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42 results for “Nuclear Envelope”
Identification of a lineage-specific protein network at the trypanosome nuclear envelope
<p>The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization, nucleocytoplasmic transport, ribosomal maturation and mRNA processing/quality control. The molecular basis for many of these functions have diverged between different eukaryotic lineages. <em>Trypanosoma brucei</em>, a member of the early branching eukaryotic lineage Discoba, highlight many of these, including a distinct lamina and kinetochore composition. Here we describe a cohort of proteins interacting with both the lamina and NPC, which we term lamina-associated proteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with <em>S. cerevisiae </em>Pom152 and <em>H. sapiens </em>Nup210, and additional peripheral components of the NPC. While many of the LAPs are specific to Trypanosomatids, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the NE proteome of trypanosomes, highlighting the diversity of nuclear biology across the eukaryotes and increasing our understanding of eukaryotic and NPC evolution.</p>
Multiple Nuclei HeLa cell ground truth images with four labels (nuclear envelope, nucleus, rest of the cell, and background) for deep learning architecture training.
<p>This is a data set that contains <strong>labelled HeLa cell images</strong>, indicating the four different classes - nuclear envelope, nucleus, rest of the cell, and background. Similar ground truth have been published for this data set, but in this case, multiple nuclei have been labelled, whilst previous ones only focused on the central cell (https://doi.org/10.5281/zenodo.3874949)</p> <p>Details of the imaging, preparation and segmentation have been published in:</p> <ul> <li>Cefa Karabağ, Martin L. Jones, Christopher J. Peddie, Anne E. Weston, Lucy M. Collinson, Constantino Carlos Reyes-Aldasoro. Segmentation and Modelling of the Nuclear Envelope of HeLa Cells Imaged with Serial Block Face Scanning Electron Microscopy. <em>J. Imaging</em> <strong>2019</strong>, <em>5</em>(9), 75; <a href="https://doi.org/10.3390/jimaging5090075">https://doi.org/10.3390/jimaging5090075</a></li> <li>Cefa Karabağ, Martin L. Jones, Christopher J. Peddie, Anne E. Weston, Lucy M. Collinson, Constantino Carlos Reyes-Aldasoro. Semantic segmentation of HeLa cells: An objective comparison between one traditional algorithm and four deep-learning architectures, PLOS ONE, <strong>2020</strong>; <a href="https://doi.org/10.1371/journal.pone.0230605">https://doi.org/10.1371/journal.pone.0230605</a></li> <li> <p>Cefa Karabağ, Martin L. Jones, Constantino Carlos Reyes-Aldasoro, Segmentation of the Plasma Membrane of HeLa Cells,<em> J. Imaging</em> <strong>2021</strong>, <em>7</em>(6), 93; <a href="https://doi.org/10.3390/jimaging7060093">https://doi.org/10.3390/jimaging7060093</a></p> </li> </ul> <ul> <li>The data sets are freely available through EMPIAR: http://dx.doi.org/10.6019/EMPIAR-10094 EMPIAR.</li> </ul>
N-glycosylation acts as a switch for FGFR1 trafficking between the plasma membrane and nuclear envelope - yet unpublished supplementary data regarding Fig. 1C
<p>Fibroblast growth factor receptor 1 (FGFR1) is a heavily N-glycosylated cell surface receptor tyrosine kinase that transmits signals across the plasma membrane, in response to fibroblast growth factors (FGFs). Balanced FGF/FGFR1 signaling is crucial for the development and homeostasis of the human body, and aberrant FGFR1 is frequently observed in various cancers. In addition to its predominant localization to the plasma membrane, FGFR1 has also been detected inside cells, mainly in the nuclear lumen, where it modulates gene expression. However, the exact mechanism of FGFR1 nuclear transport is still unknown. In this study, we generated a glycosylation-free mutant of FGFR1, FGFR1.GF, and demonstrated that it is localized primarily to the nuclear envelope. We show that reintroducing N-glycans into the D3 domain cannot redirect FGFR1 to the plasma membrane or exclude the receptor from the nuclear envelope. Reestablishment of D2 domain N-glycans largely inhibits FGFR1 accumulation in the nuclear envelope, but the receptor continues to accumulate inside the cell, mainly in the ER. Only the simultaneous presence of N-glycans of the D2 and D3 domains of FGFR1 promotes efficient transport of FGFR1 to the plasma membrane. We demonstrate that while disturbed FGFR1 folding results in partial FGFR1 accumulation in the ER, impaired FGFR1 secretion drives FGFR1 trafficking to the nuclear envelope. Intracellular FGFR1.GF displays a high level of autoactivation, suggesting the presence of nuclear FGFR1 signaling, which is independent of FGF. Using mass spectrometry and proximity ligation assay, we identified novel binding partners of the nuclear envelope-localized FGFR1, providing insights into its cellular functions. Collectively, our data define N-glycosylation of FGFR1 as an important regulator of FGFR1 kinase activity and, most importantly, as a switchable signal for FGFR1 trafficking between the nuclear envelope and plasma membrane, which, due to spatial restrictions, shapes FGFR1 interactome and cellular function.</p> <p> </p> <p>These data are raw data of Fig. 1C generated by Aleksandra Chorążewska. These data are not present in supplementary data od publication</p>
Partial-envelope stripping and nuclear-timescale mass transfer from evolved supergiants at low metallicity
<p>Model data and input files (inlists) used to compute MESA binary models to paper<br> "Partial-envelope stripping and nuclear-timescale mass transfer from evolved supergiants at low metallicity"<br> (<a href="https://ui.adsabs.harvard.edu/abs/2021arXiv211110271K/abstract">ADS link</a>)<br> MESA version r11554.<br> <br> The data consists of stellar tracks of the primary (donor) star. Provided are MESA history.data files and the final MESA model of the primary (terminated at core-He depletion).<br> <br> The data for solar metallicity models is also available on request.<br> </p>
Loss of function of the nuclear envelope protein LEMD2 causes DNA damage-dependent cardiomyopathy
GEO Series GSE194218. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Pervasive nuclear envelope ruptures precede ECM signaling and disease onset without activating cGAS-STING in Lamin-cardiomyopathy mice [mRNA-seq]
GEO Series GSE241577. Mus musculus. 46 samples. Type: Expression profiling by high throughput sequencing.
Lamin B2 controls nuclear envelope permeability and regulates cardiomyocyte regeneration
GEO Series GSE108360. Mus musculus. 33 samples. Type: Expression profiling by high throughput sequencing.
Hmga2 protein loss alters nuclear envelope and affects 3D chromatin structure upon the induction of pluripotent stem cell commitment [ChIP-seq]
GEO Series GSE200671. Mus musculus. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Pervasive nuclear envelope ruptures precede ECM signaling and disease onset without activating cGAS-STING in Lamin cardiomyopathy mice [SLAM-IT-seq]
GEO Series GSE241589. Mus musculus. 21 samples. Type: Other.
Hmga2 protein loss alters nuclear envelope and affects 3D chromatin structure upon the induction of pluripotent stem cell commitment [RNA-seq]
GEO Series GSE200691. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
Brr6 Plays a Role in Gene Recruitment and Transcriptional Regulation at the Nuclear envelope
GEO Series GSE113746. Saccharomyces cerevisiae. 17 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Accumulation of progerin affects the symmetry of cell division and is associated with impaired Wnt signaling and the mislocalization of nuclear envelope proteins [RNA-Seq]
GEO Series GSE131104. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
Hmga2 protein loss alters nuclear envelope and affects 3D chromatin structure upon the induction of pluripotent stem cell commitment
GEO Series GSE200673. Mus musculus. 24 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other.
The nuclear envelope protein Net39 is essential for nuclear integrity, chromatin organization, and muscle growth (RNA-Seq)
GEO Series GSE154849. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Loss of ER and nuclear envelope-associated neutral sphingomyelinase SMPD4 causes a severe neurodevelopmental disorder with microcephaly and congenital arthrogryposis
GEO Series GSE133264. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
HeLa cell images with four labels (nuclear envelope, nucleus, rest of the cell, and background) for deep learning architecture training.
<p>This is a data set that contains <strong>labeled HeLa cell images</strong>, generated in MATLAB® Image Labeler, indicating the four different classes - nuclear envelope, nucleus, rest of the cell, and background for <strong>deep learning</strong> architecture training. </p> <p>Details of the imaging and preparation have been published in:</p> <ul> <li>Cefa Karabağ, Martin L. Jones, Christopher J. Peddie, Anne E. Weston, Lucy M. Collinson, Constantino Carlos Reyes-Aldasoro. Segmentation and Modelling of the Nuclear Envelope of HeLa Cells Imaged with Serial Block Face Scanning Electron Microscopy. <em>J. Imaging</em> 2019, <em>5</em>(9), 75; <a href="https://doi.org/10.3390/jimaging5090075">https://doi.org/10.3390/jimaging5090075</a></li> </ul> <p>and</p> <ul> <li>The data sets are freely available through EMPIAR: http://dx.doi.org/10.6019/EMPIAR-10094 EMPIAR.</li> </ul> <p> </p> <p>Details on the segmentation and analysis of HeLa cells have been published in:</p> <ul> <li>Cefa Karabağ, Martin L. Jones, Christopher J. Peddie, Anne E. Weston, Lucy M. Collinson, Constantino Carlos Reyes-Aldasoro. Semantic Segmentation of HeLa Cells: An Objective Comparison between one Traditional Algorithm and Three Deep-Learning Architectures, BioRxiv, https://doi.org/10.1101/2020.03.05.978478</li> </ul> <p>and</p> <ul> <li> <p>Cefa Karabağ, Martin L. Jones, Christopher J. Peddie, Anne E. Weston, Lucy M. Collinson, Constantino Carlos Reyes-Aldasoro. Segmentation and Modelling of the Nuclear Envelope of HeLa Cells Imaged with Serial Block Face Scanning Electron Microscopy. <em>J. Imaging</em> 2019, <em>5</em>(9), 75; <a href="https://doi.org/10.3390/jimaging5090075">https://doi.org/10.3390/jimaging5090075</a></p> </li> </ul> <p> </p>
Nuclear Envelope Retention of LINC Complexes Is Promoted by SUN-1 Oligomerization in the Caenorhabditis elegans Germ Line
GEO Series GSE76773. Caenorhabditis elegans. 5 samples. Type: Expression profiling by high throughput sequencing.
Cellular expression of Ebola virus VP24 protein compromises the integrity of the nuclear envelope and induces a laminopathy-like cellular phenotype
GEO Series GSE155936. Chlorocebus sabaeus. 6 samples. Type: Expression profiling by high throughput sequencing.
Accumulation of progerin affects the symmetry of cell division and is associated with impaired Wnt signaling and the mislocalization of nuclear envelope proteins [Affymetrix]
GEO Series GSE131310. Mus musculus. 12 samples. Type: Expression profiling by array.
Pervasive nuclear envelope ruptures precede ECM signaling and disease onset without activating cGAS-STING in Lamin cardiomyopathy mice [sci-RNA-seq]
GEO Series GSE241587. Mus musculus. 96 samples. Type: Expression profiling by high throughput sequencing.
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