메뉴 건너뛰기




Volumn 22, Issue 2, 2012, Pages 179-187

Nuclear architecture by RNA

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; POLYCOMB GROUP PROTEIN; RNA; SINGLE STRANDED RNA; TRANSCRIPTION FACTOR CTCF; UNTRANSLATED RNA;

EID: 84860376620     PISSN: 0959437X     EISSN: 18790380     Source Type: Journal    
DOI: 10.1016/j.gde.2011.12.005     Document Type: Review
Times cited : (58)

References (72)
  • 2
    • 0013801134 scopus 로고
    • Histone-bound RNA, a component of native nucleohistone
    • Huang R.C., Bonner J. Histone-bound RNA, a component of native nucleohistone. Proc Natl Acad Sci USA 1965, 54:960-967.
    • (1965) Proc Natl Acad Sci USA , vol.54 , pp. 960-967
    • Huang, R.C.1    Bonner, J.2
  • 3
    • 0015544009 scopus 로고
    • Nuclear RNA metabolism
    • Weinberg R.A. Nuclear RNA metabolism. Annu Rev Biochem 1973, 42:329-354.
    • (1973) Annu Rev Biochem , vol.42 , pp. 329-354
    • Weinberg, R.A.1
  • 4
    • 0018791012 scopus 로고
    • Evidence for a role of RNA in eukaryotic chromosome structure. Metabolically stable, small nuclear RNA species are covalently linked to chromosomal DNA in HeLa cells
    • Pederson T., Bhorjee J.S. Evidence for a role of RNA in eukaryotic chromosome structure. Metabolically stable, small nuclear RNA species are covalently linked to chromosomal DNA in HeLa cells. J Mol Biol 1979, 128:451-480.
    • (1979) J Mol Biol , vol.128 , pp. 451-480
    • Pederson, T.1    Bhorjee, J.S.2
  • 5
    • 0016825478 scopus 로고
    • Chromatin-associated RNA content of heterochromatin and euchromatin
    • Paul J., Duerksen J.D. Chromatin-associated RNA content of heterochromatin and euchromatin. Mol Cell Biochem 1975, 9:9-16.
    • (1975) Mol Cell Biochem , vol.9 , pp. 9-16
    • Paul, J.1    Duerksen, J.D.2
  • 7
    • 0026071401 scopus 로고
    • A comprehensive study on the isolation and characterization of the HeLa S3 nuclear matrix
    • Belgrader P., Siegel A.J., Berezney R. A comprehensive study on the isolation and characterization of the HeLa S3 nuclear matrix. J Cell Sci 1991, 98:281-291.
    • (1991) J Cell Sci , vol.98 , pp. 281-291
    • Belgrader, P.1    Siegel, A.J.2    Berezney, R.3
  • 8
    • 0033538846 scopus 로고    scopus 로고
    • Association of chromosome territories with the nuclear matrix. Disruption of human chromosome territories correlates with the release of a subset of nuclear matrix proteins
    • Ma H., Siegel A., Berezney R. Association of chromosome territories with the nuclear matrix. Disruption of human chromosome territories correlates with the release of a subset of nuclear matrix proteins. J Cell Biol 1999, 146:531-542.
    • (1999) J Cell Biol , vol.146 , pp. 531-542
    • Ma, H.1    Siegel, A.2    Berezney, R.3
  • 9
    • 84860362829 scopus 로고    scopus 로고
    • Active chromatin and noncoding RNAs: an intimate relationship
    • Flynn R.A., Chang HY Active chromatin and noncoding RNAs: an intimate relationship. Curr Opin Genet Dev 2012, 22:172-178.
    • (2012) Curr Opin Genet Dev , vol.22 , pp. 172-178
    • Flynn, R.A.1    Chang, H.Y.2
  • 11
    • 80053523254 scopus 로고    scopus 로고
    • The evolution of RNAs with multiple functions
    • Dinger M.E., Gascoigne D.K., Mattick J.S. The evolution of RNAs with multiple functions. Biochimie 2011, 93:2013-2018.
    • (2011) Biochimie , vol.93 , pp. 2013-2018
    • Dinger, M.E.1    Gascoigne, D.K.2    Mattick, J.S.3
  • 12
    • 80053562921 scopus 로고    scopus 로고
    • Identification of potentially new bifunctional RNA based on genome-wide data-mining of alternative splicing events
    • Ulveling D., Francastel C., Hube F. Identification of potentially new bifunctional RNA based on genome-wide data-mining of alternative splicing events. Biochimie 2011, 93:2024-2027.
    • (2011) Biochimie , vol.93 , pp. 2024-2027
    • Ulveling, D.1    Francastel, C.2    Hube, F.3
  • 13
    • 80053560943 scopus 로고    scopus 로고
    • Coding vs non-coding: translatability of short ORFs found in putative non-coding transcripts
    • Kageyama Y., Kondo T., Hashimoto Y. Coding vs non-coding: translatability of short ORFs found in putative non-coding transcripts. Biochimie 2011, 93:1981-1986.
    • (2011) Biochimie , vol.93 , pp. 1981-1986
    • Kageyama, Y.1    Kondo, T.2    Hashimoto, Y.3
  • 15
    • 77958576363 scopus 로고    scopus 로고
    • Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes
    • Schmitz K.-M., Mayer C., Postepska A., Grummt I. Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev 2010, 24:2264-2269.
    • (2010) Genes Dev , vol.24 , pp. 2264-2269
    • Schmitz, K.-M.1    Mayer, C.2    Postepska, A.3    Grummt, I.4
  • 20
    • 77956651480 scopus 로고    scopus 로고
    • Differentiation and large scale spatial organization of the genome
    • Joffe B., Leonhardt H., Solovei I. Differentiation and large scale spatial organization of the genome. Curr Opin Genet Dev 2010, 20:562-569.
    • (2010) Curr Opin Genet Dev , vol.20 , pp. 562-569
    • Joffe, B.1    Leonhardt, H.2    Solovei, I.3
  • 21
    • 77952212771 scopus 로고    scopus 로고
    • RNA traffic control of chromatin complexes
    • Koziol M.J., Rinn J.L. RNA traffic control of chromatin complexes. Curr Opin Genet Dev 2010, 20:142-148.
    • (2010) Curr Opin Genet Dev , vol.20 , pp. 142-148
    • Koziol, M.J.1    Rinn, J.L.2
  • 23
    • 79960622503 scopus 로고    scopus 로고
    • Biogenesis and function of nuclear bodies
    • Mao Y.S., Zhang B., Spector D.L. Biogenesis and function of nuclear bodies. Trends Genet 2011, 27:295-306.
    • (2011) Trends Genet , vol.27 , pp. 295-306
    • Mao, Y.S.1    Zhang, B.2    Spector, D.L.3
  • 24
    • 69949132008 scopus 로고    scopus 로고
    • Paraspeckles: nuclear bodies built on long noncoding RNA
    • Bond C.S., Fox A.H. Paraspeckles: nuclear bodies built on long noncoding RNA. J Cell Biol 2009, 186:637-644.
    • (2009) J Cell Biol , vol.186 , pp. 637-644
    • Bond, C.S.1    Fox, A.H.2
  • 25
    • 62549117314 scopus 로고    scopus 로고
    • An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles
    • Clemson C.M., Hutchinson J.N., Sara S.A., Ensminger A.W., Fox A.H., Chess A., Lawrence J.B. An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell 2009, 33:717-726.
    • (2009) Mol Cell , vol.33 , pp. 717-726
    • Clemson, C.M.1    Hutchinson, J.N.2    Sara, S.A.3    Ensminger, A.W.4    Fox, A.H.5    Chess, A.6    Lawrence, J.B.7
  • 26
    • 62449319486 scopus 로고    scopus 로고
    • MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles
    • Sasaki Y.T., Ideue T., Sano M., Mituyama T., Hirose T. MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci USA 2009, 106:2525-2530.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 2525-2530
    • Sasaki, Y.T.1    Ideue, T.2    Sano, M.3    Mituyama, T.4    Hirose, T.5
  • 27
    • 79551593011 scopus 로고    scopus 로고
    • Nucleation of nuclear bodies by RNA
    • Shevtsov S.P., Dundr M. Nucleation of nuclear bodies by RNA. Nat Cell Biol 2011, 13:167-173.
    • (2011) Nat Cell Biol , vol.13 , pp. 167-173
    • Shevtsov, S.P.1    Dundr, M.2
  • 28
    • 78650511795 scopus 로고    scopus 로고
    • Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs
    • Mao Y.S., Sunwoo H., Zhang B., Spector D.L. Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. Nat Cell Biol 2011, 13:95-101.
    • (2011) Nat Cell Biol , vol.13 , pp. 95-101
    • Mao, Y.S.1    Sunwoo, H.2    Zhang, B.3    Spector, D.L.4
  • 29
    • 34548291568 scopus 로고    scopus 로고
    • The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons
    • Sone M., Hayashi T., Tarui H., Agata K., Takeichi M., Nakagawa S. The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. J Cell Sci 2007, 120:2498-2506.
    • (2007) J Cell Sci , vol.120 , pp. 2498-2506
    • Sone, M.1    Hayashi, T.2    Tarui, H.3    Agata, K.4    Takeichi, M.5    Nakagawa, S.6
  • 30
    • 79955103588 scopus 로고    scopus 로고
    • Competition between a noncoding exon and introns: Gomafu contains tandem UACUAAC repeats and associates with splicing factor-1
    • Tsuiji H., Yoshimoto R., Hasegawa Y., Furuno M., Yoshida M., Nakagawa S. Competition between a noncoding exon and introns: Gomafu contains tandem UACUAAC repeats and associates with splicing factor-1. Genes Cells 2011, 16:479-490.
    • (2011) Genes Cells , vol.16 , pp. 479-490
    • Tsuiji, H.1    Yoshimoto, R.2    Hasegawa, Y.3    Furuno, M.4    Yoshida, M.5    Nakagawa, S.6
  • 32
    • 79956073017 scopus 로고    scopus 로고
    • Potential in vivo roles of nucleic acid triple-helices
    • Buske F.A., Mattick J.S., Bailey T.L. Potential in vivo roles of nucleic acid triple-helices. RNA Biol 2011, 8:427-439.
    • (2011) RNA Biol , vol.8 , pp. 427-439
    • Buske, F.A.1    Mattick, J.S.2    Bailey, T.L.3
  • 33
    • 0036509836 scopus 로고    scopus 로고
    • Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component
    • Maison C., Bailly D., Peters A.H.F.M., Quivy J.-P., Roche D., Taddei A., Lachner M., Jenuwein T., Almouzni G. Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component. Nat Genet 2002, 30:329-334.
    • (2002) Nat Genet , vol.30 , pp. 329-334
    • Maison, C.1    Bailly, D.2    Peters, A.H.F.M.3    Quivy, J.-P.4    Roche, D.5    Taddei, A.6    Lachner, M.7    Jenuwein, T.8    Almouzni, G.9
  • 36
    • 77649202581 scopus 로고    scopus 로고
    • DNA binding of centromere protein C (CENPC) is stabilized by single-stranded RNA
    • Du Y., Topp C.N., Dawe R.K. DNA binding of centromere protein C (CENPC) is stabilized by single-stranded RNA. PLoS Genet 2010, 6:e1000835.
    • (2010) PLoS Genet , vol.6
    • Du, Y.1    Topp, C.N.2    Dawe, R.K.3
  • 37
    • 84979832497 scopus 로고    scopus 로고
    • Transcription of satellite DNAs in mammals
    • Vourc'h C., Biamonti G. Transcription of satellite DNAs in mammals. Prog Biophys Mol Biol 2010, 51:95-118.
    • (2010) Prog Biophys Mol Biol , vol.51 , pp. 95-118
    • Vourc'h, C.1    Biamonti, G.2
  • 38
    • 68949198783 scopus 로고    scopus 로고
    • TERRA RNA binding to TRF2 facilitates heterochromatin formation and ORC recruitment at telomeres
    • Deng Z., Norseen J., Wiedmer A., Riethman H., Lieberman P.M. TERRA RNA binding to TRF2 facilitates heterochromatin formation and ORC recruitment at telomeres. Mol Cell 2009, 35:403-413.
    • (2009) Mol Cell , vol.35 , pp. 403-413
    • Deng, Z.1    Norseen, J.2    Wiedmer, A.3    Riethman, H.4    Lieberman, P.M.5
  • 39
    • 79960290302 scopus 로고    scopus 로고
    • Fine structure of the " PcG body" in human U-2 OS cells established by correlative light-electron microscopy
    • Smigova J., Juda P., Cmarko D., Raska I. Fine structure of the " PcG body" in human U-2 OS cells established by correlative light-electron microscopy. Nucleus 2011, 2:219-228.
    • (2011) Nucleus , vol.2 , pp. 219-228
    • Smigova, J.1    Juda, P.2    Cmarko, D.3    Raska, I.4
  • 42
    • 9444244427 scopus 로고    scopus 로고
    • Chromatin compaction by a polycomb group protein complex
    • Francis N.J., Kingston R.E., Woodcock C.L. Chromatin compaction by a polycomb group protein complex. Science 2004, 306:1574-1577.
    • (2004) Science , vol.306 , pp. 1574-1577
    • Francis, N.J.1    Kingston, R.E.2    Woodcock, C.L.3
  • 45
    • 81055140863 scopus 로고    scopus 로고
    • NcRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs
    • Yang L., Lin C., Liu W., Zhang J., Ohgi K.A., Grinstein J.D., Dorrestein P.C., Rosenfeld M.G. ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. Cell 2011, 147:773-788.
    • (2011) Cell , vol.147 , pp. 773-788
    • Yang, L.1    Lin, C.2    Liu, W.3    Zhang, J.4    Ohgi, K.A.5    Grinstein, J.D.6    Dorrestein, P.C.7    Rosenfeld, M.G.8
  • 46
    • 80052413006 scopus 로고    scopus 로고
    • Chromatin structure and nuclear organization dynamics during X-chromosome inactivation
    • Nora E.P., Heard E. Chromatin structure and nuclear organization dynamics during X-chromosome inactivation. Cold Spring Harb Symp Quant Biol 2010, 75:333-344.
    • (2010) Cold Spring Harb Symp Quant Biol , vol.75 , pp. 333-344
    • Nora, E.P.1    Heard, E.2
  • 47
    • 79959948197 scopus 로고    scopus 로고
    • YY1 tethers Xist RNA to the inactive X nucleation center
    • Jeon Y., Lee J.T. YY1 tethers Xist RNA to the inactive X nucleation center. Cell 2011, 146:119-133.
    • (2011) Cell , vol.146 , pp. 119-133
    • Jeon, Y.1    Lee, J.T.2
  • 48
    • 43149100549 scopus 로고    scopus 로고
    • The facultative heterochromatin of the inactive X chromosome has a distinctive condensed ultrastructure
    • Rego A., Sinclair P.B., Tao W., Kireev I., Belmont A.S. The facultative heterochromatin of the inactive X chromosome has a distinctive condensed ultrastructure. J Cell Sci 2008, 121:1119-1127.
    • (2008) J Cell Sci , vol.121 , pp. 1119-1127
    • Rego, A.1    Sinclair, P.B.2    Tao, W.3    Kireev, I.4    Belmont, A.S.5
  • 49
    • 80054705013 scopus 로고    scopus 로고
    • A top-down analysis of Xa- and Xi-territories reveals differences of higher order structure at >/= 20 Mb genomic length scales
    • Teller K., Illner D., Thamm S., Casas-Delucchi C.S., Versteeg R., Indemans M., Cremer T., Cremer M. A top-down analysis of Xa- and Xi-territories reveals differences of higher order structure at >/= 20 Mb genomic length scales. Nucleus 2011, 2.
    • (2011) Nucleus , pp. 2
    • Teller, K.1    Illner, D.2    Thamm, S.3    Casas-Delucchi, C.S.4    Versteeg, R.5    Indemans, M.6    Cremer, T.7    Cremer, M.8
  • 52
    • 78650675579 scopus 로고    scopus 로고
    • Locked nucleic acids (LNAs) reveal sequence requirements and kinetics of Xist RNA localization to the X chromosome
    • Sarma K., Levasseur P., Aristarkhov A., Lee J.T. Locked nucleic acids (LNAs) reveal sequence requirements and kinetics of Xist RNA localization to the X chromosome. Proc Natl Acad Sci USA 2010, 107:22196-22201.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 22196-22201
    • Sarma, K.1    Levasseur, P.2    Aristarkhov, A.3    Lee, J.T.4
  • 53
    • 67549119096 scopus 로고    scopus 로고
    • CTCF: master weaver of the genome
    • Phillips J.E., Corces V.G. CTCF: master weaver of the genome. Cell 2009, 137:1194-1211.
    • (2009) Cell , vol.137 , pp. 1194-1211
    • Phillips, J.E.1    Corces, V.G.2
  • 55
    • 53149130940 scopus 로고    scopus 로고
    • The LPS-induced transcriptional upregulation of the chicken lysozyme locus involves CTCF eviction and noncoding RNA transcription
    • Lefevre P., Witham J., Lacroix C.E., Cockerill P.N., Bonifer C. The LPS-induced transcriptional upregulation of the chicken lysozyme locus involves CTCF eviction and noncoding RNA transcription. Mol Cell 2008, 32:129-139.
    • (2008) Mol Cell , vol.32 , pp. 129-139
    • Lefevre, P.1    Witham, J.2    Lacroix, C.E.3    Cockerill, P.N.4    Bonifer, C.5
  • 56
    • 78349252731 scopus 로고    scopus 로고
    • Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA
    • Yao H., Brick K., Evrard Y., Xiao T., Camerini-Otero R.D., Felsenfeld G. Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA. Genes Dev 2010, 24:2543-2555.
    • (2010) Genes Dev , vol.24 , pp. 2543-2555
    • Yao, H.1    Brick, K.2    Evrard, Y.3    Xiao, T.4    Camerini-Otero, R.D.5    Felsenfeld, G.6
  • 59
    • 84862908800 scopus 로고    scopus 로고
    • Genome-wide prediction and analysis of human chromatin boundary elements
    • 2011, published online 19 September, doi:10.1093/nar/gkr750
    • Wang J, Lunyak VV, Jordan IK: Genome-wide prediction and analysis of human chromatin boundary elements. Nucleic Acids Res 2011, published online 19 September 2011, doi:10.1093/nar/gkr750.
    • (2011) Nucleic Acids Res
    • Wang, J.1    Lunyak, V.V.2    Jordan, I.K.3
  • 61
    • 47649111278 scopus 로고    scopus 로고
    • RNA polymerase II activity is located on the surface of protein-rich transcription factories
    • Eskiw C.H., Rapp A., Carter D.R., Cook P.R. RNA polymerase II activity is located on the surface of protein-rich transcription factories. J Cell Sci 2008, 121:1999-2007.
    • (2008) J Cell Sci , vol.121 , pp. 1999-2007
    • Eskiw, C.H.1    Rapp, A.2    Carter, D.R.3    Cook, P.R.4
  • 62
    • 70450222694 scopus 로고    scopus 로고
    • A model for all genomes: the role of transcription factories
    • Cook P.R. A model for all genomes: the role of transcription factories. J Mol Biol 2010, 395:1-10.
    • (2010) J Mol Biol , vol.395 , pp. 1-10
    • Cook, P.R.1
  • 63
    • 77954814120 scopus 로고    scopus 로고
    • Genome architecture and the role of transcription
    • Papantonis A., Cook P.R. Genome architecture and the role of transcription. Curr Opin Cell Biol 2010, 22:271-276.
    • (2010) Curr Opin Cell Biol , vol.22 , pp. 271-276
    • Papantonis, A.1    Cook, P.R.2
  • 64
    • 80255137474 scopus 로고    scopus 로고
    • The proteomes of transcription factories containing polymerases I, II, or III
    • Melnik S., Deng B., Papantonis A., Babbo S., Carr I.M., Cook P.R. The proteomes of transcription factories containing polymerases I, II, or III. Nat Methods 2011, 8:963-968.
    • (2011) Nat Methods , vol.8 , pp. 963-968
    • Melnik, S.1    Deng, B.2    Papantonis, A.3    Babbo, S.4    Carr, I.M.5    Cook, P.R.6
  • 65
    • 0016699452 scopus 로고
    • Nucleolar necklaces in chick embryo fibroblast cells. II. Microscope observations of the effect of adenosine analogues on nucleolar necklace formation
    • Granick D. Nucleolar necklaces in chick embryo fibroblast cells. II. Microscope observations of the effect of adenosine analogues on nucleolar necklace formation. J Cell Biol 1975, 65:418-427.
    • (1975) J Cell Biol , vol.65 , pp. 418-427
    • Granick, D.1
  • 66
    • 0030005052 scopus 로고    scopus 로고
    • Inhibition of RNA polymerase II transcription causes chromatin decondensation, loss of nucleolar structure, and dispersion of chromosomal domains
    • Haaf T., Ward D.C. Inhibition of RNA polymerase II transcription causes chromatin decondensation, loss of nucleolar structure, and dispersion of chromosomal domains. Exp Cell Res 1996, 224:163-173.
    • (1996) Exp Cell Res , vol.224 , pp. 163-173
    • Haaf, T.1    Ward, D.C.2
  • 68
    • 57349121991 scopus 로고    scopus 로고
    • Exploring RNA transcription and turnover in vivo by using click chemistry
    • Jao C.Y., Salic A. Exploring RNA transcription and turnover in vivo by using click chemistry. Proc Natl Acad Sci USA 2008, 105:15779-15784.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 15779-15784
    • Jao, C.Y.1    Salic, A.2
  • 71
    • 79952279871 scopus 로고    scopus 로고
    • Dissecting chromatin interactions in living cells from protein mobility maps
    • Erdel F., Müller-Ott K., Baum M., Wachsmuth M., Rippe K. Dissecting chromatin interactions in living cells from protein mobility maps. Chromosome Res 2011, 19:99-115.
    • (2011) Chromosome Res , vol.19 , pp. 99-115
    • Erdel, F.1    Müller-Ott, K.2    Baum, M.3    Wachsmuth, M.4    Rippe, K.5
  • 72
    • 80555157531 scopus 로고    scopus 로고
    • Non-coding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc finger nucleases
    • Gutschner T., Baas M., Diederichs S. Non-coding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc finger nucleases. Genome Res 2011, 21:1944-1954.
    • (2011) Genome Res , vol.21 , pp. 1944-1954
    • Gutschner, T.1    Baas, M.2    Diederichs, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.