Ultrastructure of the Nucleus in Relation to Transcription and Splicing: Roles of Perichromatin Fibrils and Interchromatin Granules

By conventional electron microscopy, the formed elements of the nuclear interior include the nucleolus, chromatin, interchromatin granules, perichromatin granules, perichromatin fibrils, and various types of nuclear bodies (Figs. 1a-c). Of these structures, all have been reasonably well characterized structurally and functionally except for nuclear bodies. The most common types of nuclear bodies are simple nuclear bodies and coiled bodies (Figs. 1a,c). Since nuclear bodies are small in size (0.2-1.0 μm in diameter) and infrequent in number, they are often overlooked or simply not observed in any random thin section. The rat liver hepatocyte in Fig. 1b is a case in point. Historically, nuclear bodies are more prominent in hyperactive cells, they often occur in proximity to nucleoli (Fig. 1c), and sometimes they are observed to “bud off” from the nucleolar surface.

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Ultrastructural distribution of nuclear ribonucleoproteins as visualized by immunocytochemistry on thin sections.

The Journal of Cell Biology ◽

10.1083/jcb.98.1.358 ◽

1984 ◽

Vol 98 (1) ◽

pp. 358-363 ◽

Cited By ~ 159

Author(s):

S Fakan ◽

G Leser ◽

T E Martin

Keyword(s):

Protein A ◽

Nuclear Architecture ◽

Gold Complex ◽

Thin Sections ◽

Border Regions ◽

Core Proteins ◽

Interchromatin Granules ◽

Lowicryl K4m ◽

Perichromatin Fibrils

The ultrastructural distribution of nuclear ribonucleoproteins (RNP) has been investigated by incubation of thin sections of mouse or rat liver, embedded in Lowicryl K4M or prepared by cryoultramicrotomy, with antibodies specific for RNP. The antibodies were localized by means of a protein A-colloidal gold complex. Anti-small nuclear (sn)RNP antibodies, specific for determinants of the nucleoplasmic snRNP species containing U1, U2, U4, U5, and U6 RNAs, were found associated preferentially with perichromatin fibrils, interchromatin granules, and coiled bodies. This indicates an early association of snRNP with structural constituents containing newly synthesized heterogeneous nuclear RNA. It also suggests a possible structural role of some snRNPs in nuclear architecture. Antibodies against the core proteins of heterogeneous nuclear RNP particles associate preferentially with the border regions of condensed chromatin, and in particular with perichromatin fibrils and some perichromatin granules. These results are discussed in view of recent knowledge about the possible role of nucleoplasmic RNP-containing components in the functions of the cell nucleus.

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Subnuclear Localization and Dynamics of the Pre-mRNA 3′ End Processing Factor Mammalian Cleavage Factor I 68-kDa Subunit

Molecular Biology of the Cell ◽

10.1091/mbc.e06-09-0846 ◽

2007 ◽

Vol 18 (4) ◽

pp. 1282-1292 ◽

Cited By ~ 50

Author(s):

Stefano Cardinale ◽

Barbara Cisterna ◽

Paolo Bonetti ◽

Chiara Aringhieri ◽

Marco Biggiogera ◽

...

Keyword(s):

Rna Polymerase Ii ◽

Ultrastructural Level ◽

Essential Factor ◽

Processing Factor ◽

Nuclear Speckles ◽

Subnuclear Localization ◽

Factor I ◽

Active Transcription ◽

Interchromatin Granules ◽

Perichromatin Fibrils

Mammalian cleavage factor I (CF Im) is an essential factor that is required for the first step in pre-mRNA 3′ end processing. Here, we characterize CF Im68 subnuclear distribution and mobility. Fluorescence microscopy reveals that in addition to paraspeckles CF Im68 accumulates in structures that partially overlap with nuclear speckles. Analysis of synchronized cells shows that CF Im68 distribution in speckles and paraspeckles varies during the cell cycle. At an ultrastructural level, CF Im68 is associated with perichromatin fibrils, the sites of active transcription, and concentrates in interchromatin granules-associated zones. We show that CFIm68 colocalizes with bromouridine, RNA polymerase II, and the splicing factor SC35. On inhibition of transcription, endogenous CF Im68 no longer associates with perichromatin fibrils, but it can still be detected in interchromatin granules-associated zones. These observations support the idea that not only splicing but also 3′ end processing occurs cotranscriptionally. Finally, fluorescence recovery after photobleaching analysis reveals that the CF Im68 fraction associated with paraspeckles moves at a rate similar to the more dispersed molecules in the nucleoplasm, demonstrating the dynamic nature of this compartment. These findings suggest that paraspeckles are a functional compartment involved in RNA metabolism in the cell nucleus.

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Ribonucleoprotein components in liver cell nuclei as visualized by cryoultramicrotomy.

The Journal of Cell Biology ◽

10.1083/jcb.67.1.200 ◽

1975 ◽

Vol 67 (1) ◽

pp. 200-214 ◽

Cited By ~ 48

Author(s):

E Puvion ◽

W Bernhard

Keyword(s):

Cell Nuclei ◽

Glutaraldehyde Fixation ◽

Rat Hepatocyte ◽

Colloidal Iron ◽

Dna Structures ◽

Normal Rat ◽

Ultrathin Frozen Sections ◽

Interchromatin Granules ◽

Perichromatin Granules ◽

Perichromatin Fibrils

The interphase nucleus of the normal rat hepatocyte has been studied in ultrathin frozen sections after glutaraldehyde fixation and the modification of various staining procedures known to be specific for DNA structures (Moyne's thallium stain, Gautier's osmium-ammine) or preferential for RNP carriers and basic proteins (regressive stains based on the use of EDTA or citrate, negatively charged colloidal iron). The results are comparable to those obtained after classical dehydration and embedding. Particular attention has been paid to the nucleolus and extranucleolar RNP components, such as perichromatin fibrils and granules, as well as interchromatin granules. A striking observation was the uneven size and the strongly increased number of perichromatin granules, and the appearance of a contiguous interchromatin net, containing nucleoproteins. Cryoultramicrotomy without embedding appears to be very useful for the exploration of the nucleus in thick sections which remain sufficiently transparent even with the usual accelerating voltages.

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Nuclear RNA Is Extruded from Apoptotic Cells

Journal of Histochemistry & Cytochemistry ◽

10.1177/002215549804600903 ◽

1998 ◽

Vol 46 (9) ◽

pp. 999-1005 ◽

Cited By ~ 37

Author(s):

Marco Biggiogera ◽

Maria Grazia Bottone ◽

Carlo Pellicciari

Keyword(s):

Appreciable Amount ◽

Apoptotic Cells ◽

Spontaneous Apoptosis ◽

Systemic Autoimmune Diseases ◽

Nucleolar Material ◽

Nuclear Rna ◽

Interchromatin Granules ◽

Possible Cause ◽

Perichromatin Granules ◽

Perichromatin Fibrils

During spontaneous apoptosis of thymocytes there is extrusion of ribonucleoproteins (RNPs) from the cell. The aim of this investigation was to elucidate whether the RNP aggregates in apoptotic cells and bodies still contain RNA in an appreciable amount. We demonstrated by specific cytochemical techniques that the aggregates of nuclear RNPs extruded in the cytoplasm of spontaneously apoptotic thymocytes contain RNA in a sufficient amount to be detected cytochemically. These heterogeneous ectopic RNP-derived structures (HERDS) are formed by perichromatin fibrils, interchromatin granules, perichromatin granules, and nucleolar material. The RNA detected inside these clusters should therefore correspond to both mRNA and snRNA as well as to rRNA. We never observed DNA-contaning aggregates in the cytoplasm of apoptotic thymocytes. The presence of RNA in the HERDS that may be released from apoptotic cells suggests that the decrease in the amount of total RNA during apoptosis may be mostly linked to cellular extrusion rather than to degradation of RNA by RNase activities. Another interesting aspect of these results lies in the hypothesis of apoptosis as a possible cause for the presence of autoantibodies in the serum of patients with systemic autoimmune diseases.

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Organization of transcription and pre-mRNA splicing within the mammalian cell nucleus

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010014021x ◽

1995 ◽

Vol 53 ◽

pp. 768-769

Author(s):

D.L. Spector ◽

S. Huang ◽

S. Kaurin

Keyword(s):

Rna Polymerase Ii ◽

Cell Nucleus ◽

Functional Organization ◽

Mrna Splicing ◽

Splicing Factors ◽

Interchromatin Granule Clusters ◽

Interchromatin Granule ◽

Nuclear Regions ◽

Relationship Of ◽

Perichromatin Fibrils

We have been interested in the organization of RNA polymerase II transcription and pre-mRNA splicing within the cell nucleus. Several models have been proposed for the functional organization of RNA within the eukaryotic nucleus and for the relationship of this organization to the distribution of pre-mRNA splicing factors. One model suggests that RNAs which must be spliced are capable of recruiting splicing factors to the sites of transcription from storage and/or reassembly sites. When one examines the organization of splicing factors in the nucleus in comparison to the sites of chromatin it is clear that splicing factors are not localized in coincidence with heterochromatin (Fig. 1). Instead, they are distributed in a speckled pattern which is composed of both perichromatin fibrils and interchromatin granule clusters. The perichromatin fibrils are distributed on the periphery of heterochromatin and on the periphery of interchromatin granule clusters as well as being diffusely distributed throughout the nucleoplasm. These nuclear regions have been previously shown to represent initial sites of incorporation of 3H-uridine.

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Rearrangements of intranuclear structures involved in RNA processing in response to adenovirus infection

Journal of Cell Science ◽

10.1242/jcs.107.6.1457 ◽

1994 ◽

Vol 107 (6) ◽

pp. 1457-1468 ◽

Cited By ~ 2

Author(s):

F. Puvion-Dutilleul ◽

J.P. Bachellerie ◽

N. Visa ◽

E. Puvion

Keyword(s):

Rna Processing ◽

Rna Splicing ◽

Specific Binding ◽

Viral Rna ◽

Nuclear Transformation ◽

Adenovirus Infection ◽

Storage Site ◽

Single Stranded Dna ◽

Viral Genomes ◽

Interchromatin Granules

We have studied in HeLa cells at the electron microscope level the response to adenovirus infection of the RNA processing machinery. Components of the spliceosomes were localized by in situ hybridization with biotinylated U1 and U2 DNA probes and by immunolabeling with Y12 anti-Sm monoclonal antibody, whereas poly(A)+ RNAs were localized by specific binding of biotinylated poly(dT) probe. At early stages of nuclear transformation, the distribution of small nuclear RNPs was similar to that previously described in non-infected nuclei (Visa, N., Puvion-Dutilleul, F., Bachellerie, J.P. and Puvion, E., Eur. J. Cell Biol. 60, 308–321, 1993; Visa, N., Puvion-Dutilleul, F., Harper, F., Bachellerie, J. P. and Puvion, E., Exp. Cell Res. 208, 19–34, 1993). As the infection progresses, the large virus-induced inclusion body consists of a central storage site of functionally inactive viral genomes surrounded by a peripheral shell formed by clusters of interchromatin granules, compact rings and a fibrillogranular network in which are embedded the viral single-stranded DNA accumulation sites. Spliceosome components and poly(A)+ RNAs were then exclusively detected over the clusters of interchromatin granules and the fibrillogranular network whereas the viral single-stranded DNA accumulation sites and compact rings remained unlabeled, thus appearing to not be directly involved in splicing. Our data, therefore, suggest that the fibrillogranular network, in addition to being the site of viral transcription, is also a major site of viral RNA splicing. Like the clusters of interchromatin granules, which had been already involved in spliceosome assembly, they could also have a role in the sorting of viral spliced polyadenylated mRNAs before export to the cytoplasm. The compact rings, which contain non-polyadenylated viral RNA, might accumulate the non-used portions of the viral transcripts resulting from differential poly(A)+ site selection.

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Abscission Checkpoint Bodies Reveal a New Facet of Abscission Checkpoint Control

10.1101/2020.10.07.330290 ◽

2020 ◽

Author(s):

Lauren K. Williams ◽

Douglas R. Mackay ◽

Madeline A. Whitney ◽

Wesley I. Sundquist ◽

Katharine S. Ullman

Keyword(s):

Cell Types ◽

Aurora B ◽

Genomic Integrity ◽

Checkpoint Control ◽

Nuclear Speckles ◽

Aurora B Kinase ◽

Multiple Targets ◽

Membrane Fission ◽

Interchromatin Granules

AbstractThe abscission checkpoint regulates the ESCRT membrane fission machinery and thereby delays cytokinetic abscission to protect genomic integrity in response to residual mitotic errors. The checkpoint is maintained by Aurora B kinase, which phosphorylates multiple targets, including CHMP4C, a regulatory ESCRT-III subunit necessary for this checkpoint. We now report the discovery that cytoplasmic abscission checkpoint bodies (ACBs) containing phospho-Aurora B and tri-phospho-CHMP4C develop in telophase under an active checkpoint. ACBs are derived from Mitotic Interchromatin Granules (MIGs), transient mitotic structures whose components are housed in splicing-related nuclear speckles during interphase. ACB formation requires CHMP4C, and the ESCRT factor ALIX also contributes. ACB formation is conserved across cell types and under multiple circumstances that activate the checkpoint. Finally, ACBs retain a population of ALIX, and their presence correlates with delayed recruitment of ALIX to the midbody where it would normally promote abscission. Thus, a cytoplasmic mechanism helps regulate midbody machinery to delay abscission.

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Cytochemical study on the localization of interchromatin granules during the cell division

Acta Histochemica ◽

10.1016/s0065-1281(85)80034-9 ◽

1985 ◽

Vol 76 (1) ◽

pp. 49-55 ◽

Cited By ~ 1

Author(s):

Stefania Krzyżowska-Gruca ◽

Ewa Kulczycka ◽

Anna Zborek

Keyword(s):

Cell Division ◽

Cytochemical Study ◽

Interchromatin Granules

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INORGANIC CATIONS IN THE CELL NUCLEUS

The Journal of Cell Biology ◽

10.1083/jcb.53.2.483 ◽

1972 ◽

Vol 53 (2) ◽

pp. 483-493 ◽

Cited By ~ 16

Author(s):

Laura L. Tres ◽

A. L. Kierszenbaum ◽

C. J. Tandler

Keyword(s):

Meiotic Prophase ◽

Rna Synthesis ◽

Adult Mouse ◽

Divalent Cations ◽

Synthetic Activity ◽

Inorganic Cations ◽

Transcription Process ◽

Inorganic Cation ◽

Interchromatin Granules ◽

Potassium Pyroantimonate

Earlier reports indicated the presence of significant amounts of inorganic salts in the nucleus. In the present study the possibility that this might be related to the transcription process was tested on seminiferous epithelium of the adult mouse, using potassium pyroantimonate as a fixative. The results indicated that a correlation exists between the inorganic cations comprising the pyroantimonate-precipitable fraction and the RNA synthetic activity. During meiotic prophase an accumulation of cation-antimonate precipitates occurs dispersed through the middle pachytene nuclei, the stage in which RNA synthesis reaches a maximum. At other stages (zygotene to diplotene), where RNA synthesis falls to a low level, that pattern is not seen; cation-antimonate deposits are restricted to a few masses in areas apparently free of chromatin. The condensed sex chromosomes, the heterochromatin of the "basal knobs," the axial elements, and the synaptonemal complexes are devoid of antimonate deposits during the meiotic prophase. The Sertoli cells, active in RNA synthesis in both nucleoplasm and nucleolus, show cation-antimonate deposits at these sites. In the nucleoplasm some "patches" of precipitates appear coincident with clusters of interchromatin granules; in the nucleolus the inorganic cations are mainly located in the fibrillar and/or amorphous areas, whereas relatively few are shown by the granular component. The condensed chromatin bodies associated with the nucleolus were always free of antimonate precipitates. It is suggested that the observed sites of inorganic cation accumulation within the nucleus may at least partially indicate the presence of RNA polymerases, the activity of which is dependent on divalent cations.

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