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1.
Article in English | MEDLINE | ID: mdl-34127448

ABSTRACT

The nuclear pore complex (NPC) is a highly conserved channel in the nuclear envelope that mediates mRNA export to the cytosol and bidirectional protein transport. Many chromosomal loci physically interact with nuclear pore proteins (Nups), and interactions with Nups can promote transcriptional repression, transcriptional activation, and transcriptional poising. Interaction with the NPC also affects the spatial arrangement of genes, interchromosomal clustering, and folding of topologically associated domains. Thus, the NPC is a spatial organizer of the genome and regulator of genome function.


Subject(s)
Nuclear Pore Complex Proteins , Nuclear Pore , Active Transport, Cell Nucleus , Genome , Nuclear Pore/genetics , Nuclear Pore/metabolism , Nuclear Pore Complex Proteins/genetics , Nuclear Pore Complex Proteins/metabolism , Protein Transport
2.
Elife ; 102021 05 18.
Article in English | MEDLINE | ID: mdl-34002694

ABSTRACT

Hundreds 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 sub-diffusion and transient 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.


Subject(s)
Chromatin/metabolism , Nuclear Pore/metabolism , Saccharomyces cerevisiae/metabolism , Active Transport, Cell Nucleus , Cell Nucleus , Chromatin/genetics , Computer Simulation , Nuclear Pore/genetics , Saccharomyces cerevisiae/cytology , Saccharomyces cerevisiae/genetics
3.
J Cell Biol ; 212(6): 633-46, 2016 Mar 14.
Article in English | MEDLINE | ID: mdl-26953353

ABSTRACT

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.


Subject(s)
Chromosomes, Fungal/genetics , Gene Expression Regulation, Fungal/genetics , Multigene Family/genetics , Nuclear Pore/genetics , Transcription Factors/metabolism , Binding Sites/genetics , Cell Nucleus/genetics , Cell Nucleus/metabolism , Cluster Analysis , Fungal Proteins/genetics , Fungal Proteins/metabolism , Histone Deacetylases/metabolism , Phosphorylation/genetics , Transcriptional Activation/genetics , Up-Regulation/genetics , Yeasts/genetics , Yeasts/metabolism
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