The Journal of Cell Biology, Vol 102, 1654-1665, Copyright © 1986 by The Rockefeller University Press

ARTICLES

The nonchromatin substructures of the nucleus: the ribonucleoprotein (RNP)-containing and RNP-depleted matrices analyzed by sequential fractionation and resinless section electron microscopy

EG Fey, G Krochmalnic and S Penman

The nonchromatin structure or matrix of the nucleus has been studied using an improved fractionation in concert with resinless section electron microscopy. The resinless sections show the nucleus of the intact cell to be filled with a dense network or lattice composed of soluble proteins and chromatin in addition to the structural nuclear constituents. In the first fractionation step, soluble proteins are removed by extraction with Triton X-100, and the dense nuclear lattice largely disappears. Chromatin and nonchromatin nuclear fibers are now sharply imaged. Nuclear constituents are further separated into three well-defined, distinct protein fractions. Chromatin proteins are those that require intact DNA for their association with the nucleus and are released by 0.25 M ammonium sulfate after internucleosomal DNA is cut with DNAase I. The resulting structure retains most heterogeneous nuclear ribonucleoprotein (hnRNP) and is designated the RNP-containing nuclear matrix. The proteins of hnRNP are those associated with the nucleus only if RNA is intact. These are released when nuclear RNA is briefly digested with RNAase A. Ribonuclease digestion releases 97% of the hnRNA and its associated proteins. These proteins correspond to the hnRNP described by Pederson (Pederson, T., 1974, J. Mol. Biol., 83:163- 184) and are distinct from the proteins that remain in the ribonucleoprotein (RNP)-depleted nuclear matrix. The RNP-depleted nuclear matrix is a core structure that retains lamins A and C, the intermediate filaments, and a unique set of nuclear matrix proteins (Fey, E. G., K. M. Wan, and S. Penman, 1984, J. Cell Biol. 98:1973- 1984). This core had been previously designated the nuclear matrix- intermediate filament scaffold and its proteins are a third, distinct, and nonoverlapping subset of the nuclear nonhistone proteins. Visualizing the nuclear matrix using resinless sections shows that nuclear RNA plays an important role in matrix organization. Conventional Epon-embedded electron microscopy sections show comparatively little of the RNP-containing and RNP-depleted nuclear matrix structure. In contrast, resinless sections show matrix interior to be a three-dimensional network of thick filaments bounded by the nuclear lamina. The filaments are covered with 20-30-nm electron dense particles which may contain the hnRNA. The large electron dense bodies, enmeshed in the interior matrix fibers, have the characteristic morphology of nucleoli. Treatment of the nuclear matrix with RNAase results in the aggregation of the interior fibers and the extensive loss of the 20-30-nm particles.(ABSTRACT TRUNCATED AT 400 WORDS)
CiteULike    Complore    Connotea    Del.icio.us    Digg    Facebook    Reddit    Technorati    Twitter    What's this?

This article has been cited by other articles:

• Linnemann, A. K., Krawetz, S. A. (2009). Silencing by nuclear matrix attachment distinguishes cell-type specificity: association with increased proliferation capacity. Nucleic Acids Res 37: 2779-2788 [Abstract] [Full Text]  
• Sunwoo, H., Dinger, M. E., Wilusz, J. E., Amaral, P. P., Mattick, J. S., Spector, D. L. (2009). MEN {varepsilon}/{beta} nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19: 347-359 [Abstract] [Full Text]  
• Hirano, Y., Ishii, K., Kumeta, M., Furukawa, K., Takeyasu, K., Horigome, T. (2009). Proteomic and targeted analytical identification of BXDC1 and EBNA1BP2 as dynamic scaffold proteins in the nucleolus.. GENES CELLS 14: 155-166 [Abstract] [Full Text]  
• Nakaya, T., Kawai, T., Suzuki, T. (2008). Regulation of FE65 Nuclear Translocation and Function by Amyloid {beta}-Protein Precursor in Osmotically Stressed Cells. J. Biol. Chem. 283: 19119-19131 [Abstract] [Full Text]  
• Amazit, L., Pasini, L., Szafran, A. T., Berno, V., Wu, R.-C., Mielke, M., Jones, E. D., Mancini, M. G., Hinojos, C. A., O'Malley, B. W., Mancini, M. A. (2007). Regulation of SRC-3 Intercompartmental Dynamics by Estrogen Receptor and Phosphorylation. Mol. Cell. Biol. 27: 6913-6932 [Abstract] [Full Text]  
• Szekvolgyi, L., Rakosy, Z., Balint, B. L., Kokai, E., Imre, L., Vereb, G., Bacso, Z., Goda, K., Varga, S., Balazs, M., Dombradi, V., Nagy, L., Szabo, G. (2007). Ribonucleoprotein-masked nicks at 50-kbp intervals in the eukaryotic genomic DNA. Proc. Natl. Acad. Sci. USA 104: 14964-14969 [Abstract] [Full Text]  
• Hizume, K., Araki, S., Yoshikawa, K., Takeyasu, K. (2007). Topoisomerase II, scaffold component, promotes chromatin compaction in vitro in a linker-histone H1-dependent manner. Nucleic Acids Res 0: gkm116v1-13 [Abstract] [Full Text]  
• Grossman, H. B., Soloway, M., Messing, E., Katz, G., Stein, B., Kassabian, V., Shen, Y. (2006). Surveillance for Recurrent Bladder Cancer Using a Point-of-Care Proteomic Assay. JAMA 295: 299-305 [Abstract] [Full Text]  
• Grossman, H. B., Messing, E., Soloway, M., Tomera, K., Katz, G., Berger, Y., Shen, Y. (2005). Detection of Bladder Cancer Using a Point-of-Care Proteomic Assay. JAMA 293: 810-816 [Abstract] [Full Text]  
• Javed, A., Barnes, G. L., Pratap, J., Antkowiak, T., Gerstenfeld, L. C., van Wijnen, A. J., Stein, J. L., Lian, J. B., Stein, G. S. (2005). Impaired intranuclear trafficking of Runx2 (AML3/CBFA1) transcription factors in breast cancer cells inhibits osteolysis in vivo. Proc. Natl. Acad. Sci. USA 102: 1454-1459 [Abstract] [Full Text]  
• Itabashi, T., Terasaki, T., Asai, H. (2004). Novel Nuclear and Cytoplasmic Proteins Detected by Anti-Zoothamnium arbuscula (Protozoa) Spasmin 1 Antibody in Mammalian Cells Are Dependent on the Cell Cycle. J Biochem 136: 651-657 [Abstract] [Full Text]  
• Van Tine, B. A., Kappes, J. C., Banerjee, N. S., Knops, J., Lai, L., Steenbergen, R. D. M., Meijer, C. L. J. M., Snijders, P. J. F., Chatis, P., Broker, T. R., Moen, P. T. Jr., Chow, L. T. (2004). Clonal Selection for Transcriptionally Active Viral Oncogenes during Progression to Cancer. J. Virol. 78: 11172-11186 [Abstract] [Full Text]  
• Nesic, D., Tanackovic, G., Kramer, A. (2004). A role for Cajal bodies in the final steps of U2 snRNP biogenesis. J. Cell Sci. 117: 4423-4433 [Abstract] [Full Text]  
• Salati, L. M., Szeszel-Fedorowicz, W., Tao, H., Gibson, M. A., Amir-Ahmady, B., Stabile, L. P., Hodge, D. L. (2004). Nutritional Regulation of mRNA Processing. J. Nutr. 134: 2437S-2443S [Abstract] [Full Text]  
• CUSTODIO, N., CARVALHO, C., CONDADO, I., ANTONIOU, M., BLENCOWE, B. J., CARMO-FONSECA, M. (2004). In vivo recruitment of exon junction complex proteins to transcription sites in mammalian cell nuclei. RNA 10: 622-633 [Abstract] [Full Text]  
• Wood, J. C., Quinn, G., Suling, K. M., Oldmixon, B. A., Van Tine, B. A., Cina, R., Arn, S., Huang, C. A., Scobie, L., Onions, D. E., Sachs, D. H., Schuurman, H.-J., Fishman, J. A., Patience, C. (2004). Identification of Exogenous Forms of Human-Tropic Porcine Endogenous Retrovirus in Miniature Swine. J. Virol. 78: 2494-2501 [Abstract] [Full Text]  
• Sagara, J., Higuchi, T., Hattori, Y., Moriya, M., Sarvotham, H., Shima, H., Shirato, H., Kikuchi, K., Taniguchi, S. (2003). Scapinin, a Putative Protein Phosphatase-1 Regulatory Subunit Associated with the Nuclear Nonchromatin Structure. J. Biol. Chem. 278: 45611-45619 [Abstract] [Full Text]  
• Barseguian, K., Lutterbach, B., Hiebert, S. W., Nickerson, J., Lian, J. B., Stein, J. L., van Wijnen, A. J., Stein, G. S. (2002). Multiple subnuclear targeting signals of the leukemia-related AML1/ETO and ETO repressor proteins. Proc. Natl. Acad. Sci. USA 99: 15434-15439 [Abstract] [Full Text]  
• Tao, H., Szeszel-Fedorowicz, W., Amir-Ahmady, B., Gibson, M. A., Stabile, L. P., Salati, L. M. (2002). Inhibition of the Splicing of Glucose-6-phosphate Dehydrogenase Precursor mRNA by Polyunsaturated Fatty Acids. J. Biol. Chem. 277: 31270-31278 [Abstract] [Full Text]  
• Martens, J. H. A., Verlaan, M., Kalkhoven, E., Dorsman, J. C., Zantema, A. (2002). Scaffold/Matrix Attachment Region Elements Interact with a p300-Scaffold Attachment Factor A Complex and Are Bound by Acetylated Nucleosomes. Mol. Cell. Biol. 22: 2598-2606 [Abstract] [Full Text]  
• Kegel, K. B., Meloni, A. R., Yi, Y., Kim, Y. J., Doyle, E., Cuiffo, B. G., Sapp, E., Wang, Y., Qin, Z.-H., Chen, J. D., Nevins, J. R., Aronin, N., DiFiglia, M. (2002). Huntingtin Is Present in the Nucleus, Interacts with the Transcriptional Corepressor C-terminal Binding Protein, and Represses Transcription. J. Biol. Chem. 277: 7466-7476 [Abstract] [Full Text]  
• Didichenko, S. A., Thelen, M. (2001). Phosphatidylinositol 3-Kinase C2alpha Contains a Nuclear Localization Sequence and Associates with Nuclear Speckles. J. Biol. Chem. 276: 48135-48142 [Abstract] [Full Text]  
• Shopland, L. S., Byron, M., Stein, J. L., Lian, J. B., Stein, G. S., Lawrence, J. B. (2001). Replication-dependent Histone Gene Expression Is Related to Cajal Body (CB) Association but Does Not Require Sustained CB Contact. Mol. Biol. Cell 12: 565-576 [Abstract] [Full Text]  
• Shoeman, R. L., Hüttermann, C., Hartig, R., Traub, P. (2001). Amino-terminal Polypeptides of Vimentin Are Responsible for the Changes in Nuclear Architecture Associated with Human Immunodeficiency Virus Type 1 Protease Activity in Tissue Culture Cells. Mol. Biol. Cell 12: 143-154 [Abstract] [Full Text]  
• Smith, K. P., Lawrence, J. B. (2000). Interactions of U2 Gene Loci and Their Nuclear Transcripts with Cajal (Coiled) Bodies: Evidence for PreU2 within Cajal Bodies. Mol. Biol. Cell 11: 2987-2998 [Abstract] [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]  
• Tan, J.-h., Wooley, J. C., LeStourgeon, W. M. (2000). Nuclear Matrix-like Filaments and Fibrogranular Complexes Form through the Rearrangement of Specific Nuclear Ribonucleoproteins. Mol. Biol. Cell 11: 1547-1554 [Abstract] [Full Text]  
• Berube, N. G., Smeenk, C. A., Picketts, D. J. (2000). Cell cycle-dependent phosphorylation of the ATRX protein correlates with changes in nuclear matrix and chromatin association. Hum Mol Genet 9: 539-547 [Abstract] [Full Text]  
• Pederson, T. (2000). Half a Century of "The Nuclear Matrix". Mol. Biol. Cell 11: 799-805 [Abstract] [Full Text]  
• Miralles, F., Ofverstedt, L.-G., Sabri, N., Aissouni, Y., Hellman, U., Skoglund, U., Visa, N. (2000). Electron Tomography Reveals Posttranscriptional Binding of Pre-Mrnps to Specific Fibers in the Nucleoplasm. JCB 148: 271-282 [Abstract] [Full Text]  
• Chiodi, I, Biggiogera, M, Denegri, M, Corioni, M, Weighardt, F, Cobianchi, F, Riva, S, Biamonti, G (2000). Structure and dynamics of hnRNP-labelled nuclear bodies induced by stress treatments. J. Cell Sci. 113: 4043-4053 [Abstract]  
• Carvalho, T., Almeida, F., Calapez, A., Lafarga, M., Berciano, M. T., Carmo-Fonseca, M. (1999). The Spinal Muscular Atrophy Disease Gene Product, Smn: A Link between Snrnp Biogenesis and the Cajal (Coiled) Body. JCB 147: 715-728 [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]  
• Jolly, C., Usson, Y., Morimoto, R. I. (1999). Rapid and reversible relocalization of heat shock factor 1 within seconds to nuclear stress granules. Proc. Natl. Acad. Sci. USA 96: 6769-6774 [Abstract] [Full Text]  
• Wan, K. M., Nickerson, J. A., Krockmalnic, G., Penman, S. (1999). The nuclear matrix prepared by amine modification. Proc. Natl. Acad. Sci. USA 96: 933-938 [Abstract] [Full Text]  
• Gallina, A., Simoncini, L., Garbelli, S., Percivalle, E., Pedrali-Noy, G., Lee, K. S., Erikson, R. L., Plachter, B., Gerna, G., Milanesi, G. (1999). Polo-Like Kinase 1 as a Target for Human Cytomegalovirus pp65 Lower Matrix Protein. J. Virol. 73: 1468-1478 [Abstract] [Full Text]  
• Martini, E., Roche, D. M.J., Marheineke, K., Verreault, A., Almouzni, G. (1998). Recruitment of Phosphorylated Chromatin Assembly Factor 1 to Chromatin after UV Irradiation of Human Cells. JCB 143: 563-575 [Abstract] [Full Text]  
• Huang, S., Deerinck, T. J., Ellisman, M. H., Spector, D. L. (1998). The Perinucleolar Compartment and Transcription. JCB 143: 35-47 [Abstract] [Full Text]  
• Almeida, F., Saffrich, R., Ansorge, W., Carmo-Fonseca, M. (1998). Microinjection of Anti-coilin Antibodies Affects the Structure of Coiled Bodies. JCB 142: 899-912 [Abstract] [Full Text]  
• Clemson, C. M., Chow, J. C., Brown, C. J., Lawrence, J. B. (1998). Stabilization and Localization of Xist RNA are Controlled by Separate Mechanisms and are Not Sufficient for X Inactivation. JCB 142: 13-23 [Abstract] [Full Text]  
• Lorenz, P., Baker, B. F., Bennett, C. F., Spector, D. L. (1998). Phosphorothioate Antisense Oligonucleotides Induce the Formation of Nuclear Bodies. Mol. Biol. Cell 9: 1007-1023 [Abstract] [Full Text]  
• Van Hooser, A, Goodrich, D., Allis, C., Brinkley, B., Mancini, M. (1998). Histone H3 phosphorylation is required for the initiation, but not maintenance, of mammalian chromosome condensation. J. Cell Sci. 111: 3497-3506 [Abstract]  
• Choi, J., van Wijnen, A., Aslam, F, Leszyk, J., Stein, J., Stein, G., Lian, J., Penman, S (1998). Developmental association of the beta-galactoside-binding protein galectin-1 with the nuclear matrix of rat calvarial osteoblasts. J. Cell Sci. 111: 3035-3043 [Abstract]  
• Bridger, J., Herrmann, H, Munkel, C, Lichter, P (1998). Identification of an interchromosomal compartment by polymerization of nuclear-targeted vimentin. J. Cell Sci. 111: 1241-1253 [Abstract]  
• Sternsdorf, T., Jensen, K., Zuchner, D., Will, H. (1997). Cellular Localization, Expression, and Structure of the Nuclear Dot Protein 52. JCB 138: 435-448 [Abstract] [Full Text]  
• Seksek, O., Biwersi, J., Verkman, A.S. (1997). Translational Diffusion of Macromolecule-sized Solutes in Cytoplasm and Nucleus. JCB 138: 131-142 [Abstract] [Full Text]  
• Abney, J. R., Cutler, B., Fillbach, M. L., Axelrod, D., Scalettar, B. A. (1997). Chromatin Dynamics in Interphase Nuclei and Its Implications for Nuclear Structure. JCB 137: 1459-1468 [Abstract] [Full Text]  
• Gama-Carvalho, M., Krauss, R. D., Chiang, L., Valcarcel, J., Green, M. R., Carmo-Fonseca, M. (1997). Targeting of U2AF65 to Sites of Active Splicing in the Nucleus. JCB 137: 975-987 [Abstract] [Full Text]  
• Nickerson, J. A., Krockmalnic, G., Wan, K. M., Penman, S. (1997). The nuclear matrix revealed by eluting chromatin from a cross-linked nucleus. Proc. Natl. Acad. Sci. USA 94: 4446-4450 [Abstract] [Full Text]  
• Krauss, S. W., Larabell, C. A., Lockett, S., Gascard, P., Penman, S., Mohandas, N., Chasis, J. A. (1997). Structural Protein 4.1 in the Nucleus of Human Cells: Dynamic Rearrangements during Cell Division. JCB 137: 275-289 [Abstract] [Full Text]  
• McCaffery, J. D., Gapany, M., Faust, R. A., Davis, A. T., Adams, G. L., Ahmed, K. (1997). Nuclear Matrix Proteins as Malignant Markers in Squamous Cell Carcinoma of the Head and Neck. Arch Otolaryngol Head Neck Surg 123: 283-288 [Abstract]  
• Shimada, K, Harata, M, Mizuno, S (1997). A nuclear matrix-associated high molecular mass nuclear antigen, HMNA, of chicken and marked decrease of its immunoreactivity during the progression of S phase. J. Cell Sci. 110: 3031-3041 [Abstract]  
• Zimowska, G, Aris, J., Paddy, M. (1997). A Drosophila Tpr protein homolog is localized both in the extrachromosomal channel network and to nuclear pore complexes. J. Cell Sci. 110: 927-944 [Abstract]  
• Panning, B, Jaenisch, R (1996). DNA hypomethylation can activate Xist expression and silence X-linked genes.. Genes Dev. 10: 1991-2002 [Abstract]  
• Zhang, C, Jenkins, H, Goldberg, M., Allen, T., Hutchison, C. (1996). Nuclear lamina and nuclear matrix organization in sperm pronuclei assembled in Xenopus egg extract. J. Cell Sci. 109: 2275-2286 [Abstract]  
• van Steensel, B, Brink, M, van der Meulen, K, van Binnendijk, E., Wansink, D., de Jong, L, de Kloet, E., van Driel, R (1995). Localization of the glucocorticoid receptor in discrete clusters in the cell nucleus. J. Cell Sci. 108: 3003-3011 [Abstract]  
• Dirks, R., Daniel, K., Raap, A. (1995). RNAs radiate from gene to cytoplasm as revealed by fluorescence in situ hybridization. J. Cell Sci. 108: 2565-2572 [Abstract]  
• Diakonova, M, Payrastre, B, van Velzen, A., Hage, W., van Bergen en Henegouwen, P., Boonstra, J, Cremers, F., Humbel, B. (1995). Epidermal growth factor induces rapid and transient association of phospholipase C-gamma 1 with EGF-receptor and filamentous actin at membrane ruffles of A431 cells. J. Cell Sci. 108: 2499-2509 [Abstract]  
• Bisotto, S, Lauriault, P, Duval, M, Vincent, M (1995). Colocalization of a high molecular mass phosphoprotein of the nuclear matrix (p255) with spliceosomes. J. Cell Sci. 108: 1873-1882 [Abstract]  
• Hozak, P, Sasseville, A., Raymond, Y, Cook, P. (1995). Lamin proteins form an internal nucleoskeleton as well as a peripheral lamina in human cells. J. Cell Sci. 108: 635-644 [Abstract]  
• Hozak, P, Jackson, D., Cook, P. (1994). Replication factories and nuclear bodies: the ultrastructural characterization of replication sites during the cell cycle. J. Cell Sci. 107: 2191-2202 [Abstract]  
• Hozak, P, Cook, P., Schofer, C, Mosgoller, W, Wachtler, F (1994). Site of transcription of ribosomal RNA and intranucleolar structure in HeLa cells. J. Cell Sci. 107: 639-648 [Abstract]  
• Xing, Y, Johnson, C., Dobner, P., Lawrence, J. (1993). Higher level organization of individual gene transcription and RNA splicing. Science 259: 1326-1330 [Abstract]  
• Blencowe, B., Carmo-Fonseca, M, Behrens, S., Luhrmann, R, Lamond, A. (1993). Interaction of the human autoantigen p150 with splicing snRNPs. J. Cell Sci. 105: 685-697 [Abstract]  
• Lawrence, J.B., Carter, K.C., Xing, X. (1993). Probing Functional Organization within the Nucleus: Is Genome Structure Integrated with RNA Metabolism?. Cold Spring Harb Symp Quant Biol 58: 807-818 [Abstract]  
• Nuovo, G J, Gorgone, G A, MacConnell, P, Margiotta, M, Gorevic, P D (1992). In situ localization of PCR-amplified human and viral cDNAs.. Genome Res 2: 117-123 [Abstract]  
• Sharp, P. (1987). Splicing of messenger RNA precursors. Science 235: 766-771 [Abstract]  
• Amir-Ahmady, B., Salati, L. M. (2001). Regulation of the Processing of Glucose-6-phosphate Dehydrogenase mRNA by Nutritional Status. J. Biol. Chem. 276: 10514-10523 [Abstract] [Full Text]  
• Akileswaran, L., Taraska, J. W., Sayer, J. A., Gettemy, J. M., Coghlan, V. M. (2001). A-kinase-anchoring Protein AKAP95 Is Targeted to the Nuclear Matrix and Associates with p68 RNA Helicase. J. Biol. Chem. 276: 17448-17454 [Abstract] [Full Text]  

Home | Help | Feedback | Subscriptions | Archive | Search | Table of Contents