Functional architecture in the cell nucleus

Biochemical Journal

Volumn 356, Issue 2, 2001, Pages 297-310

  Dundr, M ^a   Misteli, T ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Chromatin; Gene expression; Nuclear compartments; Protein dynamics

Indexed keywords

BIOCHEMISTRY; PROTEINS; RNA;

MOLECULAR MECHANISMS;

GENES;

MESSENGER RNA;

CELL COMPARTMENTALIZATION; CELL FUNCTION; CELL NUCLEUS; CELL ORGANELLE; CELL STRUCTURE; CHROMATIN; GENE EXPRESSION; GENETIC TRANSCRIPTION; GENOME; HUMAN; IN VIVO STUDY; MOLECULAR GENETICS; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA SPLICING;

ANIMALS; CELL COMPARTMENTATION; CELL NUCLEOLUS; CELL NUCLEUS; CHROMATIN; CHROMOSOMES; COILED BODIES; HUMANS; MODELS, BIOLOGICAL; NEOPLASM PROTEINS; NUCLEAR PROTEINS; RNA; RNA SPLICING; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; TUMOR SUPPRESSOR PROTEINS;

EID: 0035365808     PISSN: 02646021     EISSN: None     Source Type: Journal    
DOI: 10.1042/0264-6021:3560297     Document Type: Review

References (191)

1. Macromolecular domains within the cell nucleus
2. Structure and function in the nucleus
3. Large-scale chromatin structure and function
4. Movement of mRNA from transcription site to nuclear pores
5. Protein dynamics: Implications for nuclear architecture and gene expression
6. Nuclear bodies: Multifaceted subdomains of the interchromatin space
7. Isolation of nucleoli in a medium containing spermine and magnesium acetate
8. Purification and biochemical characterization of interchromatin granule clusters
9. Half a century of "the nuclear matrix"
10. Experimental observations of a nuclear matrix
11. Structure and function of the nucleolus
12. To be or not to be in the nucleolus
13. The nucleolus: An old factory with unexpected capabilities
14. Cell Biology of transcription and pre-mRNA splicing: Nuclear architecture meets nuclear function
15. Cajal Bodies: The first 100 years
16. The transcriptional role of PML and the nuclear body
17. Visualization of focal sites of transcription within human nuclei
18. Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus
19. The organization of replication and transcription
20. Nuclear distribution of transcription factors in relation to sites of transcription and RNA polymerase II
21. Higher level organization of individual gene transcription and RNA splicing
22. RNAs radiate from gene to cytoplasm as revealed by fluorescence in situ hybridization
23. Splice site selection, rate of splicing, and alternative splicing on nascent transcripts
24. Splicing of Balbiani ring 1 gene pre-mRNA occurs simultaneously with transcription
25. Nonrandom gene organization: Structural arrangements of specific pre-mRNA transcription and splicing with SC-35 domains
26. Perichromatin fibrils are in situ forms of nascent transcripts
27. Fine structural organization of the interphase nucleus in some mammalian cells
28. In vivo evidence that transcription and splicing are coordinated by a recruiting mechanism
29. Intron-dependent recruitment of pre-mRNA splicing factors to sites of transcription
30. The dynamics of a pre-mRNA splicing factor in living cells
31. Nuclear pre-mRNA compartmentalization: Trafficking of released transcripts to splicing factor reservoirs
32. A functional interaction between the carboxy-terminal domain of RNA polymerase II and pre-mRNA splicing
33. Splicing factors associate with hyperphosphorylated RNA polymerase II in the absence of pre-mRNA
34. RNA polymerase II targets pre-mRNA splicing factors to transcription sites in vivo
35. Coupling RNA polymerase II transcription with pre-mRNA processing
36. RNA polymerase II and the integration of nuclear events
37. Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei
38. The balance sheet for transcription: An analysis of nuclear RNA metabolism in mammalian cells
39. Nonisotopic ultrastructural mapping of transcription sites within the nucleolus
40. Site of transcription of ribosomal RNA and intranucleolar structure in HeLa cells
41. Early stages of pre-rRNA formation within the nucleolar ultrastructure of mouse cells studied by in situ hybridization with a 5′ ETS leader probe
42. Ultrastructural analysis of transcription and splicing in the cell nucleus after bromo-UTP microinjection
43. Alterations of nucleolar ultrastructure and ribosome biogenesis by actinomycin D. Implications for U3 snRNP function
44. Eukaryotic ribosomal RNA: The recent excitement in the nucleotide modification problem
45. Dynamics and three-dimensional localization of ribosomal RNA within the nucleolus
46. Ribosomal RNA processing in eukaryotes
47. Function and synthesis of small nucleolar RNAs
48. The RNA world of the nucleolus: Two major families of small RNAs defined by different box elements with related functions
49. Nucleolar factors direct the 2′-O-ribose methylation and pseudouridylation of U6 spliceosomal RNA
50. NAP57, a mammalian nucleolar protein with a putative homolog in yeast and bacteria
51. The box H + ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase
52. Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly
53. Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 Å resolution
54. The road to ribosomes. Filling potholes in the export pathway
55. Protein trans-acting factors involved in ribosome biogenesis in Saccharomyces cerevisiae
56. Cytoplasmic transport of ribosomal subunits microinjected into the Xenopus laevis oocyte nucleus: A generalized, facilitated process
57. A novel in vivo assay reveals inhibition of ribosomal nuclear export in ran-cycle and nucleoporin mutants
58. Nuclear export of the small ribosomal subunit requires the ran-GTPase cycle and certain nucleoporins
59. Nmd3p is a Crm1p-dependent adapter protein for nuclear export of the large ribosomal subunit
60. Mitotic silencing of human rRNA synthesis: Inactivation of the promoter selectivity factor SL1 by cdc2/cyclin B-mediated phosphorylation
61. Mitotic phosphorylation of the TBP-containing factor SL1 represses ribosomal gene transcription
62. In vivo release of mitotic silencing of ribosomal gene transcription does not give rise to precursor ribosomal RNA processing
63. The dynamics of postmitotic reassembly of the nucleolus
64. The chromosome periphery during mitosis
65. Partially processed pre-rRNA is preserved in association with processing components in nucleolus-derived foci during mitosis
66. Initiation of nucleolar assembly is independent of RNA polymerase I transcription
67. The ribosomal RNA processing machinery is recruited to the nucleolar domain before RNA polymerase I during Xenopus laevis development
68. The nucleolus and the four ribonucleoproteins of translation
69. Signal recognition particle components in the nucleolus
70. Transient nucleolar localization of U6 small nuclear RNA in Xenopus laevis oocytes
71. A small nucleolar guide RNA functions both in 2′-O-ribose methylation and pseudouridylation of the U5 spliceosomal RNA
72. The trials and travels of tRNA
73. Localization in the nucleolus and coiled bodies of protein subunits of the ribonucleoprotein ribonuclease P
74. Control of transfer RNA maturation by phosphorylation of the human La antigen on serine 366
75. Cross talk between tRNA and rRNA synthesis in Saccharomyces cerevisiae
76. Nucleoporins nup98 and nup214 participate in nuclear export of human immunodeficiency virus type 1
77. Inhibition of human immunodeficiency virus type 1 replication by nuclear chimeric anti-HIV ribozymes in a human T lymphoblastoid cell line
78. The p53 pathway
79. Nucleolar Arf sequesters Mdm2 and activates p53
80. P19(ARF) stabilizes p53 by blocking nucleo-cytoplasmic shuttling of Mdm2
81. Mutations in human ARF exon 2 disrupt its nucleolar localization and impair its ability to block nuclear export of MDM2 and p53
82. Assembly of the nuclear transcription and processing machinery: Cajal bodies (coiled bodies) and transcriptosomes
83. Cytochemical and immunocytochemical characterization of nuclear bodies during hibernation
84. Coiled bodies in the nucleolus of breast cancer cells
85. The movement of coiled bodies visualized in living plant cells by the green fluorescent protein
86. In vivo analysis of Cajal body movement, separation, and joining in live human cells
87. Immunological and ultrastructural studies of the nuclear coiled body with autoimmune antibodies
88. Mutational analysis of p80 coilin indicates a functional interaction between coiled bodies and the nucleolus
89. Nopp140 functions as a molecular link between the nucleolus and the coiled bodies
90. Conserved composition of mammalian box H/ACA and box C/D small nucleolar ribonucleoprotein particles and their interaction with the common factor Nopp140
91. Inhibition of protein dephosphorylation results in the accumulation of splicing snRNPs and coiled bodies within the nucleolus
92. Newly assembled snRNPs associate with coiled bodies before speckles, suggesting a nuclear snRNP maturation pathway
93. The spinal muscular atrophy disease gene product. SMN: A link between snRNP biogenesis and the Cajal (coiled) body
94. Coiled bodies without coilin
95. Role of the box C/D motif in localization of small nucleolar RNAs to coiled bodies and nucleoli
96. Association of RNA with the B and C snurposomes of Xenopus oocyte nuclei
97. Human genes encoding U3 snRNA associate with coiled bodies in interphase cells and are clustered on chromosome 17p11.2 in a complex inverted repeat structure
98. Coiled bodies preferentially associate with U4, U11, and U12 small nuclear RNA genes in interphase HeLa cells but not with U6 and U7 genes
99. Association of snRNA genes with coiled bodies is mediated by nascent snRNA transcripts
100. Coiled bodies and U2 snRNA genes adjacent to coiled bodies are enriched in factors required for snRNA transcription
101. 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
102. Nuclear domains enriched in RNA 3′-processing factors associate with coiled bodies and histone genes in a cell cycle-dependent manner
103. Coiled bodies contain U7 small nuclear RNA and associate with specific DNA sequence in interphase human cells
104. Replication-dependent histone gene expression is related to Cajal body (cb) association but does not require sustained cb contact
105. Cell cycle-dependent localization of the CDK2-cyclin E complex in Cajal (coiled) bodies
106. RNA polymerase II in Cajal bodies of amphibian oocytes
107. A functional interaction between the survival motor neuron complex and RNA polymerase II
108. The PML growth-suppressor has an altered expression in human oncogenesis
109. PML nuclear bodies are general targets for inflammation and cell proliferation
110. Nuclear dots: Actors on many stages
111. The puzzling multiple lives of PML and its role in the genesis of cancer
112. Nuclear domain 10, the site of DNA virus transcription and replication
113. PML induces a novel caspase-independent death process
114. The t(15;17) translocation of acute promyelocytic leukemia fuses the retinoic acid receptor alpha gene to a novel transcribed locus
115. A novel macromolecular structure is a target of the promyelocyte-retinoic acid receptor oncoprotein
116. The t(15;17) translocation alters a nuclear body in a retinoic acid-reversible fashion
117. Visualization of gene activity in living cells
118. The transcription coactivator CBP is a dynamic component of the promyelocytic leukemia nuclear body
119. Regional and temporal specialization in the nucleus: A transcriptionally-active nuclear domain rich in PTF, Oct1 and PIKA antigens associates with specific chromosomes early in the cell cycle
120. The dynamic organization of the perinucleolar compartment in the cell nucleus
121. A perinucleolar compartment contains several RNA polymerase III transcripts as well as the polypyrimidine tract-binding protein, hnRNP I
122. Association of RNase mitochondrial RNA processing enzyme with ribonuclease P in higher ordered structures in the nucleolus: A possible coordinate role in ribosome biogenesis
123. The perinucleolar compartment and transcription
124. Chromosome territories, interchromatin domain compartment and nuclear matrix: An integrated view of the functional nuclear architecture
125. Rabl's model of the interphase chromosome arrangement tested in Chinese hamster cells by premature chromosome condensation and laser UV-microbeam experiments
126. Detection of chromosome aberrations in metaphase and interphase tumor cells by in-situ hybridization using chromosome specific library probes
127. Active and inactive genes localize preferentially in the periphery of chromosome territories
128. Spatial relationship between transcription sites and chromosome territories
129. Translational diffusion of macromolecule-sized solutes in cytoplasm and nucleus
130. Identification of an interchromosomal compartment by polymerization of nuclear-targeted vimentin
131. The EAST protein of Drosophila controls an expandable nuclear endoskeleton
132. Nuclear compartmentalization and gene activity
133. Different central nervous system cell types display distinct and nonrandom arrangements of satellite DNA sequences
134. A view of interphase chromosomes
135. Transposition of DNase hypersensitive chromatin to the nuclear periphery coincides temporally with nerve growth factor-induced up-regulation of gene expression in PC12 cells
136. Changes in morphology and spatial position of coiled bodies during NGF-induced neuronal differentiation of PC12 cells
137. Movement of the X chromosome in epilepsy
138. Gene action in the X chromosome of the mouse
139. Nuclear compartments and gene regulation
140. Locus control regions and epigenetic chromatin modifiers
141. Perturbation of nuclear architecture by long-distance chromosome interactions
142. Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin
143. Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division
144. Position effect at S. cerevisiae telomeres: Reversible repression of pol II transcription
145. Perinuclear localization of chromatin facilitates transcriptional silencing
146. Alteration of nucleosome structure as a mechanism of transcriptional regulation
147. Chromatin dynamics in interphase nuclei and its implications for nuclear structure
148. Interphase chromosomes undergo constrained diffusional motion in living cells
149. Histone-GFP fusion protein enables sensitive analysis of chromosome dynamics in living mammalian cells
150. In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition
151. Large-scale chromatin unfolding and remodeling induced by VP16 acidic activation domain
152. Interphase movements of a DNA chromosome region modulated by VP16 transcriptional activator
153. The glucocorticoid receptor: Rapid exchange with regulatory sites in living cells
154. H3-uridine incorporation in lampbrush chromosomes
155. Transcription in polytene chromosomes
156. Gene gating: A hypothesis
157. Discrete nuclear domains of poly(A) RNA and their relationship to the functional organization of the nucleus
158. A three-dimensional view of precursor messenger RNA metabolism within the mammalian nucleus
159. Nuclear RNA tracks: Structural basis for transcription and splicing?
160. Repression and turnover pattern of fusi tarazu RNA in the early Drosophila embryo
161. Apical localization of pair-rule transcripts requires 3′ sequences and limits protein diffusion in the Drosophila blastoderm embryo
162. Squid hnRNP proteins promotes apical cytoplasmic transport and localization of Drosophila pair-rule transcripts
163. Evidence for channeled diffusion of pre-mRNAs during nuclear RNA transport in metazoans
164. Intranuclear diffusion and hybridization state of oligonucleotides measured by fluorescence correlation spectroscopy in living cells
165. Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells
166. The intranuclear movement of Balbiani ring premessenger ribonucleoprotein particles
167. FRAP reveals that mobility of oestrogen receptor-α is ligand and proteasome-dependent
168. Reduced mobility of the alternate splicing factor (ASF) through the nucleoplasm and steady state speckle compartments
169. High mobility of proteins in the mammalian cell nucleus
170. Mutational analysis of fibrillarin and its mobility in living human cells
171. Action of DNA repair endonuclease ERCC1/XPF in living cells
172. Rapid exchange of histone H1.1 on chromatin in living cells
173. Dynamic binding of histone H1 to chromatin in living cells
174. Higher concentration of histone macro-H2A in the Barr body are correlated with higher nucleosome density
175. Dynamics of DNA replication factories in living cells
176. Human SWI/SNF nucleosome remodeling activity is partially inhibited by linker histone H1
177. In vivo footprinting of rat TAT gene: Dynamic interplay between the glucocorticoid receptor and a liver-specific factor
178. Rapid and reversible relocalization of heat shock factor 1 within seconds to nuclear stress granules
179. The reversible action of a-amanitin on nuclear structure and molecular composition
180. The dynamics of a pre-mRNA splicing factor in living cells
181. Self-association of p80 coilin reveals a common theme in nuclaer body formation
182. PML is critical for ND10 formation and recruits the PML-interacting protein Daxx to this nuclear structure when modified by SUMO-1
183. SMN oligomerization defect correlates with spinal muscular atrophy severity
184. Structural alterations of the nucleolus in mutants of Saccharomyces cerevisiae defective in RNA polymerase I
185. The nucleolus: An organelle formed by the act of building a ribosome
186. A Drosophila rRNA gene located in euchromatin is active in transcription and nucleolus formation
187. Mutational analysis of the structure and localization of the nucleolus in the yeast Saccharomyces cerevisiae
188. Organization of replication and transcription
189. Dynamic organization of DNA replication in mammalian cell nuclei: Spatially and temporally defined replication of chromosome-specific alpha-satellite DNA sequences
190. Spatial and temporal dynamics of DNA replication sites in mammalian cells