Connecting the transcription site to the nuclear pore: a multi-tether process that regulates gene expression

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.

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Caenorhabditis elegans Nuclear Pore Complexes in Genome Organization and Gene Expression

Nuclear Pore Complexes in Genome Organization, Function and Maintenance ◽

10.1007/978-3-319-71614-5_6 ◽

2018 ◽

pp. 137-158

Author(s):

Celia María Muñoz-Jiménez ◽

Peter Askjaer

Keyword(s):

Gene Expression ◽

Caenorhabditis Elegans ◽

Genome Organization ◽

Nuclear Pore ◽

Nuclear Pore Complexes ◽

Pore Complexes

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Abstract P217: Nuclear Protein Import as the Missing Link in Phenylephrine-Induced Cardiomyocyte Hypertrophy

Circulation Research ◽

10.1161/res.109.suppl_1.ap217 ◽

2011 ◽

Vol 109 (suppl_1) ◽

Author(s):

Mirna N Chahine ◽

Maxime Mioulane ◽

Gabor Földes ◽

Alexander Lyon ◽

Sian E Harding

Keyword(s):

Gene Expression ◽

Nuclear Export ◽

Protein Import ◽

Nuclear Protein ◽

Nuclear Translocation ◽

Cardiomyocyte Hypertrophy ◽

Nuclear Pore ◽

Nucleocytoplasmic Trafficking ◽

Adult Rat ◽

Nuclear Protein Import

During cardiac hypertrophy, cardiomyocytes (CM) present alterations in gene expression and increased contractile protein content. Nuclear protein import (NPI) is critical in regulating gene expression, transcription, and subsequently cell hypertrophy. However, it is unknown how the nuclear transport machinery (transport receptors and nuclear pore complex (NPC)) functions to sustain increased demands for nucleocytoplasmic trafficking. The aim of this study was to determine if exposure of adult CM to phenylephrine (PE) affects hypertrophy by altering NPI and NPC density. Comparisons were made to adult failing rat and human CM. Rat myocytes were enzymatically isolated from adult hearts, and used for immunocytochemistry, qPCR and western immunoblotting. Failing CM were obtained from explanted human hearts at the time of transplant and from a rat model of myocardial infarction-induced hypertrophy and failure. Rat adult CM exposed for 48h to PE were injected with a protein import substrate (Alexa488-BSA-NLS) to visually monitor nuclear import with the confocal microscope. The effects of P38 MAPK inhibitor, HDAC inhibitor, Exportin-1 (CRM-1) inhibitor, and GSK-3 β inhibitor were investigated. Cell and nuclear sizes were increased in PE treated-adult rat CM and in the adult failing rat and human CM compared to normal CM. In contrast, PE depressed the rate and maximal NPI (by 65 +/- 3.4 % (3.55 from 5.46), p<0.05) as well as nucleoporin p62 mRNA and protein expression levels in adult rat CM compared to non-treated CM. Nucleoporin p62, cytoplasmic Ranbp1, and nuclear translocation of importins (Imp.α and β) relative densities were also decreased in PE treated-adult rat CM and in adult failing rat CM and human heart tissue compared to normal controls. On the contrary, CRM-1 nuclear export relative density was increased during the same pathological conditions. Thus NPI downregulation is linked to an increased nuclear export required by CM to generate the hypertrophic phenotype. All these effects were P38MAPK, HDAC and CRM-1 dependent but GSK-3Beta independent in rat CM. Our results show that alterations in NPI and NPC density occur in failing CM as well as in CM under hypertrophic stimuli. NPI may represent a critical therapeutic target in hypertrophic conditions.

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Actin-based motility drives baculovirus transit to the nucleus and cell surface

The Journal of Cell Biology ◽

10.1083/jcb.201001162 ◽

2010 ◽

Vol 190 (2) ◽

pp. 187-195 ◽

Cited By ~ 143

Author(s):

Taro Ohkawa ◽

Loy E. Volkman ◽

Matthew D. Welch

Keyword(s):

Gene Expression ◽

Actin Polymerization ◽

Nuclear Periphery ◽

Viral Gene Expression ◽

Early Gene ◽

Evolutionary Strategy ◽

Viral Gene ◽

Nuclear Pore ◽

Nuclear Pore Complexes ◽

Nuclear Entry

Most viruses move intracellularly to and from their sites of replication using microtubule-based mechanisms. In this study, we show that nucleocapsids of the baculovirus Autographa californica multiple nucleopolyhedrovirus undergo intracellular motility driven by actin polymerization. Motility requires the viral P78/83 capsid protein and the host Arp2/3 complex. Surprisingly, the virus directs two sequential and coordinated phases of actin-based motility. Immediately after cell entry, motility enables exploration of the cytoplasm and collision with the nuclear periphery, speeding nuclear entry and the initiation of viral gene expression. Nuclear entry itself requires transit through nuclear pore complexes. Later, after the onset of early gene expression, motility is required for accumulation of a subpopulation of nucleocapsids in the tips of actin-rich surface spikes. Temporal coordination of actin-based nuclear and surface translocation likely enables rapid transmission to neighboring cells during infection in insects and represents a distinctive evolutionary strategy for overcoming host defenses.

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The autophagy protein Ambra1 regulates gene expression by supporting novel transcriptional complexes

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.012565 ◽

2020 ◽

Vol 295 (34) ◽

pp. 12045-12057

Author(s):

Christina Schoenherr ◽

Adam Byron ◽

Billie Griffith ◽

Alexander Loftus ◽

Jimi C. Wills ◽

...

Keyword(s):

Gene Expression ◽

Cancer Cell ◽

Cell Invasion ◽

Cell Biology ◽

Protein Complexes ◽

Transcriptional Regulators ◽

Adaptor Proteins ◽

Nuclear Pore ◽

Biochemical Fractionation

Ambra1 is considered an autophagy and trafficking protein with roles in neurogenesis and cancer cell invasion. Here, we report that Ambra1 also localizes to the nucleus of cancer cells, where it has a novel nuclear scaffolding function that controls gene expression. Using biochemical fractionation and proteomics, we found that Ambra1 binds to multiple classes of proteins in the nucleus, including nuclear pore proteins, adaptor proteins such as FAK and Akap8, chromatin-modifying proteins, and transcriptional regulators like Brg1 and Atf2. We identified biologically important genes, such as Angpt1, Tgfb2, Tgfb3, Itga8, and Itgb7, whose transcription is regulated by Ambra1-scaffolded complexes, likely by altering histone modifications and Atf2 activity. Therefore, in addition to its recognized roles in autophagy and trafficking, Ambra1 scaffolds protein complexes at chromatin, regulating transcriptional signaling in the nucleus. This novel function for Ambra1, and the specific genes impacted, may help to explain the wider role of Ambra1 in cancer cell biology.

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Nuclear Envelope and Nuclear Pore Complexes in Neurodegenerative Diseases—New Perspectives for Therapeutic Interventions

Molecular Neurobiology ◽

10.1007/s12035-020-02168-x ◽

2020 ◽

Author(s):

Naomi Hachiya ◽

Marta Sochocka ◽

Anna Brzecka ◽

Takuto Shimizu ◽

Kazimierz Gąsiorowski ◽

...

Keyword(s):

Gene Expression ◽

Neurodegenerative Diseases ◽

Nuclear Envelope ◽

Neurodegenerative Disorders ◽

Nuclear Transport ◽

Therapeutic Interventions ◽

Nuclear Pore ◽

Nuclear Pore Complexes ◽

Pore Complexes ◽

Bidirectional Exchange

Abstract Transport of proteins, transcription factors, and other signaling molecules between the nucleus and cytoplasm is necessary for signal transduction. The study of these transport phenomena is particularly challenging in neurons because of their highly polarized structure. The bidirectional exchange of molecular cargoes across the nuclear envelope (NE) occurs through nuclear pore complexes (NPCs), which are aqueous channels embedded in the nuclear envelope. The NE and NPCs regulate nuclear transport but are also emerging as relevant regulators of chromatin organization and gene expression. The alterations in nuclear transport are regularly identified in affected neurons associated with human neurodegenerative diseases. This review presents insights into the roles played by nuclear transport defects in neurodegenerative disease, focusing primarily on NE proteins and NPCs. The subcellular mislocalization of proteins might be a very desirable means of therapeutic intervention in neurodegenerative disorders.

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The nuclear basket proteins Mlp1p and Mlp2p are part of a dynamic interactome including Esc1p and the proteasome

Molecular Biology of the Cell ◽

10.1091/mbc.e13-07-0412 ◽

2013 ◽

Vol 24 (24) ◽

pp. 3920-3938 ◽

Cited By ~ 63

Author(s):

Mario Niepel ◽

Kelly R. Molloy ◽

Rosemary Williams ◽

Julia C. Farr ◽

Anne C. Meinema ◽

...

Keyword(s):

Gene Expression ◽

Nuclear Pore Complex ◽

Nuclear Export ◽

Regulation Of Gene Expression ◽

Nuclear Pore ◽

Docking Site ◽

Discrete Structure ◽

Transport Channel ◽

Macromolecular Complexes ◽

Nuclear Stability

The basket of the nuclear pore complex (NPC) is generally depicted as a discrete structure of eight protein filaments that protrude into the nucleoplasm and converge in a ring distal to the NPC. We show that the yeast proteins Mlp1p and Mlp2p are necessary components of the nuclear basket and that they also embed the NPC within a dynamic protein network, whose extended interactome includes the spindle organizer, silencing factors, the proteasome, and key components of messenger ribonucleoproteins (mRNPs). Ultrastructural observations indicate that the basket reduces chromatin crowding around the central transporter of the NPC and might function as a docking site for mRNP during nuclear export. In addition, we show that the Mlps contribute to NPC positioning, nuclear stability, and nuclear envelope morphology. Our results suggest that the Mlps are multifunctional proteins linking the nuclear transport channel to multiple macromolecular complexes involved in the regulation of gene expression and chromatin maintenance.

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The inner nuclear membrane protein Src1 associates with subtelomeric genes and alters their regulated gene expression

The Journal of Cell Biology ◽

10.1083/jcb.200803098 ◽

2008 ◽

Vol 182 (5) ◽

pp. 897-910 ◽

Cited By ~ 75

Author(s):

Stefanie E. Grund ◽

Tamás Fischer ◽

Ghislain G. Cabal ◽

Oreto Antúnez ◽

José E. Pérez-Ortín ◽

...

Keyword(s):

Gene Expression ◽

Membrane Protein ◽

Nuclear Membrane ◽

Genetic Interaction ◽

Nuclear Pore ◽

Inner Nuclear Membrane ◽

Regulated Gene Expression ◽

Inner Nuclear Membrane Protein ◽

Subtelomeric Regions ◽

Nuclear Membrane Protein

Inner nuclear membrane proteins containing a LEM (LAP2, emerin, and MAN1) domain participate in different processes, including chromatin organization, gene expression, and nuclear envelope biogenesis. In this study, we identify a robust genetic interaction between transcription export (TREX) factors and yeast Src1, an integral inner nuclear membrane protein that is homologous to vertebrate LEM2. DNA macroarray analysis revealed that the expression of the phosphate-regulated genes PHO11, PHO12, and PHO84 is up-regulated in src1Δ cells. Notably, these PHO genes are located in subtelomeric regions of chromatin and exhibit a perinuclear location in vivo. Src1 spans the nuclear membrane twice and exposes its N and C domains with putative DNA-binding motifs to the nucleoplasm. Genome-wide chromatin immunoprecipitation–on-chip analyses indicated that Src1 is highly enriched at telomeres and subtelomeric regions of the yeast chromosomes. Our data show that the inner nuclear membrane protein Src1 functions at the interface between subtelomeric gene expression and TREX-dependent messenger RNA export through the nuclear pore complexes.

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