scholarly journals Subnuclear positioning and interchromosomal clustering of the GAL1-10 locus are controlled by separable, interdependent mechanisms

2016 ◽  
Vol 27 (19) ◽  
pp. 2980-2993 ◽  
Author(s):  
Donna Garvey Brickner ◽  
Varun Sood ◽  
Evelina Tutucci ◽  
Robert Coukos ◽  
Kayla Viets ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Nuclear Pore Complex ◽  
Molecular Mechanisms ◽  
Nuclear Periphery ◽  
Gene Clustering ◽  
Nuclear Pore ◽  
Cis Acting ◽  
Gene Positioning ◽  
Gal Genes ◽  
Necessary And Sufficient

On activation, the GAL genes in yeast are targeted to the nuclear periphery through interaction with the nuclear pore complex. Here we identify two cis-acting “DNA zip codes” from the GAL1-10 promoter that are necessary and sufficient to induce repositioning to the nuclear periphery. One of these zip codes, GRS4, is also necessary and sufficient to promote clustering of GAL1-10 alleles. GRS4, and to a lesser extent GRS5, contribute to stronger expression of GAL1 and GAL10 by increasing the fraction of cells that respond to the inducer. The molecular mechanism controlling targeting to the NPC is distinct from the molecular mechanism controlling interchromosomal clustering. Targeting to the nuclear periphery and interaction with the nuclear pore complex are prerequisites for gene clustering. However, once formed, clustering can be maintained in the nucleoplasm, requires distinct nuclear pore proteins, and is regulated differently through the cell cycle. In addition, whereas targeting of genes to the NPC is independent of transcription, interchromosomal clustering requires transcription. These results argue that zip code–dependent gene positioning at the nuclear periphery and interchromosomal clustering represent interdependent phenomena with distinct molecular mechanisms.

scholarly journals P granules extend the nuclear pore complex environment in the C. elegans germ line

2011 ◽  
Vol 192 (6) ◽  
pp. 939-948 ◽  
Author(s):  
Dustin L. Updike ◽  
Stephanie J. Hachey ◽  
Jeremy Kreher ◽  
Susan Strome
Keyword(s):  
Nuclear Pore Complex ◽  
Germ Plasm ◽  
Germ Line ◽  
Hydrophobic Interactions ◽  
Nuclear Periphery ◽  
Size Exclusion ◽  
Nuclear Pore ◽  
Complex Environment ◽  
P Granules ◽  
C Elegans

The immortal and totipotent properties of the germ line depend on determinants within the germ plasm. A common characteristic of germ plasm across phyla is the presence of germ granules, including P granules in Caenorhabditis elegans, which are typically associated with the nuclear periphery. In C. elegans, nuclear pore complex (NPC)–like FG repeat domains are found in the VASA-related P-granule proteins GLH-1, GLH-2, and GLH-4 and other P-granule components. We demonstrate that P granules, like NPCs, are held together by weak hydrophobic interactions and establish a size-exclusion barrier. Our analysis of intestine-expressed proteins revealed that GLH-1 and its FG domain are not sufficient to form granules, but require factors like PGL-1 to nucleate the localized concentration of GLH proteins. GLH-1 is necessary but not sufficient for the perinuclear location of granules in the intestine. Our results suggest that P granules extend the NPC environment in the germ line and provide insights into the roles of the PGL and GLH family proteins.

scholarly journals Cotranscriptional Recruitment to the mRNA Export Receptor Mex67p Contributes to Nuclear Pore Anchoring of Activated Genes

2006 ◽  
Vol 26 (21) ◽  
pp. 7858-7870 ◽  
Author(s):  
Guennaelle Dieppois ◽  
Nahid Iglesias ◽  
Françoise Stutz
Keyword(s):  
Transcriptional Activation ◽  
Mrna Export ◽  
Nuclear Periphery ◽  
Nuclear Pore ◽  
Coding Region ◽  
Messenger Ribonucleoprotein ◽  
Gene Positioning ◽  
Independent Process ◽  
Stable Association ◽  
Early Recruitment

ABSTRACT Transcription activation of some Saccharomyces cerevisiae genes is paralleled by their repositioning to the nuclear periphery, but the mechanism underlying gene anchoring is poorly defined. We show that the nuclear pore complex-associated Mlp1p and the shuttling mRNA export receptor Mex67p contribute to the stable association of the activated GAL10 and HSP104 genes with the nuclear periphery. However, we find no obligatory link between gene positioning and gene expression. Furthermore, gene anchoring correlates with the cotranscriptional recruitment of Mex67p to transcribing genes. Notably, the association of Mex67p with chromatin is not mediated by RNA. Interestingly, a mutant GAL2 gene lacking the coding region is still able to recruit Mex67p upon transcriptional activation and to relocate to the nuclear periphery. Together these data suggest that, at least for GAL2, nascent messenger ribonucleoprotein does not play a major role in gene anchoring and that the early recruitment of Mex67p contributes to gene repositioning by virtue of an RNA-independent process.

scholarly journals Strategies to regulate transcription factor–mediated gene positioning and interchromosomal clustering at the nuclear periphery

2016 ◽  
Vol 212 (6) ◽  
pp. 633-646 ◽  
Author(s):  
Carlo Randise-Hinchliff ◽  
Robert Coukos ◽  
Varun Sood ◽  
Michael Chas Sumner ◽  
Stefan Zdraljevic ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Binding Sites ◽  
Nuclear Periphery ◽  
Mitogen Activated Protein Kinase ◽  
Nuclear Pore ◽  
General Function ◽  
Gene Promoters ◽  
Protein Levels ◽  
Gene Positioning

In budding yeast, targeting of active genes to the nuclear pore complex (NPC) and interchromosomal clustering is mediated by transcription factor (TF) binding sites in the gene promoters. For example, the binding sites for the TFs Put3, Ste12, and Gcn4 are necessary and sufficient to promote positioning at the nuclear periphery and interchromosomal clustering. However, in all three cases, gene positioning and interchromosomal clustering are regulated. Under uninducing conditions, local recruitment of the Rpd3(L) histone deacetylase by transcriptional repressors blocks Put3 DNA binding. This is a general function of yeast repressors: 16 of 21 repressors blocked Put3-mediated subnuclear positioning; 11 of these required Rpd3. In contrast, Ste12-mediated gene positioning is regulated independently of DNA binding by mitogen-activated protein kinase phosphorylation of the Dig2 inhibitor, and Gcn4-dependent targeting is up-regulated by increasing Gcn4 protein levels. These different regulatory strategies provide either qualitative switch-like control or quantitative control of gene positioning over different time scales.

scholarly journals Telomere relocalization to the nuclear pore complex in response to replication stress

2020 ◽  
Author(s):  
Alexandra M Pinzaru ◽  
Noa Lamm ◽  
Mike al-Kareh ◽  
Eros Lazzerini-Denchi ◽  
Anthony J Cesare ◽  
...  
Keyword(s):  
Nuclear Pore Complex ◽  
Actin Polymerization ◽  
Nuclear Periphery ◽  
Tumor Development ◽  
Replication Stress ◽  
Nuclear Pore ◽  
Telomere Repeat ◽  
Telomere Binding Protein ◽  
The Impact ◽  
In Cells

AbstractMutations in the telomere binding protein, POT1 are associated with solid tumors and leukemias. POT1 alterations cause rapid telomere elongation, ATR kinase activation, telomere fragility, and accelerated tumor development. Here, we investigated the impact of mutant POT1 alleles through complementary genetic and proteomic approaches based on CRISPR-interference and biotin-based proximity labelling, respectively. These screens revealed that replication stress is a major vulnerability in cells expressing mutant POT1 and manifest in increased mitotic DNA synthesis (MiDAS) at telomeres. Our study also unveiled a role for the nuclear pore complex (NPC) in resolving replication defects at telomeres. Depletion of NPC subunits in the context of POT1 dysfunction increased DNA damage signaling and telomere fragility. Furthermore, we observed telomere repositioning to the nuclear periphery driven by nuclear F-actin polymerization in cells with POT1 mutations. In conclusion, our study establishes that relocalization of dysfunctional telomeres to the nuclear periphery is critical to preserve telomere repeat integrity.

scholarly journals Nuclear Envelope Proteins Modulating the Heterochromatin Formation and Functions in Fission Yeast

Cells ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1908 ◽  
Author(s):  
Yasuhiro Hirano ◽  
Haruhiko Asakawa ◽  
Takeshi Sakuno ◽  
Tokuko Haraguchi ◽  
Yasushi Hiraoka
Keyword(s):  
Endoplasmic Reticulum ◽  
Nuclear Envelope ◽  
Fission Yeast ◽  
Histone Deacetylase ◽  
Nuclear Pore Complex ◽  
Molecular Mechanisms ◽  
Nuclear Pore ◽  
Double Membrane ◽  
Heterochromatin Formation ◽  
Nuclear Membranes

The nuclear envelope (NE) consists of the inner and outer nuclear membranes (INM and ONM), and the nuclear pore complex (NPC), which penetrates the double membrane. ONM continues with the endoplasmic reticulum (ER). INM and NPC can interact with chromatin to regulate the genetic activities of the chromosome. Studies in the fission yeast Schizosaccharomyces pombe have contributed to understanding the molecular mechanisms underlying heterochromatin formation by the RNAi-mediated and histone deacetylase machineries. Recent studies have demonstrated that NE proteins modulate heterochromatin formation and functions through interactions with heterochromatic regions, including the pericentromeric and the sub-telomeric regions. In this review, we first introduce the molecular mechanisms underlying the heterochromatin formation and functions in fission yeast, and then summarize the NE proteins that play a role in anchoring heterochromatic regions and in modulating heterochromatin formation and functions, highlighting roles for a conserved INM protein, Lem2.

Carrier-Independent Nuclear Import of the Transcription Factor PU.1.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3561-3561
Author(s):  
Nabeel R. Yaseen ◽  
Akiko Takeda ◽  
Reza Nazari ◽  
Helen Shio ◽  
Gunter Blobel ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Nuclear Localization ◽  
Nuclear Pore Complex ◽  
Nuclear Import ◽  
Nuclear Pore ◽  
Permeabilized Cells ◽  
Ultrastructural Studies ◽  
Ets Family ◽  
Ets Domain ◽  
Necessary And Sufficient

Abstract PU.1 is a transcription factor of the Ets family with important functions in hematopoietic cell differentiation. Using GFP-PU.1 fusions, we show that the Ets DNA-binding domain of PU.1 is necessary and sufficient for its nuclear localization. Fluorescence and ultrastructural nuclear import assays showed that PU.1 nuclear import requires energy but not soluble carriers. PU.1 interacted with the FG repeats of nucleoporins Nup62 and Nup153. The binding of PU.1 to Nup153, but not to Nup62, dramatically increased in the presence of RanGMPPNP, indicating the formation of a PU.1/RanGTP/Nup153 complex. The Ets domain accounted for the bulk of the interaction of PU.1 with Nup153 and RanGMPPNP. Since Nup62 is located close to the midplane of the nuclear pore complex (NPC) while Nup153 is at its nuclear side, these findings suggest a model whereby RanGTP propels PU.1 towards the nuclear side of the NPC by increasing its affinity for Nup153. This notion was confirmed by ultrastructural studies using gold-labeled PU.1 in permeabilized cells.

scholarly journals Nuclear pore complex evolution: a trypanosome Mlp analogue functions in chromosomal segregation but lacks transcriptional barrier activity

2014 ◽  
Vol 25 (9) ◽  
pp. 1421-1436 ◽  
Author(s):  
Jennifer M. Holden ◽  
Ludek Koreny ◽  
Samson Obado ◽  
Alexander V. Ratushny ◽  
Wei-Ming Chen ◽  
...  
Keyword(s):  
Nuclear Pore Complex ◽  
Mitotic Spindle ◽  
Nuclear Periphery ◽  
Coiled Coil ◽  
Nuclear Lamina ◽  
Nucleocytoplasmic Transport ◽  
Nuclear Pore ◽  
Dependent Manner ◽  
Major Barrier ◽  
African Trypanosomes

The nuclear pore complex (NPC) has dual roles in nucleocytoplasmic transport and chromatin organization. In many eukaryotes the coiled-coil Mlp/Tpr proteins of the NPC nuclear basket have specific functions in interactions with chromatin and defining specialized regions of active transcription, whereas Mlp2 associates with the mitotic spindle/NPC in a cell cycle–dependent manner. We previously identified two putative Mlp-related proteins in African trypanosomes, TbNup110 and TbNup92, the latter of which associates with the spindle. We now provide evidence for independent ancestry for TbNup92/TbNup110 and Mlp/Tpr proteins. However, TbNup92 is required for correct chromosome segregation, with knockout cells exhibiting microaneuploidy and lowered fidelity of telomere segregation. Further, TbNup92 is intimately associated with the mitotic spindle and spindle anchor site but apparently has minimal roles in control of gene transcription, indicating that TbNup92 lacks major barrier activity. TbNup92 therefore acts as a functional analogue of Mlp/Tpr proteins, and, together with the lamina analogue NUP-1, represents a cohort of novel proteins operating at the nuclear periphery of trypanosomes, uncovering complex evolutionary trajectories for the NPC and nuclear lamina.

scholarly journals Random sub-diffusion and capture of genes by the nuclear pore reduces dynamics and coordinates interchromosomal movement

2021 ◽  
Author(s):  
Michael Chas Sumner ◽  
Steven B. Torrisi ◽  
Donna Garvey Brickner ◽  
Jason H. Brickner
Keyword(s):  
Brownian Motion ◽  
Fractional Brownian Motion ◽  
Nuclear Pore Complex ◽  
Nuclear Periphery ◽  
Experimental Models ◽  
Nuclear Pore ◽  
Dynamic Tracking ◽  
Diffusive Movement ◽  
Chromosomal Loci

ABSTRACTHundreds of genes interact with the yeast nuclear pore complex (NPC), localizing at the nuclear periphery and clustering with co-regulated genes. Dynamic tracking of peripheral genes shows that they cycle on and off the NPC and that interaction with the NPC slows their sub-diffusive movement. Furthermore, NPC-dependent inter-chromosomal clustering leads to coordinated movement of pairs of loci separated by hundreds of nanometers. We developed Fractional Brownian Motion simulations for chromosomal loci in the nucleoplasm and interacting with NPCs. These simulations predict the rate and nature of random sub-diffusion during repositioning from nucleoplasm to periphery and match measurements from two different experimental models, arguing that recruitment to the nuclear periphery is due to random subdiffusion, collision, and capture by NPCs. Finally, the simulations do not lead to inter-chromosomal clustering or coordinated movement, suggesting that interaction with the NPC is necessary, but not sufficient, to cause clustering.

scholarly journals Evolutionary conserved protein motifs drive attachment of the plant nucleoskeleton at nuclear pores

2021 ◽  
Author(s):  
Sarah Mermet ◽  
Maxime Voisin ◽  
Joris Mordier ◽  
Tristan Dubos ◽  
Sylvie Tutois ◽  
...  
Keyword(s):  
Nuclear Pore Complex ◽  
Evolutionary History ◽  
Nuclear Periphery ◽  
Land Plants ◽  
Nuclear Pore ◽  
Nuclear Pores ◽  
Protein Motifs ◽  
Peptide Motifs ◽  
Functional Regions ◽  
Computational Predictions

ABSTRACTThe nucleoskeleton forms a filamentous meshwork under the nuclear envelope and contributes to the regulation of nuclear morphology and gene expression. To understand how the Arabidopsis nucleoskeleton physically connects to the nuclear periphery, we investigated the nucleoskeleton protein KAKU4 and sought for functional regions responsible for its localization at the nuclear periphery. Computational predictions identified three evolutionary conserved peptide motifs within the N-terminal region of KAKU4. Functional analysis revealed that these motifs are required for homomerization of KAKU4, interaction with the nucleoskeleton proteins CROWDED NUCLEI (CRWN) and localization at the nuclear periphery. We find that similar protein motifs are present in NUP82 and NUP136, two plant specific nucleoporins from the Nuclear Pore Complex (NPC) basket. These conserved motifs allow the two nucleoporins to bind CRWN proteins, thus revealing a physical link between the nucleoskeleton and nuclear pores in plants. Finally, whilst NUP82, NUP136 and KAKU4 have a common evolutionary history predating non-vascular land plants, KAKU4 mainly localizes outside the NPC suggesting neofunctionalization of an ancient nucleoporin into a new nucleoskeleton component.

scholarly journals Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding at cis-regulatory elements and TAD boundaries

2020 ◽  
Author(s):  
Shinichi Kadota ◽  
Jianhong Ou ◽  
Yuming Shi ◽  
Jiayu Sun ◽  
Eda Yildirim
Keyword(s):  
Nuclear Pore Complex ◽  
Mammalian Cells ◽  
Molecular Mechanisms ◽  
Es Cells ◽  
Embryonic Stem ◽  
Regulatory Elements ◽  
Temporal Organization ◽  
Nuclear Pore ◽  
Developmental Genes ◽  
Chromatin Architecture

ABSTRACTThe nuclear pore complex (NPC) components, nucleoporins (Nups), have been proposed to mediate spatial and temporal organization of chromatin during gene regulation. Nevertheless, we have little understanding on the molecular mechanisms that underlie Nup-mediated chromatin structure and transcription in mammals. Here, we show that Nucleoporin 153 (NUP153) interacts with the chromatin architectural proteins, CTCF and cohesin, and mediates their binding across cis-regulatory elements and TAD boundaries in mouse embryonic stem (ES) cells. NUP153 depletion results in altered CTCF and cohesin occupancy and differential gene expression. This function of NUP153 is most prevalent at the developmental genes that show bivalent chromatin state. To dissect the functional relevance of NUP153-mediated CTCF and cohesin binding during transcriptional activation or silencing, we utilized epidermal growth factor (EGF)-inducible immediate early genes (IEGs). We found that NUP153 binding at the cis-regulatory elements controls CTCF and cohesin binding and subsequent POL II pausing during the transcriptionally silent state. Furthermore, efficient and timely transcription initiation of IEGs relies on NUP153 and occurs around the nuclear periphery suggesting that NUP153 acts as an activator of IEG transcription. Collectively, these results uncover a key role for NUP153 in chromatin architecture and transcription by mediating CTCF and cohesin binding in mammalian cells. We propose that NUP153 links NPCs to chromatin architecture allowing developmental genes and IEGs that are poised to respond rapidly to developmental cues to be properly modulated.

Sign in / Sign up

Export Citation Format

Share Document