scholarly journals Mapping the micro-proteome of the nuclear lamina and lamina-associated domains

2021 ◽  
Vol 4 (5) ◽  
pp. e202000774
Author(s):  
Xianrong Wong ◽  
Jevon A Cutler ◽  
Victoria E Hoskins ◽  
Molly Gordon ◽  
Anil K Madugundu ◽  
...  
Keyword(s):  
Large Fraction ◽  
Nuclear Periphery ◽  
Nuclear Lamina ◽  
Mammalian Genome ◽  
Live Cells ◽  
H3k9 Methylation ◽  
Tracer System ◽  
Membrane Bound ◽  
Gene Regulatory ◽  
Regulatory Functions

The nuclear lamina is a proteinaceous network of filaments that provide both structural and gene regulatory functions by tethering proteins and large domains of DNA, the so-called lamina-associated domains (LADs), to the periphery of the nucleus. LADs are a large fraction of the mammalian genome that are repressed, in part, by their association to the nuclear periphery. The genesis and maintenance of LADs is poorly understood as are the proteins that participate in these functions. In an effort to identify proteins that reside at the nuclear periphery and potentially interact with LADs, we have taken a two-pronged approach. First, we have undertaken an interactome analysis of the inner nuclear membrane bound LAP2β to further characterize the nuclear lamina proteome. To accomplish this, we have leveraged the BioID system, which previously has been successfully used to characterize the nuclear lamina proteome. Second, we have established a system to identify proteins that bind to LADs by developing a chromatin-directed BioID system. We combined the BioID system with the m6A-tracer system which binds to LADs in live cells to identify both LAD proximal and nuclear lamina proteins. In combining these datasets, we have further characterized the protein network at the nuclear lamina, identified putative LAD proximal proteins and found several proteins that appear to interface with both micro-proteomes. Importantly, several proteins essential for LAD function, including heterochromatin regulating proteins related to H3K9 methylation, were identified in this study.

scholarly journals Mapping the micro-proteome of the nuclear lamina and lamin associated domains

2019 ◽  
Author(s):  
Jevon A. Cutler ◽  
Xianrong Wong ◽  
Victoria E. Hoskins ◽  
Molly Gordon ◽  
Anil K. Madugundu ◽  
...  
Keyword(s):  
Large Fraction ◽  
Nuclear Periphery ◽  
Nuclear Lamina ◽  
Mammalian Genome ◽  
Live Cells ◽  
H3k9 Methylation ◽  
Tracer System ◽  
Membrane Bound ◽  
Gene Regulatory ◽  
Regulatory Functions

AbstractThe nuclear lamina is a proteinaceous network of filaments that provide both structural and gene regulatory functions by tethering proteins and large domains of DNA, so-called lamin associated domains (LADs), to the periphery of the nucleus. LADs are a large fraction of the mammalian genome that are repressed, in part, by their association to the nuclear periphery. The genesis and maintenance of LADs is poorly understood as are the proteins that participate in these functions. In an effort to identify proteins that reside at the nuclear periphery and potentially interact with LADs, we have taken a two-pronged approach. First, we have undertaken an interactome analysis of the inner nuclear membrane bound LAP2β to further characterize the nuclear lamina proteome. To accomplish this, we have leveraged the BioID system, which previously has been successfully used to characterize the nuclear lamina proteome. Second, we have established a system to identify proteins that bind to LADs by developing a chromatin directed BioID system. We combined the BioID system with the m6A-tracer system which binds to LADs in live cells to identify both LAD proximal and nuclear lamina proteins. In combining these datasets, we have further characterized the protein network at the nuclear lamina, identified putative LAD proximal proteins and found several proteins that appear to interface with both micro-proteomes. Importantly, several proteins essential for LAD function, including heterochromatin regulating proteins related to H3K9 methylation, were identified in this study.

scholarly journals Prdm16-mediated H3K9 methylation controls fibro-adipogenic progenitors identity during skeletal muscle repair

2021 ◽  
Vol 7 (23) ◽  
pp. eabd9371
Author(s):  
Beatrice Biferali ◽  
Valeria Bianconi ◽  
Daniel Fernandez Perez ◽  
Sophie Pöhle Kronawitter ◽  
Fabrizia Marullo ◽  
...  
Keyword(s):  
Envelope Protein ◽  
Nuclear Periphery ◽  
Nuclear Lamina ◽  
H3k9 Methylation ◽  
Cell Type ◽  
Specific Manner ◽  
A Cell ◽  
Cell Type Specific ◽  
Genomic Regions

H3K9 methylation maintains cell identity orchestrating stable silencing and anchoring of alternate fate genes within the heterochromatic compartment underneath the nuclear lamina (NL). However, how cell type–specific genomic regions are specifically targeted to the NL is still elusive. Using fibro-adipogenic progenitors (FAPs) as a model, we identified Prdm16 as a nuclear envelope protein that anchors H3K9-methylated chromatin in a cell-specific manner. We show that Prdm16 mediates FAP developmental capacities by orchestrating lamina-associated domain organization and heterochromatin sequestration at the nuclear periphery. We found that Prdm16 localizes at the NL where it cooperates with the H3K9 methyltransferases G9a/GLP to mediate tethering and silencing of myogenic genes, thus repressing an alternative myogenic fate in FAPs. Genetic and pharmacological disruption of this repressive pathway confers to FAP myogenic competence, preventing fibro-adipogenic degeneration of dystrophic muscles. In summary, we reveal a druggable mechanism of heterochromatin perinuclear sequestration exploitable to reprogram FAPs in vivo.

scholarly journals The PRR14 heterochromatin tether encodes modular domains that mediate and regulate nuclear lamina targeting

2019 ◽  
Author(s):  
Kelly L. Dunlevy ◽  
Valentina Medvedeva ◽  
Jade E. Wilson ◽  
Mohammed Hoque ◽  
Trinity Pellegrin ◽  
...  
Keyword(s):  
Nuclear Membrane ◽  
Large Fraction ◽  
Nuclear Periphery ◽  
Nuclear Lamina ◽  
Binding Domain ◽  
Recognition Site ◽  
Evolutionarily Conserved ◽  
Engineering Strategy ◽  
Necessary And Sufficient ◽  
Modular Domains

AbstractA large fraction of epigenetically silent heterochromatin is anchored to the nuclear periphery via “tethering proteins” that function to bridge heterochromatin and the nuclear membrane or nuclear lamina. We identified previously a human tethering protein, PRR14, that binds heterochromatin through an N-terminal domain, but the mechanism and regulation of nuclear lamina association remained to be investigated. Here we identify a centrally located, evolutionarily conserved PRR14 nuclear lamina binding domain (LBD) that is both necessary and sufficient for positioning of PRR14 at the nuclear lamina. We also show that PRR14 associates dynamically with the nuclear lamina, and provide evidence that such dynamics are regulated through phosphorylation of the LBD. We also show that the evolutionary conserved PRR14 C-terminal Tantalus domain encodes a PP2A phosphatase recognition site that regulates PRR14 nuclear lamina association. The overall findings demonstrate a heterochromatin anchoring mechanism whereby the PRR14 tether simultaneously binds heterochromatin and the nuclear lamina through two modular domains. Furthermore, the identification of a modular LBD may provide an engineering strategy for delivery of cargo to the nuclear lamina.

scholarly journals Lamin B1 acetylation slows the G1 to S cell cycle transition through inhibition of DNA repair

2021 ◽  
Author(s):  
Laura A Murray-Nerger ◽  
Joshua L Justice ◽  
Pranav Rekapalli ◽  
Josiah E Hutton ◽  
Ileana M Cristea
Keyword(s):  
Cell Cycle ◽  
Dna Repair ◽  
Posttranslational Modifications ◽  
Cell Cycle Progression ◽  
Nuclear Periphery ◽  
Virus Production ◽  
Nuclear Lamina ◽  
Regulatory Function ◽  
Herpesvirus Type ◽  
Lamin B1

Abstract The integrity and regulation of the nuclear lamina is essential for nuclear organization and chromatin stability, with its dysregulation being linked to laminopathy diseases and cancer. Although numerous posttranslational modifications have been identified on lamins, few have been ascribed a regulatory function. Here, we establish that lamin B1 (LMNB1) acetylation at K134 is a molecular toggle that controls nuclear periphery stability, cell cycle progression, and DNA repair. LMNB1 acetylation prevents lamina disruption during herpesvirus type 1 (HSV-1) infection, thereby inhibiting virus production. We also demonstrate the broad impact of this site on laminar processes in uninfected cells. LMNB1 acetylation negatively regulates canonical nonhomologous end joining by impairing the recruitment of 53BP1 to damaged DNA. This defect causes a delay in DNA damage resolution and a persistent activation of the G1/S checkpoint. Altogether, we reveal LMNB1 acetylation as a mechanism for controlling DNA repair pathway choice and stabilizing the nuclear periphery.

scholarly journals Differences in size, structure and function of free and membrane-bound polyribosomes of rat liver. Evidence for a single class of membrane-bound polyribosomes

1977 ◽  
Vol 168 (1) ◽  
pp. 1-8 ◽  
Author(s):  
J C Ramsey ◽  
W J Steele
Keyword(s):  
Protein Synthesis ◽  
Rat Liver ◽  
Size Structure ◽  
Large Fraction ◽  
Liver Homogenate ◽  
Structure And Function ◽  
Structural And Functional Properties ◽  
Membrane Bound ◽  
And Function

Free loosely bound and tightly bound polyribosomes were separated from rat liver homogenate by salt extraction followed by differential centrifugation, and several of their structural and functional properties were compared to resolve the existence of loosely bound polyribosomes and verify the specificity of the separation. The free and loosely bound polyribosomes have similar sedimentation profiles and polyribosome contents, their subunit proteins have similar electrophoretic patterns and their products of protein synthesis in vitro show a close correspondence in size and amounts synthesized. In contrast, the tightly bound polyribosomes have different properties from those of the free and loosely bound polyribosomes; their average size is significantly smaller; their polyribosome content is higher; their 60 S-subunit proteins lack two components and contain four or more components not found elsewhere; their products of protein synthesis in vitro differ in size and amounts synthesized. These observations show that rat liver membranes entrap a large fraction of the free polyribosomes at low salt concentrations and that these polyribosomes are similar to those of the free-polyribosome fraction and are different from those of the tightly bound polyribosome fraction in size, structure and function.

scholarly journals Nuclear Cytoskeleton in Virus Infection

2022 ◽  
Vol 23 (1) ◽  
pp. 578
Author(s):  
Lenka Horníková ◽  
Kateřina Bruštíková ◽  
Sandra Huérfano ◽  
Jitka Forstová
Keyword(s):  
Virus Infection ◽  
Nuclear Periphery ◽  
Nuclear Lamina ◽  
Nuclear Actin ◽  
Nuclear Egress ◽  
Viral Particles ◽  
Replication Sites ◽  
Main Component ◽  
Virus Egress ◽  
Natural Barrier

The nuclear lamina is the main component of the nuclear cytoskeleton that maintains the integrity of the nucleus. However, it represents a natural barrier for viruses replicating in the cell nucleus. The lamina blocks viruses from being trafficked to the nucleus for replication, but it also impedes the nuclear egress of the progeny of viral particles. Thus, viruses have evolved mechanisms to overcome this obstacle. Large viruses induce the assembly of multiprotein complexes that are anchored to the inner nuclear membrane. Important components of these complexes are the viral and cellular kinases phosphorylating the lamina and promoting its disaggregation, therefore allowing virus egress. Small viruses also use cellular kinases to induce lamina phosphorylation and the subsequent disruption in order to facilitate the import of viral particles during the early stages of infection or during their nuclear egress. Another component of the nuclear cytoskeleton, nuclear actin, is exploited by viruses for the intranuclear movement of their particles from the replication sites to the nuclear periphery. This study focuses on exploitation of the nuclear cytoskeleton by viruses, although this is just the beginning for many viruses, and promises to reveal the mechanisms and dynamic of physiological and pathological processes in the nucleus.

scholarly journals Exosomic microRNAs as emerging key regulators of intercellular communication in the tumor microenvironment and beyond

2016 ◽  
Vol 2 (1) ◽  
Author(s):  
Mariam Murtadha ◽  
Muller Fabbri
Keyword(s):  
Tumor Microenvironment ◽  
Cancer Patients ◽  
Intercellular Communication ◽  
Potential Role ◽  
Biological Fluids ◽  
Healthy Controls ◽  
Gene Regulatory ◽  
Non Coding Rnas ◽  
Regulatory Functions

AbstractMicroRNAs (miRs) are small non-coding RNAs with key gene regulatory functions. Recent evidence has shown that miRs have a central role in shaping the biology of the Tumor Microenvironment (TME). The discovery that some exosomes contain high levels of miR cargo that shuttle between cells and mediate intercellular cross-talk has shifted the focus of miR research towards understanding the biological role of exosomic miRs. In this review, we highlight the emerging role of exosomic miRs in molding the tumor microenvironment towards pro-tumor conditions by altering intercellular communication. We briefly discuss some mechanisms of selective loading of miRs into exosomes, as well as emerging evidence that exosomic miRs are present in all biological fluids. Furthermore, we describe the differences in the exosomic miR signatures between cancer patients and healthy controls, and the potential role of exosomic miRs as diagnostic, prognostic, and therapeutic biomarkers.

scholarly journals H3K9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Andrey Poleshko ◽  
Cheryl L Smith ◽  
Son C Nguyen ◽  
Priya Sivaramakrishnan ◽  
Karen G Wong ◽  
...  
Keyword(s):  
Cell Division ◽  
Spatial Organization ◽  
Nuclear Periphery ◽  
Nuclear Lamina ◽  
Positional Information ◽  
Specific Gene ◽  
Cell Type ◽  
Histone 3 ◽  
Spatial Positioning ◽  
Peripheral Heterochromatin

Cell-type-specific 3D organization of the genome is unrecognizable during mitosis. It remains unclear how essential positional information is transmitted through cell division such that a daughter cell recapitulates the spatial genome organization of the parent. Lamina-associated domains (LADs) are regions of repressive heterochromatin positioned at the nuclear periphery that vary by cell type and contribute to cell-specific gene expression and identity. Here we show that histone 3 lysine 9 dimethylation (H3K9me2) is an evolutionarily conserved, specific mark of nuclear peripheral heterochromatin and that it is retained through mitosis. During mitosis, phosphorylation of histone 3 serine 10 temporarily shields the H3K9me2 mark allowing for dissociation of chromatin from the nuclear lamina. Using high-resolution 3D immuno-oligoFISH, we demonstrate that H3K9me2-enriched genomic regions, which are positioned at the nuclear lamina in interphase cells prior to mitosis, re-associate with the forming nuclear lamina before mitotic exit. The H3K9me2 modification of peripheral heterochromatin ensures that positional information is safeguarded through cell division such that individual LADs are re-established at the nuclear periphery in daughter nuclei. Thus, H3K9me2 acts as a 3D architectural mitotic guidepost. Our data establish a mechanism for epigenetic memory and inheritance of spatial organization of the genome.

The nuclear lamina and heterochromatin: a complex relationship

2011 ◽  
Vol 39 (6) ◽  
pp. 1705-1709 ◽  
Author(s):  
Erin M. Bank ◽  
Yosef Gruenbaum
Keyword(s):  
Nuclear Periphery ◽  
Gene Activation ◽  
Nuclear Lamina ◽  
Current Evidence ◽  
Specific Gene ◽  
Nuclear Interior ◽  
Gene Retention ◽  
Gene Positioning ◽  
Review Current ◽  
Active Genes

In metazoan cells, the heterochromatin is generally localized at the nuclear periphery, whereas active genes are preferentially found in the nuclear interior. In the present paper, we review current evidence showing that components of the nuclear lamina interact directly with heterochromatin, which implicates the nuclear lamina in a mechanism of specific gene retention at the nuclear periphery and release to the nuclear interior upon gene activation. We also discuss recent data showing that mutations in lamin proteins affect gene positioning and expression, providing a potential mechanism for how these mutations lead to tissue-specific diseases.

Ammonium utilization in Bacillus subtilis: transport and regulatory functions of NrgA and NrgB

Microbiology ◽  
2003 ◽  
Vol 149 (11) ◽  
pp. 3289-3297 ◽  
Author(s):  
Christian Detsch ◽  
Jörg Stülke
Keyword(s):  
Bacillus Subtilis ◽  
Large Fraction ◽  
Glutamate Synthase ◽  
Nitrogen Sources ◽  
Covalent Modification ◽  
Ammonium Transporter ◽  
Ammonium Ion ◽  
Ammonium Transport ◽  
Low Concentrations ◽  
Regulatory Functions

Bacillus subtilis uses glutamine as the best source of nitrogen. In the absence of glutamine, alternative nitrogen sources such as ammonium can be used. Ammonium utilization involves the uptake of the gas or the ammonium ion, the synthesis of glutamine by the glutamine synthetase and the recycling of the glutamate by the glutamate synthase. In this work, ammonium transport in B. subtilis was studied. At high ammonium concentrations, a large fraction of the ammonium is present as ammonia, which may enter the cell via diffusion. In contrast, the ammonium transporter NrgA is required for ammonium utilization at low concentrations or at low pH values when the equilibrium between uncharged ammonia and the ammonium ion is shifted towards ammonium. Moreover, a functional NrgA is essential for the transport of the ammonium analogue methylammonium. NrgA is encoded in the nrgAB operon. The product of the second gene, NrgB, is a member of the PII family of regulatory proteins. In contrast to PII proteins from other organisms, there is no indication for a covalent modification of NrgB in response to the nitrogen supply of the cell. It is demonstrated here that NrgB is localized at the membrane, most likely in association with the ammonium transporter NrgA. The presence of a functional NrgB is required for full-level expression of the nrgAB operon in response to nitrogen limitation, suggesting that NrgB might relay the information on ammonium availability to downstream regulatory factors and thus fine-tune their activity.

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