Three-dimensional Visualization of Transcription Sites and Their Association with Splicing Factor–rich Nuclear Speckles

doi:10.1083/jcb.146.3.543

This Article

	Full Text
	Full Text (PDF, 1360K)
	Alert me when this article is cited
	Citation Map

Services

	Email this article
	Similar articles in this journal
	Similar articles in PubMed
	Alert me to new content in the JCB
	Download to citation manager

Citing Articles

	Citing Articles via HighWire
	Citing Articles via CrossRef
	Citing Articles via Google Scholar

Google Scholar

	Articles by Wei, X.
	Articles by Berezney, R.
	Search for Related Content

PubMed

	PubMed Citation
	Articles by Wei, X.
	Articles by Berezney, R.


Social Bookmarking

	What's this?

J. Cell Biol., Volume 146, Number 3, August 9, 1999 543-558
Copyright © 1999 by The Rockefeller University Press.

Three-dimensional Visualization of Transcription Sites and Their Association with Splicing Factor–rich Nuclear Speckles

Xiangyun Wei^a, Suryanarayan Somanathan^a, Jagath Samarabandu^a, and Ronald Berezney^a
^a Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York 14260

Correspondence to: Ronald Berezney, Department of Biological Sciences, SUNY at Buffalo, Buffalo, NY 14260. Tel:716-645-2874 (2350/2362) Fax:716-645-2975 E-mail:berezney{at}acsu.buffalo.edu.

Transcription sites are detected by labeling nascent transcriptswith BrUTP in permeabilized 3T3 mouse fibroblasts followed bylaser scanning confocal microscopy. Inhibition and enzyme digestionstudies confirm that the labeled sites are from RNA transcriptsand that RNA polymerase I (RP I) and II (RP II) are responsiblefor nucleolar and extranucleolar transcription, respectively.An average of 2,000 sites are detected per nucleus with over90% in the extranucleolar compartment where they are arrangedin clusters and three-dimensional networklike arrays. The numberof transcription sites, their three-dimensional organizationand arrangement into functional zones (Wei et al. 1998 ) isstrikingly maintained after extraction for nuclear matrix. Significantlevels of total RP II mediated transcription sites (45%) wereassociated with splicing factor–rich nuclear speckles eventhough the speckles occupied <10% of the total extranucleolarspace. Moreover, the vast majority of nuclear speckles (>90%)had moderate to high levels of associated transcription activity.Transcription sites were found along the periphery as well asinside the speckles themselves. These spatial relations wereconfirmed in optical sections through individual speckles andafter in vivo labeling of nascent transcripts. Our results demonstratethat nuclear speckles and their surrounding regions are majorsites of RP II-mediated transcription in the cell nucleus, andsupport the view that both speckle- and nonspeckle-associatedregions of the nucleus contain sites for the coordination oftranscription and splicing processes.

Key Words: transcription sites, nuclear matrix, nuclear speckles, splicingfactors, laser scanning confocal microscopy

Add to CiteULike CiteULike Add to Complore Complore Add to Connotea Connotea Add to Del.icio.us Del.icio.us Add to Digg Digg Add to Reddit Reddit Add to Technorati Technorati What's this?

This article has been cited by other articles:

Ellis, J. D., Lleres, D., Denegri, M., Lamond, A. I., Caceres, J. F. (2008). Spatial mapping of splicing factor complexes involved in exon and intron definition. JCB 181: 921-934 [Abstract] [Full Text]
Jao, C. Y., Salic, A. (2008). Exploring RNA transcription and turnover in vivo by using click chemistry. Proc. Natl. Acad. Sci. USA 105: 15779-15784 [Abstract] [Full Text]
Zhang, H.-M., Li, L., Papadopoulou, N., Hodgson, G., Evans, E., Galbraith, M., Dear, M., Vougier, S., Saxton, J., Shaw, P. E. (2008). Mitogen-induced recruitment of ERK and MSK to SRE promoter complexes by ternary complex factor Elk-1. Nucleic Acids Res 36: 2594-2607 [Abstract] [Full Text]
Smith, K. P., Byron, M., Johnson, C., Xing, Y., Lawrence, J. B. (2007). Defining early steps in mRNA transport: mutant mRNA in myotonic dystrophy type I is blocked at entry into SC-35 domains. JCB 178: 951-964 [Abstract] [Full Text]
Saijo, M., Hirai, T., Ogawa, A., Kobayashi, A., Kamiuchi, S., Tanaka, K. (2007). Functional TFIIH Is Required for UV-Induced Translocation of CSA to the Nuclear Matrix. Mol. Cell. Biol. 27: 2538-2547 [Abstract] [Full Text]
Grunwald, D., Spottke, B., Buschmann, V., Kubitscheck, U. (2006). Intranuclear Binding Kinetics and Mobility of Single Native U1 snRNP Particles in Living Cells. Mol. Biol. Cell 17: 5017-5027 [Abstract] [Full Text]
Sanchez-Alvarez, M., Goldstrohm, A. C., Garcia-Blanco, M. A., Sune, C. (2006). Human Transcription Elongation Factor CA150 Localizes to Splicing Factor-Rich Nuclear Speckles and Assembles Transcription and Splicing Components into Complexes through Its Amino and Carboxyl Regions.. Mol. Cell. Biol. 26: 4998-5014 [Abstract] [Full Text]
Xie, S. Q., Martin, S., Guillot, P. V., Bentley, D. L., Pombo, A. (2006). Splicing Speckles Are Not Reservoirs of RNA Polymerase II, but Contain an Inactive Form, Phosphorylated on Serine2 Residues of the C-Terminal Domain. Mol. Biol. Cell 17: 1723-1733 [Abstract] [Full Text]
Molenaar, C., Abdulle, A., Gena, A., Tanke, H. J., Dirks, R. W. (2004). Poly(A)+ RNAs roam the cell nucleus and pass through speckle domains in transcriptionally active and inactive cells. JCB 165: 191-202 [Abstract] [Full Text]
Zimowska, G., Shi, J., Munguba, G., Jackson, M. R., Alpatov, R., Simmons, M. N., Shi, Y., Sugrue, S. P. (2003). Pinin/DRS/memA Interacts with SRp75, SRm300 and SRrp130 in Corneal Epithelial Cells. IOVS 44: 4715-4723 [Abstract] [Full Text]
Shopland, L. S., Johnson, C. V., Byron, M., McNeil, J., Lawrence, J. B. (2003). Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains: evidence for local euchromatic neighborhoods. JCB 162: 981-990 [Abstract] [Full Text]
Zhang, C., Dowd, D. R., Staal, A., Gu, C., Lian, J. B., van Wijnen, A. J., Stein, G. S., MacDonald, P. N. (2003). Nuclear Coactivator-62 kDa/Ski-interacting Protein Is a Nuclear Matrix-associated Coactivator That May Couple Vitamin D Receptor-mediated Transcription and RNA Splicing. J. Biol. Chem. 278: 35325-35336 [Abstract] [Full Text]
Pilipuk, G. P., Galigniana, M. D., Schwartz, J. (2003). Subnuclear Localization of C/EBP{beta} Is Regulated by Growth Hormone and Dependent on MAPK. J. Biol. Chem. 278: 35668-35677 [Abstract] [Full Text]
POLLOCK, A. S., TURCK, J., LOVETT, D. H. (2003). The prodomain of interleukin 1{alpha} interacts with elements of the RNA processing apparatus and induces apoptosis in malignant cells. FASEB J. 17: 203-213 [Abstract] [Full Text]
Kumaran, R. I., Muralikrishna, B., Parnaik, V. K. (2002). Lamin A/C speckles mediate spatial organization of splicing factor compartments and RNA polymerase II transcription. JCB 159: 783-793 [Abstract] [Full Text]
Mauldin, S. K., Getts, R. C., Liu, W., Stamato, T. D. (2002). DNA-PK-dependent binding of DNA ends to plasmids containing nuclear matrix attachment region DNA sequences: evidence for assembly of a repair complex. Nucleic Acids Res 30: 4075-4087 [Abstract] [Full Text]
Hall, L. L., Byron, M., Sakai, K., Carrel, L., Willard, H. F., Lawrence, J. B. (2002). An ectopic human XIST gene can induce chromosome inactivation in postdifferentiation human HT-1080 cells. Proc. Natl. Acad. Sci. USA 99: 8677-8682 [Abstract] [Full Text]
Chatterjee, T. K., Fisher, R. A. (2002). RGS12TS-S Localizes at Nuclear Matrix-Associated Subnuclear Structures and Represses Transcription: Structural Requirements for Subnuclear Targeting and Transcriptional Repression. Mol. Cell. Biol. 22: 4334-4345 [Abstract] [Full Text]
Elbi, C., Misteli, T., Hager, G. L. (2002). Recruitment of Dioxin Receptor to Active Transcription Sites. Mol. Biol. Cell 13: 2001-2015 [Abstract] [Full Text]
Kimura, Y., Sakai, F., Nakano, O., Kisaki, O., Sugimoto, H., Sawamura, T., Sadano, H., Osumi, T. (2002). The Newly Identified Human Nuclear Protein NXP-2 Possesses Three Distinct Domains, the Nuclear Matrix-binding, RNA-binding, and Coiled-coil Domains. J. Biol. Chem. 277: 20611-20617 [Abstract] [Full Text]
Rodgers, W., Jordan, S. J., Capra, J. D. (2002). Transient Association of Ku with Nuclear Substrates Characterized Using Fluorescence Photobleaching. J. Immunol. 168: 2348-2355 [Abstract] [Full Text]
Sacco-Bubulya, P., Spector, D. L. (2002). Disassembly of interchromatin granule clusters alters the coordination of transcription and pre-mRNA splicing. JCB 156: 425-436 [Abstract] [Full Text]
Dimitrova, D. S., Berezney, R. (2002). The spatio-temporal organization of DNA replication sites is identical in primary, immortalized and transformed mammalian cells. J. Cell Sci. 115: 4037-4051 [Abstract] [Full Text]
Nielsen, J. A., Hudson, L. D., Armstrong, R. C. (2002). Nuclear organization in differentiating oligodendrocytes. J. Cell Sci. 115: 4071-4079 [Abstract] [Full Text]
Kamiuchi, S., Saijo, M., Citterio, E., de Jager, M., Hoeijmakers, J. H. J., Tanaka, K. (2002). Translocation of Cockayne syndrome group A protein to the nuclear matrix: Possible relevance to transcription-coupled DNA repair. Proc. Natl. Acad. Sci. USA 99: 201-206 [Abstract] [Full Text]
Campbell, T. J., Liscum, E. (2001). Plant Photobiology 2001: A Thousand Points of Enlightenment from Receptor Structures to Ecological Adaptation. Plant Cell 13: 1704-1710 [Full Text]
Shav-Tal, Y., Cohen, M., Lapter, S., Dye, B., Patton, J. G., Vandekerckhove, J., Zipori, D. (2001). Nuclear Relocalization of the Pre-mRNA Splicing Factor PSF during Apoptosis Involves Hyperphosphorylation, Masking of Antigenic Epitopes, and Changes in Protein Interactions. Mol. Biol. Cell 12: 2328-2340 [Abstract] [Full Text]
Caron, H., Schaik, B. v., Mee, M. v. d., Baas, F., Riggins, G., Sluis, P. v., Hermus, M.-C., Asperen, R. v., Boon, K., Voûte, P. A., Heisterkamp, S., Kampen, A. v., Versteeg, R. (2001). The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains. Science 291: 1289-1292 [Abstract] [Full Text]
Zaidi, S. K., Javed, A., Choi, J.-Y., van Wijnen, A. J., Stein, J. L., Lian, J. B., Stein, G. S. (2001). A specific targeting signal directs Runx2/Cbfa1 to subnuclear domains and contributes to transactivation of the osteocalcin gene. J. Cell Sci. 114: 3093-3102 [Abstract] [Full Text]
Herrmann, C., Mancini, M. (2001). The Cdk9 and cyclin T subunits of TAK/P-TEFb localize to splicing factor-rich nuclear speckle regions. J. Cell Sci. 114: 1491-1503 [Abstract]
Nickerson, J (2001). Experimental observations of a nuclear matrix. J. Cell Sci. 114: 463-474 [Abstract]
Bhattacharya, D., Lutzoni, F., Reeb, V., Simon, D., Nason, J., Fernandez, F. (2000). Widespread Occurrence of Spliceosomal Introns in the rDNA Genes of Ascomycetes. Mol Biol Evol 17: 1971-1984 [Abstract] [Full Text]
He, L., Weber, A., Levens, D. (2000). Nuclear targeting determinants of the far upstream element binding protein, a c-myc transcription factor. Nucleic Acids Res 28: 4558-4565 [Abstract] [Full Text]
Lemon, B., Tjian, R. (2000). Orchestrated response: a symphony of transcription factors for gene control. Genes Dev. 14: 2551-2569 [Full Text]
Johnson, C., Primorac, D., McKinstry, M., McNeil, J., Rowe, D., Lawrence, J. B. (2000). Tracking COL1A1 RNA in Osteogenesis Imperfecta: Splice-defective Transcripts Initiate Transport from the Gene but Are Retained within the SC35 Domain. JCB 150: 417-432 [Abstract] [Full Text]
Kruhlak, M. J., Lever, M. A., Fischle, W., Verdin, E., Bazett-Jones, D. P., Hendzel, M. J. (2000). Reduced Mobility of the Alternate Splicing Factor (ASF) through the Nucleoplasm and Steady State Speckle Compartments. JCB 150: 41-52 [Abstract] [Full Text]
Stein, G., van Wijnen, A., Stein, J., Lian, J., Montecino, M, Choi, J, Zaidi, K, Javed, A (2000). Intranuclear trafficking of transcription factors: implications for biological control. J. Cell Sci. 113: 2527-2533 [Abstract]
McNeil, S., Zeng, C., Harrington, K. S., Hiebert, S., Lian, J. B., Stein, J. L., van Wijnen, A. J., Stein, G. S. (1999). The t(8;21) chromosomal translocation in acute myelogenous leukemia modifies intranuclear targeting of the AML1/CBFalpha 2 transcription factor. Proc. Natl. Acad. Sci. USA 96: 14882-14887 [Abstract] [Full Text]
Ma, H., Siegel, A. J., Berezney, R. (1999). Association of Chromosome Territories with the Nuclear Matrix: Disruption of Human Chromosome Territories Correlates with the Release of a Subset of Nuclear Matrix Proteins. JCB 146: 531-542 [Abstract] [Full Text]
Sacco-Bubulya, P., Spector, D. L. (2002). Disassembly of interchromatin granule clusters alters the coordination of transcription and pre-mRNA splicing. JCB 156: 425-436 [Abstract] [Full Text]