. Cell. Biol. 24: 2118-2131.
    • (2004) Mol. Cell. Biol. , vol.24 , pp. 2118-2131
    • Bi, X.1    Yu, Q.2    Sandmeier, J.J.3    Zou, Y.4
  • 12
    • 0026597313 scopus 로고
    • Biological significance of unwinding capability of nuclear matrix-associating DNAs
    • Bode, J., Kohwi, Y., Dickinson, L., Joh, T., Klehr, D., Mielke, C., and Kohwi-Shigematsu, T. (1992). Biological significance of unwinding capability of nuclear matrix-associating DNAs. Science 255: 195-197.
    • (1992) Science , vol.255 , pp. 195-197
    • Bode, J.1    Kohwi, Y.2    Dickinson, L.3    Joh, T.4    Klehr, D.5    Mielke, C.6    Kohwi-Shigematsu, T.7
  • 13
    • 0027215759 scopus 로고
    • Nature of DNA sequences at the attachment regions of genes to the nuclear matrix
    • Boulikas, T. (1993). Nature of DNA sequences at the attachment regions of genes to the nuclear matrix. J. Cell. Biochem. 52: 14-22.
    • (1993) J. Cell. Biochem. , vol.52 , pp. 14-22
    • Boulikas, T.1
  • 14
    • 42149187766 scopus 로고    scopus 로고
    • Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets
    • Buisine, N., Quesneville, H., and Colot, V. (2008). Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets. Genomics 91: 467-475.
    • (2008) Genomics , vol.91 , pp. 467-475
    • Buisine, N.1    Quesneville, H.2    Colot, V.3
  • 16
    • 0042978644 scopus 로고    scopus 로고
    • Visualization of chromatin domains created by the gypsy insulator of Drosophila
    • Byrd, K., and Corces, V.G. (2003). Visualization of chromatin domains created by the gypsy insulator of Drosophila. J. Cell Biol. 162: 565-574.
    • (2003) J. Cell Biol. , vol.162 , pp. 565-574
    • Byrd, K.1    Corces, V.G.2
  • 17
    • 0038369968 scopus 로고    scopus 로고
    • Tissue-specific nuclear architecture and gene expression regulated by SATB1
    • Cai, S., Han, H.J., and Kohwi-Shigematsu, T. (2003). Tissue-specific nuclear architecture and gene expression regulated by SATB1. Nat. Genet. 34: 42-51.
    • (2003) Nat. Genet. , vol.34 , pp. 42-51
    • Cai, S.1    Han, H.J.2    Kohwi-Shigematsu, T.3
  • 18
    • 70249121045 scopus 로고    scopus 로고
    • The logic of chromatin architecture and remodelling at promoters
    • Cairns, B.R. (2009). The logic of chromatin architecture and remodelling at promoters. Nature 461: 193-198.
    • (2009) Nature , vol.461 , pp. 193-198
    • Cairns, B.R.1
  • 19
    • 0141529726 scopus 로고    scopus 로고
    • A proteomic study of the Arabidopsis nuclear matrix
    • Calikowski, T.T., Meulia, T., and Meier, I. (2003). A proteomic study of the Arabidopsis nuclear matrix. J. Cell. Biochem. 90: 361-378.
    • (2003) J. Cell. Biochem. , vol.90 , pp. 361-378
    • Calikowski, T.T.1    Meulia, T.2    Meier, I.3
  • 20
    • 0020162216 scopus 로고
    • The nuclear matrix: Threedimensional architecture and protein composition
    • Capco, D.G., Wan, K.M., and Penman, S. (1982). The nuclear matrix: Threedimensional architecture and protein composition. Cell 29: 847-858.
    • (1982) Cell , vol.29 , pp. 847-858
    • Capco, D.G.1    Wan, K.M.2    Penman, S.3
  • 21
    • 77954659099 scopus 로고    scopus 로고
    • Relationship between nucleosome positioning and DNA methylation
    • Chodavarapu, R.K., et al. (2010). Relationship between nucleosome positioning and DNA methylation. Nature 466: 388-392.
    • (2010) Nature , vol.466 , pp. 388-392
    • Chodavarapu, R.K.1
  • 22
    • 0022553738 scopus 로고
    • Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites
    • Cockerill, P.N., and Garrard, W.T. (1986). Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell 44: 273-282.
    • (1986) Cell , vol.44 , pp. 273-282
    • Cockerill, P.N.1    Garrard, W.T.2
  • 24
    • 0347492019 scopus 로고    scopus 로고
    • AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors
    • Davuluri, R.V., Sun, H., Palaniswamy, S.K., Matthews, N., Molina, C., Kurtz, M., and Grotewold, E. (2003). AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics 4: 25.
    • (2003) BMC Bioinformatics , vol.4 , pp. 25
    • Davuluri, R.V.1    Sun, H.2    Palaniswamy, S.K.3    Matthews, N.4    Molina, C.5    Kurtz, M.6    Grotewold, E.7
  • 25
    • 0033763825 scopus 로고    scopus 로고
    • Separable whorl-specific expression and negative regulation by enhancer elements within the AGAMOUS second intron
    • Deyholos, M.K., and Sieburth, L.E. (2000). Separable whorl-specific expression and negative regulation by enhancer elements within the AGAMOUS second intron. Plant Cell 12: 1799-1810.
    • (2000) Plant Cell , vol.12 , pp. 1799-1810
    • Deyholos, M.K.1    Sieburth, L.E.2
  • 26
    • 0026758357 scopus 로고
    • A tissue-specific MAR/SAR DNA-binding protein with unusual binding site recognition
    • Dickinson, L.A., Joh, T., Kohwi, Y., and Kohwi-Shigematsu, T. (1992). A tissue-specific MAR/SAR DNA-binding protein with unusual binding site recognition. Cell 70: 631-645.
    • (1992) Cell , vol.70 , pp. 631-645
    • Dickinson, L.A.1    Joh, T.2    Kohwi, Y.3    Kohwi-Shigematsu, T.4
  • 27
    • 84860761301 scopus 로고    scopus 로고
    • The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element
    • Dinh, T.T., Girke, T., Liu, X., Yant, L., Schmid, M., and Chen, X. (2012). The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element. Development 139: 1978-1986.
    • (2012) Development , vol.139 , pp. 1978-1986
    • Dinh, T.T.1    Girke, T.2    Liu, X.3    Yant, L.4    Schmid, M.5    Chen, X.6
  • 31
    • 0036180490 scopus 로고    scopus 로고
    • In silico prediction of scaffold/matrix attachment regions in large genomic sequences
    • Frisch, M., Frech, K., Klingenhoff, A., Cartharius, K., Liebich, I., and Werner, T. (2002). In silico prediction of scaffold/matrix attachment regions in large genomic sequences. Genome Res. 12: 349-354.
    • (2002) Genome Res. , vol.12 , pp. 349-354
    • Frisch, M.1    Frech, K.2    Klingenhoff, A.3    Cartharius, K.4    Liebich, I.5    Werner, T.6
  • 32
    • 12444346207 scopus 로고    scopus 로고
    • Identification of a novel plant MAR DNA binding protein localized on chromosomal surfaces
    • Fujimoto, S., Matsunaga, S., Yonemura, M., Uchiyama, S., Azuma, T., and Fukui, K. (2004). Identification of a novel plant MAR DNA binding protein localized on chromosomal surfaces. Plant Mol. Biol. 56: 225-239.
    • (2004) Plant Mol. Biol. , vol.56 , pp. 225-239
    • Fujimoto, S.1    Matsunaga, S.2    Yonemura, M.3    Uchiyama, S.4    Azuma, T.5    Fukui, K.6
  • 33
    • 0023050122 scopus 로고
    • Cohabitation of scaffold binding regions with upstream/enhancer elements of three developmentally regulated genes of D. melanogaster
    • Gasser, S.M., and Laemmli, U.K. (1986). Cohabitation of scaffold binding regions with upstream/enhancer elements of three developmentally regulated genes of D. melanogaster. Cell 46: 521-530.
    • (1986) Cell , vol.46 , pp. 521-530
    • Gasser, S.M.1    Laemmli, U.K.2
  • 34
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: Open software development for computational biology and bioinformatics
    • Gentleman, R.C., et al. (2004). Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 5: R80.
    • (2004) Genome Biol. , vol.5
    • Gentleman, R.C.1
  • 35
    • 0033638334 scopus 로고    scopus 로고
    • A chromatin insulator determines the nuclear localization of DNA
    • Gerasimova, T.I., Byrd, K., and Corces, V.G. (2000). A chromatin insulator determines the nuclear localization of DNA. Mol. Cell 6: 1025-1035.
    • (2000) Mol. Cell , vol.6 , pp. 1025-1035
    • Gerasimova, T.I.1    Byrd, K.2    Corces, V.G.3
  • 37
    • 37249012276 scopus 로고    scopus 로고
    • Nucleosome destabilization in the epigenetic regulation of gene expression
    • Henikoff, S. (2008). Nucleosome destabilization in the epigenetic regulation of gene expression. Nat. Rev. Genet. 9: 15-26.
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 15-26
    • Henikoff, S.1
  • 38
    • 0032918558 scopus 로고    scopus 로고
    • Plant cis-acting regulatory DNA elements (PLACE) database: 1999
    • Higo, K., Ugawa, Y., Iwamoto, M., and Korenaga, T. (1999). Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res. 27: 297-300.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 297-300
    • Higo, K.1    Ugawa, Y.2    Iwamoto, M.3    Korenaga, T.4
  • 39
    • 0037781051 scopus 로고    scopus 로고
    • Regulatory elements of the floral homeotic gene AGAMOUS identified by phylogenetic footprinting and shadowing
    • Hong, R.L., Hamaguchi, L., Busch, M.A., and Weigel, D. (2003). Regulatory elements of the floral homeotic gene AGAMOUS identified by phylogenetic footprinting and shadowing. Plant Cell 15: 1296-1309.
    • (2003) Plant Cell , vol.15 , pp. 1296-1309
    • Hong, R.L.1    Hamaguchi, L.2    Busch, M.A.3    Weigel, D.4
  • 40
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang, W., Sherman, B.T., and Lempicki, R.A. (2009a). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4: 44-57.
    • (2009) Nat. Protoc. , vol.4 , pp. 44-57
    • Huang, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 41
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
    • Huang, W., Sherman, B.T., and Lempicki, R.A. (2009b). Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37: 1-13.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1-13
    • Huang, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 42
    • 0036947892 scopus 로고    scopus 로고
    • Robust estimators for expression analysis
    • Hubbell, E., Liu, W.M., and Mei, R. (2002). Robust estimators for expression analysis. Bioinformatics 18: 1585-1592.
    • (2002) Bioinformatics , vol.18 , pp. 1585-1592
    • Hubbell, E.1    Liu, W.M.2    Mei, R.3
  • 43
    • 84867371116 scopus 로고    scopus 로고
    • A functional evolutionary approach to identify determinants of nucleosome positioning: A unifying model for establishing the genome-wide pattern
    • Hughes, A.L., Jin, Y., Rando, O.J., and Struhl, K. (2012). A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern. Mol. Cell 48: 5-15.
    • (2012) Mol. Cell , vol.48 , pp. 5-15
    • Hughes, A.L.1    Jin, Y.2    Rando, O.J.3    Struhl, K.4
  • 44
    • 0029026719 scopus 로고
    • Poly(dA: DT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure
    • Iyer, V., and Struhl, K. (1995). Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J. 14: 2570-2579.
    • (1995) EMBO J. , vol.14 , pp. 2570-2579
    • Iyer, V.1    Struhl, K.2
  • 46
    • 0037301560 scopus 로고    scopus 로고
    • Origin of a substantial fraction of human regulatory sequences from transposable elements
    • Jordan, I.K., Rogozin, I.B., Glazko, G.V., and Koonin, E.V. (2003). Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet. 19: 68-72.
    • (2003) Trends Genet. , vol.19 , pp. 68-72
    • Jordan, I.K.1    Rogozin, I.B.2    Glazko, G.V.3    Koonin, E.V.4
  • 48
    • 0024820573 scopus 로고
    • Specific inhibition of DNA binding to nuclear scaffolds and histone H1 by distamycin. The role of oligo(dA). oligo(dT) tracts
    • Käs, E., Izaurralde, E., and Laemmli, U.K. (1989). Specific inhibition of DNA binding to nuclear scaffolds and histone H1 by distamycin. The role of oligo(dA). oligo(dT) tracts. J. Mol. Biol. 210: 587-599.
    • (1989) J. Mol. Biol. , vol.210 , pp. 587-599
    • Käs, E.1    Izaurralde, E.2    Laemmli, U.K.3
  • 49
    • 79952642782 scopus 로고    scopus 로고
    • Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes
    • Keaton, M.A., Taylor, C.M., Layer, R.M., and Dutta, A. (2011). Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes. PLoS ONE 6: e17912.
    • (2011) PLoS ONE , vol.6
    • Keaton, M.A.1    Taylor, C.M.2    Layer, R.M.3    Dutta, A.4
  • 50
    • 33845871732 scopus 로고    scopus 로고
    • Functional interaction between PML and SATB1 regulates chromatin-loop architecture and transcription of the MHC class I locus
    • Kumar, P.P., Bischof, O., Purbey, P.K., Notani, D., Urlaub, H., Dejean, A., and Galande, S. (2007). Functional interaction between PML and SATB1 regulates chromatin-loop architecture and transcription of the MHC class I locus. Nat. Cell Biol. 9: 45-56.
    • (2007) Nat. Cell Biol. , vol.9 , pp. 45-56
    • Kumar, P.P.1    Bischof, O.2    Purbey, P.K.3    Notani, D.4    Urlaub, H.5    Dejean, A.6    Galande, S.7
  • 51
    • 23844540311 scopus 로고    scopus 로고
    • Characterization of Arabidopsis thaliana SMC1 and SMC3: Evidence that AtSMC3 may function beyond chromosome cohesion
    • Lam, W.S., Yang, X., and Makaroff, C.A. (2005). Characterization of Arabidopsis thaliana SMC1 and SMC3: evidence that AtSMC3 may function beyond chromosome cohesion. J. Cell Sci. 118: 3037-3048.
    • (2005) J. Cell Sci. , vol.118 , pp. 3037-3048
    • Lam, W.S.1    Yang, X.2    Makaroff, C.A.3
  • 52
    • 77954155284 scopus 로고    scopus 로고
    • Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state
    • Lee, T.-J., et al. (2010). Arabidopsis thaliana chromosome 4 replicates in two phases that correlate with chromatin state. PLoS Genet. 6: e1000982.
    • (2010) PLoS Genet. , vol.6
    • Lee, T.-J.1
  • 53
    • 0036682334 scopus 로고    scopus 로고
    • Evaluation of sequence motifs found in scaffold/matrix-attached regions (S/MARs)
    • Liebich, I., Bode, J., Reuter, I., and Wingender, E. (2002). Evaluation of sequence motifs found in scaffold/matrix-attached regions (S/MARs). Nucleic Acids Res. 30: 3433-3442.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3433-3442
    • Liebich, I.1    Bode, J.2    Reuter, I.3    Wingender, E.4
  • 54
    • 59049098879 scopus 로고    scopus 로고
    • Differential nuclear scaffold/matrix attachment marks expressed genes
    • Linnemann, A.K., Platts, A.E., and Krawetz, S.A. (2009). Differential nuclear scaffold/matrix attachment marks expressed genes. Hum. Mol. Genet. 18: 645-654.
    • (2009) Hum. Mol. Genet. , vol.18 , pp. 645-654
    • Linnemann, A.K.1    Platts, A.E.2    Krawetz, S.A.3
  • 55
    • 77952500831 scopus 로고    scopus 로고
    • Histone methylation in higher plants
    • Liu, C., Lu, F., Cui, X., and Cao, X. (2010). Histone methylation in higher plants. Annu. Rev. Plant Biol. 61: 395-420.
    • (2010) Annu. Rev. Plant Biol. , vol.61 , pp. 395-420
    • Liu, C.1    Lu, F.2    Cui, X.3    Cao, X.4
  • 56
    • 84862732690 scopus 로고    scopus 로고
    • New insights into nucleosome and chromatin structure: An ordered state or a disordered affair?
    • Luger, K., Dechassa, M.L., and Tremethick, D.J. (2012). New insights into nucleosome and chromatin structure: An ordered state or a disordered affair? Nat. Rev. Mol. Cell Biol. 13: 436-447.
    • (2012) Nat. Rev. Mol. Cell Biol. , vol.13 , pp. 436-447
    • Luger, K.1    Dechassa, M.L.2    Tremethick, D.J.3
  • 57
    • 0037452978 scopus 로고    scopus 로고
    • The matrix attachment region in the Chinese hamster dihydrofolate reductase origin of replication may be required for local chromatid separation
    • Mesner, L.D., Hamlin, J.L., and Dijkwel, P.A. (2003). The matrix attachment region in the Chinese hamster dihydrofolate reductase origin of replication may be required for local chromatid separation. Proc. Natl. Acad. Sci. USA 100: 3281-3286.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 3281-3286
    • Mesner, L.D.1    Hamlin, J.L.2    Dijkwel, P.A.3
  • 58
    • 0033613104 scopus 로고    scopus 로고
    • Characterization of randomly-obtained matrix attachment regions (MARs) from higher plants
    • Michalowski, S.M., Allen, G.C., Hall, G.E., Jr., Thompson, W.F., and Spiker, S. (1999). Characterization of randomly-obtained matrix attachment regions (MARs) from higher plants. Biochemistry 38: 12795-12804.
    • (1999) Biochemistry , vol.38 , pp. 12795-12804
    • Michalowski, S.M.1    Allen, G.C.2    Hall Jr., G.E.3    Thompson, W.F.4    Spiker, S.5
  • 59
    • 0023923131 scopus 로고
    • Scaffold attachment of DNA loops in metaphase chromosomes
    • Mirkovitch, J., Gasser, S.M., and Laemmli, U.K. (1988). Scaffold attachment of DNA loops in metaphase chromosomes. J. Mol. Biol. 200: 101-109.
    • (1988) J. Mol. Biol. , vol.200 , pp. 101-109
    • Mirkovitch, J.1    Gasser, S.M.2    Laemmli, U.K.3
  • 60
    • 0021675784 scopus 로고
    • Organization of the higher-order chromatin loop: Specific DNA attachment sites on nuclear scaffold
    • Mirkovitch, J., Mirault, M.-E., and Laemmli, U.K. (1984). Organization of the higher-order chromatin loop: Specific DNA attachment sites on nuclear scaffold. Cell 39: 223-232.
    • (1984) Cell , vol.39 , pp. 223-232
    • Mirkovitch, J.1    Mirault, M.-E.2    Laemmli, U.K.3
  • 61
    • 0033758607 scopus 로고    scopus 로고
    • AHM1, a novel type of nuclear matrixlocalized, MAR binding protein with a single AT hook and a J domain-homologous region
    • Morisawa, G., Han-Yama, A., Moda, I., Tamai, A., Iwabuchi, M., and Meshi, T. (2000). AHM1, a novel type of nuclear matrixlocalized, MAR binding protein with a single AT hook and a J domain-homologous region. Plant Cell 12: 1903-1916.
    • (2000) Plant Cell , vol.12 , pp. 1903-1916
    • Morisawa, G.1    Han-Yama, A.2    Moda, I.3    Tamai, A.4    Iwabuchi, M.5    Meshi, T.6
  • 62
    • 0031915974 scopus 로고    scopus 로고
    • A nuclear matrix/ scaffold attachment region co-localizes with the gypsy retrotransposon insulator sequence
    • Nabirochkin, S., Ossokina, M., and Heidmann, T. (1998). A nuclear matrix/ scaffold attachment region co-localizes with the gypsy retrotransposon insulator sequence. J. Biol. Chem. 273: 2473-2479.
    • (1998) J. Biol. Chem. , vol.273 , pp. 2473-2479
    • Nabirochkin, S.1    Ossokina, M.2    Heidmann, T.3
  • 63
    • 77956620942 scopus 로고    scopus 로고
    • Shedding light on the role of AT-hook/PPC domain protein in Arabidopsis thaliana
    • Ng, K.-H., and Ito, T. (2010). Shedding light on the role of AT-hook/PPC domain protein in Arabidopsis thaliana. Plant Signal. Behavior 5: 200-201.
    • (2010) Plant Signal. Behavior , vol.5 , pp. 200-201
    • Ng, K.-H.1    Ito, T.2
  • 64
    • 72949097670 scopus 로고    scopus 로고
    • AGAMOUS controls GIANT KILLER, a multifunctional chromatin modifier in reproductive organ patterning and differentiation
    • Ng, K.H., Yu, H., and Ito, T. (2009). AGAMOUS controls GIANT KILLER, a multifunctional chromatin modifier in reproductive organ patterning and differentiation. PLoS Biol. 7: e1000251.
    • (2009) PLoS Biol. , vol.7
    • Ng, K.H.1    Yu, H.2    Ito, T.3
  • 65
  • 66
    • 55549084895 scopus 로고    scopus 로고
    • Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex
    • Ottaviani, D., et al. (2008). Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex. Genome Res. 18: 1778-1786.
    • (2008) Genome Res. , vol.18 , pp. 1778-1786
    • Ottaviani, D.1
  • 67
    • 33646907417 scopus 로고    scopus 로고
    • AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks
    • Palaniswamy, S.K., James, S., Sun, H., Lamb, R.S., Davuluri, R.V., and Grotewold, E. (2006). AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks. Plant Physiol. 140: 818-829.
    • (2006) Plant Physiol. , vol.140 , pp. 818-829
    • Palaniswamy, S.K.1    James, S.2    Sun, H.3    Lamb, R.S.4    Davuluri, R.V.5    Grotewold, E.6
  • 68
    • 0017652886 scopus 로고
    • The structure of histonedepleted metaphase chromosomes
    • Paulson, J.R., and Laemmli, U.K. (1977). The structure of histonedepleted metaphase chromosomes. Cell 12: 817-828.
    • (1977) Cell , vol.12 , pp. 817-828
    • Paulson, J.R.1    Laemmli, U.K.2
  • 70
    • 70149113077 scopus 로고    scopus 로고
    • R Development Core Team, (Vienna, Austria: R Foundation for Statistical Computing)
    • R Development Core Team (2009). R: A Language and Environment for Statistical Computing. (Vienna, Austria: R Foundation for Statistical Computing).
    • (2009) R: A Language and Environment for Statistical Computing
  • 71
    • 70350686719 scopus 로고    scopus 로고
    • The role of DNA shape in protein-DNA recognition
    • Rohs, R., West, S.M., Sosinsky, A., Liu, P., Mann, R.S., and Honig, B. (2009). The role of DNA shape in protein-DNA recognition. Nature 461: 1248-1253.
    • (2009) Nature , vol.461 , pp. 1248-1253
    • Rohs, R.1    West, S.M.2    Sosinsky, A.3    Liu, P.4    Mann, R.S.5    Honig, B.6
  • 72
    • 0033215297 scopus 로고    scopus 로고
    • Identification and characterization of nuclear matrixattachment regions in the human serpin gene cluster at 14q32.1
    • Rollini, P., Namciu, S.J., Marsden, M.D., and Fournier, R.E.K. (1999). Identification and characterization of nuclear matrixattachment regions in the human serpin gene cluster at 14q32.1. Nucleic Acids Res. 27: 3779-3791.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 3779-3791
    • Rollini, P.1    Namciu, S.J.2    Marsden, M.D.3    Fournier, R.E.K.4
  • 73
    • 79956066320 scopus 로고    scopus 로고
    • Integrative epigenomic mapping defines four main chromatin states in Arabidopsis
    • Roudier, F., et al. (2011). Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J. 30: 1928-1938.
    • (2011) EMBO J. , vol.30 , pp. 1928-1938
    • Roudier, F.1
  • 74
    • 3042667241 scopus 로고    scopus 로고
    • Genome-wide in silico mapping of scaffold/ matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression
    • Rudd, S., Frisch, M., Grote, K., Meyers, B.C., Mayer, K., and Werner, T. (2004). Genome-wide in silico mapping of scaffold/ matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression. Plant Physiol. 135: 715-722.
    • (2004) Plant Physiol. , vol.135 , pp. 715-722
    • Rudd, S.1    Frisch, M.2    Grote, K.3    Meyers, B.C.4    Mayer, K.5    Werner, T.6
  • 75
    • 0033953635 scopus 로고    scopus 로고
    • An economic method for the fluorescent labeling of PCR fragments
    • Schuelke, M. (2000). An economic method for the fluorescent labeling of PCR fragments. Nat. Biotechnol. 18: 233-234.
    • (2000) Nat. Biotechnol. , vol.18 , pp. 233-234
    • Schuelke, M.1
  • 76
    • 60349115060 scopus 로고    scopus 로고
    • Poly(dA: DT) tracts: Major determinants of nucleosome organization
    • Segal, E., and Widom, J. (2009). Poly(dA:dT) tracts: Major determinants of nucleosome organization. Curr. Opin. Struct. Biol. 19: 65-71.
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 65-71
    • Segal, E.1    Widom, J.2
  • 77
    • 0031106359 scopus 로고    scopus 로고
    • Molecular dissection of the AGAMOUS control region shows that cis elements for spatial regulation are located intragenically
    • Sieburth, L.E., and Meyerowitz, E.M. (1997). Molecular dissection of the AGAMOUS control region shows that cis elements for spatial regulation are located intragenically. Plant Cell 9: 355-365.
    • (1997) Plant Cell , vol.9 , pp. 355-365
    • Sieburth, L.E.1    Meyerowitz, E.M.2
  • 78
    • 80054902318 scopus 로고    scopus 로고
    • The nucleoskeleton as a genome-associated dynamic 'network of networks'
    • Simon, D.N., and Wilson, K.L. (2011). The nucleoskeleton as a genome-associated dynamic 'network of networks'. Nat. Rev. Mol. Cell Biol. 12: 695-708.
    • (2011) Nat. Rev. Mol. Cell Biol. , vol.12 , pp. 695-708
    • Simon, D.N.1    Wilson, K.L.2
  • 79
    • 33644872577 scopus 로고    scopus 로고
    • Limma: Linear models for microarray data
    • In, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, andW. Huber, eds (New York: Springer)
    • Smyth, G.K. (2005). Limma: Linear models for microarray data. In Bioinformatics and Computational Biology Solutions Using R and Bioconductor, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, andW. Huber, eds (New York: Springer), pp. 397-420.
    • (2005) Bioinformatics and Computational Biology Solutions Using R and Bioconductor , pp. 397-420
    • Smyth, G.K.1
  • 80
    • 80053539409 scopus 로고    scopus 로고
    • Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
    • Song, L., et al. (2011). Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res. 21: 1757-1767.
    • (2011) Genome Res. , vol.21 , pp. 1757-1767
    • Song, L.1
  • 81
    • 84875196326 scopus 로고    scopus 로고
    • Determinants of nucleosome positioning
    • Struhl, K., and Segal, E. (2013). Determinants of nucleosome positioning. Nat. Struct. Mol. Biol. 20: 267-273.
    • (2013) Nat. Struct. Mol. Biol. , vol.20 , pp. 267-273
    • Struhl, K.1    Segal, E.2
  • 82
    • 62749122796 scopus 로고    scopus 로고
    • Dissecting nucleosome free regions by a segmental semi-Markov model
    • Sun, W., Xie, W., Xu, F., Grunstein, M., and Li, K.-C. (2009). Dissecting nucleosome free regions by a segmental semi-Markov model. PLoS ONE 4: e4721.
    • (2009) PLoS ONE , vol.4
    • Sun, W.1    Xie, W.2    Xu, F.3    Grunstein, M.4    Li, K.-C.5
  • 83
    • 38549144806 scopus 로고    scopus 로고
    • The Arabidopsis Information Resource (TAIR): Gene structure and function annotation
    • Swarbreck, D., et al. (2008). The Arabidopsis Information Resource (TAIR): Gene structure and function annotation. Nucleic Acids Res. 36: D1009-D1014.
    • (2008) Nucleic Acids Res. , vol.36
    • Swarbreck, D.1
  • 84
    • 67649410722 scopus 로고    scopus 로고
    • Determination of the in vivo distribution of nuclear matrix attachment regions using a polymerase chain reaction-based assay in Arabidopsis thaliana
    • Tachiki, K., Kodama, Y., Nakayama, H., and Shinmyo, A. (2009). Determination of the in vivo distribution of nuclear matrix attachment regions using a polymerase chain reaction-based assay in Arabidopsis thaliana. J. Biosci. Bioeng. 108: 11-19.
    • (2009) J. Biosci. Bioeng. , vol.108 , pp. 11-19
    • Tachiki, K.1    Kodama, Y.2    Nakayama, H.3    Shinmyo, A.4
  • 86
    • 33645787282 scopus 로고    scopus 로고
    • Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana
    • Tetko, I.V., Haberer, G., Rudd, S., Meyers, B., Mewes, H.W., and Mayer, K.F. (2006). Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana. PLOS Comput. Biol. 2: e21.
    • (2006) PLOS Comput. Biol. , vol.2
    • Tetko, I.V.1    Haberer, G.2    Rudd, S.3    Meyers, B.4    Mewes, H.W.5    Mayer, K.F.6
  • 87
  • 88
    • 0034143275 scopus 로고    scopus 로고
    • Structural domains and matrix attachment regions along colinear chromosomal segments of maize and sorghum
    • Tikhonov, A.P., Bennetzen, J.L., and Avramova, Z.V. (2000). Structural domains and matrix attachment regions along colinear chromosomal segments of maize and sorghum. Plant Cell 12: 249-264.
    • (2000) Plant Cell , vol.12 , pp. 249-264
    • Tikhonov, A.P.1    Bennetzen, J.L.2    Avramova, Z.V.3
  • 89
    • 0030963738 scopus 로고    scopus 로고
    • Analysis of the chromatin domain organisation around the plastocyanin gene reveals an MAR-specific sequence element in Arabidopsis thaliana
    • van Drunen, C.M., Oosterling, R.W., Keultjes, G.M., Weisbeek, P. J., van Driel, R., and Smeekens, S.C.M. (1997). Analysis of the chromatin domain organisation around the plastocyanin gene reveals an MAR-specific sequence element in Arabidopsis thaliana. Nucleic Acids Res. 25: 3904-3911.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3904-3911
    • van Drunen, C.M.1    Oosterling, R.W.2    Keultjes, G.M.3    Weisbeek, P.J.4    van Driel, R.5    Smeekens, S.C.M.6
  • 91
    • 0025965095 scopus 로고
    • A matrix/ scaffold attachment region binding protein: Identification, purification, and mode of binding
    • von Kries, J.P., Buhrmester, H., and Strätling, W.H. (1991). A matrix/ scaffold attachment region binding protein: Identification, purification, and mode of binding. Cell 64: 123-135.
    • (1991) Cell , vol.64 , pp. 123-135
    • von Kries, J.P.1    Buhrmester, H.2    Strätling, W.H.3
  • 93
    • 84865331447 scopus 로고    scopus 로고
    • Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis
    • Zhang, W., Zhang, T., Wu, Y., and Jiang, J. (2012). Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant Cell 24: 2719-2731.
    • (2012) Plant Cell , vol.24 , pp. 2719-2731
    • Zhang, W.1    Zhang, T.2    Wu, Y.3    Jiang, J.4
  • 94
    • 67650091251 scopus 로고    scopus 로고
    • Genome-wide analysis of mono-, di-and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana
    • Zhang, X., Bernatavichute, Y.V., Cokus, S., Pellegrini, M., and Jacobsen, S.E. (2009a). Genome-wide analysis of mono-, di-and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol. 10: R62.
    • (2009) Genome Biol. , vol.10
    • Zhang, X.1    Bernatavichute, Y.V.2    Cokus, S.3    Pellegrini, M.4    Jacobsen, S.E.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.