Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.
A Kinetic Framework for a Mammalian RNA Polymerase in Vivo
Miroslav Dundr,1Urs Hoffmann-Rohrer,2Qiyue Hu,3Ingrid Grummt,2Lawrence I. Rothblum,3Robert D. Phair,4Tom Misteli*1
We have analyzed the kinetics of assembly and
elongation of the mammalian RNA polymerase I complex on endogenous
ribosomalgenes in the nuclei of living cells with the use of in vivo
microscopy.We show that components of the RNA polymerase I machinery
arebrought to ribosomal genes as distinct subunits and that assemblyoccurs via metastable intermediates. With the use of computationalmodeling of imaging data, we have determined the in vivo elongationtime of the polymerase, and measurements of recruitment and
incorporationfrequencies show that incorporation of components into
the assemblingpolymerase is inefficient. Our data provide a kinetic
and mechanisticframework for the function of a mammalian RNA
polymerase in livingcells.
1 National Cancer Institute (NCI),
National Institutes of Health, Bethesda, MD 20892, USA.
2 German Cancer Research Center, 69120 Heidelberg,
Germany.
3 Weis Center for Research, Danville, PA
17821, USA.
4 BioInformatics Services,
Rockville, MD 20854, USA.
*
To whom correspondence should be addressed. E-mail:
mistelit{at}mail.nih.gov
The editors suggest the following Related Resources on Science sites:
In Science Magazine
NEWS OF THE WEEK
Jennifer Couzin (22 November 2002) Science298 (5598), 1538a.
[DOI: 10.1126/science.298.5598.1538a] |Summary »|Full Text »|PDF »
THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Fibroblast Growth Factor Receptor-1 (FGFR1) Nuclear Dynamics Reveal a Novel Mechanism in Transcription Control.
S. M. Dunham-Ems, Y.-W. Lee, E. K. Stachowiak, H. Pudavar, P. Claus, P. N. Prasad, and M. K. Stachowiak (2009)
Mol. Biol. Cell
20, 2401-2412
|Abstract »|Full Text »|PDF »
Transcription, chromatin condensation, and gene migration.
Assembly of multiprotein complexes that control genome function.
C. Dinant, M. S. Luijsterburg, T. Hofer, G. von Bornstaedt, W. Vermeulen, A. B. Houtsmuller, and R. van Driel (2009)
J. Cell Biol.
185, 21-26
|Abstract »|Full Text »|PDF »
Mutant Huntingtin Impairs Post-Golgi Trafficking to Lysosomes by Delocalizing Optineurin/Rab8 Complex from the Golgi Apparatus.
D. del Toro, J. Alberch, F. Lazaro-Dieguez, R. Martin-Ibanez, X. Xifro, G. Egea, and J. M. Canals (2009)
Mol. Biol. Cell
20, 1478-1492
|Abstract »|Full Text »|PDF »
Regulation of TATA-binding protein dynamics in living yeast cells.
R. O. Sprouse, T. S. Karpova, F. Mueller, A. Dasgupta, J. G. McNally, and D. T. Auble (2008)
PNAS
105, 13304-13308
|Abstract »|Full Text »|PDF »
Phosphorylation by Casein Kinase 2 Facilitates rRNA Gene Transcription by Promoting Dissociation of TIF-IA from Elongating RNA Polymerase I.
H. Bierhoff, M. Dundr, A. A. Michels, and I. Grummt (2008)
Mol. Cell. Biol.
28, 4988-4998
|Abstract »|Full Text »|PDF »
Visual Analysis of the Yeast 5S rRNA Gene Transcriptome: Regulation and Role of La Protein.
S. L. French, Y. N. Osheim, D. A. Schneider, M. L. Sikes, C. F. Fernandez, L. A. Copela, V. A. Misra, M. Nomura, S. L. Wolin, and A. L. Beyer (2008)
Mol. Cell. Biol.
28, 4576-4587
|Abstract »|Full Text »|PDF »
Microplate-based chromatin immunoprecipitation method, Matrix ChIP: a platform to study signaling of complex genomic events.
S. Flanagin, J. D. Nelson, D. G. Castner, O. Denisenko, and K. Bomsztyk (2008)
Nucleic Acids Res.
36, e17
|Abstract »|Full Text »|PDF »
Control and Regulation of Gene Expression: QUANTITATIVE ANALYSIS OF THE EXPRESSION OF PHOSPHOGLYCERATE KINASE IN BLOODSTREAM FORM TRYPANOSOMA BRUCEI.
J. R. Haanstra, M. Stewart, V.-D. Luu, A. van Tuijl, H. V. Westerhoff, C. Clayton, and B. M. Bakker (2008)
J. Biol. Chem.
283, 2495-2507
|Abstract »|Full Text »|PDF »
A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence.
The transcriptional cycle of HIV-1 in real-time and live cells.
S. Boireau, P. Maiuri, E. Basyuk, M. de la Mata, A. Knezevich, B. Pradet-Balade, V. Backer, A. Kornblihtt, A. Marcello, and E. Bertrand (2007)
J. Cell Biol.
179, 291-304
|Abstract »|Full Text »|PDF »
Functional association of Sun1 with nuclear pore complexes.
Q. Liu, N. Pante, T. Misteli, M. Elsagga, M. Crisp, D. Hodzic, B. Burke, and K. J. Roux (2007)
J. Cell Biol.
178, 785-798
|Abstract »|Full Text »|PDF »
Recruitment of factors linking transcription and processing of pre-rRNA to NOR chromatin is UBF-dependent and occurs independent of transcription in human cells.
Show and tell: visualizing gene expression in living cells.
I. U. Rafalska-Metcalf and S. M. Janicki (2007)
J. Cell Sci.
120, 2301-2307
|Abstract »|Full Text »|PDF »
Mass spectrometric identification of phosphorylation sites of rRNA transcription factor upstream binding factor.
C. H. Lin, M. D. Platt, S. B. Ficarro, M. H. Hoofnagle, J. Shabanowitz, L. Comai, D. F. Hunt, and G. K. Owens (2007)
Am J Physiol Cell Physiol
292, C1617-C1624
|Abstract »|Full Text »|PDF »
Epigenetic disruption of ribosomal RNA genes and nucleolar architecture in DNA methyltransferase 1 (Dnmt1) deficient cells.
J. Espada, E. Ballestar, R. Santoro, M. F. Fraga, A. Villar-Garea, A. Nemeth, L. Lopez-Serra, S. Ropero, A. Aranda, H. Orozco, et al. (2007)
Nucleic Acids Res.
35, 2191-2198
|Abstract »|Full Text »|PDF »
Mutant huntingtin Impairs the Post-Golgi Trafficking of Brain-Derived Neurotrophic Factor But Not Its Val66Met Polymorphism.
D. del Toro, J. M. Canals, S. Gines, M. Kojima, G. Egea, and J. Alberch (2006)
J. Neurosci.
26, 12748-12757
|Abstract »|Full Text »|PDF »
Enhancement of U4/U6 Small Nuclear Ribonucleoprotein Particle Association in Cajal Bodies Predicted by Mathematical Modeling.
M. Klingauf, D. Stanek, and K. M. Neugebauer (2006)
Mol. Biol. Cell
17, 4972-4981
|Abstract »|Full Text »|PDF »
Dynamic Interactions between Pit-1 and C/EBP{alpha} in the Pituitary Cell Nucleus.
I. A. Demarco, T. C. Voss, C. F. Booker, and R. N. Day (2006)
Mol. Cell. Biol.
26, 8087-8098
|Abstract »|Full Text »|PDF »
Estrogen-receptor-{alpha} exchange and chromatin dynamics are ligand- and domain-dependent.
Z. D. Sharp, M. G. Mancini, C. A. Hinojos, F. Dai, V. Berno, A. T. Szafran, K. P. Smith, T. T. Lele, D. E. Ingber, and M. A. Mancini (2006)
J. Cell Sci.
119, 4101-4116
|Abstract »|Full Text »|PDF »
FBPs Are Calibrated Molecular Tools To Adjust Gene Expression..
H.-J. Chung, J. Liu, M. Dundr, Z. Nie, S. Sanford, and D. Levens (2006)
Mol. Cell. Biol.
26, 6584-6597
|Abstract »|Full Text »|PDF »
Functional spliceosomal A complexes can be assembled in vitro in the absence of a penta-snRNP.
N. Behzadnia, K. Hartmuth, C. L. Will, and R. Luhrmann (2006)
RNA
12, 1738-1746
|Abstract »|Full Text »|PDF »
Potential Roles for Ubiquitin and the Proteasome during Ribosome Biogenesis..
D. A. Stavreva, M. Kawasaki, M. Dundr, K. Koberna, W. G. Muller, T. Tsujimura-Takahashi, W. Komatsu, T. Hayano, T. Isobe, I. Raska, et al. (2006)
Mol. Cell. Biol.
26, 5131-5145
|Abstract »|Full Text »|PDF »
Structural and Functional Organization of Ribosomal Genes within the Mammalian Cell Nucleolus.
M. Derenzini, G. Pasquinelli, M.-F. O'Donohue, D. Ploton, and M. Thiry (2006)
J. Histochem. Cytochem.
54, 131-145
|Abstract »|Full Text »|PDF »
The methyl-CpG binding protein MBD1 is required for PML-RAR{alpha} function.
R. Villa, L. Morey, V. A. Raker, M. Buschbeck, A. Gutierrez, F. De Santis, M. Corsaro, F. Varas, D. Bossi, S. Minucci, et al. (2006)
PNAS
103, 1400-1405
|Abstract »|Full Text »|PDF »
Fast chromatin immunoprecipitation assay.
J. D. Nelson, O. Denisenko, P. Sova, and K. Bomsztyk (2006)
Nucleic Acids Res.
34, e2
|Abstract »|Full Text »|PDF »
Calcineurin Localization in Skeletal Muscle Offers Insights into Potential New Targets.
The Constitutive Centromere Component CENP-50 Is Required for Recovery from Spindle Damage.
Y. Minoshima, T. Hori, M. Okada, H. Kimura, T. Haraguchi, Y. Hiraoka, Y.-C. Bao, T. Kawashima, T. Kitamura, and T. Fukagawa (2005)
Mol. Cell. Biol.
25, 10315-10328
|Abstract »|Full Text »|PDF »
Partner-regulated interaction of IFN regulatory factor 8 with chromatin visualized in live macrophages.
L. Laricchia-Robbio, T. Tamura, T. Karpova, B. L. Sprague, J. G. McNally, and K. Ozato (2005)
PNAS
102, 14368-14373
|Abstract »|Full Text »|PDF »
High Mobility of Flap Endonuclease 1 and DNA Polymerase {eta} Associated with Replication Foci in Mammalian S-Phase Nucleus.
L. Solovjeva, M. Svetlova, L. Sasina, K. Tanaka, M. Saijo, I. Nazarov, M. Bradbury, and N. Tomilin (2005)
Mol. Biol. Cell
16, 2518-2528
|Abstract »|Full Text »|PDF »
Glutamine Rich and Basic Region/Leucine Zipper (bZIP) Domains Stabilize cAMP-response Element-binding Protein (CREB) Binding to Chromatin.
B. M. Mayr, E. Guzman, and M. Montminy (2005)
J. Biol. Chem.
280, 15103-15110
|Abstract »|Full Text »|PDF »
Cholesterol and Fatty Acids Regulate Dynamic Caveolin Trafficking through the Golgi Complex and between the Cell Surface and Lipid Bodies.
A. Pol, S. Martin, M. A. Fernandez, M. Ingelmo-Torres, C. Ferguson, C. Enrich, and R. G. Parton (2005)
Mol. Biol. Cell
16, 2091-2105
|Abstract »|Full Text »|PDF »
RNA Polymerase I Transcription Factors in Active Yeast rRNA Gene Promoters Enhance UV Damage Formation and Inhibit Repair.
The Functional Region of CENP-H Interacts with the Nuf2 Complex That Localizes to Centromere during Mitosis.
Y. Mikami, T. Hori, H. Kimura, and T. Fukagawa (2005)
Mol. Cell. Biol.
25, 1958-1970
|Abstract »|Full Text »|PDF »
Kinetic and Molecular Analysis of Nuclear Export Factor CRM1 Association with Its Cargo In Vivo.
D. Daelemans, S. V. Costes, S. Lockett, and G. N. Pavlakis (2005)
Mol. Cell. Biol.
25, 728-739
|Abstract »|Full Text »|PDF »
Condensed mitotic chromatin is accessible to transcription factors and chromatin structural proteins.
D. Chen, M. Dundr, C. Wang, A. Leung, A. Lamond, T. Misteli, and S. Huang (2005)
J. Cell Biol.
168, 41-54
|Abstract »|Full Text »|PDF »
UBF-binding site arrays form pseudo-NORs and sequester the RNA polymerase I transcription machinery.
C. Mais, J. E. Wright, J.-L. Prieto, S. L. Raggett, and B. McStay (2005)
Genes & Dev.
19, 50-64
|Abstract »|Full Text »|PDF »
Cajal Bodies, Nucleoli, and Speckles in the Xenopus Oocyte Nucleus Have a Low-Density, Sponge-like Structure.
K. E. Handwerger, J. A. Cordero, and J. G. Gall (2005)
Mol. Biol. Cell
16, 202-211
|Abstract »|Full Text »|PDF »
Nonphosphorylated Human La Antigen Interacts with Nucleolin at Nucleolar Sites Involved in rRNA Biogenesis.
R. V. Intine, M. Dundr, A. Vassilev, E. Schwartz, Y. Zhao, Y. Zhao, M. L. DePamphilis, and R. J. Maraia (2004)
Mol. Cell. Biol.
24, 10894-10904
|Abstract »|Full Text »|PDF »
In vivo dynamics of chromatin-associated complex formation in mammalian nucleotide excision repair.
M. J. Mone, T. Bernas, C. Dinant, F. A. Goedvree, E. M. M. Manders, M. Volker, A. B. Houtsmuller, J. H. J. Hoeijmakers, W. Vermeulen, and R. van Driel (2004)
PNAS
101, 15933-15937
|Abstract »|Full Text »|PDF »
Upstream binding factor association induces large-scale chromatin decondensation.
Quantitative kinetic analysis of nucleolar breakdown and reassembly during mitosis in live human cells.
A. K. L. Leung, D. Gerlich, G. Miller, C. Lyon, Y. W. Lam, D. Lleres, N. Daigle, J. Zomerdijk, J. Ellenberg, and A. I. Lamond (2004)
J. Cell Biol.
166, 787-800
|Abstract »|Full Text »|PDF »
Global Nature of Dynamic Protein-Chromatin Interactions In Vivo: Three-Dimensional Genome Scanning and Dynamic Interaction Networks of Chromatin Proteins.
R. D. Phair, P. Scaffidi, C. Elbi, J. Vecerova, A. Dey, K. Ozato, D. T. Brown, G. Hager, M. Bustin, and T. Misteli (2004)
Mol. Cell. Biol.
24, 6393-6402
|Abstract »|Full Text »|PDF »
The Pleckstrin Homology Domain of Phosphoinositide-specific Phospholipase C{delta}4 Is Not a Critical Determinant of the Membrane Localization of the Enzyme.
S. B. Lee, P. Varnai, A. Balla, K. Jalink, S.-G. Rhee, and T. Balla (2004)
J. Biol. Chem.
279, 24362-24371
|Abstract »|Full Text »|PDF »
Rapid Glucocorticoid Receptor Exchange at a Promoter Is Coupled to Transcription and Regulated by Chaperones and Proteasomes.
D. A. Stavreva, W. G. Muller, G. L. Hager, C. L. Smith, and J. G. McNally (2004)
Mol. Cell. Biol.
24, 2682-2697
|Abstract »|Full Text »|PDF »
Distinct Functional Domains within Nucleoporins Nup153 and Nup98 Mediate Transcription-dependent Mobility.
E. R. Griffis, B. Craige, C. Dimaano, K. S. Ullman, and M. A. Powers (2004)
Mol. Biol. Cell
15, 1991-2002
|Abstract »|Full Text »|PDF »
In vivo kinetics of Cajal body components.
M. Dundr, M. D. Hebert, T. S. Karpova, D. Stanek, H. Xu, K. B. Shpargel, U. T. Meier, K. M. Neugebauer, A. G. Matera, and T. Misteli (2004)
J. Cell Biol.
164, 831-842
|Abstract »|Full Text »|PDF »
Putative involvement of the histone acetyltransferase Tip60 in ribosomal gene transcription.
K. Halkidou, I. R. Logan, S. Cook, D. E. Neal, and C. N. Robson (2004)
Nucleic Acids Res.
32, 1654-1665
|Abstract »|Full Text »|PDF »
The Carboxyl-Terminus Directs TAFI48 to the Nucleus and Nucleolus and Associates with Multiple Nuclear Import Receptors.
J. L. Dynes, S. Xu, S. Bothner, J. M. Lahti, and R. T. Hori (2004)
J. Biochem.
135, 429-438
|Abstract »|Full Text »|PDF »
Multiple States of Stalled T7 RNA Polymerase at DNA Lesions Generated by Platinum Anticancer Agents.
Rrn3 Becomes Inactivated in the Process of Ribosomal DNA Transcription.
I. Hirschler-Laszkiewicz, A. H. Cavanaugh, A. Mirza, M. Lun, Q. Hu, T. Smink, and L. I. Rothblum (2003)
J. Biol. Chem.
278, 18953-18959
|Abstract »|Full Text »|PDF »
In Exponentially Growing Saccharomyces cerevisiae Cells, rRNA Synthesis Is Determined by the Summed RNA Polymerase I Loading Rate Rather than by the Number of Active Genes.
S. L. French, Y. N. Osheim, F. Cioci, M. Nomura, and A. L. Beyer (2003)
Mol. Cell. Biol.
23, 1558-1568
|Abstract »|Full Text »|PDF »
Steady-state dynamics of Cajal body components in the Xenopus germinal vesicle.
K. E. Handwerger, C. Murphy, and J. G. Gall (2003)
J. Cell Biol.
160, 495-504
|Abstract »|Full Text »|PDF »