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Biology  2013 

The Role of Nuclear Bodies in Gene Expression and Disease

DOI: 10.3390/biology2030976

Keywords: nuclear bodies, transcription, gene expression, genome organization

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Abstract:

This review summarizes the current understanding of the role of nuclear bodies in regulating gene expression. The compartmentalization of cellular processes, such as ribosome biogenesis, RNA processing, cellular response to stress, transcription, modification and assembly of spliceosomal snRNPs, histone gene synthesis and nuclear RNA retention, has significant implications for gene regulation. These functional nuclear domains include the nucleolus, nuclear speckle, nuclear stress body, transcription factory, Cajal body, Gemini of Cajal body, histone locus body and paraspeckle. We herein review the roles of nuclear bodies in regulating gene expression and their relation to human health and disease.

References

[1]  Venters, B.J.; Pugh, B.F. How eukaryotic genes are transcribed. Crit. Rev. Biochem. Mol. Biol. 2009, 44, 117–141.
[2]  Hocine, S.; Singer, R.H.; Grunwald, D. RNA processing and export. Cold Spring Harb. Perspect. Biol. 2010, 2, a000752, doi:10.1101/cshperspect.a000752.
[3]  Gebauer, F.; Hentze, M.W. Molecular mechanisms of translational control. Nat. Rev. Mol. Cell Biol. 2004, 5, 827–835, doi:10.1038/nrm1488.
[4]  Carmo-Fonseca, M.; Berciano, M.T.; Lafarga, M. Orphan nuclear bodies. Cold Spring Harb. Perspect. Biol. 2010, 2, a000703, doi:10.1101/cshperspect.a000703.
[5]  Lallemand-Breitenbach, V.; de The, H. PML nuclear bodies. Cold Spring Harb. Perspect. Biol. 2010, 2, a000661, doi:10.1101/cshperspect.a000661.
[6]  Wagner, R. Einige bemerkungen und fragen über das keimbl?schen (vesicular germinativa). Müller's Arch. Anat. Physiol.Wissenschaftliche Med. 1835, 373–377.
[7]  Valentin, G. Repertorium für anatomie und physiologie; Verlag von Veit und Comp: Berlin, Germany, 1836; Volume 1, pp. 1–293.
[8]  Brown, D.D.; Gurdon, J.B. Absence of ribosomal RNA synthesis in the anucleolate mutant of Xenopus laevis. Proc. Natl. Acad. Sci. USA 1964, 51, 139–146, doi:10.1073/pnas.51.1.139.
[9]  Boisvert, F.M.; van Koningsbruggen, S.; Navascues, J.; Lamond, A.I. The multifunctional nucleolus. Nat. Rev. Mol. Cell Biol. 2007, 8, 574–585, doi:10.1038/nrm2184.
[10]  Boulon, S.; Westman, B.J.; Hutten, S.; Boisvert, F.M.; Lamond, A.I. The nucleolus under stress. Mol. Cell 2010, 40, 216–227, doi:10.1016/j.molcel.2010.09.024.
[11]  Gerbi, S.A.; Borovjagin, A.V.; Lange, T.S. The nucleolus: A site of ribonucleoprotein maturation. Curr. Opin. Cell Biol. 2003, 15, 318–325, doi:10.1016/S0955-0674(03)00049-8.
[12]  Andersen, J.S.; Lyon, C.E.; Fox, A.H.; Leung, A.K.; Lam, Y.W.; Steen, H.; Mann, M.; Lamond, A.I. Directed proteomic analysis of the human nucleolus. Curr. Biol. 2002, 12, 1–11.
[13]  Scherl, A.; Coute, Y.; Deon, C.; Calle, A.; Kindbeiter, K.; Sanchez, J.C.; Greco, A.; Hochstrasser, D.; Diaz, J.J. Functional proteomic analysis of human nucleolus. Mol. Biol. Cell 2002, 13, 4100–4109, doi:10.1091/mbc.E02-05-0271.
[14]  Maggi, L.B., Jr.; Kuchenruether, M.; Dadey, D.Y.; Schwope, R.M.; Grisendi, S.; Townsend, R.R.; Pandolfi, P.P.; Weber, J.D. Nucleophosmin serves as a rate-limiting nuclear export chaperone for the mammalian ribosome. Mol. Cell. Biol. 2008, 28, 7050–7065, doi:10.1128/MCB.01548-07.
[15]  Ginisty, H.; Amalric, F.; Bouvet, P. Nucleolin functions in the first step of ribosomal RNA processing. EMBO J. 1998, 17, 1476–1486, doi:10.1093/emboj/17.5.1476.
[16]  Rickards, B.; Flint, S.J.; Cole, M.D.; LeRoy, G. Nucleolin is required for RNA polymerase I transcription in vivo. Mol. Cell. Biol. 2007, 27, 937–948, doi:10.1128/MCB.01584-06.
[17]  Kiss, T. Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J. 2001, 20, 3617–3622, doi:10.1093/emboj/20.14.3617.
[18]  Isaac, C.; Yang, Y.; Meier, U.T. Nopp140 functions as a molecular link between the nucleolus and the coiled bodies. J. Cell Biol. 1998, 142, 319–329, doi:10.1083/jcb.142.2.319.
[19]  Spector, D.L.; Ochs, R.L.; Busch, H. Silver staining, immunofluorescence, and immunoelectron microscopic localization of nucleolar phosphoproteins B23 and C2. Chromosoma 1984, 90, 139–148, doi:10.1007/BF00292451.
[20]  Ochs, R.L.; Lischwe, M.A.; Spohn, W.H.; Busch, H. Fibrillarin: A new protein of the nucleolus identified by autoimmune sera. Biol. Cell 1985, 54, 123–133, doi:10.1111/j.1768-322X.1985.tb00387.x.
[21]  Leung, A.K.; Lamond, A.I. In vivo analysis of NHPX reveals a novel nucleolar localization pathway involving a transient accumulation in splicing speckles. J. Cell Biol. 2002, 157, 615–629, doi:10.1083/jcb.200201120.
[22]  Gautier, T.; Berges, T.; Tollervey, D.; Hurt, E. Nucleolar KKE/D repeat proteins Nop56p and Nop58p interact with Nop1p and are required for ribosome biogenesis. Mol. Cell. Biol. 1997, 17, 7088–7098.
[23]  Heiss, N.S.; Girod, A.; Salowsky, R.; Wiemann, S.; Pepperkok, R.; Poustka, A. Dyskerin localizes to the nucleolus and its mislocalization is unlikely to play a role in the pathogenesis of dyskeratosis congenita. Hum. Mol. Genet. 1999, 8, 2515–2524, doi:10.1093/hmg/8.13.2515.
[24]  Girard, J.P.; Lehtonen, H.; Caizergues-Ferrer, M.; Amalric, F.; Tollervey, D.; Lapeyre, B. GAR1 is an essential small nucleolar RNP protein required for pre-rRNA processing in yeast. EMBO J. 1992, 11, 673–682.
[25]  Henras, A.; Henry, Y.; Bousquet-Antonelli, C.; Noaillac-Depeyre, J.; Gelugne, J.P.; Caizergues-Ferrer, M. Nhp2p and Nop10p are essential for the function of H/ACA snoRNPs. EMBO J. 1998, 17, 7078–7090.
[26]  Meier, U.T.; Blobel, G. Nopp140 shuttles on tracks between nucleolus and cytoplasm. Cell 1992, 70, 127–138, doi:10.1016/0092-8674(92)90539-O.
[27]  Scheer, U.; Rose, K.M. Localization of RNA polymerase I in interphase cells and mitotic chromosomes by light and electron microscopic immunocytochemistry. Proc. Natl. Acad. Sci. USA 1984, 81, 1431–1435, doi:10.1073/pnas.81.5.1431.
[28]  Tyc, K.; Steitz, J.A. U3, U8 and U13 comprise a new class of mammalian snRNPs localized in the cell nucleolus. EMBO J. 1989, 8, 3113–3119.
[29]  Lange, T.S.; Borovjagin, A.; Maxwell, E.S.; Gerbi, S.A. Conserved boxes C and D are essential nucleolar localization elements of U14 and U8 snoRNAs. EMBO J. 1998, 17, 3176–3187, doi:10.1093/emboj/17.11.3176.
[30]  Selvamurugan, N.; Joost, O.H.; Haas, E.S.; Brown, J.W.; Galvin, N.J.; Eliceiri, G.L. Intracellular localization and unique conserved sequences of three small nucleolar RNAs. Nucleic Acids Res. 1997, 25, 1591–1596, doi:10.1093/nar/25.8.1591.
[31]  Caceres, J.F.; Misteli, T.; Screaton, G.R.; Spector, D.L.; Krainer, A.R. Role of the modular domains of SR proteins in subnuclear localization and alternative splicing specificity. J. Cell Biol. 1997, 138, 225–238, doi:10.1083/jcb.138.2.225.
[32]  Fu, X.D.; Maniatis, T. Factor required for mammalian spliceosome assembly is localized to discrete regions in the nucleus. Nature 1990, 343, 437–441, doi:10.1038/343437a0.
[33]  Mintz, P.J.; Patterson, S.D.; Neuwald, A.F.; Spahr, C.S.; Spector, D.L. Purification and biochemical characterization of interchromatin granule clusters. EMBO J. 1999, 18, 4308–4320.
[34]  Saitoh, N.; Spahr, C.S.; Patterson, S.D.; Bubulya, P.; Neuwald, A.F.; Spector, D.L. Proteomic analysis of interchromatin granule clusters. Mol. Biol. Cell 2004, 15, 3876–3890, doi:10.1091/mbc.E04-03-0253.
[35]  Colwill, K.; Pawson, T.; Andrews, B.; Prasad, J.; Manley, J.L.; Bell, J.C.; Duncan, P.I. The Clk/Sty protein kinase phosphorylates SR splicing factors and regulates their intranuclear distribution. EMBO J. 1996, 15, 265–275.
[36]  Bregman, D.B.; Du, L.; van der Zee, S.; Warren, S.L. Transcription-dependent redistribution of the large subunit of RNA polymerase II to discrete nuclear domains. J. Cell Biol. 1995, 129, 287–298, doi:10.1083/jcb.129.2.287.
[37]  Huang, S.; Spector, D.L. U1 and U2 small nuclear RNAs are present in nuclear speckles. Proc. Natl. Acad. Sci. USA 1992, 89, 305–308, doi:10.1073/pnas.89.1.305.
[38]  Hutchinson, J.N.; Ensminger, A.W.; Clemson, C.M.; Lynch, C.R.; Lawrence, J.B.; Chess, A. A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics 2007, 8, 39.
[39]  Carter, K.C.; Taneja, K.L.; Lawrence, J.B. Discrete nuclear domains of poly(A) RNA and their relationship to the functional organization of the nucleus. J. Cell Biol. 1991, 115, 1191–1202, doi:10.1083/jcb.115.5.1191.
[40]  Sarge, K.D.; Murphy, S.P.; Morimoto, R.I. Activation of heat shock gene transcription by heat shock factor 1 involves oligomerization, acquisition of DNA-binding activity, and nuclear localization and can occur in the absence of stress. Mol. Cell. Biol. 1993, 13, 1392–1407.
[41]  Alastalo, T.P.; Hellesuo, M.; Sandqvist, A.; Hietakangas, V.; Kallio, M.; Sistonen, L. Formation of nuclear stress granules involves HSF2 and coincides with the nucleolar localization of Hsp70. J. Cell Sci. 2003, 116, 3557–3570, doi:10.1242/jcs.00671.
[42]  Weighardt, F.; Cobianchi, F.; Cartegni, L.; Chiodi, I.; Villa, A.; Riva, S.; Biamonti, G. A novel hnRNP protein (HAP/SAF-B) enters a subset of hnRNP complexes and relocates in nuclear granules in response to heat shock. J. Cell Sci. 1999, 112, 1465–1476.
[43]  Denegri, M.; Chiodi, I.; Corioni, M.; Cobianchi, F.; Riva, S.; Biamonti, G. Stress-induced nuclear bodies are sites of accumulation of pre-mRNA processing factors. Mol. Biol. Cell 2001, 12, 3502–3514, doi:10.1091/mbc.12.11.3502.
[44]  Jolly, C.; Metz, A.; Govin, J.; Vigneron, M.; Turner, B.M.; Khochbin, S.; Vourc'h, C. Stress-induced transcription of satellite III repeats. J. Cell Biol. 2004, 164, 25–33, doi:10.1083/jcb.200306104.
[45]  Jackson, D.A.; Iborra, F.J.; Manders, E.M.; Cook, P.R. Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei. Mol. Biol. Cell 1998, 9, 1523–1536, doi:10.1091/mbc.9.6.1523.
[46]  Melnik, S.; Deng, B.; Papantonis, A.; Baboo, S.; Carr, I.M.; Cook, P.R. The proteomes of transcription factories containing RNA polymerases I, II or III. Nat. Methods 2011, 8, 963–968, doi:10.1038/nmeth.1705.
[47]  Raska, I.; Andrade, L.E.; Ochs, R.L.; Chan, E.K.; Chang, C.M.; Roos, G.; Tan, E.M. Immunological and ultrastructural studies of the nuclear coiled body with autoimmune antibodies. Exp. Cell Res. 1991, 195, 27–37, doi:10.1016/0014-4827(91)90496-H.
[48]  Andrade, L.E.; Chan, E.K.; Raska, I.; Peebles, C.L.; Roos, G.; Tan, E.M. Human autoantibody to a novel protein of the nuclear coiled body: Immunological characterization and cDNA cloning of p80-coilin. J. Exp. Med. 1991, 173, 1407–1419, doi:10.1084/jem.173.6.1407.
[49]  Raska, I.; Ochs, R.L.; Andrade, L.E.; Chan, E.K.; Burlingame, R.; Peebles, C.; Gruol, D.; Tan, E.M. Association between the nucleolus and the coiled body. J. Struct. Biol. 1990, 104, 120–127, doi:10.1016/1047-8477(90)90066-L.
[50]  Verheggen, C.; Lafontaine, D.L.; Samarsky, D.; Mouaikel, J.; Blanchard, J.M.; Bordonne, R.; Bertrand, E. Mammalian and yeast U3 snoRNPs are matured in specific and related nuclear compartments. EMBO J. 2002, 21, 2736–2745, doi:10.1093/emboj/21.11.2736.
[51]  Meier, U.T.; Blobel, G. NAP57, a mammalian nucleolar protein with a putative homolog in yeast and bacteria. J. Cell Biol. 1994, 127, 1505–1514, doi:10.1083/jcb.127.6.1505.
[52]  Pogacic, V.; Dragon, F.; Filipowicz, W. Human H/ACA small nucleolar RNPs and telomerase share evolutionarily conserved proteins NHP2 and NOP10. Mol. Cell. Biol. 2000, 20, 9028–9040, doi:10.1128/MCB.20.23.9028-9040.2000.
[53]  Zhu, Y.; Tomlinson, R.L.; Lukowiak, A.A.; Terns, R.M.; Terns, M.P. Telomerase RNA accumulates in Cajal bodies in human cancer cells. Mol. Biol. Cell 2004, 15, 81–90.
[54]  Venteicher, A.S.; Abreu, E.B.; Meng, Z.; McCann, K.E.; Terns, R.M.; Veenstra, T.D.; Terns, M.P.; Artandi, S.E. A human telomerase holoenzyme protein required for Cajal body localization and telomere synthesis. Science 2009, 323, 644–648, doi:10.1126/science.1165357.
[55]  Carvalho, T.; Almeida, F.; Calapez, A.; Lafarga, M.; Berciano, M.T.; Carmo-Fonseca, M. The spinal muscular atrophy disease gene product, SMN: A link between snRNP biogenesis and the Cajal (coiled) body. J. Cell Biol. 1999, 147, 715–728, doi:10.1083/jcb.147.4.715.
[56]  Darzacq, X.; Jady, B.E.; Verheggen, C.; Kiss, A.M.; Bertrand, E.; Kiss, T. Cajal body-specific small nuclear RNAs: A novel class of 2'-O-methylation and pseudouridylation guide RNAs. EMBO J. 2002, 21, 2746–2756, doi:10.1093/emboj/21.11.2746.
[57]  Carmo-Fonseca, M.; Pepperkok, R.; Carvalho, M.T.; Lamond, A.I. Transcription-dependent colocalization of the U1, U2, U4/U6, and U5 snRNPs in coiled bodies. J. Cell Biol. 1992, 117, 1–14, doi:10.1083/jcb.117.1.1.
[58]  Matera, A.G.; Ward, D.C. Nucleoplasmic organization of small nuclear ribonucleoproteins in cultured human cells. J. Cell Biol. 1993, 121, 715–727, doi:10.1083/jcb.121.4.715.
[59]  Narayanan, A.; Speckmann, W.; Terns, R.; Terns, M.P. Role of the box C/D motif in localization of small nucleolar RNAs to coiled bodies and nucleoli. Mol. Biol. Cell 1999, 10, 2131–2147, doi:10.1091/mbc.10.7.2131.
[60]  Liu, Q.; Dreyfuss, G. A novel nuclear structure containing the survival of motor neurons protein. EMBO J. 1996, 15, 3555–3565.
[61]  Liu, Q.; Fischer, U.; Wang, F.; Dreyfuss, G. The spinal muscular atrophy disease gene product, SMN, and its associated protein SIP1 are in a complex with spliceosomal snRNP proteins. Cell 1997, 90, 1013–1021, doi:10.1016/S0092-8674(00)80367-0.
[62]  Charroux, B.; Pellizzoni, L.; Perkinson, R.A.; Shevchenko, A.; Mann, M.; Dreyfuss, G. Gemin3: A novel DEAD box protein that interacts with SMN, the spinal muscular atrophy gene product, and is a component of gems. J. Cell Biol. 1999, 147, 1181–1194, doi:10.1083/jcb.147.6.1181.
[63]  Charroux, B.; Pellizzoni, L.; Perkinson, R.A.; Yong, J.; Shevchenko, A.; Mann, M.; Dreyfuss, G. Gemin4: A novel component of the SMN complex that is found in both gems and nucleoli. J. Cell Biol. 2000, 148, 1177–1186, doi:10.1083/jcb.148.6.1177.
[64]  Gubitz, A.K.; Mourelatos, Z.; Abel, L.; Rappsilber, J.; Mann, M.; Dreyfuss, G. Gemin5, a novel WD repeat protein component of the SMN complex that binds Sm proteins. J. Biol. Chem. 2002, 277, 5631–5636.
[65]  Pellizzoni, L.; Baccon, J.; Rappsilber, J.; Mann, M.; Dreyfuss, G. Purification of native survival of motor neurons complexes and identification of Gemin6 as a novel component. J. Biol. Chem. 2002, 277, 7540–7545.
[66]  Baccon, J.; Pellizzoni, L.; Rappsilber, J.; Mann, M.; Dreyfuss, G. Identification and characterization of Gemin7, a novel component of the survival of motor neuron complex. J. Biol. Chem. 2002, 277, 31957–31962.
[67]  Carissimi, C.; Saieva, L.; Baccon, J.; Chiarella, P.; Maiolica, A.; Sawyer, A.; Rappsilber, J.; Pellizzoni, L. Gemin8 is a novel component of the survival motor neuron complex and functions in small nuclear ribonucleoprotein assembly. J. Biol. Chem. 2006, 281, 8126–8134, doi:10.1074/jbc.M512243200.
[68]  Gangwani, L.; Mikrut, M.; Theroux, S.; Sharma, M.; Davis, R.J. Spinal muscular atrophy disrupts the interaction of ZPR1 with the SMN protein. Nat. Cell Biol. 2001, 3, 376–383, doi:10.1038/35070059.
[69]  Ma, T.; Van Tine, B.A.; Wei, Y.; Garrett, M.D.; Nelson, D.; Adams, P.D.; Wang, J.; Qin, J.; Chow, L.T.; Harper, J.W. Cell cycle-regulated phosphorylation of p220(NPAT) by cyclin E/Cdk2 in Cajal bodies promotes histone gene transcription. Genes Dev. 2000, 14, 2298–2313, doi:10.1101/gad.829500.
[70]  Ghule, P.N.; Dominski, Z.; Yang, X.C.; Marzluff, W.F.; Becker, K.A.; Harper, J.W.; Lian, J.B.; Stein, J.L.; van Wijnen, A.J.; Stein, G.S. Staged assembly of histone gene expression machinery at subnuclear foci in the abbreviated cell cycle of human embryonic stem cells. Proc. Natl. Acad. Sci. USA 2008, 105, 16964–16969, doi:10.1073/pnas.0809273105.
[71]  Liu, J.L.; Murphy, C.; Buszczak, M.; Clatterbuck, S.; Goodman, R.; Gall, J.G. The Drosophila melanogaster Cajal body. J. Cell Biol. 2006, 172, 875–884, doi:10.1083/jcb.200511038.
[72]  Barcaroli, D.; Dinsdale, D.; Neale, M.H.; Bongiorno-Borbone, L.; Ranalli, M.; Munarriz, E.; Sayan, A.E.; McWilliam, J.M.; Smith, T.M.; Fava, E.; et al. FLASH is an essential component of Cajal bodies. Proc. Natl. Acad. Sci. USA 2006, 103, 14802–14807, doi:10.1073/pnas.0604225103.
[73]  Narita, T.; Yung, T.M.; Yamamoto, J.; Tsuboi, Y.; Tanabe, H.; Tanaka, K.; Yamaguchi, Y.; Handa, H. NELF interacts with CBC and participates in 3' end processing of replication-dependent histone mRNAs. Mol. Cell 2007, 26, 349–365, doi:10.1016/j.molcel.2007.04.011.
[74]  Miele, A.; Braastad, C.D.; Holmes, W.F.; Mitra, P.; Medina, R.; Xie, R.; Zaidi, S.K.; Ye, X.; Wei, Y.; Harper, J.W.; et al. HiNF-P directly links the cyclin E/CDK2/p220NPAT pathway to histone H4 gene regulation at the G1/S phase cell cycle transition. Mol. Cell. Biol. 2005, 25, 6140–6153, doi:10.1128/MCB.25.14.6140-6153.2005.
[75]  Gangwani, L. Deficiency of the zinc finger protein ZPR1 causes defects in transcription and cell cycle progression. J. Biol. Chem. 2006, 281, 40330–40340, doi:10.1074/jbc.M608165200.
[76]  Liu, J.L.; Wu, Z.; Nizami, Z.; Deryusheva, S.; Rajendra, T.K.; Beumer, K.J.; Gao, H.; Matera, A.G.; Carroll, D.; Gall, J.G. Coilin is essential for Cajal body organization in Drosophila melanogaster. Mol. Biol. Cell 2009, 20, 1661–1670, doi:10.1091/mbc.E08-05-0525.
[77]  Frey, M.R.; Matera, A.G. Coiled bodies contain U7 small nuclear RNA and associate with specific DNA sequences in interphase human cells. Proc. Natl. Acad. Sci. USA 1995, 92, 5915–5919, doi:10.1073/pnas.92.13.5915.
[78]  Fox, A.H.; Lam, Y.W.; Leung, A.K.; Lyon, C.E.; Andersen, J.; Mann, M.; Lamond, A.I. Paraspeckles: A novel nuclear domain. Curr. Biol. 2002, 12, 13–25, doi:10.1016/S0960-9822(01)00632-7.
[79]  Prasanth, K.V.; Prasanth, S.G.; Xuan, Z.; Hearn, S.; Freier, S.M.; Bennett, C.F.; Zhang, M.Q.; Spector, D.L. Regulating gene expression through RNA nuclear retention. Cell 2005, 123, 249–263, doi:10.1016/j.cell.2005.08.033.
[80]  Dettwiler, S.; Aringhieri, C.; Cardinale, S.; Keller, W.; Barabino, S.M. Distinct sequence motifs within the 68-kDa subunit of cleavage factor Im mediate RNA binding, protein-protein interactions, and subcellular localization. J. Biol. Chem. 2004, 279, 35788–35797, doi:10.1074/jbc.M403927200.
[81]  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, doi:10.1016/j.molcel.2009.01.026.
[82]  Sunwoo, H.; Dinger, M.E.; Wilusz, J.E.; Amaral, P.P.; Mattick, J.S.; Spector, D.L. MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res. 2009, 19, 347–359.
[83]  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.
[84]  Tollervey, D.; Lehtonen, H.; Carmo-Fonseca, M.; Hurt, E.C. The small nucleolar RNP protein NOP1 (fibrillarin) is required for pre-rRNA processing in yeast. EMBO J. 1991, 10, 573–583.
[85]  Jack, K.; Bellodi, C.; Landry, D.M.; Niederer, R.O.; Meskauskas, A.; Musalgaonkar, S.; Kopmar, N.; Krasnykh, O.; Dean, A.M.; Thompson, S.R.; et al. rRNA pseudouridylation defects affect ribosomal ligand binding and translational fidelity from yeast to human cells. Mol. Cell 2011, 44, 660–666, doi:10.1016/j.molcel.2011.09.017.
[86]  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, doi:10.1006/excr.1996.0124.
[87]  Flygare, J.; Aspesi, A.; Bailey, J.C.; Miyake, K.; Caffrey, J.M.; Karlsson, S.; Ellis, S.R. Human RPS19, the gene mutated in Diamond-Blackfan anemia, encodes a ribosomal protein required for the maturation of 40S ribosomal subunits. Blood 2007, 109, 980–986.
[88]  Hughes, J.M.; Ares, M., Jr. Depletion of U3 small nucleolar RNA inhibits cleavage in the 5' external transcribed spacer of yeast pre-ribosomal RNA and impairs formation of 18S ribosomal RNA. EMBO J. 1991, 10, 4231–4239.
[89]  Tripathi, V.; Song, D.Y.; Zong, X.; Shevtsov, S.P.; Hearn, S.; Fu, X.D.; Dundr, M.; Prasanth, K.V. SRSF1 regulates the assembly of pre-mRNA processing factors in nuclear speckles. Mol. Biol. Cell 2012, 23, 3694–3706.
[90]  Sacco-Bubulya, P.; Spector, D.L. Disassembly of interchromatin granule clusters alters the coordination of transcription and pre-mRNA splicing. J. Cell Biol. 2002, 156, 425–436, doi:10.1083/jcb.200107017.
[91]  Tripathi, V.; Ellis, J.D.; Shen, Z.; Song, D.Y.; Pan, Q.; Watt, A.T.; Freier, S.M.; Bennett, C.F.; Sharma, A.; Bubulya, P.A.; et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol. Cell 2010, 39, 925–938, doi:10.1016/j.molcel.2010.08.011.
[92]  Sharma, A.; Takata, H.; Shibahara, K.; Bubulya, A.; Bubulya, P.A. Son is essential for nuclear speckle organization and cell cycle progression. Mol. Biol. Cell 2010, 21, 650–663, doi:10.1091/mbc.E09-02-0126.
[93]  Okada, M.; Jang, S.W.; Ye, K. Akt phosphorylation and nuclear phosphoinositide association mediate mRNA export and cell proliferation activities by ALY. Proc. Natl. Acad. Sci. USA 2008, 105, 8649–8654, doi:10.1073/pnas.0802533105.
[94]  Dias, A.P.; Dufu, K.; Lei, H.; Reed, R. A role for TREX components in the release of spliced mRNA from nuclear speckle domains. Nat. Commun. 2010, 1, 97, doi:10.1038/ncomms1103.
[95]  Nakagawa, S.; Ip, J.Y.; Shioi, G.; Tripathi, V.; Zong, X.; Hirose, T.; Prasanth, K.V. Malat1 is not an essential component of nuclear speckles in mice. RNA 2012, 18, 1487–1499, doi:10.1261/rna.033217.112.
[96]  Eissmann, M.; Gutschner, T.; Hammerle, M.; Gunther, S.; Caudron-Herger, M.; Gross, M.; Schirmacher, P.; Rippe, K.; Braun, T.; Zornig, M.; et al. Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development. RNA Biol. 2012, 9, 1076–1087.
[97]  O'Keefe, R.T.; Mayeda, A.; Sadowski, C.L.; Krainer, A.R.; Spector, D.L. Disruption of pre-mRNA splicing in vivo results in reorganization of splicing factors. J. Cell Biol. 1994, 124, 249–260, doi:10.1083/jcb.124.3.249.
[98]  Sandqvist, A.; Bjork, J.K.; Akerfelt, M.; Chitikova, Z.; Grichine, A.; Vourc'h, C.; Jolly, C.; Salminen, T.A.; Nymalm, Y.; Sistonen, L. Heterotrimerization of heat-shock factors 1 and 2 provides a transcriptional switch in response to distinct stimuli. Mol. Biol. Cell 2009, 20, 1340–1347, doi:10.1091/mbc.E08-08-0864.
[99]  Jackson, D.A.; Hassan, A.B.; Errington, R.J.; Cook, P.R. Visualization of focal sites of transcription within human nuclei. EMBO J. 1993, 12, 1059–1065.
[100]  Pombo, A.; Jackson, D.A.; Hollinshead, M.; Wang, Z.; Roeder, R.G.; Cook, P.R. Regional specialization in human nuclei: Visualization of discrete sites of transcription by RNA polymerase III. EMBO J. 1999, 18, 2241–2253, doi:10.1093/emboj/18.8.2241.
[101]  Tucker, K.E.; Berciano, M.T.; Jacobs, E.Y.; LePage, D.F.; Shpargel, K.B.; Rossire, J.J.; Chan, E.K.; Lafarga, M.; Conlon, R.A.; Matera, A.G. Residual Cajal bodies in coilin knockout mice fail to recruit Sm snRNPs and SMN, the spinal muscular atrophy gene product. J. Cell Biol. 2001, 154, 293–307, doi:10.1083/jcb.200104083.
[102]  Walker, M.P.; Tian, L.; Matera, A.G. Reduced viability, fertility and fecundity in mice lacking the cajal body marker protein, coilin. PLoS One 2009, 4, e6171, doi:10.1371/journal.pone.0006171.
[103]  Bauer, D.W.; Gall, J.G. Coiled bodies without coilin. Mol. Biol. Cell 1997, 8, 73–82.
[104]  Deryusheva, S.; Gall, J.G. Small Cajal body-specific RNAs of Drosophila function in the absence of Cajal bodies. Mol. Biol. Cell 2009, 20, 5250–5259, doi:10.1091/mbc.E09-09-0777.
[105]  Batista, L.F.; Pech, M.F.; Zhong, F.L.; Nguyen, H.N.; Xie, K.T.; Zaug, A.J.; Crary, S.M.; Choi, J.; Sebastiano, V.; Cherry, A.; et al. Telomere shortening and loss of self-renewal in dyskeratosis congenita induced pluripotent stem cells. Nature 2011, 474, 399–402, doi:10.1038/nature10084.
[106]  Renvoise, B.; Colasse, S.; Burlet, P.; Viollet, L.; Meier, U.T.; Lefebvre, S. The loss of the snoRNP chaperone Nopp140 from Cajal bodies of patient fibroblasts correlates with the severity of spinal muscular atrophy. Hum. Mol. Genet. 2009, 18, 1181–1189, doi:10.1093/hmg/ddp009.
[107]  Lefebvre, S.; Burlet, P.; Liu, Q.; Bertrandy, S.; Clermont, O.; Munnich, A.; Dreyfuss, G.; Melki, J. Correlation between severity and SMN protein level in spinal muscular atrophy. Nat. Genet. 1997, 16, 265–269.
[108]  Coovert, D.D.; Le, T.T.; McAndrew, P.E.; Strasswimmer, J.; Crawford, T.O.; Mendell, J.R.; Coulson, S.E.; Androphy, E.J.; Prior, T.W.; Burghes, A.H. The survival motor neuron protein in spinal muscular atrophy. Hum. Mol. Genet. 1997, 6, 1205–1214.
[109]  Girard, C.; Neel, H.; Bertrand, E.; Bordonne, R. Depletion of SMN by RNA interference in HeLa cells induces defects in Cajal body formation. Nucleic Acids Res. 2006, 34, 2925–2932, doi:10.1093/nar/gkl374.
[110]  Feng, W.; Gubitz, A.K.; Wan, L.; Battle, D.J.; Dostie, J.; Golembe, T.J.; Dreyfuss, G. Gemins modulate the expression and activity of the SMN complex. Hum. Mol. Genet. 2005, 14, 1605–1611.
[111]  Shpargel, K.B.; Matera, A.G. Gemin proteins are required for efficient assembly of Sm-class ribonucleoproteins. Proc. Natl. Acad. Sci. USA 2005, 102, 17372–17377, doi:10.1073/pnas.0508947102.
[112]  Frugier, T.; Tiziano, F.D.; Cifuentes-Diaz, C.; Miniou, P.; Roblot, N.; Dierich, A.; Le Meur, M.; Melki, J. Nuclear targeting defect of SMN lacking the C-terminus in a mouse model of spinal muscular atrophy. Hum. Mol. Genet. 2000, 9, 849–858, doi:10.1093/hmg/9.5.849.
[113]  Gabanella, F.; Butchbach, M.E.; Saieva, L.; Carissimi, C.; Burghes, A.H.; Pellizzoni, L. Ribonucleoprotein assembly defects correlate with spinal muscular atrophy severity and preferentially affect a subset of spliceosomal snRNPs. PLoS One 2007, 2, e921.
[114]  Zhang, Z.; Lotti, F.; Dittmar, K.; Younis, I.; Wan, L.; Kasim, M.; Dreyfuss, G. SMN deficiency causes tissue-specific perturbations in the repertoire of snRNAs and widespread defects in splicing. Cell 2008, 133, 585–600.
[115]  Campion, Y.; Neel, H.; Gostan, T.; Soret, J.; Bordonne, R. Specific splicing defects in S. pombe carrying a degron allele of the Survival of Motor Neuron gene. EMBO J. 2010, 29, 1817–1829, doi:10.1038/emboj.2010.70.
[116]  Shpargel, K.B.; Praveen, K.; Rajendra, T.K.; Matera, A.G. Gemin3 is an essential gene required for larval motor function and pupation in Drosophila. Mol. Biol. Cell 2009, 20, 90–101.
[117]  Gangwani, L.; Flavell, R.A.; Davis, R.J. ZPR1 is essential for survival and is required for localization of the survival motor neurons (SMN) protein to Cajal bodies. Mol. Cell. Biol. 2005, 25, 2744–2756, doi:10.1128/MCB.25.7.2744-2756.2005.
[118]  Doran, B.; Gherbesi, N.; Hendricks, G.; Flavell, R.A.; Davis, R.J.; Gangwani, L. Deficiency of the zinc finger protein ZPR1 causes neurodegeneration. Proc. Natl. Acad. Sci. USA 2006, 103, 7471–7475.
[119]  Di Fruscio, M.; Weiher, H.; Vanderhyden, B.C.; Imai, T.; Shiomi, T.; Hori, T.A.; Jaenisch, R.; Gray, D.A. Proviral inactivation of the Npat gene of Mpv 20 mice results in early embryonic arrest. Mol. Cell. Biol. 1997, 17, 4080–4086.
[120]  Sullivan, K.D.; Mullen, T.E.; Marzluff, W.F.; Wagner, E.J. Knockdown of SLBP results in nuclear retention of histone mRNA. RNA 2009, 15, 459–472, doi:10.1261/rna.1205409.
[121]  Sullivan, E.; Santiago, C.; Parker, E.D.; Dominski, Z.; Yang, X.; Lanzotti, D.J.; Ingledue, T.C.; Marzluff, W.F.; Duronio, R.J. Drosophila stem loop binding protein coordinates accumulation of mature histone mRNA with cell cycle progression. Genes Dev. 2001, 15, 173–187, doi:10.1101/gad.862801.
[122]  White, A.E.; Leslie, M.E.; Calvi, B.R.; Marzluff, W.F.; Duronio, R.J. Developmental and cell cycle regulation of the Drosophila histone locus body. Mol. Biol. Cell 2007, 18, 2491–2502, doi:10.1091/mbc.E06-11-1033.
[123]  Godfrey, A.C.; White, A.E.; Tatomer, D.C.; Marzluff, W.F.; Duronio, R.J. The Drosophila U7 snRNP proteins Lsm10 and Lsm11 are required for histone pre-mRNA processing and play an essential role in development. RNA 2009, 15, 1661–1672, doi:10.1261/rna.1518009.
[124]  Barcaroli, D.; Bongiorno-Borbone, L.; Terrinoni, A.; Hofmann, T.G.; Rossi, M.; Knight, R.A.; Matera, A.G.; Melino, G.; De Laurenzi, V. FLASH is required for histone transcription and S-phase progression. Proc. Natl. Acad. Sci. USA 2006, 103, 14808–14812, doi:10.1073/pnas.0604227103.
[125]  De Cola, A.; Bongiorno-Borbone, L.; Bianchi, E.; Barcaroli, D.; Carletti, E.; Knight, R.A.; Di Ilio, C.; Melino, G.; Sette, C.; De Laurenzi, V. FLASH is essential during early embryogenesis and cooperates with p73 to regulate histone gene transcription. Oncogene 2012, 31, 573–582.
[126]  Xie, R.; Medina, R.; Zhang, Y.; Hussain, S.; Colby, J.; Ghule, P.; Sundararajan, S.; Keeler, M.; Liu, L.J.; van der Deen, M.; et al. The histone gene activator HINFP is a nonredundant cyclin E/CDK2 effector during early embryonic cell cycles. Proc. Natl. Acad. Sci. USA 2009, 106, 12359–12364, doi:10.1073/pnas.0905651106.
[127]  Godfrey, A.C.; Kupsco, J.M.; Burch, B.D.; Zimmerman, R.M.; Dominski, Z.; Marzluff, W.F.; Duronio, R.J. U7 snRNA mutations in Drosophila block histone pre-mRNA processing and disrupt oogenesis. RNA 2006, 12, 396–409, doi:10.1261/rna.2270406.
[128]  Salzler, H.R.; Tatomer, D.C.; Malek, P.Y.; McDaniel, S.L.; Orlando, A.N.; Marzluff, W.F.; Duronio, R.J. A Sequence in the Drosophila H3-H4 Promoter Triggers Histone Locus Body Assembly and Biosynthesis of Replication-Coupled Histone mRNAs. Dev. Cell 2013, 24, 623–634, doi:10.1016/j.devcel.2013.02.014.
[129]  Hata, K.; Nishimura, R.; Muramatsu, S.; Matsuda, A.; Matsubara, T.; Amano, K.; Ikeda, F.; Harley, V.R.; Yoneda, T. Paraspeckle protein p54nrb links Sox9-mediated transcription with RNA processing during chondrogenesis in mice. J. Clin. Invest. 2008, 118, 3098–3108, doi:10.1172/JCI31373.
[130]  Brown, S.A.; Ripperger, J.; Kadener, S.; Fleury-Olela, F.; Vilbois, F.; Rosbash, M.; Schibler, U. PERIOD1-associated proteins modulate the negative limb of the mammalian circadian oscillator. Science 2005, 308, 693–696, doi:10.1126/science.1107373.
[131]  Chen, L.L.; Carmichael, G.G. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: Functional role of a nuclear noncoding RNA. Mol. Cell 2009, 35, 467–478, doi:10.1016/j.molcel.2009.06.027.
[132]  Kowalska, E.; Ripperger, J.A.; Muheim, C.; Maier, B.; Kurihara, Y.; Fox, A.H.; Kramer, A.; Brown, S.A. Distinct roles of DBHS family members in the circadian transcriptional feedback loop. Mol. Cell. Biol. 2012, 32, 4585–4594, doi:10.1128/MCB.00334-12.
[133]  Nakagawa, S.; Naganuma, T.; Shioi, G.; Hirose, T. Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice. J. Cell Biol. 2011, 193, 31–39, doi:10.1083/jcb.201011110.
[134]  Murano, K.; Okuwaki, M.; Hisaoka, M.; Nagata, K. Transcription regulation of the rRNA gene by a multifunctional nucleolar protein, B23/nucleophosmin, through its histone chaperone activity. Mol. Cell. Biol. 2008, 28, 3114–3126.
[135]  Cong, R.; Das, S.; Ugrinova, I.; Kumar, S.; Mongelard, F.; Wong, J.; Bouvet, P. Interaction of nucleolin with ribosomal RNA genes and its role in RNA polymerase I transcription. Nucleic Acids Res. 2012, 40, 9441–9454.
[136]  Lessard, F.; Stefanovsky, V.; Tremblay, M.G.; Moss, T. The cellular abundance of the essential transcription termination factor TTF-I regulates ribosome biogenesis and is determined by MDM2 ubiquitinylation. Nucleic Acids Res. 2012, 40, 5357–5367, doi:10.1093/nar/gks198.
[137]  Boyd, M.T.; Vlatkovic, N.; Rubbi, C.P. The nucleolus directly regulates p53 export and degradation. J. Cell Biol. 2011, 194, 689–703.
[138]  Richardson, L.A.; Reed, B.J.; Charette, J.M.; Freed, E.F.; Fredrickson, E.K.; Locke, M.N.; Baserga, S.J.; Gardner, R.G. A conserved deubiquitinating enzyme controls cell growth by regulating RNA polymerase I stability. Cell Rep. 2012, 2, 372–385, doi:10.1016/j.celrep.2012.07.009.
[139]  Westman, B.J.; Verheggen, C.; Hutten, S.; Lam, Y.W.; Bertrand, E.; Lamond, A.I. A proteomic screen for nucleolar SUMO targets shows SUMOylation modulates the function of Nop5/Nop58. Mol. Cell 2010, 39, 618–631, doi:10.1016/j.molcel.2010.07.025.
[140]  Haindl, M.; Harasim, T.; Eick, D.; Muller, S. The nucleolar SUMO-specific protease SENP3 reverses SUMO modification of nucleophosmin and is required for rRNA processing. EMBO Rep. 2008, 9, 273–279, doi:10.1038/embor.2008.3.
[141]  Bernardi, R.; Scaglioni, P.P.; Bergmann, S.; Horn, H.F.; Vousden, K.H.; Pandolfi, P.P. PML regulates p53 stability by sequestering Mdm2 to the nucleolus. Nat. Cell Biol. 2004, 6, 665–672, doi:10.1038/ncb1147.
[142]  Mekhail, K.; Gunaratnam, L.; Bonicalzi, M.E.; Lee, S. HIF activation by pH-dependent nucleolar sequestration of VHL. Nat. Cell Biol. 2004, 6, 642–647.
[143]  Fatyol, K.; Szalay, A.A. The p14ARF tumor suppressor protein facilitates nucleolar sequestration of hypoxia-inducible factor-1alpha (HIF-1alpha ) and inhibits HIF-1-mediated transcription. J. Biol. Chem. 2001, 276, 28421–28429, doi:10.1074/jbc.M102847200.
[144]  Lin, D.Y.; Shih, H.M. Essential role of the 58-kDa microspherule protein in the modulation of Daxx-dependent transcriptional repression as revealed by nucleolar sequestration. J. Biol. Chem. 2002, 277, 25446–25456.
[145]  Bywater, M.J.; Pearson, R.B.; McArthur, G.A.; Hannan, R.D. Dysregulation of the basal RNA polymerase transcription apparatus in cancer. Nat. Rev. Cancer 2013, 13, 299–314.
[146]  The Treacher Collins Syndrome Collaborative Group. Positional cloning of a gene involved in the pathogenesis of Treacher Collins syndrome. Nat. Genet 1996, 12, 130–136, doi:10.1038/ng0296-130.
[147]  Dauwerse, J.G.; Dixon, J.; Seland, S.; Ruivenkamp, C.A.; van Haeringen, A.; Hoefsloot, L.H.; Peters, D.J.; Boers, A.C.; Daumer-Haas, C.; Maiwald, R.; et al. Mutations in genes encoding subunits of RNA polymerases I and III cause Treacher Collins syndrome. Nat. Genet. 2011, 43, 20–22.
[148]  Draptchinskaia, N.; Gustavsson, P.; Andersson, B.; Pettersson, M.; Willig, T.N.; Dianzani, I.; Ball, S.; Tchernia, G.; Klar, J.; Matsson, H.; et al. The gene encoding ribosomal protein S19 is mutated in Diamond-Blackfan anaemia. Nat. Genet. 1999, 21, 169–175.
[149]  Gazda, H.T.; Grabowska, A.; Merida-Long, L.B.; Latawiec, E.; Schneider, H.E.; Lipton, J.M.; Vlachos, A.; Atsidaftos, E.; Ball, S.E.; Orfali, K.A.; et al. Ribosomal protein S24 gene is mutated in Diamond-Blackfan anemia. Am. J. Hum. Genet. 2006, 79, 1110–1118, doi:10.1086/510020.
[150]  Cmejla, R.; Cmejlova, J.; Handrkova, H.; Petrak, J.; Pospisilova, D. Ribosomal protein S17 gene (RPS17) is mutated in Diamond-Blackfan anemia. Hum. Mutat. 2007, 28, 1178–1182, doi:10.1002/humu.20608.
[151]  Farrar, J.E.; Nater, M.; Caywood, E.; McDevitt, M.A.; Kowalski, J.; Takemoto, C.M.; Talbot, C.C., Jr.; Meltzer, P.; Esposito, D.; Beggs, A.H.; et al. Abnormalities of the large ribosomal subunit protein, Rpl35a, in Diamond-Blackfan anemia. Blood 2008, 112, 1582–1592, doi:10.1182/blood-2008-02-140012.
[152]  Gazda, H.T.; Sheen, M.R.; Vlachos, A.; Choesmel, V.; O'Donohue, M.F.; Schneider, H.; Darras, N.; Hasman, C.; Sieff, C.A.; Newburger, P.E.; et al. Ribosomal protein L5 and L11 mutations are associated with cleft palate and abnormal thumbs in Diamond-Blackfan anemia patients. Am. J. Hum. Genet. 2008, 83, 769–780, doi:10.1016/j.ajhg.2008.11.004.
[153]  Doherty, L.; Sheen, M.R.; Vlachos, A.; Choesmel, V.; O'Donohue, M.F.; Clinton, C.; Schneider, H.E.; Sieff, C.A.; Newburger, P.E.; Ball, S.E.; et al. Ribosomal protein genes RPS10 and RPS26 are commonly mutated in Diamond-Blackfan anemia. Am. J. Hum. Genet. 2010, 86, 222–228, doi:10.1016/j.ajhg.2009.12.015.
[154]  Gazda, H.T.; Preti, M.; Sheen, M.R.; O'Donohue, M.F.; Vlachos, A.; Davies, S.M.; Kattamis, A.; Doherty, L.; Landowski, M.; Buros, C.; et al. Frameshift mutation in p53 regulator RPL26 is associated with multiple physical abnormalities and a specific pre-ribosomal RNA processing defect in diamond-blackfan anemia. Hum. Mutat. 2012, 33, 1037–1044, doi:10.1002/humu.22081.
[155]  Yu, C.E.; Oshima, J.; Fu, Y.H.; Wijsman, E.M.; Hisama, F.; Alisch, R.; Matthews, S.; Nakura, J.; Miki, T.; Ouais, S.; et al. Positional cloning of the Werner's syndrome gene. Science 1996, 272, 258–262.
[156]  Ellis, N.A.; Groden, J.; Ye, T.Z.; Straughen, J.; Lennon, D.J.; Ciocci, S.; Proytcheva, M.; German, J. The Bloom's syndrome gene product is homologous to RecQ helicases. Cell 1995, 83, 655–666, doi:10.1016/0092-8674(95)90105-1.
[157]  Chakarova, C.F.; Hims, M.M.; Bolz, H.; Abu-Safieh, L.; Patel, R.J.; Papaioannou, M.G.; Inglehearn, C.F.; Keen, T.J.; Willis, C.; Moore, A.T.; et al. Mutations in HPRP3, a third member of pre-mRNA splicing factor genes, implicated in autosomal dominant retinitis pigmentosa. Hum. Mol. Genet. 2002, 11, 87–92, doi:10.1093/hmg/11.1.87.
[158]  Tanackovic, G.; Ransijn, A.; Ayuso, C.; Harper, S.; Berson, E.L.; Rivolta, C. A missense mutation in PRPF6 causes impairment of pre-mRNA splicing and autosomal-dominant retinitis pigmentosa. Am. J. Hum. Genet. 2011, 88, 643–649, doi:10.1016/j.ajhg.2011.04.008.
[159]  McKie, A.B.; McHale, J.C.; Keen, T.J.; Tarttelin, E.E.; Goliath, R.; van Lith-Verhoeven, J.J.; Greenberg, J.; Ramesar, R.S.; Hoyng, C.B.; Cremers, F.P.; et al. Mutations in the pre-mRNA splicing factor gene PRPC8 in autosomal dominant retinitis pigmentosa (RP13). Hum. Mol. Genet. 2001, 10, 1555–1562, doi:10.1093/hmg/10.15.1555.
[160]  Zhao, C.; Bellur, D.L.; Lu, S.; Zhao, F.; Grassi, M.A.; Bowne, S.J.; Sullivan, L.S.; Daiger, S.P.; Chen, L.J.; Pang, C.P.; et al. Autosomal-dominant retinitis pigmentosa caused by a mutation in SNRNP200, a gene required for unwinding of U4/U6 snRNAs. Am. J. Hum. Genet. 2009, 85, 617–627, doi:10.1016/j.ajhg.2009.09.020.
[161]  Lines, M.A.; Huang, L.; Schwartzentruber, J.; Douglas, S.L.; Lynch, D.C.; Beaulieu, C.; Guion-Almeida, M.L.; Zechi-Ceide, R.M.; Gener, B.; Gillessen-Kaesbach, G.; et al. Haploinsufficiency of a spliceosomal GTPase encoded by EFTUD2 causes mandibulofacial dysostosis with microcephaly. Am. J. Hum. Genet. 2012, 90, 369–377, doi:10.1016/j.ajhg.2011.12.023.
[162]  Albers, C.A.; Paul, D.S.; Schulze, H.; Freson, K.; Stephens, J.C.; Smethurst, P.A.; Jolley, J.D.; Cvejic, A.; Kostadima, M.; Bertone, P.; et al. Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome. Nat. Genet. 2012, 44, 435–439, S431–S432.
[163]  Bernard, G.; Chouery, E.; Putorti, M.L.; Tetreault, M.; Takanohashi, A.; Carosso, G.; Clement, I.; Boespflug-Tanguy, O.; Rodriguez, D.; Delague, V.; et al. Mutations of POLR3A encoding a catalytic subunit of RNA polymerase Pol III cause a recessive hypomyelinating leukodystrophy. Am. J. Hum. Genet. 2011, 89, 415–423, doi:10.1016/j.ajhg.2011.07.014.
[164]  Saitsu, H.; Osaka, H.; Sasaki, M.; Takanashi, J.; Hamada, K.; Yamashita, A.; Shibayama, H.; Shiina, M.; Kondo, Y.; Nishiyama, K.; et al. Mutations in POLR3A and POLR3B encoding RNA Polymerase III subunits cause an autosomal-recessive hypomyelinating leukoencephalopathy. Am. J. Hum. Genet. 2011, 89, 644–651.
[165]  Tetreault, M.; Choquet, K.; Orcesi, S.; Tonduti, D.; Balottin, U.; Teichmann, M.; Fribourg, S.; Schiffmann, R.; Brais, B.; Vanderver, A.; et al. Recessive mutations in POLR3B, encoding the second largest subunit of Pol III, cause a rare hypomyelinating leukodystrophy. Am. J. Hum. Genet. 2011, 89, 652–655, doi:10.1016/j.ajhg.2011.10.006.
[166]  Schwartz, C.E.; Tarpey, P.S.; Lubs, H.A.; Verloes, A.; May, M.M.; Risheg, H.; Friez, M.J.; Futreal, P.A.; Edkins, S.; Teague, J.; et al. The original Lujan syndrome family has a novel missense mutation (p.N1007S) in the MED12 gene. J. Med. Genet. 2007, 44, 472–477.
[167]  Risheg, H.; Graham, J.M., Jr.; Clark, R.D.; Rogers, R.C.; Opitz, J.M.; Moeschler, J.B.; Peiffer, A.P.; May, M.; Joseph, S.M.; Jones, J.R.; et al. A recurrent mutation in MED12 leading to R961W causes Opitz-Kaveggia syndrome. Nat. Genet. 2007, 39, 451–453.
[168]  Kaufmann, R.; Straussberg, R.; Mandel, H.; Fattal-Valevski, A.; Ben-Zeev, B.; Naamati, A.; Shaag, A.; Zenvirt, S.; Konen, O.; Mimouni-Bloch, A.; et al. Infantile cerebral and cerebellar atrophy is associated with a mutation in the MED17 subunit of the transcription preinitiation mediator complex. Am. J. Hum. Genet. 2010, 87, 667–670.
[169]  Hashimoto, S.; Boissel, S.; Zarhrate, M.; Rio, M.; Munnich, A.; Egly, J.M.; Colleaux, L. MED23 mutation links intellectual disability to dysregulation of immediate early gene expression. Science 2011, 333, 1161–1163.
[170]  Leal, A.; Huehne, K.; Bauer, F.; Sticht, H.; Berger, P.; Suter, U.; Morera, B.; Del Valle, G.; Lupski, J.R.; Ekici, A.; et al. Identification of the variant Ala335Val of MED25 as responsible for CMT2B2: molecular data, functional studies of the SH3 recognition motif and correlation between wild-type MED25 and PMP22 RNA levels in CMT1A animal models. Neurogenetics 2009.
[171]  Arrand, J.E.; Bone, N.M.; Johnson, R.T. Molecular cloning and characterization of a mammalian excision repair gene that partially restores UV resistance to xeroderma pigmentosum complementation group D cells. Proc. Natl. Acad. Sci. USA 1989, 86, 6997–7001, doi:10.1073/pnas.86.18.6997.
[172]  Graham, J.M., Jr.; Anyane-Yeboa, K.; Raams, A.; Appeldoorn, E.; Kleijer, W.J.; Garritsen, V.H.; Busch, D.; Edersheim, T.G.; Jaspers, N.G. Cerebro-oculo-facio-skeletal syndrome with a nucleotide excision-repair defect and a mutated XPD gene, with prenatal diagnosis in a triplet pregnancy. Am. J. Hum. Genet. 2001, 69, 291–300, doi:10.1086/321295.
[173]  Broughton, B.C.; Steingrimsdottir, H.; Weber, C.A.; Lehmann, A.R. Mutations in the xeroderma pigmentosum group D DNA repair/transcription gene in patients with trichothiodystrophy. Nat. Genet. 1994, 7, 189–194.
[174]  Weeda, G.; van Ham, R.C.; Vermeulen, W.; Bootsma, D.; van der Eb, A.J.; Hoeijmakers, J.H. A presumed DNA helicase encoded by ERCC-3 is involved in the human repair disorders xeroderma pigmentosum and Cockayne's syndrome. Cell 1990, 62, 777–791, doi:10.1016/0092-8674(90)90122-U.
[175]  Weeda, G.; Eveno, E.; Donker, I.; Vermeulen, W.; Chevallier-Lagente, O.; Taieb, A.; Stary, A.; Hoeijmakers, J.H.; Mezzina, M.; Sarasin, A. A mutation in the XPB/ERCC3 DNA repair transcription gene, associated with trichothiodystrophy. Am. J. Hum. Genet. 1997, 60, 320–329.
[176]  Giglia-Mari, G.; Coin, F.; Ranish, J.A.; Hoogstraten, D.; Theil, A.; Wijgers, N.; Jaspers, N.G.; Raams, A.; Argentini, M.; van der Spek, P.J.; et al. A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A. Nat. Genet. 2004, 36, 714–719.
[177]  Lefebvre, S.; Burglen, L.; Reboullet, S.; Clermont, O.; Burlet, P.; Viollet, L.; Benichou, B.; Cruaud, C.; Millasseau, P.; Zeviani, M.; et al. Identification and characterization of a spinal muscular atrophy-determining gene. Cell 1995, 80, 155–165, doi:10.1016/0092-8674(95)90460-3.
[178]  Heiss, N.S.; Knight, S.W.; Vulliamy, T.J.; Klauck, S.M.; Wiemann, S.; Mason, P.J.; Poustka, A.; Dokal, I. X-linked dyskeratosis congenita is caused by mutations in a highly conserved gene with putative nucleolar functions. Nat. Genet. 1998, 19, 32–38.
[179]  Knight, S.W.; Heiss, N.S.; Vulliamy, T.J.; Aalfs, C.M.; McMahon, C.; Richmond, P.; Jones, A.; Hennekam, R.C.; Poustka, A.; Mason, P.J.; et al. Unexplained aplastic anaemia, immunodeficiency, and cerebellar hypoplasia (Hoyeraal-Hreidarsson syndrome) due to mutations in the dyskeratosis congenita gene, DKC1. Br. J. Haematol. 1999, 107, 335–339, doi:10.1046/j.1365-2141.1999.01690.x.
[180]  Vulliamy, T.; Beswick, R.; Kirwan, M.; Marrone, A.; Digweed, M.; Walne, A.; Dokal, I. Mutations in the telomerase component NHP2 cause the premature ageing syndrome dyskeratosis congenita. Proc. Natl. Acad. Sci. USA 2008, 105, 8073–8078.
[181]  Walne, A.J.; Vulliamy, T.; Marrone, A.; Beswick, R.; Kirwan, M.; Masunari, Y.; Al-Qurashi, F.H.; Aljurf, M.; Dokal, I. Genetic heterogeneity in autosomal recessive dyskeratosis congenita with one subtype due to mutations in the telomerase-associated protein NOP10. Hum. Mol. Genet. 2007, 16, 1619–1629, doi:10.1093/hmg/ddm111.
[182]  Armanios, M.; Chen, J.L.; Chang, Y.P.; Brodsky, R.A.; Hawkins, A.; Griffin, C.A.; Eshleman, J.R.; Cohen, A.R.; Chakravarti, A.; Hamosh, A.; et al. Haploinsufficiency of telomerase reverse transcriptase leads to anticipation in autosomal dominant dyskeratosis congenita. Proc. Natl. Acad. Sci. USA 2005, 102, 15960–15964, doi:10.1073/pnas.0508124102.
[183]  Marrone, A.; Walne, A.; Tamary, H.; Masunari, Y.; Kirwan, M.; Beswick, R.; Vulliamy, T.; Dokal, I. Telomerase reverse-transcriptase homozygous mutations in autosomal recessive dyskeratosis congenita and Hoyeraal-Hreidarsson syndrome. Blood 2007, 110, 4198–4205, doi:10.1182/blood-2006-12-062851.
[184]  Zhong, F.; Savage, S.A.; Shkreli, M.; Giri, N.; Jessop, L.; Myers, T.; Chen, R.; Alter, B.P.; Artandi, S.E. Disruption of telomerase trafficking by TCAB1 mutation causes dyskeratosis congenita. Genes Dev. 2011, 25, 11–16, doi:10.1101/gad.2006411.
[185]  Vulliamy, T.; Marrone, A.; Goldman, F.; Dearlove, A.; Bessler, M.; Mason, P.J.; Dokal, I. The RNA component of telomerase is mutated in autosomal dominant dyskeratosis congenita. Nature 2001, 413, 432–435, doi:10.1038/35096585.
[186]  Cajal, S.R. El núcleo de las células piramidales del cerebro humano y de algunos mamíferos. Trab. Lab. Inv. Biol. Univ. Madr. 1910, 8, 27–62.
[187]  Beck, J.S. Variations in the morphological patterns of "autoimmune" nuclear fluorescence. Lancet 1961, 1, 1203–1205, doi:10.1016/S0140-6736(61)91944-4.
[188]  Swift, H. Studies on nuclear fine structure. Brookhaven Symp. Biol. 1959, 12, 134–152.
[189]  Perraud, M.; Gioud, M.; Monier, J.C. Intranuclear structures recognized by autoantibodies against ribonucleoproteins: Study on monkey kidney cells in culture using immunofluorescent techniques and immunoelectron microscopy. Ann. Immunol. (Paris) 1970, 130, 635–647.
[190]  Lerner, E.A.; Lerner, M.R.; Janeway, C.A., Jr.; Steitz, J.A. Monoclonal antibodies to nucleic acid-containing cellular constituents: Probes for molecular biology and autoimmune disease. Proc. Natl. Acad. Sci. USA 1981, 78, 2737–2741, doi:10.1073/pnas.78.5.2737.
[191]  Spector, D.L.; Schrier, W.H.; Busch, H. Immunoelectron microscopic localization of snRNPs. Biol. Cell 1983, 49, 1–10, doi:10.1111/j.1768-322X.1984.tb00215.x.
[192]  Girard, C.; Will, C.L.; Peng, J.; Makarov, E.M.; Kastner, B.; Lemm, I.; Urlaub, H.; Hartmuth, K.; Luhrmann, R. Post-transcriptional spliceosomes are retained in nuclear speckles until splicing completion. Nat. Commun. 2012, 3, 994.
[193]  Lin, S.; Coutinho-Mansfield, G.; Wang, D.; Pandit, S.; Fu, X.D. The splicing factor SC35 has an active role in transcriptional elongation. Nat. Struct. Mol. Biol. 2008, 15, 819–826.
[194]  Zhong, X.Y.; Wang, P.; Han, J.; Rosenfeld, M.G.; Fu, X.D. SR proteins in vertical integration of gene expression from transcription to RNA processing to translation. Mol. Cell 2009, 35, 1–10, doi:10.1016/j.molcel.2009.06.016.
[195]  Chang, Y.F.; Imam, J.S.; Wilkinson, M.F. The nonsense-mediated decay RNA surveillance pathway. Annu. Rev. Biochem. 2007, 76, 51–74, doi:10.1146/annurev.biochem.76.050106.093909.
[196]  Wei, X.; Somanathan, S.; Samarabandu, J.; Berezney, R. Three-dimensional visualization of transcription sites and their association with splicing factor-rich nuclear speckles. J. Cell Biol. 1999, 146, 543–558, doi:10.1083/jcb.146.3.543.
[197]  Long, J.C.; Caceres, J.F. The SR protein family of splicing factors: Master regulators of gene expression. Biochem. J. 2009, 417, 15–27, doi:10.1042/BJ20081501.
[198]  Misteli, T.; Caceres, J.F.; Clement, J.Q.; Krainer, A.R.; Wilkinson, M.F.; Spector, D.L. Serine phosphorylation of SR proteins is required for their recruitment to sites of transcription in vivo. J. Cell Biol. 1998, 143, 297–307.
[199]  Strasser, K.; Masuda, S.; Mason, P.; Pfannstiel, J.; Oppizzi, M.; Rodriguez-Navarro, S.; Rondon, A.G.; Aguilera, A.; Struhl, K.; Reed, R.; et al. TREX is a conserved complex coupling transcription with messenger RNA export. Nature 2002, 417, 304–308, doi:10.1038/nature746.
[200]  Cmarko, D.; Verschure, P.J.; Martin, T.E.; Dahmus, M.E.; Krause, S.; Fu, X.D.; van Driel, R.; Fakan, S. Ultrastructural analysis of transcription and splicing in the cell nucleus after bromo-UTP microinjection. Mol. Biol. Cell 1999, 10, 211–223, doi:10.1091/mbc.10.1.211.
[201]  Jolly, C.; Usson, Y.; Morimoto, R.I. Rapid and reversible relocalization of heat shock factor 1 within seconds to nuclear stress granules. Proc. Natl. Acad. Sci. USA 1999, 96, 6769–6774, doi:10.1073/pnas.96.12.6769.
[202]  Cotto, J.; Fox, S.; Morimoto, R. HSF1 granules: A novel stress-induced nuclear compartment of human cells. J. Cell Sci. 1997, 110, 2925–2934.
[203]  Denegri, M.; Moralli, D.; Rocchi, M.; Biggiogera, M.; Raimondi, E.; Cobianchi, F.; De Carli, L.; Riva, S.; Biamonti, G. Human chromosomes 9, 12, and 15 contain the nucleation sites of stress-induced nuclear bodies. Mol. Biol. Cell 2002, 13, 2069–2079, doi:10.1091/mbc.01-12-0569.
[204]  Morton, E.A.; Lamitina, T. Caenorhabditis elegans HSF-1 is an essential nuclear protein that forms stress granule-like structures following heat shock. Aging Cell 2012.
[205]  Prasanth, K.V.; Rajendra, T.K.; Lal, A.K.; Lakhotia, S.C. Omega speckles—a novel class of nuclear speckles containing hnRNPs associated with noncoding hsr-omega RNA in Drosophila. J. Cell Sci. 2000, 113, 3485–3497.
[206]  Mahl, P.; Lutz, Y.; Puvion, E.; Fuchs, J.P. Rapid effect of heat shock on two heterogeneous nuclear ribonucleoprotein-associated antigens in HeLa cells. J. Cell Biol. 1989, 109, 1921–1935, doi:10.1083/jcb.109.5.1921.
[207]  Xiao, H.; Lis, J.T. Germline transformation used to define key features of heat-shock response elements. Science 1988, 239, 1139–1142.
[208]  Jolly, C.; Konecny, L.; Grady, D.L.; Kutskova, Y.A.; Cotto, J.J.; Morimoto, R.I.; Vourc'h, C. In vivo binding of active heat shock transcription factor 1 to human chromosome 9 heterochromatin during stress. J. Cell Biol. 2002, 156, 775–781, doi:10.1083/jcb.200109018.
[209]  Oesterreich, S.; Lee, A.V.; Sullivan, T.M.; Samuel, S.K.; Davie, J.R.; Fuqua, S.A. Novel nuclear matrix protein HET binds to and influences activity of the HSP27 promoter in human breast cancer cells. J. Cell. Biochem. 1997, 67, 275–286, doi:10.1002/(SICI)1097-4644(19971101)67:2<275::AID-JCB13>3.0.CO;2-E.
[210]  Townson, S.M.; Kang, K.; Lee, A.V.; Oesterreich, S. Structure-function analysis of the estrogen receptor alpha corepressor scaffold attachment factor-B1: identification of a potent transcriptional repression domain. J. Biol. Chem. 2004, 279, 26074–26081.
[211]  Montgomery, T.H. Comparative cytological studies, with especial regard to the morphology of the nucleolus. J. Morphol. 1898, 15, 265–582.
[212]  Islinger, M.; Willimski, D.; Volkl, A.; Braunbeck, T. Effects of 17a-ethinylestradiol on the expression of three estrogen-responsive genes and cellular ultrastructure of liver and testes in male zebrafish. Aquat. Toxicol. 2003, 62, 85–103, doi:10.1016/S0166-445X(02)00049-8.
[213]  Knibiehler, B.; Mirre, C.; Rosset, R. Nucleolar organizer structure and activity in a nucleolus without fibrillar centres: The nucleolus in an established Drosophila cell line. J. Cell Sci. 1982, 57, 351–364.
[214]  Lee, L.W.; Lee, C.C.; Huang, C.R.; Lo, S.J. The nucleolus of Caenorhabditis elegans. J. Biomed. Biotechnol. 2012, 2012, 601274.
[215]  Smitt, W.W.; Vlak, J.M.; Molenaar, I.; Rozijn, T.H. Nucleolar function of the dense crescent in the yeast nucleus. A biochemical and ultrastructural study. Exp. Cell Res. 1973, 80, 313–321.
[216]  Monneron, A.; Bernhard, W. Fine structural organization of the interphase nucleus in some mammalian cells. J. Ultrastruct. Res. 1969, 27, 266–288, doi:10.1016/S0022-5320(69)80017-1.
[217]  Wu, Z.A.; Murphy, C.; Callan, H.G.; Gall, J.G. Small nuclear ribonucleoproteins and heterogeneous nuclear ribonucleoproteins in the amphibian germinal vesicle: loops, spheres, and snurposomes. J. Cell Biol. 1991, 113, 465–483, doi:10.1083/jcb.113.3.465.
[218]  Segalat, L.; Lepesant, J.A. Spatial distribution of the Sm antigen in Drosophila early embryos. Biol. Cell 1992, 75, 181–185.
[219]  Potashkin, J.A.; Derby, R.J.; Spector, D.L. Differential distribution of factors involved in pre-mRNA processing in the yeast cell nucleus. Mol. Cell. Biol. 1990, 10, 3524–3534.
[220]  Schoenfelder, S.; Sexton, T.; Chakalova, L.; Cope, N.F.; Horton, A.; Andrews, S.; Kurukuti, S.; Mitchell, J.A.; Umlauf, D.; Dimitrova, D.S.; et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat. Genet. 2010, 42, 53–61.
[221]  Cajal, S.R. Un sencillo método de coloración seletiva del retículo protoplasmático y sus efectos en los diversos órganos nerviosos de vertebrados e invertebrados. Trab. Lab. Inv. Biol. Univ. Madr. 1903, 2, 129–221.
[222]  Nizami, Z.F.; Gall, J.G. Pearls are novel Cajal body-like structures in the Xenopus germinal vesicle that are dependent on RNA pol III transcription. Chromosome Res. 2012, 20, 953–969, doi:10.1007/s10577-012-9320-1.
[223]  Strzelecka, M.; Oates, A.C.; Neugebauer, K.M. Dynamic control of Cajal body number during zebrafish embryogenesis. Nucleus 2010, 1, 96–108.
[224]  Verheggen, C.; Mouaikel, J.; Thiry, M.; Blanchard, J.M.; Tollervey, D.; Bordonne, R.; Lafontaine, D.L.; Bertrand, E. Box C/D small nucleolar RNA trafficking involves small nucleolar RNP proteins, nucleolar factors and a novel nuclear domain. EMBO J. 2001, 20, 5480–5490, doi:10.1093/emboj/20.19.5480.
[225]  Francis, J.W.; Sandrock, A.W.; Bhide, P.G.; Vonsattel, J.P.; Brown, R.H., Jr. Heterogeneity of subcellular localization and electrophoretic mobility of survival motor neuron (SMN) protein in mammalian neural cells and tissues. Proc. Natl. Acad. Sci. USA 1998, 95, 6492–6497.
[226]  Cauchi, R.J. Gem formation upon constitutive Gemin3 overexpression in Drosophila. Cell Biol. Int. 2011, 35, 1233–1238, doi:10.1042/CBI20110147.
[227]  Wu, C.H.; Gall, J.G. U7 small nuclear RNA in C snurposomes of the Xenopus germinal vesicle. Proc. Natl. Acad. Sci. USA 1993, 90, 6257–6259, doi:10.1073/pnas.90.13.6257.
[228]  Bongiorno-Borbone, L.; De Cola, A.; Vernole, P.; Finos, L.; Barcaroli, D.; Knight, R.A.; Melino, G.; De Laurenzi, V. FLASH and NPAT positive but not Coilin positive Cajal Bodies correlate with cell ploidy. Cell Cycle 2008, 7, 2357–2367.
[229]  Ge, H.; Manley, J.L. A protein factor, ASF, controls cell-specific alternative splicing of SV40 early pre-mRNA in vitro. Cell 1990, 62, 25–34.
[230]  Wu, H.; Sun, S.; Tu, K.; Gao, Y.; Xie, B.; Krainer, A.R.; Zhu, J. A splicing-independent function of SF2/ASF in microRNA processing. Mol. Cell 2010, 38, 67–77, doi:10.1016/j.molcel.2010.02.021.
[231]  Jolly, C.; Vourc'h, C.; Robert-Nicoud, M.; Morimoto, R.I. Intron-independent association of splicing factors with active genes. J. Cell Biol. 1999, 145, 1133–1143, doi:10.1083/jcb.145.6.1133.
[232]  Fu, X.D. Specific commitment of different pre-mRNAs to splicing by single SR proteins. Nature 1993, 365, 82–85.
[233]  Busa, R.; Geremia, R.; Sette, C. Genotoxic stress causes the accumulation of the splicing regulator Sam68 in nuclear foci of transcriptionally active chromatin. Nucleic Acids Res. 2010, 38, 3005–3018, doi:10.1093/nar/gkq004.
[234]  Metz, A.; Soret, J.; Vourc'h, C.; Tazi, J.; Jolly, C. A key role for stress-induced satellite III transcripts in the relocalization of splicing factors into nuclear stress granules. J. Cell Sci. 2004, 117, 4551–4558.
[235]  Shevtsov, S.P.; Dundr, M. Nucleation of nuclear bodies by RNA. Nat. Cell Biol. 2011, 13, 167–173.
[236]  Fritah, S.; Col, E.; Boyault, C.; Govin, J.; Sadoul, K.; Chiocca, S.; Christians, E.; Khochbin, S.; Jolly, C.; Vourc'h, C. Heat-shock factor 1 controls genome-wide acetylation in heat-shocked cells. Mol. Biol. Cell 2009, 20, 4976–4984.
[237]  Papantonis, A.; Larkin, J.D.; Wada, Y.; Ohta, Y.; Ihara, S.; Kodama, T.; Cook, P.R. Active RNA polymerases: Mobile or immobile molecular machines? PLoS Biol. 2010, 8, e1000419, doi:10.1371/journal.pbio.1000419.
[238]  Dickinson, P.; Cook, P.R.; Jackson, D.A. Active RNA polymerase I is fixed within the nucleus of HeLa cells. EMBO J. 1990, 9, 2207–2214.
[239]  Mitchell, J.A.; Fraser, P. Transcription factories are nuclear subcompartments that remain in the absence of transcription. Genes Dev. 2008, 22, 20–25, doi:10.1101/gad.454008.
[240]  Cook, P.R. Predicting three-dimensional genome structure from transcriptional activity. Nat. Genet. 2002, 32, 347–352, doi:10.1038/ng1102-347.
[241]  McCracken, S.; Fong, N.; Yankulov, K.; Ballantyne, S.; Pan, G.; Greenblatt, J.; Patterson, S.D.; Wickens, M.; Bentley, D.L. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 1997, 385, 357–361, doi:10.1038/385357a0.
[242]  Gall, J.G. The centennial of the Cajal body. Nat. Rev. Mol. Cell Biol. 2003, 4, 975–980, doi:10.1038/nrm1262.
[243]  Dundr, M. Nuclear bodies: Multifunctional companions of the genome. Curr. Opin. Cell Biol. 2012, 24, 415–422, doi:10.1016/j.ceb.2012.03.010.
[244]  Machyna, M.; Heyn, P.; Neugebauer, K.M. Cajal bodies: Where form meets function. Wiley Interdiscip Rev RNA 2013, 4, 17–34, doi:10.1002/wrna.1139.
[245]  Jady, B.E.; Bertrand, E.; Kiss, T. Human telomerase RNA and box H/ACA scaRNAs share a common Cajal body-specific localization signal. J. Cell Biol. 2004, 164, 647–652, doi:10.1083/jcb.200310138.
[246]  Baillat, D.; Hakimi, M.A.; Naar, A.M.; Shilatifard, A.; Cooch, N.; Shiekhattar, R. Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II. Cell 2005, 123, 265–276, doi:10.1016/j.cell.2005.08.019.
[247]  Takata, H.; Nishijima, H.; Maeshima, K.; Shibahara, K. The integrator complex is required for integrity of Cajal bodies. J. Cell Sci. 2012, 125, 166–175, doi:10.1242/jcs.090837.
[248]  Xu, H.; Pillai, R.S.; Azzouz, T.N.; Shpargel, K.B.; Kambach, C.; Hebert, M.D.; Schumperli, D.; Matera, A.G. The C-terminal domain of coilin interacts with Sm proteins and U snRNPs. Chromosoma 2005, 114, 155–166, doi:10.1007/s00412-005-0003-y.
[249]  Broome, H.J.; Hebert, M.D. Coilin displays differential affinity for specific RNAs in vivo and is linked to telomerase RNA biogenesis. J. Mol. Biol. 2013.
[250]  Hebert, M.D.; Szymczyk, P.W.; Shpargel, K.B.; Matera, A.G. Coilin forms the bridge between Cajal bodies and SMN, the spinal muscular atrophy protein. Genes Dev. 2001, 15, 2720–2729, doi:10.1101/gad.908401.
[251]  Broome, H.J.; Hebert, M.D. In vitro RNase and nucleic acid binding activities implicate coilin in U snRNA processing. PLoS One 2012, 7, e36300, doi:10.1371/journal.pone.0036300.
[252]  Sleeman, J.E.; Lamond, A.I. Newly assembled snRNPs associate with coiled bodies before speckles, suggesting a nuclear snRNP maturation pathway. Curr. Biol. 1999, 9, 1065–1074, doi:10.1016/S0960-9822(99)80475-8.
[253]  Stanek, D.; Neugebauer, K.M. Detection of snRNP assembly intermediates in Cajal bodies by fluorescence resonance energy transfer. J. Cell Biol. 2004, 166, 1015–1025, doi:10.1083/jcb.200405160.
[254]  Nesic, D.; Tanackovic, G.; Kramer, A. A role for Cajal bodies in the final steps of U2 snRNP biogenesis. J. Cell Sci. 2004, 117, 4423–4433, doi:10.1242/jcs.01308.
[255]  Kiss, T.; Fayet, E.; Jady, B.E.; Richard, P.; Weber, M. Biogenesis and intranuclear trafficking of human box C/D and H/ACA RNPs. Cold Spring Harb. Symp. Quant. Biol. 2006, 71, 407–417, doi:10.1101/sqb.2006.71.025.
[256]  Mahmoudi, S.; Henriksson, S.; Weibrecht, I.; Smith, S.; Soderberg, O.; Stromblad, S.; Wiman, K.G.; Farnebo, M. WRAP53 is essential for Cajal body formation and for targeting the survival of motor neuron complex to Cajal bodies. PLoS Biol. 2010, 8, e1000521, doi:10.1371/journal.pbio.1000521.
[257]  Davis, D.R. Stabilization of RNA stacking by pseudouridine. Nucleic Acids Res. 1995, 23, 5020–5026, doi:10.1093/nar/23.24.5020.
[258]  Wu, G.; Xiao, M.; Yang, C.; Yu, Y.T. U2 snRNA is inducibly pseudouridylated at novel sites by Pus7p and snR81 RNP. EMBO J. 2011, 30, 79–89, doi:10.1038/emboj.2010.316.
[259]  Frey, M.R.; Bailey, A.D.; Weiner, A.M.; Matera, A.G. Association of snRNA genes with coiled bodies is mediated by nascent snRNA transcripts. Curr. Biol. 1999, 9, 126–135, doi:10.1016/S0960-9822(99)80066-9.
[260]  Smith, K.P.; Carter, K.C.; Johnson, C.V.; Lawrence, J.B. U2 and U1 snRNA gene loci associate with coiled bodies. J. Cell. Biochem. 1995, 59, 473–485.
[261]  Smith, K.P.; Lawrence, J.B. Interactions of U2 gene loci and their nuclear transcripts with Cajal (coiled) bodies: Evidence for PreU2 within Cajal bodies. Mol. Biol. Cell 2000, 11, 2987–2998, doi:10.1091/mbc.11.9.2987.
[262]  Sleeman, J.E.; Lamond, A.I. Newly assembled snRNPs associate with coiled bodies before speckles, suggesting a nuclear snRNP maturation pathway. Curr. Biol. 1999, 9, 1065–1074, doi:10.1016/S0960-9822(99)80475-8.
[263]  Cristofari, G.; Adolf, E.; Reichenbach, P.; Sikora, K.; Terns, R.M.; Terns, M.P.; Lingner, J. Human telomerase RNA accumulation in Cajal bodies facilitates telomerase recruitment to telomeres and telomere elongation. Mol. Cell 2007, 27, 882–889.
[264]  Tomlinson, R.L.; Abreu, E.B.; Ziegler, T.; Ly, H.; Counter, C.M.; Terns, R.M.; Terns, M.P. Telomerase reverse transcriptase is required for the localization of telomerase RNA to Cajal bodies and telomeres in human cancer cells. Mol. Biol. Cell 2008, 19, 3793–3800, doi:10.1091/mbc.E08-02-0184.
[265]  Tomlinson, R.L.; Ziegler, T.D.; Supakorndej, T.; Terns, R.M.; Terns, M.P. Cell cycle-regulated trafficking of human telomerase to telomeres. Mol. Biol. Cell 2006, 17, 955–965.
[266]  Jady, B.E.; Richard, P.; Bertrand, E.; Kiss, T. Cell cycle-dependent recruitment of telomerase RNA and Cajal bodies to human telomeres. Mol. Biol. Cell 2006, 17, 944–954.
[267]  Werdnig, G. Zwei frühinfantile heredit?re f?lle von progressiver muskelatrophie unter dem bilde der dystrophie, aber auf neurotischer grundlage. Arch. Psychiatr. Nervenkr. 1891, 22, 437–481, doi:10.1007/BF01776636.
[268]  Hoffmann, J. Weitere beitr?ge zur lehre von der progressiven neurotischen muskeldystrophie. Dtsch. Z. Nervenheilkd. 1891, 1, 95–120, doi:10.1007/BF01669211.
[269]  Strasswimmer, J.; Lorson, C.L.; Breiding, D.E.; Chen, J.J.; Le, T.; Burghes, A.H.; Androphy, E.J. Identification of survival motor neuron as a transcriptional activator-binding protein. Hum. Mol. Genet. 1999, 8, 1219–1226.
[270]  Pellizzoni, L.; Charroux, B.; Rappsilber, J.; Mann, M.; Dreyfuss, G. A functional interaction between the survival motor neuron complex and RNA polymerase II. J. Cell Biol. 2001, 152, 75–85.
[271]  Sanchez, G.; Dury, A.Y.; Murray, L.M.; Biondi, O.; Tadesse, H.; El Fatimy, R.; Kothary, R.; Charbonnier, F.; Khandjian, E.W.; Cote, J. A novel function for the survival motoneuron protein as a translational regulator. Hum. Mol. Genet. 2012.
[272]  Battle, D.J.; Lau, C.K.; Wan, L.; Deng, H.; Lotti, F.; Dreyfuss, G. The Gemin5 protein of the SMN complex identifies snRNAs. Mol. Cell 2006, 23, 273–279.
[273]  Galcheva-Gargova, Z.; Gangwani, L.; Konstantinov, K.N.; Mikrut, M.; Theroux, S.J.; Enoch, T.; Davis, R.J. The cytoplasmic zinc finger protein ZPR1 accumulates in the nucleolus of proliferating cells. Mol. Biol. Cell 1998, 9, 2963–2971, doi:10.1091/mbc.9.10.2963.
[274]  Galcheva-Gargova, Z.; Konstantinov, K.N.; Wu, I.H.; Klier, F.G.; Barrett, T.; Davis, R.J. Binding of zinc finger protein ZPR1 to the epidermal growth factor receptor. Science 1996, 272, 1797–1802.
[275]  Hebert, M.D.; Shpargel, K.B.; Ospina, J.K.; Tucker, K.E.; Matera, A.G. Coilin methylation regulates nuclear body formation. Dev. Cell 2002, 3, 329–337, doi:10.1016/S1534-5807(02)00222-8.
[276]  Shafey, D.; Cote, P.D.; Kothary, R. Hypomorphic Smn knockdown C2C12 myoblasts reveal intrinsic defects in myoblast fusion and myotube morphology. Exp. Cell Res. 2005, 311, 49–61, doi:10.1016/j.yexcr.2005.08.019.
[277]  Yang, X.C.; Sabath, I.; Debski, J.; Kaus-Drobek, M.; Dadlez, M.; Marzluff, W.F.; Dominski, Z. A complex containing the CPSF73 endonuclease and other polyadenylation factors associates with U7 snRNP and is recruited to histone pre-mRNA for 3'-end processing. Mol. Cell. Biol. 2013, 33, 28–37, doi:10.1128/MCB.00653-12.
[278]  Sanchez, R.; Marzluff, W.F. The stem-loop binding protein is required for efficient translation of histone mRNA in vivo and in vitro. Mol. Cell. Biol. 2002, 22, 7093–7104, doi:10.1128/MCB.22.20.7093-7104.2002.
[279]  Krishnan, N.; Lam, T.T.; Fritz, A.; Rempinski, D.; O'Loughlin, K.; Minderman, H.; Berezney, R.; Marzluff, W.F.; Thapar, R. The prolyl isomerase Pin1 targets stem-loop binding protein (SLBP) to dissociate the SLBP-histone mRNA complex linking histone mRNA decay with SLBP ubiquitination. Mol. Cell. Biol. 2012, 32, 4306–4322, doi:10.1128/MCB.00382-12.
[280]  Fox, A.H.; Bond, C.S.; Lamond, A.I. p54nrb forms a heterodimer with PSP1 that localizes to paraspeckles in an RNA-dependent manner. Mol. Biol. Cell 2005, 16, 5304–5315, doi:10.1091/mbc.E05-06-0587.
[281]  Naganuma, T.; Nakagawa, S.; Tanigawa, A.; Sasaki, Y.F.; Goshima, N.; Hirose, T. Alternative 3'-end processing of long noncoding RNA initiates construction of nuclear paraspeckles. EMBO J. 2012, 31, 4020–4034, doi:10.1038/emboj.2012.251.
[282]  Rosonina, E.; Ip, J.Y.; Calarco, J.A.; Bakowski, M.A.; Emili, A.; McCracken, S.; Tucker, P.; Ingles, C.J.; Blencowe, B.J. Role for PSF in mediating transcriptional activator-dependent stimulation of pre-mRNA processing in vivo. Mol. Cell. Biol. 2005, 25, 6734–6746, doi:10.1128/MCB.25.15.6734-6746.2005.
[283]  Kaneko, S.; Rozenblatt-Rosen, O.; Meyerson, M.; Manley, J.L. The multifunctional protein p54nrb/PSF recruits the exonuclease XRN2 to facilitate pre-mRNA 3' processing and transcription termination. Genes Dev. 2007, 21, 1779–1789, doi:10.1101/gad.1565207.
[284]  Patton, J.G.; Porro, E.B.; Galceran, J.; Tempst, P.; Nadal-Ginard, B. Cloning and characterization of PSF, a novel pre-mRNA splicing factor. Genes Dev. 1993, 7, 393–406, doi:10.1101/gad.7.3.393.
[285]  Peng, R.; Dye, B.T.; Perez, I.; Barnard, D.C.; Thompson, A.B.; Patton, J.G. PSF and p54nrb bind a conserved stem in U5 snRNA. RNA 2002, 8, 1334–1347, doi:10.1017/S1355838202022070.
[286]  Kameoka, S.; Duque, P.; Konarska, M.M. p54(nrb) associates with the 5' splice site within large transcription/splicing complexes. EMBO J. 2004, 23, 1782–1791, doi:10.1038/sj.emboj.7600187.
[287]  Bladen, C.L.; Udayakumar, D.; Takeda, Y.; Dynan, W.S. Identification of the polypyrimidine tract binding protein-associated splicing factor p54(nrb) complex as a candidate DNA double-strand break rejoining factor. J. Biol. Chem. 2005, 280, 5205–5210.
[288]  Li, S.; Kuhne, W.W.; Kulharya, A.; Hudson, F.Z.; Ha, K.; Cao, Z.; Dynan, W.S. Involvement of p54(nrb), a PSF partner protein, in DNA double-strand break repair and radioresistance. Nucleic Acids Res. 2009, 37, 6746–6753, doi:10.1093/nar/gkp741.
[289]  Salton, M.; Lerenthal, Y.; Wang, S.Y.; Chen, D.J.; Shiloh, Y. Involvement of Matrin 3 and SFPQ/NONO in the DNA damage response. Cell Cycle 2010, 9, 1568–1576, doi:10.4161/cc.9.8.11298.
[290]  Ha, K.; Takeda, Y.; Dynan, W.S. Sequences in PSF/SFPQ mediate radioresistance and recruitment of PSF/SFPQ-containing complexes to DNA damage sites in human cells. DNA Repair (Amst) 2011, 10, 252–259, doi:10.1016/j.dnarep.2010.11.009.
[291]  Lowery, L.A.; Rubin, J.; Sive, H. Whitesnake/sfpq is required for cell survival and neuronal development in the zebrafish. Dev. Dyn. 2007, 236, 1347–1357.
[292]  Auboeuf, D.; Dowhan, D.H.; Li, X.; Larkin, K.; Ko, L.; Berget, S.M.; O'Malley, B.W. CoAA, a nuclear receptor coactivator protein at the interface of transcriptional coactivation and RNA splicing. Mol. Cell. Biol. 2004, 24, 442–453, doi:10.1128/MCB.24.1.442-453.2004.
[293]  Ruegsegger, U.; Beyer, K.; Keller, W. Purification and characterization of human cleavage factor Im involved in the 3' end processing of messenger RNA precursors. J. Biol. Chem. 1996, 271, 6107–6113, doi:10.1074/jbc.271.11.6107.
[294]  Ruepp, M.D.; Aringhieri, C.; Vivarelli, S.; Cardinale, S.; Paro, S.; Schumperli, D.; Barabino, S.M. Mammalian pre-mRNA 3' end processing factor CF I m 68 functions in mRNA export. Mol. Biol. Cell 2009, 20, 5211–5223, doi:10.1091/mbc.E09-05-0389.
[295]  Zhang, Z.; Carmichael, G.G. The fate of dsRNA in the nucleus: A p54(nrb)-containing complex mediates the nuclear retention of promiscuously A-to-I edited RNAs. Cell 2001, 106, 465–475, doi:10.1016/S0092-8674(01)00466-4.
[296]  Moncada, S.; Higgs, A. The L-arginine-nitric oxide pathway. N. Engl. J. Med. 1993, 329, 2002–2012, doi:10.1056/NEJM199312303292706.
[297]  Herman, R.C.; Williams, J.G.; Penman, S. Message and non-message sequences adjacent to poly(A) in steady state heterogeneous nuclear RNA of HeLa cells. Cell 1976, 7, 429–437.
[298]  Athanasiadis, A.; Rich, A.; Maas, S. Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol. 2004, 2, e391, doi:10.1371/journal.pbio.0020391.
[299]  Kim, D.D.; Kim, T.T.; Walsh, T.; Kobayashi, Y.; Matise, T.C.; Buyske, S.; Gabriel, A. Widespread RNA editing of embedded alu elements in the human transcriptome. Genome Res. 2004, 14, 1719–1725, doi:10.1101/gr.2855504.
[300]  Levanon, E.Y.; Eisenberg, E.; Yelin, R.; Nemzer, S.; Hallegger, M.; Shemesh, R.; Fligelman, Z.Y.; Shoshan, A.; Pollock, S.R.; Sztybel, D.; et al. Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat. Biotechnol. 2004, 22, 1001–1005.
[301]  Rabl, C. über Zelltheilung. Morphol. Jahrbuch 1885, 10, 214–330.
[302]  Bischoff, A.; Albers, J.; Kharboush, I.; Stelzer, E.; Cremer, T.; Cremer, C. Differences of size and shape of active and inactive X-chromosome domains in human amniotic fluid cell nuclei. Microsc. Res. Tech. 1993, 25, 68–77, doi:10.1002/jemt.1070250110.
[303]  Cremer, T.; Cremer, C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet. 2001, 2, 292–301, doi:10.1038/35066075.
[304]  Cremer, T.; Lichter, P.; Borden, J.; Ward, D.C.; Manuelidis, L. Detection of chromosome aberrations in metaphase and interphase tumor cells by in situ hybridization using chromosome-specific library probes. Hum. Genet. 1988, 80, 235–246, doi:10.1007/BF01790091.
[305]  Lichter, P.; Cremer, T.; Borden, J.; Manuelidis, L.; Ward, D.C. Delineation of individual human chromosomes in metaphase and interphase cells by in situ suppression hybridization using recombinant DNA libraries. Hum. Genet. 1988, 80, 224–234, doi:10.1007/BF01790090.
[306]  Pinkel, D.; Landegent, J.; Collins, C.; Fuscoe, J.; Segraves, R.; Lucas, J.; Gray, J. Fluorescence in situ hybridization with human chromosome-specific libraries: detection of trisomy 21 and translocations of chromosome 4. Proc. Natl. Acad. Sci. USA 1988, 85, 9138–9142.
[307]  Chambeyron, S.; Bickmore, W.A. Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev. 2004, 18, 1119–1130, doi:10.1101/gad.292104.
[308]  Chambeyron, S.; Da Silva, N.R.; Lawson, K.A.; Bickmore, W.A. Nuclear re-organisation of the Hoxb complex during mouse embryonic development. Development 2005, 132, 2215–2223, doi:10.1242/dev.01813.
[309]  Dietzel, S.; Schiebel, K.; Little, G.; Edelmann, P.; Rappold, G.A.; Eils, R.; Cremer, C.; Cremer, T. The 3D positioning of ANT2 and ANT3 genes within female X chromosome territories correlates with gene activity. Exp. Cell Res. 1999, 252, 363–375, doi:10.1006/excr.1999.4635.
[310]  Ferrai, C.; Xie, S.Q.; Luraghi, P.; Munari, D.; Ramirez, F.; Branco, M.R.; Pombo, A.; Crippa, M.P. Poised transcription factories prime silent uPA gene prior to activation. PLoS Biol. 2010, 8, e1000270, doi:10.1371/journal.pbio.1000270.
[311]  Kurz, A.; Lampel, S.; Nickolenko, J.E.; Bradl, J.; Benner, A.; Zirbel, R.M.; Cremer, T.; Lichter, P. Active and inactive genes localize preferentially in the periphery of chromosome territories. J. Cell Biol. 1996, 135, 1195–1205, doi:10.1083/jcb.135.5.1195.
[312]  Mahy, N.L.; Perry, P.E.; Bickmore, W.A. Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH. J. Cell Biol. 2002, 159, 753–763, doi:10.1083/jcb.200207115.
[313]  Mahy, N.L.; Perry, P.E.; Gilchrist, S.; Baldock, R.A.; Bickmore, W.A. Spatial organization of active and inactive genes and noncoding DNA within chromosome territories. J. Cell Biol. 2002, 157, 579–589, doi:10.1083/jcb.200111071.
[314]  Morey, C.; Da Silva, N.R.; Perry, P.; Bickmore, W.A. Nuclear reorganisation and chromatin decondensation are conserved, but distinct, mechanisms linked to Hox gene activation. Development 2007, 134, 909–919, doi:10.1242/dev.02779.
[315]  Scheuermann, M.O.; Tajbakhsh, J.; Kurz, A.; Saracoglu, K.; Eils, R.; Lichter, P. Topology of genes and nontranscribed sequences in human interphase nuclei. Exp. Cell Res. 2004, 301, 266–279, doi:10.1016/j.yexcr.2004.08.031.
[316]  Volpi, E.V.; Chevret, E.; Jones, T.; Vatcheva, R.; Williamson, J.; Beck, S.; Campbell, R.D.; Goldsworthy, M.; Powis, S.H.; Ragoussis, J.; et al. Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. J. Cell Sci. 2000, 113, 1565–1576.
[317]  Williams, R.R.; Broad, S.; Sheer, D.; Ragoussis, J. Subchromosomal positioning of the epidermal differentiation complex (EDC) in keratinocyte and lymphoblast interphase nuclei. Exp. Cell Res. 2002, 272, 163–175, doi:10.1006/excr.2001.5400.
[318]  Bridger, J.M.; Herrmann, H.; Munkel, C.; Lichter, P. Identification of an interchromosomal compartment by polymerization of nuclear-targeted vimentin. J. Cell Sci. 1998, 111, 1241–1253.
[319]  Clemson, C.M.; Lawrence, J.B. Multifunctional compartments in the nucleus: Insights from DNA and RNA localization. J. Cell. Biochem. 1996, 62, 181–190, doi:10.1002/(SICI)1097-4644(199608)62:2<181::AID-JCB6>3.0.CO;2-O.
[320]  Lampel, S.; Bridger, J.M.; Zirbel, R.M.; Mathieu, U.R.; Lichter, P. Nuclear RNA accumulations contain released transcripts and exhibit specific distributions with respect to Sm antigen foci. DNA Cell Biol. 1997, 16, 1133–1142, doi:10.1089/dna.1997.16.1133.
[321]  Xing, Y.; Johnson, C.V.; Moen, P.T., Jr.; McNeil, J.A.; Lawrence, J. Nonrandom gene organization: Structural arrangements of specific pre-mRNA transcription and splicing with SC-35 domains. J. Cell Biol. 1995, 131, 1635–1647, doi:10.1083/jcb.131.6.1635.
[322]  Zirbel, R.M.; Mathieu, U.R.; Kurz, A.; Cremer, T.; Lichter, P. Evidence for a nuclear compartment of transcription and splicing located at chromosome domain boundaries. Chromosome Res. 1993, 1, 93–106, doi:10.1007/BF00710032.
[323]  Bickmore, W.A.; Chubb, J.R. Dispatch. Chromosome position: Now, where was I? Curr. Biol. 2003, 13, R357–R359.
[324]  Gerlich, D.; Beaudouin, J.; Kalbfuss, B.; Daigle, N.; Eils, R.; Ellenberg, J. Global chromosome positions are transmitted through mitosis in mammalian cells. Cell 2003, 112, 751–764, doi:10.1016/S0092-8674(03)00189-2.
[325]  Parada, L.A.; Roix, J.J.; Misteli, T. An uncertainty principle in chromosome positioning. Trends Cell Biol. 2003, 13, 393–396, doi:10.1016/S0962-8924(03)00149-1.
[326]  Walter, J.; Schermelleh, L.; Cremer, M.; Tashiro, S.; Cremer, T. Chromosome order in HeLa cells changes during mitosis and early G1, but is stably maintained during subsequent interphase stages. J. Cell Biol. 2003, 160, 685–697, doi:10.1083/jcb.200211103.
[327]  Williams, R.R.; Fisher, A.G. Chromosomes, positions please! Nat. Cell Biol. 2003, 5, 388–390, doi:10.1038/ncb0503-388.
[328]  Harewood, L.; Schutz, F.; Boyle, S.; Perry, P.; Delorenzi, M.; Bickmore, W.A.; Reymond, A. The effect of translocation-induced nuclear reorganization on gene expression. Genome Res. 2010, 20, 554–564, doi:10.1101/gr.103622.109.
[329]  Campalans, A.; Amouroux, R.; Bravard, A.; Epe, B.; Radicella, J.P. UVA irradiation induces relocalisation of the DNA repair protein hOGG1 to nuclear speckles. J. Cell Sci. 2007, 120, 23–32.
[330]  Ishitani, K.; Yoshida, T.; Kitagawa, H.; Ohta, H.; Nozawa, S.; Kato, S. p54nrb acts as a transcriptional coactivator for activation function 1 of the human androgen receptor. Biochem. Biophys. Res. Commun. 2003, 306, 660–665, doi:10.1016/S0006-291X(03)01021-0.
[331]  Kuwahara, S.; Ikei, A.; Taguchi, Y.; Tabuchi, Y.; Fujimoto, N.; Obinata, M.; Uesugi, S.; Kurihara, Y. PSPC1, NONO, and SFPQ are expressed in mouse Sertoli cells and may function as coregulators of androgen receptor-mediated transcription. Biol. Reprod. 2006, 75, 352–359, doi:10.1095/biolreprod.106.051136.
[332]  Mayer, C.; Bierhoff, H.; Grummt, I. The nucleolus as a stress sensor: JNK2 inactivates the transcription factor TIF-IA and down-regulates rRNA synthesis. Genes Dev. 2005, 19, 933–941, doi:10.1101/gad.333205.
[333]  Velma, V.; Carrero, Z.I.; Cosman, A.M.; Hebert, M.D. Coilin interacts with Ku proteins and inhibits in vitro non-homologous DNA end joining. FEBS Lett. 2010, 584, 4735–4739, doi:10.1016/j.febslet.2010.11.004.
[334]  Xu, M.; Cook, P.R. The role of specialized transcription factories in chromosome pairing. Biochim. Biophys. Acta 2008, 1783, 2155–2160.
[335]  Zhao, J.; Kennedy, B.K.; Lawrence, B.D.; Barbie, D.A.; Matera, A.G.; Fletcher, J.A.; Harlow, E. NPAT links cyclin E-Cdk2 to the regulation of replication-dependent histone gene transcription. Genes Dev. 2000, 14, 2283–2297, doi:10.1101/gad.827700.
[336]  Mao, Y.S.; Zhang, B.; Spector, D.L. Biogenesis and function of nuclear bodies. Trends Genet. 2011, 27, 295–306, doi:10.1016/j.tig.2011.05.006.
[337]  Dundr, M.; Misteli, T. Biogenesis of nuclear bodies. Cold Spring Harb. Perspect. Biol. 2010, 2, a000711, doi:10.1101/cshperspect.a000711.
[338]  Shav-Tal, Y.; Blechman, J.; Darzacq, X.; Montagna, C.; Dye, B.T.; Patton, J.G.; Singer, R.H.; Zipori, D. Dynamic sorting of nuclear components into distinct nucleolar caps during transcriptional inhibition. Mol. Biol. Cell 2005, 16, 2395–2413, doi:10.1091/mbc.E04-11-0992.
[339]  Spector, D.L.; Fu, X.D.; Maniatis, T. Associations between distinct pre-mRNA splicing components and the cell nucleus. EMBO J. 1991, 10, 3467–3481.
[340]  Young, P.J.; Le, T.T.; Dunckley, M.; Nguyen, T.M.; Burghes, A.H.; Morris, G.E. Nuclear gems and Cajal (coiled) bodies in fetal tissues: nucleolar distribution of the spinal muscular atrophy protein, SMN. Exp. Cell Res. 2001, 265, 252–261, doi:10.1006/excr.2001.5186.
[341]  Gdula, M.R.; Poterlowicz, K.; Mardaryev, A.N.; Sharov, A.A.; Peng, Y.; Fessing, M.Y.; Botchkarev, V.A. Remodeling of Three-Dimensional Organization of the Nucleus during Terminal Keratinocyte Differentiation in the Epidermis. J. Invest. Dermatol. 2013.
[342]  Berrios, S.; Fernandez-Donoso, R.; Pincheira, J.; Page, J.; Manterola, M.; Cerda, M.C. Number and nuclear localisation of nucleoli in mammalian spermatocytes. Genetica 2004, 121, 219–228, doi:10.1023/B:GENE.0000039843.78522.99.
[343]  McClintock, B. The relation of a particular chromosomal element to the development of the nucleoli in Zea mays. Z. Zellforsch. 1934, 21, 294–328, doi:10.1007/BF00374060.
[344]  Pardue, M.L.; Hsu, T.C. Locations of 18S and 28S ribosomal genes on the chromosomes of the Indian muntjac. J. Cell Biol. 1975, 64, 251–254, doi:10.1083/jcb.64.1.251.
[345]  Lima-de-Faria, A. The relation between chromomeres, replicons, operons, transcription units, genes, viruses and palindromes. Hereditas 1975, 81, 249–284, doi:10.1111/j.1601-5223.1975.tb01039.x.
[346]  Lima-de-Faria, A. Classification of genes, rearrangements and chromosomes according to the chromosome field. Hereditas 1980, 93, 1–46, doi:10.1111/j.1601-5223.1980.tb01043.x.
[347]  Thatcher, T.H.; Gorovsky, M.A. Phylogenetic analysis of the core histones H2A, H2B, H3, and H4. Nucleic Acids Res. 1994, 22, 174–179, doi:10.1093/nar/22.2.174.

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