Nuclear Domains and the Nuclear Matrix

Driel, Roel van; Wansink, Derick G.; Steensel, Bas van; Grande, M.A.; Schul, Wouter; Jong, Luitzen de

doi:10.1016/s0074-7696(08)61231-0

Cited by 68 publications

(59 citation statements)

References 264 publications

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“…are coupled tightly, and they occur together at or near discrete sites in the nucleoplasm (1)(2)(3)(4)(5). Initially, these sites seem to include mainly the relatively larger nuclear substructures such as the SC35 speckles (34)(35)(36). However, later studies investigating the sites of UTP incorporation and locations of RNA polymerase II suggested the following scenario.…”

Section: Discussionmentioning

confidence: 99%

Higher order arrangement of the eukaryotic nuclear bodies

Wang

Reddy

Shen

2002

Proc. Natl. Acad. Sci. U.S.A.

176

133

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The nuclei of eukaryotic cells consist of discrete substructures. These substructures include the nuclear bodies, which have been implicated in a number of biological processes such as transcription and splicing. However, for most nuclear bodies, the details of involvement in these processes in relation to their three-dimensional distributions in the nucleus are still unclear. Through the analysis of TDP, a protein functional in both transcriptional repression and alternative splicing, we have identified a new category of nuclear bodies within which the TDP molecules reside. Remarkably, the TDP bodies (TBs) colocalize or overlap with several different types of nuclear bodies previously suggested to function in transcription or splicing. Of these nuclear bodies, the Gemini of coiled bodies (GEM) seems to associate with TB through the interaction between survival motor neuron (SMN) protein and TDP. Furthermore, TB sometimes appears to be the bridge of two or more of these other nuclear bodies. Our data suggest the existence of a hierarchy and possibly functional arrangement of the nuclear bodies within the eukaryotic nuclei.nuclear structure ͉ splicing ͉ transcription

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Section: Discussionmentioning

confidence: 99%

Higher order arrangement of the eukaryotic nuclear bodies

Wang

Reddy

Shen

2002

Proc. Natl. Acad. Sci. U.S.A.

176

133

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“…Moreover, these investigations have demonstrated that perichromatin fibrils (PFs) are the in situ form of the nascent transcripts and further indicated a migration of a portion of PFs toward the interchromatin space while their RNA was undergoing processing (for reviews, see Fakan and Puvion, 1980;Puvion and Moyne, 1981). Furthermore, immunocytochemical (Fakan et al, 1984;Puvion et al, 1984;Spector et al, 1991) and in situ hybridization (Visa et al, 1993b) analyses strongly support the idea that splicing and polyadenylation of pre-mRNA also occur in association with PFs (for reviews, see Spector, 1993;Fakan, 1994;van Driel et al, 1995;Puvion and Puvion-Dutilleul, 1996). These observations were later confirmed by means of nonradioactive RNA-labeling methods and immunofluorescence microscopy (Jackson et al, 1993;Wansink et al, 1993;Fay et al, 1997).…”

Section: Introductionmentioning

confidence: 87%

Ultrastructural Analysis of Transcription and Splicing in the Cell Nucleus after Bromo-UTP Microinjection

Cmarko

Verschure

Martin

et al. 1999

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229

195

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In this study we demonstrate, at an ultrastructural level, the in situ distribution of heterogeneous nuclear RNA transcription sites after microinjection of 5-bromo-UTP (BrUTP) into the cytoplasm of living cells and subsequent postembedding immunoelectron microscopic visualization after different labeling periods. Moreover, immunocytochemical localization of several pre-mRNA transcription and processing factors has been carried out in the same cells. This high-resolution approach allowed us to reveal perichromatin regions as the most important sites of nucleoplasmic RNA transcription and the perichromatin fibrils (PFs) as in situ forms of nascent transcripts. Furthermore, we show that transcription takes place in a rather diffuse pattern, without notable local accumulation of transcription sites. RNA polymerase II, heterogeneous nuclear ribonucleoprotein (hnRNP) core proteins, general transcription factor TFIIH, poly(A) polymerase, splicing factor SC-35, and Sm complex of small nuclear ribonucleoproteins (snRNPs) are associated with PFs. This strongly supports the idea that PFs are also sites of major pre-mRNA processing events. The absence of nascent transcripts, RNA polymerase II, poly(A) polymerase, and hnRNPs within the clusters of interchromatin granules rules out the possibility that this domain plays a role in pre-mRNA transcription and polyadenylation; however, interchromatin granule-associated zones contain RNA polymerase II, TFIIH, and Sm complex of snRNPs and, after longer periods of BrUTP incubation, also Br-labeled RNA. Their role in nuclear functions still remains enigmatic. In the nucleolus, transcription sites occur in the dense fibrillar component. Our fine structural results show that PFs represent the major nucleoplasmic structural domain involved in active premRNA transcriptional and processing events.

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confidence: 99%

“…The chromosomes form chromosomal territories, each consisting of several more-or-less condensed and variable domains (1,2). The individual territories are separated by a delicate network of thin channels, the interchromosomal space (2)(3)(4). The active genes are usually situated in the periphery of the domains and deliver the transcription products into the channel system (5,6).…”

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confidence: 99%

Assembly and transport of a premessenger RNP particle

Daneholt

2001

Proc. Natl. Acad. Sci. U.S.A.

131

124

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Salivary gland cells in the larvae of the dipteran Chironomus tentans offer unique possibilities to visualize the assembly and nucleocytoplasmic transport of a specific transcription product. Each nucleus harbors four giant polytene chromosomes, whose transcription sites are expanded, or puffed. On chromosome IV, there are two puffs of exceptional size, Balbiani ring (BR) 1 and BR 2. A BR gene is 35-40 kb, contains four short introns, and encodes a 1-MDa salivary polypeptide. The BR transcript is packed with proteins into a ribonucleoprotein (RNP) fibril that is folded into a compact ring-like structure. The completed RNP particle is released into the nucleoplasm and transported to the nuclear pore, where the RNP fibril is gradually unfolded and passes through the pore. On the cytoplasmic side, the exiting extended RNP fibril becomes engaged in protein synthesis and the ensuing polysome is anchored to the endoplasmic reticulum. Several of the BR particle proteins have been characterized, and their fate during the assembly and transport of the BR particle has been elucidated. The proteins studied are all added cotranscriptionally to the pre-mRNA molecule. The various proteins behave differently during RNA transport, and the flow pattern of each protein is related to the particular function of the protein. Because the cotranscriptional assembly of the pre-mRNP particle involves proteins functioning in the nucleus as well as proteins functioning in the cytoplasm, it is concluded that the fate of the mRNA molecule is determined to a considerable extent already at the gene level.

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Nuclear Domains and the Nuclear Matrix

Cited by 68 publications

References 264 publications

Higher order arrangement of the eukaryotic nuclear bodies

Higher order arrangement of the eukaryotic nuclear bodies

Ultrastructural Analysis of Transcription and Splicing in the Cell Nucleus after Bromo-UTP Microinjection

Assembly and transport of a premessenger RNP particle

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