The mammalian cell nucleus is a multifunctional, highly organized and complex compartment that contains structural and functional sub-domains (Figure 7).
Compartmentalization of the nucleus appears to be prerequisite for the organization of all the molecular machineries involved in activities such as replication, transcription, splicing, rRNA biosynthesis etc. Some of the subnuclear compartments are the nucleolus, promyelocytic leukemia protein (PML) bodies, Cajal or coiled bodies (CBs), Gemini of coiled bodies (gems), speckles and paraspeckles (Lamond and Sleeman, 2003; Platani and Lamond, 2004).
Figure 7. The cell nucleus (Spector, 2001). A cartoon of the cell nucleus with some of its most ‘popular’ subnuclear compartments like the nucleolus, Cajal bodies, PML bodies etc.
Nucleolus
(Boisvert et al., 2007; Sirri et al., 2008)
The nucleolus is probably the most well-studied compartment of the nucleus, and new information is continuously emerging regarding its roles in the cell. It is characterized as the ribosome factory of the cell, but also implicated in other functions such as the control of cell survival and proliferation. Mammalian cell nuclei contain from one to four nucleoli. These are present throughout the cell cycle, but, because of their dynamic nature, they reorganize in response to certain stimuli, like RNA Pol I or Pol II inhibition.
Interestingly, during RNA Pol II transcription inhibition, apart from their reorganization, nucleoli also attract various nucleoplasmic components to their vicinity, which form perinucleolar caps. Components of all of the below mentioned sub-nuclear structures move to the same or distinct perinucleolar caps in transcriptionally arrested cells (Shav-Tal et al., 2005). The function of these caps is not understood.
PML bodies
(Bernardi and Pandolfi, 2007)
PML bodies are focal nuclear structures present in most mammalian nuclei. They vary in number from 10 to 30 per nucleus, and their integrity depends on the PML protein, which is concentrated in these structures. Because PML bodies contain a large number of different molecules, they have been linked to many nuclear functions such as transcription, DNA repair, and apoptosis.
Cajal bodies
(Cioce and Lamond, 2005; Morris, 2008)
CBs were named after their discoverer Santiago Ramon y Cajal, who first reported them in 1903. They are small, round sub-nuclear compartments, often found in the vicinity of nucleoli and present in nuclei of cells that are transcriptionally highly active.
Their number depends on the cell type as well as on the stage of the cell cycle and varies from zero to ten per nucleus. A major constituent of CBs is p80 coilin, which also serves as a marker for these structures. CBs have been associated with several cellular functions, like stress response, aging and transcription, but their main role appears to be in snRNP and snoRNP biogenesis and trafficking.
Gems
(Liu and Dreyfuss, 1996)
Gems are characterized by the presence of the Survival of motor neuron (SMN) protein, as well as several gemins. These structures are often structurally associated with CBs, hence their name “gemini of CBs”. They are also very similar in terms of size and number to CBs and in some cases the two structures colocalise. Their function remains obscure. Although they do not contain any snRNPs, their close relationship to CBs and the presence of SMN, a protein involved in snRNP biogenesis, implies a role for them in this process.
Speckles
(Lamond and Spector, 2003)
Mammalian cells contain 10-30 splicing speckles, which are irregular, but discrete domains that correspond to interchromatin granule clusters (IGCs). They can be visualized by an antibody against splicing factor SC35, which has been widely used as
a marker for speckles (Fu and Maniatis, 1990). Since they are devoid of pre-mRNA, it was thought until recently that splicing speckles (also termed SC35 domains) were storage sites for the majority of snRNPs and non-snRNP splicing factors that, in addition to being diffusely distributed throughout the nucleoplasm, concentrate in these domains in nuclei of interphase cells when they are not forming spliceosomes.
However, a recent report has shown that splicing proteins move constantly by Brownian diffusion in the nucleus and collide randomly, transiently and independently of splicing activity with pre-mRNAs and speckle components (Rino et al., 2007). These authors suggested that the concentration of splicing proteins in speckles does not indicate storage, but is a result of a higher number of binding sites available for splicing factors inside the speckles as compared to the nucleoplasm.
Paraspeckles
(Bond and Fox, 2009)
Splicing speckles are found closely associated with paraspeckles, a relatively novel subnuclear compartment (Fox et al., 2002). Paraspeckles are irregularly shaped structures scattered throughout the nucleoplasm and within the interchromatin space.
Mammalian cells contain 2-20 paraspeckles, the number varying depending on the cell cycle. Paraspeckles contain a marker protein, named paraspeckle protein 1 (PSP1), and to date only a few other proteins (PSP2, p54nrb, PSF, CFIm68 and RNA polymerase II) have been found associated with them.
The role of paraspeckles is not clear yet, but their protein content suggests that they are involved in transcriptional control and RNA metabolism. More specifically, PSP1 has been shown to concentrate in testis. It has been suggested that PSP1 regulates early mRNA processing in germ cells and assists in chromatin remodeling and nuclear shaping during spermatogenesis (Myojin et al., 2004). PSP2 is a steroid hormone receptor coactivator, implicated in transcription and RNA splicing (Auboeuf et al., 2004). The third component of paraspeckles, p54nrb, forms a dimer with PSP1 (Fox et al., 2005) and is involved in numerous nuclear events, including transcriptional regulation and splicing (Shav-Tal and Zipori, 2002). p54nrb also dimerises with polypyrimidine tract-binding protein (PTB)-associated splicing factor (PSF) (Peng et al., 2002), another paraspeckle resident. PSF is an RNA-binding component of the spliceosome, but also interacts with DNA and functions as transcriptional regulator (Shav-Tal and Zipori, 2002). Finally, the 68-kDa subunit of mammalian cleavage factor
Im (CFIm68) is an RNA-binding protein required for the first step in pre-mRNA 3’ end processing (Dettwiler et al., 2004).
In addition to their proposed role in transcriptional control and RNA metabolism, paraspeckles have also been implicated in nuclear retention of RNAs that undergo A to I RNA-editing (Prasanth et al., 2005). Furthermore, it has been reported recently that the non-coding (nc) RNAs Men-ε and Men-β are retained in paraspeckles and are essential structural units of these subnuclear structures. A link has therefore been established between paraspeckles and non-coding RNAs (Clemson et al., 2009;
Sasaki et al., 2009; Sunwoo et al., 2009).
As in the nucleus, concentrations of proteins with similar functions are also observed at distinct cytoplasmic sites. Some of these structures are processing (P) bodies, uridine-rich (U) bodies and stress granules (SG), the latter appearing only upon induction of stress.
Cytoplasmic Stress Granules (Anderson and Kedersha, 2008)
SGs are aggregates of proteins and untranslated mRNAs that form in the cytoplasm when cells are exposed to stress. Many functions have been proposed for these structures, such as protection of RNA from exposure to harmful agents, as temporary storage sites for mRNA, and as a decision-making compartment between translation and decay. Recent data however demonstrates that a wide variety of proteins with distinct functions accumulate in SGs (transcription and splicing factors, adhesion and signaling molecules, etc.), making their role even more obscure. The typical protein marker for this compartment is TIA-1 (T-cell-restricted intracellular antigen-1), which is also involved in splicing.