Spector, D. L.

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Nuclear domainsDavid L. SpectorCold Spring Harbor Laboratory, One BungtownRoad, Cold Spring Harbor, NY 11724, USA(e-mail: spector@cshl.org)Journal of Cell Science 114, 2891-2893 (2001)© The Company of Biologists LtdThe mammalian cell nucleus is amembrane-bound organelle that containsthe machinery essential for geneexpression. Although early studiessuggested that little organization existswithin this compartment, morecontemporary studies have identified anincreasing number of specializeddomains or subnuclear organelles withinthe nucleus (Lamond and Earnshaw,1998; Spector, 1993). In some cases,these domains have been shown to bedynamic structures and, in addition,rapid protein exchange occurs betweenmany of the domains and thenucleoplasm (Misteli, 2001). Anextensive effort is currently underway bynumerous laboratories to determine thebiological function(s) associated witheach domain. The accompanying posterpresents an overview of commonlyobserved nuclear domains.The nucleus is bounded by a nuclearenvelope, a double-membrane structure,of which the outer membrane iscontiguous with the rough endoplasmicreticulum and is often studded withribosomes. The inner and outer nuclearmembranes are fused together in places,forming nuclear pores that serve in thetransit of materials between the nucleusand cytoplasm (Stoffler et al., 1999). Thenuclear pore complex has been shown tohave a remarkable substructure, in whicha basket extends into the nucleoplasm.The peripheral nuclear lamina liesinside the nuclear envelope and iscomposed of lamins A/C and B and isthought to play a role in regulatingnuclear envelope structure andanchoring interphase chromatin at thenuclear periphery. Internal patches oflamin protein are also present in thenucleoplasm (Moir et al., 2000). Thecartoon depicts much of the nuclearenvelope/peripheral lamina astransparent, so that internal structurescan be more easily observed.Within the nucleoplasm, the chromo-somes are arranged into chromosometerritories, and active genes are thoughtto reside throughout the surface of theCELL SCIENCE AT A GLANCE 2891(See poster insert)2892loosely packed territories (Cremer et al.,2000). Homologues do not appear to bepaired in interphase mammalian nuclei.In some cell types, a band ofheterochromatin (inactive chromatin)is observed just internal to andassociated with the nuclear lamina. Inaddition, varying amounts ofheterochromatin are also observed inmore internal nuclear regions. PcGbodies containing polycomb groupproteins (i.e. RING1, BMI1 and hPc2)have been observed associated withpericentromeric heterochromatin (Saurinet al., 1998). These domains vary innumber (two to several hundred), size(0.2-1.5 m m) and protein composition. Itis currently unclear whether thesedomains are storage compartments or aredirectly involved in silencing.Pre-mRNA splicing factors arelocalized in a pattern of 25-50 nuclearspeckles as well as being diffuselydistributed throughout the nucleoplasm(Spector, 1993). Many of the largerspeckles correspond to interchromatingranule clusters (IGCs). These clustersmeasure 0.8-1.8 m m in diameter and arecomposed of 20-25-nm diameterparticles that appear connected inplaces. IGCs have been proposed to beinvolved in the assembly and/ormodification of pre-mRNA splicingfactors. Nuclear speckles are dynamicstructures, and factors are recruitedfrom them to sites of transcription(perichromatin fibrils). Transcriptionsites are observed throughout thenucleoplasm, including on theperiphery of IGCs, as several thousandfoci. In addition to being diffuselydistributed, several transcription factorshave also been shown to be con-centrated in one to three compartmentstermed OPT (Oct1/PTF/transcription)domains. These domains are 1.0-1.5m m in diameter and also contain nascenttranscripts as well as other transcriptionfactors, but they contain few, if any,factors involved in RNA processing(Grande et al., 1997; Pombo et al.,1998). The OPT domain appears in G1phase, when it often resides next tonucleoli, and it disappears during Sphase. Its function is unknown.In many cell types, pre-mRNA splicingfactors are also localized in 1-10 Cajalbodies, previously called Coiled Bodies(Gall, 2000). These dynamic nuclearbodies are 0.2-1.0 m m in diameter andare thought to play a role in snRNPbiogenesis and in the trafficking ofsnRNPs and snoRNPs. SpliceosomalU1, U2, U4/U6 and U5 snRNPs, as wellas the U7 snRNP involved in histone 3 ¢ -end processing, and U3 and U8 snoRNPsinvolved in processing of pre-rRNA, alllocalize to this structure. It has beenproposed that these factors movethrough the Cajal body en route tonuclear speckles (snRNPs) or nucleoli(snoRNPs). In addition, the Cajal bodyhas been shown to associate with histoneloci as well as U1, U2 and U3 geneclusters (Matera, 1999).Gems (gemini of Cajal bodies) are foundin the nucleoplasm and are coincidentwith or adjacent to Cajal bodies,depending upon the cell line examined,and they have been characterized by thepresence of the survival of motorneurons gene product (SMN) and anassociated factor, Gemin2 (Matera,1999). The cytoplasmic pool of SMNand Gemin2 has been implicated in theassembly of snRNPs, and the nuclearpool may play an additional role insnRNP maturation. Interestingly, spinalmuscular atrophy, a motor neurondegenerative disease, results fromreduced levels of, or a mutation in, theSMN protein.Several factors specifically involved inthe cleavage and polyadenylation stepsof pre-mRNA processing (e.g. CstF andCPSF) have a diffuse distribution patternin the nucleus and in addition areconcentrated in 1-4 foci, each 0.3-1.0 m min diameter, called cleavage bodies(Schul et al., 1996). These structureseither overlap with or are localizedadjacent to Cajal bodies. The subset ofcleavage bodies that do not overlap withCajal bodies contain newly synthesizedRNA.The Nucleolus is the site of rRNAsynthesis, rRNA processing, andassembly of ribosomal subunits(Spector, 1993) and is perhaps the mostobvious internal nuclear compartment.Most mamalian cells contain 1-5nucleoli, each 0.5-5.0 m m in diameter.The nucleolus is differentiated into threeclearly identifiable regions. The fibrillarcenters (shown as green ovals within thenucleolus) are regions that are thought tobe the interphase equivalent ofnucleolar-organizing regions (NORs) ofchromosomes. Human cells containapproximately 250 copies of rDNAlocated at NORs on five different pairsof chromosomes. Transcription andprocessing of rRNA is thought to occurwithin the dense fibrillar component(shown as a blue reticulum), a regionthat surrounds and in some cases extendsbetween the fibrillar centers. Thegranular region (shown as greengranules) of the nucleolus is made up ofpre-ribosomal particles at differentstages of maturation, as well as large andsmall ribosomal subunits.The perinucleolar compartment(PNC) and the SAM68 nuclear body(Huang, 2000) have been identified asunique structures that are associatedwith the surface of nucleoli and arethought to play a role in RNAmetabolism. They range in size from0.25-1.0 m m in diameter, and 1-10 areobserved per nucleus. The PNC containsa series of small RNAs transcribed byRNA polymerase III and several RNA-binding proteins, including poly-pyrimidine-tract-binding (PTB) protein.SAM68 nuclear bodies containmembers of a group of RNA-bindingproteins that contain a GSG domain,also called the STAR (signaltransduction and activation of RNA)domain, which is a 100-residuesequence highly homologous to the KHdomain found in hnRNP K. Althoughthe functions of the PNC and SAM68nuclear bodies are unknown, both ofthese structures are predominantlyfound in cancer cells, and they are rarelyobserved in primary cells.PML bodies (Maul et al., 2000) vary insize from 0.3 m m to 1.0 m m in diameter,and a typical mammalian nucleuscontains 10-30 of these structures. PMLbodies have also been called ND10,PODs (PML oncogenic domains) and Krbodies. In addition to the PML protein,several other proteins, including Sp100,SUMO1, HAUSP and CBP, have beenlocalized to this nuclear domain inaddition to being diffusely distributed inthe nucleoplasm. PML bodies have beensuggested to play a role in aspects oftranscriptional regulation and appear tobe targets of viral infection.JOURNAL OF CELL SCIENCE 114 (16)Interestingly, individuals suffering fromacute promyelocytic leukemia (APL)have a t(15,17) translocation, in whichthe the PML gene is fused to the genethat encodes the a -retinoic acid receptor,which results in the production of afusion protein. Cells from theseindividuals exhibit a break-up of PMLbodies into a large number of smallerdomains, which are scattered throughoutthe nucleoplasm. Treatment withretinoic acid, which results in theseindividuals going into remission, alsoresults in a reformation of typical PMLbodies.In addition to the above domainsgenerally observed in mammaliannuclei, other domains that are specific tocell type or physiological state have alsobeen reported. For example, GATA-1nuclear bodies containing GATAtranscription factors have been observedin murine haemopoietic cells (Elefantyet al., 1996). However, these domainsare not active in transcription. HSF1foci containing the transcription factor,heat shock factor 1, have been observedin nuclei of cells that have beensubjected to heat shock, however; thesedomains do not coincide with HSP70 orHSP90 transcription sites (Jolly et al.,1997).The above text provides an expandedlegend to the accompanying poster; it isnot meant to serve as a review of primaryresearch papers, and as such much of theprimary literature has not been citedhere. Readers are encouraged to accessthe cited reviews in order to locate theprimary research papers on particularnuclear bodies. I thank Jim Duffy for hisoutstanding artistic skills in developingthe cartoon, and the followingindividuals who providedimmunofluorescent images for thisposter: Mark Frey and Greg Matera(Cajal body and Gem), Paul Mintz (RNApolymerase II transcription factor,nucleoli, peripheral nuclear lamina,perinucleolar compartment, PML body,nuclear speckles), Ana Pombo (OPTdomain), Stéphane Richard (Sam68nuclear body), Thomas Ried and EvelinSchröck (chromosome territory). Inaddition, I thank Edith Heard, GregMatera and members of my laboratoryfor their insight and useful discussions.Research in my laboratory is funded byNIH/NIGMS 42694-12.ReferencesCremer, T., Kreth, G., Koester, H., Fink, R. H.,Heintzmann, R., Cremer, M., Solovei, I., Zink,D. and Cremer, C. (2000). Chromosometerritories, interchromatin domain compartment,and nuclear matrix: an integrated view of thefunctional nuclear architecture. Crit. Rev.Eukaryotic Gene Expr. 10, 179-212.Elefanty, A. G., Antoniou, M., Custodio, N.,Carmo-Fonseca, M. and Grosveld, F. G. (1996).GATA transcription factors associate with a novelclass of nuclear bodies in erythroblasts andmegakaryocytes. EMBO J. 15, 319-333.Gall, J. G. (2000). Cajal bodies: the first 100 years.Annu. Rev. Cell Dev. Biol. 16, 273-300.Grande, M. A., van der Kraan, I., de Jong, L.and van Driel, R. (1997). Nuclear distribution oftranscription factors in relation to sites oftranscription and RNA polymerase II. J. Cell Sci.110, 1781-1791.Huang, S. (2000). Review: perinucleolarstructures. J. Struct. Biol. 129, 233-240.Jolly, C., Morimoto, R., Robert-Nicoud, M. andVourc’h, C. (1997). HSF1 transcription factorconcentrates in nuclear foci during heat shock:relationship with transcription sites. J. Cell Sci.110, 2935-2941.Lamond, A. I. and Earnshaw, W. C. (1998).Structure and function in the nucleus. Science 280,547-553.Matera, A. G. (1999). Nuclear bodies:multifaceted subdomains of the interchromatinspace. Trends Cell Biol. 9, 302-309.Maul, G. G., Negorev, D., Bell, P. and Ishov, A.M. (2000). Review: properties and assemblymechanisms of ND10, PML bodies, or PODs. J.Struct. Biol. 129, 278-287.Misteli, T. (2001). Protein dynamics: implicationsfor nuclear architecture and gene expression.Science 291, 843-847.Moir, R. D., Yoon, M., Khuon, S. and Goldman,R. D. (2000). Nuclear lamins A and B1: differentpathways of assembly during nuclear envelopeformation in living cells. J. Cell Biol. 151, 1155-1168.Pombo, A., Cuello, P., Schul, W., Yoon, J.-B.,Roeder, R. G., Cook, P. R. and Murphy, S.(1998). Regional and temporal specialization in thenucleus: a transcriptionally-active nuclear domainrich in PTE, Oct1 and PIKA antigens associateswith specific chromosomes early in the cell cycle.EMBO J. 17, 1768-1778.Saurin, A. J., Shiels, C., Williamson, J., Satijn,D. P., Otte, A. P., Sheer, D. and Freemont, P. S.(1998). The human polycomb group complexassociates with pericentromeric heterochromatin toform 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 andCPSF 100 kDa are concentrated in nucleardomains closely associated with coiled bodies andnewly synthesized RNA. EMBO J. 15, 2883-2892.Spector, D. L. (1993). Macromolecular domainswithin the cell nucleus. Annu. Rev. Cell Biol. 9,265-315.Stoffler, D., Fahrenkrog, B. and Aebi, U. (1999).The nuclear pore complex: from moleculararchitecture to functional dynamics. Curr. Opin.Cell Biol. 11, 391-401.CELL SCIENCE AT A GLANCE 2893Cell Science at a Glance on the WebElectronic copies of the full-size posterinsert are available in the online version ofthis article (see www.biologists.com/jcs).Files in several formats are provided andmay be downloaded for use as slides.Year 2001 Travelling FellowshipsJCS offers fellowships of up to US$4000 to graduate students and post-docs wishing to make collaborative visits to otherlaboratories. These are designed to cover the cost of travel and other expenses, and there is no restriction on nationality. Applicantsshould be working in the field of cell biology and intend to visit a laboratory in another country. Each application is judged on theexcellence of the candidate, and the importance and innovative quality of the work to be done.Application forms can be downloaded from our Web site at jcs.biologists.org. Please send the completed application form, togetherwith a copy of your CV, an account of the work to be done and a breakdown of the costs involved, as well as letters ofrecommendation from the heads of the laboratory in which you currently work and the laboratory you hope to visit, to the ProductionEditor at the address below.Journal of Cell Science Editorial Office, The Company of Biologists Limited, Bidder Building, 140 Cowley Road, Cambridge CB4 0DL, UKDeadline: 30 September 2001

Nuclear domains

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