scholarly journals Chromatin targeting of nuclear pore proteins induces chromatin decondensation

2019 ◽  
Vol 218 (9) ◽  
pp. 2945-2961 ◽  
Author(s):  
Terra M. Kuhn ◽  
Pau Pascual-Garcia ◽  
Alejandro Gozalo ◽  
Shawn C. Little ◽  
Maya Capelson
Keyword(s):  
Target Gene ◽  
Nuclear Periphery ◽  
Nuclear Pore ◽  
Open Chromatin ◽  
Nuclear Pore Complexes ◽  
Chromatin Binding ◽  
Chromatin Decondensation ◽  
Chromatin Remodeling Complex ◽  
Biochemical Interaction ◽  
Pore Complexes

Nuclear pore complexes have emerged in recent years as chromatin-binding nuclear scaffolds, able to influence target gene expression. However, how nucleoporins (Nups) exert this control remains poorly understood. Here we show that ectopically tethering Drosophila Nups, especially Sec13, to chromatin is sufficient to induce chromatin decondensation. This decondensation is mediated through chromatin-remodeling complex PBAP, as PBAP is both robustly recruited by Sec13 and required for Sec13-induced decondensation. This phenomenon is not correlated with localization of the target locus to the nuclear periphery, but is correlated with robust recruitment of Nup Elys. Furthermore, we identified a biochemical interaction between endogenous Sec13 and Elys with PBAP, and a role for endogenous Elys in global as well as gene-specific chromatin decompaction. Together, these findings reveal a functional role and mechanism for specific nuclear pore components in promoting an open chromatin state.

scholarly journals Phosphorylation-dependent mitotic SUMOylation drives nuclear envelope–chromatin interactions

2021 ◽  
Vol 220 (12) ◽  
Author(s):  
Christopher Ptak ◽  
Natasha O. Saik ◽  
Ashwini Premashankar ◽  
Diego L. Lapetina ◽  
John D. Aitchison ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nuclear Envelope ◽  
Spatial Organization ◽  
G1 Phase ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Chromatin Binding ◽  
Chromatin Interactions ◽  
Sumo Ligase ◽  
Pore Complexes

In eukaryotes, chromatin binding to the inner nuclear membrane (INM) and nuclear pore complexes (NPCs) contributes to spatial organization of the genome and epigenetic programs important for gene expression. In mitosis, chromatin–nuclear envelope (NE) interactions are lost and then formed again as sister chromosomes segregate to postmitotic nuclei. Investigating these processes in S. cerevisiae, we identified temporally and spatially controlled phosphorylation-dependent SUMOylation events that positively regulate postmetaphase chromatin association with the NE. Our work establishes a phosphorylation-mediated targeting mechanism of the SUMO ligase Siz2 to the INM during mitosis, where Siz2 binds to and SUMOylates the VAP protein Scs2. The recruitment of Siz2 through Scs2 is further responsible for a wave of SUMOylation along the INM that supports the assembly and anchorage of subtelomeric chromatin at the INM and localization of an active gene (INO1) to NPCs during the later stages of mitosis and into G1-phase.

scholarly journals Functional evolution of nuclear structure

2011 ◽  
Vol 195 (2) ◽  
pp. 171-181 ◽  
Author(s):  
Katherine L. Wilson ◽  
Scott C. Dawson
Keyword(s):  
Membrane Proteins ◽  
Nuclear Structure ◽  
Common Ancestor ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Chromatin Binding ◽  
Endomembrane System ◽  
Tightly Coupled ◽  
Pore Complexes ◽  
Eukaryotic Supergroup

The evolution of the nucleus, the defining feature of eukaryotic cells, was long shrouded in speculation and mystery. There is now strong evidence that nuclear pore complexes (NPCs) and nuclear membranes coevolved with the endomembrane system, and that the last eukaryotic common ancestor (LECA) had fully functional NPCs. Recent studies have identified many components of the nuclear envelope in living Opisthokonts, the eukaryotic supergroup that includes fungi and metazoan animals. These components include diverse chromatin-binding membrane proteins, and membrane proteins with adhesive lumenal domains that may have contributed to the evolution of nuclear membrane architecture. Further discoveries about the nucleoskeleton suggest that the evolution of nuclear structure was tightly coupled to genome partitioning during mitosis.

scholarly journals The dynamic three-dimensional organization of the diploid yeast genome

2016 ◽  
Author(s):  
Seungsoo Kim ◽  
Ivan Liachko ◽  
Donna G Brickner ◽  
Kate Cook ◽  
William S Noble ◽  
...  
Keyword(s):  
Nuclear Periphery ◽  
Three Dimensional ◽  
Culture Conditions ◽  
Yeast Genome ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Chromosome Conformation ◽  
Homolog Pairing ◽  
Pore Complexes ◽  
Eukaryotic Genomes

AbstractThe budding yeast Saccharomyces cerevisiae is a long-standing model for the three-dimensional organization of eukaryotic genomes. Even in this well-studied model, it is unclear how homolog pairing in diploids and environment-induced gene relocalization influence overall genome organization. Here, we performed high-throughput chromosome conformation capture on diverged Saccharomyces hybrid diploids to obtain the first global view of chromosome conformation in diploid yeasts. After controlling for the Rabl-like orientation, we observe significant homolog proximity that increased in saturated culture conditions. Surprisingly, we observe a localized increase in homologous interactions between the HAS1 alleles specifically under galactose induction and saturated growth, mediated by association with nuclear pore complexes at the nuclear periphery. Together, these results reveal that the diploid yeast genome has a dynamic and complex 3D organization.

Relationships at the nuclear envelope: lamins and nuclear pore complexes in animals and plants

2010 ◽  
Vol 38 (3) ◽  
pp. 829-831 ◽  
Author(s):  
Jindriska Fiserova ◽  
Martin W. Goldberg
Keyword(s):  
Nuclear Envelope ◽  
Nuclear Periphery ◽  
Nuclear Lamina ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Nucleocytoplasmic Trafficking ◽  
Animal Cells ◽  
Cellular Processes ◽  
Associated Proteins ◽  
Pore Complexes

The nuclear envelope comprises a distinct compartment at the nuclear periphery that provides a platform for communication between the nucleus and cytoplasm. Signal transfer can proceed by multiple means. Primarily, this is by nucleocytoplasmic trafficking facilitated by NPCs (nuclear pore complexes). Recently, it has been indicated that signals can be transmitted from the cytoskeleton to the intranuclear structures via interlinking transmembrane proteins. In animal cells, the nuclear lamina tightly underlies the inner nuclear membrane and thus represents the protein structure located at the furthest boundary of the nucleus. It enables communication between the nucleus and the cytoplasm via its interactions with chromatin-binding proteins, transmembrane and membrane-associated proteins. Of particular interest is the interaction of the nuclear lamina with NPCs. As both structures fulfil essential roles in close proximity at the nuclear periphery, their interactions have a large impact on cellular processes resulting in affects on tissue differentiation and development. The present review concentrates on the structural and functional lamina–NPC relationship in animal cells and its potential implications to plants.

Sequential recruitment of NPC proteins to the nuclear periphery at the end of mitosis

1999 ◽  
Vol 112 (13) ◽  
pp. 2253-2264 ◽  
Author(s):  
K. Bodoor ◽  
S. Shaikh ◽  
D. Salina ◽  
W.H. Raharjo ◽  
R. Bastos ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Nuclear Envelope ◽  
Nuclear Membrane ◽  
Time Course ◽  
Nuclear Periphery ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Confocal Immunofluorescence Microscopy ◽  
Pore Complexes ◽  
Nuclear Membrane Protein

Nuclear pore complexes (NPCs) are extremely elaborate structures that mediate the bidirectional movement of macromolecules between the nucleus and cytoplasm. With a mass of about 125 MDa, NPCs are thought to be composed of 50 or more distinct protein subunits, each present in multiple copies. During mitosis in higher cells the nuclear envelope is disassembled and its components, including NPC subunits, are dispersed throughout the mitotic cytoplasm. At the end of mitosis, all of these components are reutilized. Using both conventional and digital confocal immunofluorescence microscopy we have been able to define a time course of post-mitotic assembly for a group of NPC components (CAN/Nup214, Nup153, POM121, p62 and Tpr) relative to the integral nuclear membrane protein LAP2 and the NPC membrane glycoprotein gp210. Nup153, a component of the nuclear basket, associates with chromatin towards the end of anaphase, in parallel with the inner nuclear membrane protein, LAP2. However, immunogold labeling suggests that the initial Nup153 chromatin association is membrane-independent. Assembly of the remaining proteins follows that of the nuclear membranes and occurs in the sequence POM121, p62, CAN/Nup214 and gp210/Tpr. Since p62 remains as a complex with three other NPC proteins (p58, 54, 45) during mitosis and CAN/Nup214 maintains a similar interaction with its partner, Nup84, the relative timing of assembly of these additional four proteins may also be inferred. These observations suggest that there is a sequential association of NPC proteins with chromosomes during nuclear envelope reformation and the recruitment of at least eight of these precedes that of gp210. These findings support a model in which it is POM121 rather than gp210 that defines initial membrane-associated NPC assembly intermediates.

Peripheral Localization and Regulation of the Murine β-Globin Locus.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 4070-4070
Author(s):  
Tobias Ragoczy ◽  
Agnes Telling ◽  
Rachel Byron ◽  
M.A. Bender ◽  
Mark Groudine
Keyword(s):  
Gene Expression ◽  
Globin Gene ◽  
Nuclear Periphery ◽  
Embryonic Stem ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Erythroid Progenitor ◽  
Interphase Cell ◽  
Pore Complexes ◽  
Globin Gene Expression

Abstract The interphase cell nucleus is structurally and functionally compartmentalized, making the subnuclear position of genes an important determinant of their activity. During cellular differentiation, as tissue-specific expression programs unfold, dynamic reorganization of the nucleus positions sets of genes in active or repressive compartments. The nuclear periphery has emerged as an unusually complex compartment in this process. While it is marked by facultative heterochromatin and has been considered primarily as a repressive compartment, recent work suggests that active genes may also associate with the periphery. Moreover, the nuclear envelope is riddled with nuclear pore complexes, the gateways for molecular exchange between the cytoplasm and the nucleus, resulting in substantial traffic through this compartment. Using murine erythropoiesis as a model system, our recent three dimensional analysis of the positioning of the β-globin locus revealed that, when inactive in undifferentiated embryonic stem cells and erythroid progenitor cells, the locus is positioned predominantly at the nuclear periphery and appears to contact the lamina. This association is lost with progressing erythroid maturation, and the locus is repositioned towards the nuclear interior concomitant with increasing β-globin gene expression. Importantly, however, β-major globin expression begins at the nuclear periphery prior to relocalization, suggesting that associations of the locus at the periphery may shift from repressive to activating complexes. We are investigating the interactions of the β-globin locus with the nuclear periphery by two approaches: Using enhanced imaging permitted by Cryo-ImmunoFISH, we are analyzing the position of the locus relative to specific components of the nuclear lamina and nuclear pore complexes at distinct differentiation stages. In addition, we are probing the physical interactions of the locus with the periphery by biochemical means. To this end we are using ChIP-chip to identify lamina associated proteins binding the β-globin locus and to determine what sequence elements within the locus mediate these interactions. Ultimately these experiments will shed further light on mechanisms regulating β-globin gene expression during erythropoiesis and how stage-specific nuclear localization contributes to this process.

scholarly journals Mutation or deletion of the Saccharomyces cerevisiae RAT3/NUP133 gene causes temperature-dependent nuclear accumulation of poly(A)+ RNA and constitutive clustering of nuclear pore complexes.

1995 ◽  
Vol 6 (4) ◽  
pp. 401-417 ◽  
Author(s):  
O Li ◽  
C V Heath ◽  
D C Amberg ◽  
T C Dockendorff ◽  
C S Copeland ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Messenger Rna ◽  
Nuclear Periphery ◽  
Nuclear Accumulation ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Permissive Temperature ◽  
Temperature Dependent ◽  
Pore Complexes ◽  
Mutant Cells

To identify genes whose products play potential roles in the nucleocytoplasmic export of messenger RNA, we isolated temperature-sensitive strains of Saccharomyces cerevisiae and examined them by fluorescent in situ hybridization. With the use of a digoxigen-tagged oligo-(dT)50 probe, we identified those that showed nuclear accumulation of poly(A)+ RNA when cells were shifted to the nonpermissive temperature. We describe here the properties of yeast strains bearing the rat3-1 mutation (RAT-ribonucleic acid trafficking) and the cloning of the RAT3 gene. When cultured at the permissive temperature of 23 degrees C, fewer than 10% of cells carrying the rat3-1 allele showed nuclear accumulation of poly(A)+ RNA, whereas approximately 70% showed nuclear accumulation of poly(A)+ RNA, whereas approximately 70% showed nuclear accumulation of poly(A)+ RNA after a shift to 37 degrees C for 4 h. In wild-type cells, nuclear pore complexes (NPCs) are distributed relatively evenly around the nuclear envelope. Both indirect immunofluorescence analysis and electron microscopy of rat3-1 cells indicated that NPCs were clustered into one or a few regions of the NE in mutant cells. Similar NPC clustering was seen in mutant cells cultured at temperatures between 15 degrees C and 37 degrees C. The RAT3 gene encodes an 1157-amino acid protein without similarity to other known proteins. It is essential for growth only at 37 degrees C. Cells carrying a disruption of the RAT3 gene were very similar to cells carrying the original rat3-1 mutation; they showed temperature-dependent nuclear accumulation of poly(A)+ RNA and exhibited constitutive clustering of NPCs. Epitope tagging of Rat3p demonstrated that it is located at the nuclear periphery and co-localizes with nuclear pore proteins recognized by the RL1 monoclonal antibody. We refer to this nucleoporin as Rat3p/Nup133p.

scholarly journals Members of the RSC Chromatin-Remodeling Complex Are Required for Maintaining Proper Nuclear Envelope Structure and Pore Complex Localization

2010 ◽  
Vol 21 (6) ◽  
pp. 1072-1087 ◽  
Author(s):  
Laura C. Titus ◽  
T. Renee Dawson ◽  
Deborah J. Rexer ◽  
Kathryn J. Ryan ◽  
Susan R. Wente
Keyword(s):  
Nuclear Envelope ◽  
Chromatin Remodeling ◽  
Fluorescent Protein ◽  
Nuclear Periphery ◽  
Structural Defects ◽  
Nuclear Pore ◽  
Temperature Sensitive ◽  
Nuclear Pore Complexes ◽  
Chromatin Remodeling Complex ◽  
Green Fluorescent

The assembly, distribution, and functional integrity of nuclear pore complexes (NPCs) in the nuclear envelope (NE) are key determinants in the nuclear periphery architecture. However, the mechanisms controlling proper NPC and NE structure are not fully defined. We used two different genetic screening approaches to identify Saccharomyces cerevisiae mutants with defects in NPC localization. The first approach examined green fluorescent protein (GFP)-Nic96 in 531 strains from the yeast Tet-promoters Hughes Collection with individual essential genes expressed from a doxycycline-regulated promoter (TetO7-orf). Under repressive conditions, depletion of the protein encoded by 44 TetO7-orf strains resulted in mislocalized GFP-Nic96. These included STH1, RSC4, RSC8, RSC9, RSC58, ARP7, and ARP9, each encoding components of the RSC chromatin remodeling complex. Second, a temperature-sensitive sth1-F793S (npa18-1) mutant was identified in an independent genetic screen for NPC assembly (npa) mutants. NPC mislocalization in the RSC mutants required new protein synthesis and ongoing transcription, confirming that lack of global transcription did not underlie the phenotypes. Electron microscopy studies showed significantly altered NEs and nuclear morphology, with coincident cytoplasmic membrane sheet accumulation. Strikingly, increasing membrane fluidity with benzyl alcohol treatment prevented the sth1-F793S NE structural defects and NPC mislocalization. We speculate that NE structure is functionally linked to proper chromatin architecture.

scholarly journals Esc1, a Nuclear Periphery Protein Required for Sir4-Based Plasmid Anchoring and Partitioning

2002 ◽  
Vol 22 (23) ◽  
pp. 8292-8301 ◽  
Author(s):  
Erik D. Andrulis ◽  
David C. Zappulla ◽  
Athar Ansari ◽  
Severine Perrod ◽  
Catherine V. Laiosa ◽  
...  
Keyword(s):  
Fluorescent Protein ◽  
Nuclear Periphery ◽  
Nuclear Pore ◽  
Nuclear Pore Complexes ◽  
Uncharacterized Protein ◽  
Telomeric Silencing ◽  
Green Fluorescent ◽  
Pore Complexes ◽  
Redundant Pathway

ABSTRACT A targeted silencing screen was performed to identify yeast proteins that, when tethered to a telomere, suppress a telomeric silencing defect caused by truncation of Rap1. A previously uncharacterized protein, Esc1 (establishes silent chromatin), was recovered, in addition to well-characterized proteins Rap1, Sir1, and Rad7. Telomeric silencing was slightly decreased in Δesc1 mutants, but silencing of the HM loci was unaffected. On the other hand, targeted silencing by various tethered proteins was greatly weakened in Δesc1 mutants. Two-hybrid analysis revealed that Esc1 and Sir4 interact via a 34-amino-acid portion of Esc1 (residues 1440 to 1473) and a carboxyl-terminal domain of Sir4 known as PAD4 (residues 950 to 1262). When tethered to DNA, this Sir4 domain confers efficient partitioning to otherwise unstable plasmids and blocks the ability of bound DNA segments to rotate freely in vivo. Here, both phenomena were shown to require ESC1. Sir protein-mediated partitioning of a telomere-based plasmid also required ESC1. Fluorescence microscopy of cells expressing green fluorescent protein (GFP)-Esc1 showed that the protein localized to the nuclear periphery, a region of the nucleus known to be functionally important for silencing. GFP-Esc1 localization, however, was not entirely coincident with telomeres, the nucleolus, or nuclear pore complexes. Our data suggest that Esc1 is a component of a redundant pathway that functions to localize silencing complexes to the nuclear periphery.

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