Snapshot: Cellular Bodies David L

Home , Cajal body, Nuclear bodies, Nuclear protein, Paraspeckle

SnapShot: Cellular Bodies David L. Spector Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA

Number/ Typical Size Marker Body Name Description Image Cell and Shape Protein

Involved in snRNP and snoRNP biogenesis and 0.1–2.0 µm; Cajal Body 0–6 Coilin posttranscriptional modification of newly assembled round spliceosomal snRNAs.

20S core Contains ubiquitin conjugates, the proteolytically active 0.2–1.2 µm; catalytic Clastosome 0–3 20S core and 19S regulatory complexes of the 26S irregular component of proteasome, and protein substrates of the proteasome. proteasome

Contains several factors involved in 3′ cleavage of mRNAs. 0.2–1.0 µm; Cleavage Body 1–4 CstF 64 kDa ?20% contain newly synthesized RNA. Some cleavage round bodies localize adjacent to Cajal and PML bodies.

Nuclear Contains proteins for pre-mRNA processing. Involved in Speckle or 0.8–1.8 µm; SC35, 25–50 the storage, assembly, and/or modification of pre-mRNA Interchromatin irregular SF2/ASF splicing factors. Granule Cluster

Induced by heat shock response. Associates with Nuclear Stress 0.3–3.0 µm; satellite III repeats on human chromosome 9q12 and 2–10 HSF1 Body irregular other pericentromeric regions; recruits various RNA- binding proteins.

Contains several transcription factors (Oct1/PTF) and 1.0–1.5 µm; OPT Domain 1–3 PTF RNA transcripts; predominant in late G1 cells. Often round

Nuclear Bodies localizes close to nucleolus.

0.5 µm; Contains several RNA-binding proteins and nuclear- Paraspeckle 10–20 p54nrb, PSP1 round retained CTN-RNA.

Cap on surface of nucleolus; found mainly in transformed Perinucleolar 0.3–1.0 µm; 1–4 hnRNPI (PTB) cells. Contains RNA pol III transcripts and several RNA- Compartment cap binding proteins.

0.3–1.0 µm; Suggested to play a role in aspects of transcriptional PML Body 10–30 PML round regulation and/or nuclear protein sequestration.

0.3–1.0 µm; Contains silencing proteins associated with Polycomb Polycomb Body 12–16 round/ Bmi1, Pc2 repressive complex 1; associates with heterochromatin. irregular

Forms when proteasome’s degradative capacity is 2.0–10.0 µm; exceeded. May sequester aggregated proteins/substrates Aggresome 1 CFTR irregular for lysosomal degradation via autophagy. Associated with microtubule organizing center; encaged by vimentin.

Contains decapping enzymes, a 5′-to-3′ exoribonuclease, Processing 0.1–1.0 µm; Ago1/2, 0–30 LSm proteins, and RNAi machinery components. Also Body (P Body) round GW182 involved in storage of miRNA-repressed mRNAs.

Formed upon stress. Contains “stalled” mRNAs, mRNA- 0.4–5.0 µm; binding proteins, translation initiation factors, and 40S Cytoplasmic Bodies Stress Granule 5–30 eIF3 irregular ribosomal subunits. mRNAs can shuttle between stress granules and P bodies.

See online version for references and acknowledgements. 1070 Cell 127, December 1, 2006 ©2006 Elsevier Inc. DOI 10.1016/j.cell.2006.11.026 SnapShot: Cellular Bodies David L. Spector Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA

For the purposes of this table, cellular bodies are defined as non-membrane-bound structures that can be visualized as independent domains by transmission electron microscopy without antibody labeling.

References

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Biamonte, G. (2004). Nuclear stress bodies: A heterochromatin affair? Nat. Rev. Mol. Cell Biol. 5, 493–498.

Fox, A.H., Lam, Y.W., Leung, A.K., Lyon, C.E., Andersen, J., Mann, M., and Lamond, A.I. (2002). Paraspeckles: A novel nuclear domain. Curr. Biol. 12, 13–25.

Grande, M.A., van der Kraan, I., de Jong, L., and van Driel, R. (1997). Nuclear distribution of transcription factors in relation to sites of transcription and RNA polymerase II. J. Cell Sci. 110, 1781–1791.

Huang, S. (2000). Review: perinucleolar structures. J. Struct. Biol. 129, 233–240.

Johnston, J.A., Ward, C.L., and Kopito, R.R. (1998). Aggresomes: A cellular response to misfolded proteins. J. Cell Biol. 143, 1883–1898.

Lafarga, M., Berciano, M.T., Pena, E., Mayo, I., Castano, J.G., Bohmann, D., Rodrigues, J.P., Tavanez, J.P., and Carmo-Fonseca, M. (2002). Clastosome: A subtype of nuclear body enriched in 19S and 20S proteasomes, ubiquitin, and protein substrates of proteasome. Mol. Biol. Cell 13, 2771–2782.

Lamond, A.I., and Spector, D.L. (2003). Nuclear speckles: A model for nuclear organelles. Nat. Rev. Mol. Cell Biol. 4, 605–612.

Matera, A.G., and Shpargel, K.B. (2006). Pumping RNA: nuclear bodybuilding along the RNP pipeline. Curr. Opin. Cell Biol. 18, 317–324.

Maul, G.G., Negorev, D., Bell, P., and Ishov, A.M. (2000). Review: Properties and assembly mechanisms of ND10, PML bodies, or PODs. J. Struct. Biol. 129, 278–287.

Pombo, A., Cuello, P., Schul, W., Yoon, J.-B., Roeder, R.G., Cook, P.R., and Murphy, S. (1998). Regional and temporal specialization in the nucleus: A transcriptionally- active nuclear domain rich in PTE, Oct1 and PIKA antigens associates with specific chromosomes early in the cell cycle. EMBO J. 17, 1768–1778.

Prasanth, K.V., Prasanth, S.G., Xuan, Z., Hearn, S., Freier, S.M., Bennett, C.F., Zhang, M.Q., and Spector, D.L. (2005). Regulating gene expression through RNA nuclear retention. Cell 123, 249–263.

Saitoh, N., Spahr, C.S., Patterson, S.D., Bubulya, P., Neuwald, A.F., and Spector, D.L. (2004). Proteomic analysis of interchromatin granule clusters. Mol. Biol. Cell 15, 3876–3890.

Saurin, A.J., Shiels, C., Williamson, J., Satijn, D.P., Otte, A.P., Sheer, D., and Freemont, P.S. (1998). The human polycomb group complex associates with pericentromeric heterochromatin to form a novel nuclear domain. J. Cell Biol. 142, 887–898.

Schul, W., Groenhout, B., Koberna, K., Takagaki, Y., Jenny, A., Manders, E.M., Raska, I., van Driel, R., and de Jong, L. (1996). The RNA 3′ cleavage factors CstF 64 kDa and CPSF 100 kDa are concentrated in nuclear domains closely associated with coiled bodies and newly synthesized RNA. EMBO J. 15, 2883–2892.

Acknowledgments

I thank P. Bubulya, G. Matera, and members of my lab for helpful discussions and NIGMS for funding (42694, 71407). Many thanks to the following for providing images:

Aggresome (Ron Kopito, Stanford University) Cajal Body (Yi-Chun Maria Chen, Cold Spring Harbor Laboratory) Clastosome (Maria Carmo-Fonseca, Institute of Molecular Medicine, University of Lisbon) Cleavage Body (Lei Li and Roseline Godbout, University of Alberta, Canada) Nuclear Speckles (Paula Bubulya, Cold Spring Harbor Laboratory) Nuclear Stress Body (Giuseppe Biamonti, Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy) OPT Domain (Ana Pombo, MRC Clinical Sciences Centre, Imperial College, London, UK) Paraspeckles (Kannanganattu V. Prasanth, Cold Spring Harbor Laboratory) Perinucleolar Compartment (Sui Huang, Northwestern University, Feinberg School of Medicine, Chicago, Illinois) PML Bodies (Yi-Chun Maria Chen, Cold Spring Harbor Laboratory) Polycomb Bodies (Michael Hübner, Cold Spring Harbor Laboratory) Processing Bodies (Nancy Kedersha, Harvard Medical School, Brigham and Women’s Hospital) Stress Granules (Nancy Kedersha, Harvard Medical School, Brigham and Women’s Hospital)