scholarly journals Nuclear Organization in Stress and Aging

Cells ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 664 ◽  
Author(s):  
Romero-Bueno ◽  
de la Cruz Ruiz ◽  
Artal-Sanz ◽  
Askjaer ◽  
Dobrzynska
Keyword(s):  
Gene Expression ◽  
Nuclear Envelope ◽  
Nuclear Organization ◽  
3 Dimensional ◽  
Cellular Processes ◽  
Nuclear Lamins ◽  
Nuclear Composition ◽  
Histone Modifiers ◽  
And Function ◽  
Gene Expression Alterations

The eukaryotic nucleus controls most cellular processes. It is isolated from the cytoplasm by the nuclear envelope, which plays a prominent role in the structural organization of the cell, including nucleocytoplasmic communication, chromatin positioning, and gene expression. Alterations in nuclear composition and function are eminently pronounced upon stress and during premature and physiological aging. These alterations are often accompanied by epigenetic changes in histone modifications. We review, here, the role of nuclear envelope proteins and histone modifiers in the 3-dimensional organization of the genome and the implications for gene expression. In particular, we focus on the nuclear lamins and the chromatin-associated protein BAF, which are linked to Hutchinson–Gilford and Nestor–Guillermo progeria syndromes, respectively. We also discuss alterations in nuclear organization and the epigenetic landscapes during normal aging and various stress conditions, ranging from yeast to humans.

scholarly journals Bend, Push, Stretch: Remarkable Structure and Mechanics of Single Intermediate Filaments and Meshworks

Cells ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1960
Author(s):  
K. Tanuj Sapra ◽  
Ohad Medalia
Keyword(s):  
Intermediate Filaments ◽  
Eukaryotic Cell ◽  
Coiled Coils ◽  
Cellular Functions ◽  
Mechanical Pressure ◽  
Mechanical Feature ◽  
Cellular Processes ◽  
Nuclear Lamins ◽  
Filament Networks ◽  
And Function

The cytoskeleton of the eukaryotic cell provides a structural and functional scaffold enabling biochemical and cellular functions. While actin and microtubules form the main framework of the cell, intermediate filament networks provide unique mechanical properties that increase the resilience of both the cytoplasm and the nucleus, thereby maintaining cellular function while under mechanical pressure. Intermediate filaments (IFs) are imperative to a plethora of regulatory and signaling functions in mechanotransduction. Mutations in all types of IF proteins are known to affect the architectural integrity and function of cellular processes, leading to debilitating diseases. The basic building block of all IFs are elongated α-helical coiled-coils that assemble hierarchically into complex meshworks. A remarkable mechanical feature of IFs is the capability of coiled-coils to metamorphize into β-sheets under stress, making them one of the strongest and most resilient mechanical entities in nature. Here, we discuss structural and mechanical aspects of IFs with a focus on nuclear lamins and vimentin.

Closing the (nuclear) envelope on the genome: How nuclear lamins interact with promoters and modulate gene expression

BioEssays ◽  
2013 ◽  
Vol 36 (1) ◽  
pp. 75-83 ◽  
Author(s):  
Philippe Collas ◽  
Eivind G. Lund ◽  
Anja R. Oldenburg
Keyword(s):  
Gene Expression ◽  
Nuclear Envelope ◽  
Nuclear Lamins

scholarly journals Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy

2019 ◽  
Author(s):  
Alessandro Bertero ◽  
Paul A. Fields ◽  
Alec S. T. Smith ◽  
Andrea Leonard ◽  
Kevin Beussman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Induced Pluripotent Stem Cell ◽  
Lamin A ◽  
Chromosome Conformation ◽  
Human Cardiomyocytes ◽  
Nuclear Lamins ◽  
Genome Wide ◽  
Induced Pluripotent ◽  
Gene Expression Alterations

AbstractPathogenic mutations in A-type nuclear lamins cause dilated cardiomyopathy, which is postulated to result from dysregulated gene expression due to changes in chromatin organization into active and inactive compartments. To test this, we performed genome-wide chromosome conformation analyses (Hi-C) in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) with a haploinsufficient mutation for lamin A/C. Compared to gene-corrected cells, mutant hiPSC-CMs have marked electrophysiological and contractile alterations, with modest gene expression changes. While large-scale changes in chromosomal topology are evident, differences in chromatin compartmentalization are limited to a few hotspots that escape inactivation during cardiogenesis. These regions exhibit upregulation of multiple non-cardiac genes including CACNA1A, encoding for neuronal P/Q-type calcium channels. Pharmacological inhibition of the resulting current partially mitigates the electrical alterations. On the other hand, A/B compartment changes do not explain most gene expression alterations in mutant hiPSC-CMs. We conclude that global errors in chromosomal compartmentation are not the primary pathogenic mechanism in heart failure due to lamin A/C haploinsufficiency.SummaryBertero et al. observe that lamin A/C haploinsufficiency in human cardiomyocytes markedly alters electrophysiology, contractility, gene expression, and chromosomal topology. Contrary to expectations, however, changes in chromatin compartments involve just few regions, and most dysregulated genes lie outside these hotspots.Condensed titleGenomic effects of lamin A/C haploinsufficiency

The structure and function of the nuclear lamins

1995 ◽  
Vol 53 ◽  
pp. 762-763
Author(s):  
R.D. Goldman ◽  
A. Goldman ◽  
S. Khuon ◽  
M. Montag-Lowy ◽  
R. Moir ◽  
...  
Keyword(s):  
Nuclear Envelope ◽  
Nuclear Lamina ◽  
Structure And Function ◽  
Supramolecular Organization ◽  
Intermediate Filament Proteins ◽  
Nuclear Envelope Breakdown ◽  
Nuclear Lamins ◽  
Interphase Cells ◽  
Type V ◽  
And Function

The nuclear lamins are the Type V intermediate filament proteins comprising the nuclear lamina. The lamina is located subjacent to the nucleoplasmic face of the nuclear envelope where it interfaces with chromatin. The lamins are major karyoskeletal proteins which are thought to play important roles in the formation and maintenance of nuclear shape and architecture, as well as in the supramolecular organization of chromatin. The lamins have long been thought to be stable polymeric constituents of the interphase nuclear matrix, due to their insolubility in solutions containing detergents and high salt concentrations. During mitosis, however, the nuclear lamins depolymerize during nuclear envelope breakdown. Subsequently, the lamins repolymerize around the decondensing chromosomes as the nuclear envelope reassembles at the end of mitosis. Although there is a significant amount known about the properties and potential functions of the lamins during mitosis, surprisingly little is known about their properties during interphase. In light of this, we have undertaken experiments which are aimed at determining the properties of the lamins in interphase cells.

scholarly journals The nuclear envelope protein Net39 is essential for muscle nuclear integrity and chromatin organization

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Andres Ramirez-Martinez ◽  
Yichi Zhang ◽  
Kenian Chen ◽  
Jiwoong Kim ◽  
Bercin K. Cenik ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nuclear Envelope ◽  
Envelope Protein ◽  
Transmembrane Protein ◽  
Chromatin Accessibility ◽  
Chromatin Organization ◽  
Potential Contribution ◽  
Molecular Etiology ◽  
And Function

AbstractLamins and transmembrane proteins within the nuclear envelope regulate nuclear structure and chromatin organization. Nuclear envelope transmembrane protein 39 (Net39) is a muscle nuclear envelope protein whose functions in vivo have not been explored. We show that mice lacking Net39 succumb to severe myopathy and juvenile lethality, with concomitant disruption in nuclear integrity, chromatin accessibility, gene expression, and metabolism. These abnormalities resemble those of Emery–Dreifuss muscular dystrophy (EDMD), caused by mutations in A-type lamins (LMNA) and other genes, like Emerin (EMD). We observe that Net39 is downregulated in EDMD patients, implicating Net39 in the pathogenesis of this disorder. Our findings highlight the role of Net39 at the nuclear envelope in maintaining muscle chromatin organization, gene expression and function, and its potential contribution to the molecular etiology of EDMD.

Embryonic exposure to an aqueous coal dust extract results in gene expression alterations associated with the development and function of connective tissue and the hematological system, immunological and inflammatory disease, and cancer in zebrafish

Metallomics ◽  
2018 ◽  
Vol 10 (3) ◽  
pp. 463-473 ◽  
Author(s):  
Karina Caballero-Gallardo ◽  
Sara E. Wirbisky-Hershberger ◽  
Jesus Olivero-Verbel ◽  
Jesus de la Rosa ◽  
Jennifer L. Freeman
Keyword(s):  
Gene Expression ◽  
Connective Tissue ◽  
Inflammatory Disease ◽  
Coal Dust ◽  
Developmental Toxicity ◽  
Embryonic Exposure ◽  
And Function ◽  
Gene Expression Alterations ◽  
Dust Extract

This is the first study to identify the developmental toxicity of an aqueous coal dust extract in zebrafish.

Quantitative 3d Analysis Of Intra-Nuclear Organization In The Tissue Context

1999 ◽  
Vol 5 (S2) ◽  
pp. 1320-1321
Author(s):  
S.J. Lockett ◽  
D.W. Knowles ◽  
D. Pinkel ◽  
C. Ortiz de Solórzano
Keyword(s):  
Spatial Organization ◽  
Nuclear Organization ◽  
Center Of Mass ◽  
Visual Observation ◽  
3D Analysis ◽  
Computer Algorithms ◽  
Cellular Processes ◽  
Segmented Nucleus ◽  
Tissue Specimens ◽  
And Function

Confocal microscopy is revealing associations between the internal organization of the nucleus and tissue architecture and function. Such associations may exist which are too subtle or complex for visual observation or quantitative analysis may be required, for example as input data to mathematical modeling of cellular processes. In these circumstances, it is necessary to perform the analysis using computer algorithms. We have developed 3D image analysis (IA) algorithms for segmenting nuclei from within intact tissue specimens, measuring the structure of the nuclei and for segmenting specifically- labeled punctate entities within nuclei. In this study we developed algorithms for measuring the spatial organization of the two copies of a specific DNA locus (labeled using fluorescence in situ hybridization (FISH) ) inside diploid nuclei and with respect to the nuclear organization of the tissue.For each segmented nucleus, its center of mass (CoM) was determined, which informed us about its position in the tissue.

scholarly journals Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy

2019 ◽  
Vol 218 (9) ◽  
pp. 2919-2944 ◽  
Author(s):  
Alessandro Bertero ◽  
Paul A. Fields ◽  
Alec S.T. Smith ◽  
Andrea Leonard ◽  
Kevin Beussman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Induced Pluripotent Stem Cell ◽  
Nuclear Lamina ◽  
Lamin A ◽  
Chromosome Conformation ◽  
Nuclear Lamins ◽  
Genome Wide ◽  
Induced Pluripotent ◽  
Gene Expression Alterations

Mutations in A-type nuclear lamins cause dilated cardiomyopathy, which is postulated to result from dysregulated gene expression due to changes in chromatin organization into active and inactive compartments. To test this, we performed genome-wide chromosome conformation analyses in human induced pluripotent stem cell–derived cardiomyocytes (hiPSC-CMs) with a haploinsufficient mutation for lamin A/C. Compared with gene-corrected cells, mutant hiPSC-CMs have marked electrophysiological and contractile alterations, with modest gene expression changes. While large-scale changes in chromosomal topology are evident, differences in chromatin compartmentalization are limited to a few hotspots that escape segregation to the nuclear lamina and inactivation during cardiogenesis. These regions exhibit up-regulation of multiple noncardiac genes including CACNA1A, encoding for neuronal P/Q-type calcium channels. Pharmacological inhibition of the resulting current partially mitigates the electrical alterations. However, chromatin compartment changes do not explain most gene expression alterations in mutant hiPSC-CMs. Thus, global errors in chromosomal compartmentation are not the primary pathogenic mechanism in heart failure due to lamin A/C haploinsufficiency.

scholarly journals Ultrasound Imaging of Gene Expression in Mammalian Cells

2019 ◽  
Author(s):  
Arash Farhadi ◽  
Gabrielle H. Ho ◽  
Daniel P. Sawyer ◽  
Raymond W. Bourdeau ◽  
Mikhail G. Shapiro
Keyword(s):  
Gene Expression ◽  
Mammalian Cells ◽  
Reporter Genes ◽  
Tissue Imaging ◽  
Cellular Functions ◽  
Cellular Processes ◽  
Deep Tissue Imaging ◽  
And Function ◽  
Expression In Mammalian Cells

ABSTRACTThe study of cellular processes occurring inside intact organisms and the development of cell-based diagnostic and therapeutic agents requires methods to visualize cellular functions such as gene expression in deep tissues. Ultrasound is a widely used biomedical technology enabling deep-tissue imaging with high spatial and temporal resolution. However, no genetically encoded molecular reporters are available to connect ultrasound contrast to gene expression in mammalian cells. To address this limitation, we introduce the first mammalian acoustic reporter genes. Starting with an eleven-gene polycistronic gene cluster derived from bacteria, we engineered a eukaryotic genetic program whose introduction into mammalian cells results in the expression of a unique class of intracellular air-filled protein nanostructures called gas vesicles. The scattering of ultrasound by these nanostructures allows mammalian cells to be visualized at volumetric densities below 0.5%, enables the monitoring of dynamic circuit-driven gene expression, and permits high-resolution imaging of gene expression in living animals. These mammalian acoustic reporter genes enable previously impossible approaches to monitoring the location, viability and function of mammalian cellsin vivo.

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