Separation of replication and transcription domains in nucleoli

Journal of Structural Biology

Volumn 188, Issue 3, 2014, Pages 259-266

  Smirnov, E ^a   Borkovec, J ^a   Kovacik L ^a   Svidenska S ^a   Schrofel A ^a   Skalnikova M ^a   Svindrych Z ^a   Krizek P ^a   Ovesny M ^a   Hagen, G M ^a   Juda, P ^a   Michalova K ^a   Cardoso, M V ^b   Cmarko, D ^a   Raska I ^a  

^a CHARLES UNIVERSITY   (Czech Republic)

^b DARMSTADT UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

Nucleolus; RDNA; Replication; Single molecule localization microscopy; Super resolution; Transcription

Indexed keywords

DNA DIRECTED RNA POLYMERASE; FIBRILLARIN; FLUOROURIDINE; RIBOSOME DNA;

3T3 CELL LINE; ARTICLE; CELL CYCLE G2 PHASE; CELL CYCLE S PHASE; CELL SEPARATION; COMPUTER PROGRAM; CONTROLLED STUDY; DNA REPLICATION; ENZYME LOCALIZATION; FEMALE; FIBROSARCOMA; FIBROSARCOMA CELL; GENE EXPRESSION; GENETIC TRANSCRIPTION; HELA CELL LINE; HUMAN; HUMAN CELL; IMAGE ANALYSIS; IMMUNOCYTOCHEMISTRY; MICROSCOPY; NUCLEOLUS; SINGLE MOLECULE LOCALIZATION MICROSCOPY; CELL LINE; GENETICS; METABOLISM;

MAMMALIA;

CELL LINE; CELL NUCLEOLUS; DNA REPLICATION; HELA CELLS; HUMANS; TRANSCRIPTION, GENETIC;

EID: 84918508759     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2014.10.001     Document Type: Article

References (39)

1. Baddeley D., Chagin V.O., Schermelleh L., Martin S., Pombo A., Carlton P.M., Gahl A., Domaing P., Birk U., Leonhardt H., Cremer C., Cardoso M.C. Measurement of replication structures at the nanometer scale using super-resolution light microscopy. Nucleic Acids Res. 2009, 38(2):1-11.
2. Berezney R., Dubey D.D., Huberman J.A. Heterogeneity of eukaryotic replicons, replicon clusters, and replication foci. Chromosoma 2000, 108:471-484.
3. Berger C., Horlebein A., Gogel E., Grummt F. Temporal order of replication of mouse ribosomal RNA genes during the cell cycle. Chromosoma 1997, 106:479-484.
4. Casafont I., Navascues J., Pena E., Lafarga M., Berciano M.T. Nuclear organization and dynamics of transcription sites in rat sensory ganglia neurons detected by incorporation of 5'-fluorouridine into nascent RNA. Neuroscience 2006, 14:453-462.
5. Casas-Delucchi C.S., Cardoso M.C. Epigenetic control of DNA replication dynamics in mammals. Nucleus 2011, 5:370-382.
6. 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(1):211-223.
7. Cmarko D., Verschure P.J., Rothblum L.I., Hernandez-Verdun D., Amalric F., van Driel R., Fakan S. Ultrastructural analysis of nucleolar transcription in cells microinjected with 5-bromo-UTP. Histochem. Cell Biol. 2000, 113:181-187.
8. Cmarko D., Smigova J., Minichova L., Popov A. Nucleolus: the ribosome factory. Histol. Histopathol. 2008, 23(10):1291-1298.
9. Dimitrova D.S. DNA replication initiation patterns and spatial dynamics of the human ribosomal RNA gene loci. J. Cell Sci. 2011, 124(Pt 16):2743-2752.
10. Dundr M., Hoffmann-Rohrer U., Hu Q., Grummt I., Rothblum L.I., Phair R.D., Misteli T. A kinetic framework for a mammalian RNA polymerase in vivo. Science 2002, 298(5598):1623-1626.
11. Gorski S.A., Snyder S.K., John S., Grummt I., Misteli T. Modulation of RNA polymerase assembly dynamics in transcriptional regulation. Mol. Cell 2008, 30(4):486-497.
12. Grummt I., Pikaard C.S. Epigenetic silencing of RNA polymerase I transcription. Nat. Rev. Mol. Cell Biol. 2003, 4:641-649.
13. Henderson A.S., Warburton D., Atwood K.C. Location of ribosomal DNA in the human chromosome complement. Proc. Natl. Acad. Sci. U.S.A. 1972, 69:3394-3398.
14. Jackson D.A., Pombo A. Replicon clusters are stable units of chromosome structure: evidence that nuclear organization contributes to the efficient activation and propagation of S phase in human cells. J. Cell Biol. 1998, 140(6):1285-1295.
15. Koberna K., Malínský J., Pliss A., Mavata M., Vecerova J., Fialová M., Bednár J., Raška I. Ribosomal genes in focus: new transcripts label the dense fibrillar components and form clusters indicative of "Christmas trees" in situ. J. Cell Biol. 2002, 157:743-748.
16. Koberna K., Ligasova A., Malinsky J., Pliss A., Siegel A.J., Cvacková Z., Fidlerová H., Masata M., Fialová M., Raška I., Berezney R. Electron microscopy of DNA replication in 3-D: evidence for similar-sized replication foci throughout S-phase. J. Cell. Biochem. 2005, 94(1):126-138.
17. Křížek P., Raška I., Hagen G.M. Minimizing detection errors in single molecule localization microscopy. Opt. Express 2011, 19:3226-3235.
18. Li J., Santoro R., Koberna K., Grummt I. The chromatin remodeling complex NoRC controls replication timing of rRNA genes. EMBO J. 2004, 24(1):120-127.
19. Little R.D., Platt T.H., Schildkraut C.L. Initiation and termination of DNA replication in human rRNA genes. Mol. Cell. Biol. 1993, 13(10):6600-6613.
20. Long E.O., Dawid I.B. Repeated genes in eukaryotes. Annu. Rev. Biochem. 1980, 49:727-764.
21. Malinský J., Koberna K., Bednar J., Stulik J., Raška I. Searching for active ribosomal genes in situ: light microscopy in light of the electron beam. J. Struct. Biol. 2002, 140(1-3):227-231.
22. Melčak I., Risueno M.C., Raška I. Ultrastructural non-isotopic mapping of nucleolar transcription sites in onion protoplasts. J. Struct. Biol. 1996, 116(2):253-263.
23. 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(2):123-133.
24. Ovesný M., Křížek P., Borkovec J., Švindrych Z., Hagen G.M. ThunderSTORM: a comprehensive ImageJ plugin for PALM and STORM data analysis and super-resolution imaging. Bioinformatics 2014, (Advance access). 10.1093/bioinformatics/btu202.
25. Pliss A., Koberna K., Vecerová J., Malínský J., Masata M., Fialová M., Raška I., Berezney R. Spatio-temporal dynamics at rDNA foci: global switching between DNA replication and transcription. J. Cell. Biochem. 2005, 94(3):554-565.
26. Puvion-Dutilleul F., Bachellerie J.P., Puvion E. Nucleolar organization of HeLa cells as studied by in situ hybridization. Chromosoma 1991, 100:395-409.
27. Raška I. Oldies but goldies: searching for Christmas trees within the nucleolar architecture. Trends Cell Biol. 2003, 13:517-525.
28. Raška I., Rychter Z., Smetana K. Fibrillar centers and condensed nucleolar chromatin in resting and stimulated human lymphocytes. Zeitschrift fur mikroskopischanatomische Forschung 1983, 97(1):15-32.
29. Raška I., Armbruster B.L., Frey J.R., Smetana K. Analysis of ring-shaped nucleoli in serially sectioned human lymphocytes. Cell Tissue Res. 1983, 234(3):707-711.
30. Raška I., Dundr M., Koberna K., Melcak I., Risueno M.M., Torok I. Does the synthesis of ribosomal RNA take place within nucleolar fibrillar centres or dense fibrillar components? A critical appraisal. J. Struct. Biol. 1995, 114:1-22.
31. Raška I., Shaw P.J., Cmarko D. New insights into nucleolar architecture and activity. Int. Rev. Cytol. 2006, 255:177-235.
32. Raška I., Shaw P.J., Cmarko D. Structure and function of the nucleolus in the spotlight. Curr. Opin. Cell Biol. 2006, 18:325-334.
33. Reinhart M., Casas-Delucchi C.S., Cardoso M.C. Spatiotemporal visualization of DNA replication dynamics. Methods Mol. Biol. 2013, 1042:213-225.
34. Scheer U., Benavente R. Functional and dynamic aspects of the mammalian nucleolus. Bioessays 1990, 12:14-21.
35. Schermelleh L., Solovei I., Zink D., Cremer T. Two-color fluorescence labeling of early and mid-to-late replicating chromatin in living cells. Chromosome Res. 2001, 9:77-80.
36. Sirri V., Urcuqui-Inchima S., Roussel P., Hernandez-Verdun D. Nucleolus: the fascinating nuclear body. Histochem. Cell Biol. 2008, 129:13-31.
37. Smirnov E., Cmarko D., Kováčik L., Hagen G.M., Popov A., Raška O., Prieto J.L., Ryabchenko B., Amim F., McStay B., Ravka I. Replication timing of pseudo-NORs. J. Struct. Biol. 2011, 173(2):213-218.
38. Warner J.R. The economics of ribosome biosynthesis in yeast. Trends Biochem. Sci. 1999, 24:437-440.
39. Yoon Y., Sanchez J.A., Brun C., Huberman J.A. Mapping of replication initiation sites in human ribosomal DNA by nascent-strand abundance analysis. Mol. Cell. Biol. 1995, 15:2482-2489.