Actin Functions in the Cytoplasmic and Nuclear Compartments

2010 ◽  
pp. 3-32
Author(s):  
Richard B. Meagher ◽  
Muthugapatti K. Kandasamy ◽  
Lori King
Keyword(s):  
Nuclear Compartments

scholarly journals Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

2018 ◽  
Vol 217 (11) ◽  
pp. 4025-4048 ◽  
Author(s):  
Yu Chen ◽  
Yang Zhang ◽  
Yuchuan Wang ◽  
Liguo Zhang ◽  
Eva K. Brinkman ◽  
...  
Keyword(s):  
Genome Organization ◽  
Spatial Organization ◽  
Essential Feature ◽  
K562 Cells ◽  
Housekeeping Genes ◽  
Mapping Method ◽  
Spatial Gradient ◽  
Nuclear Speckles ◽  
Nuclear Compartments ◽  
Genome Wide

While nuclear compartmentalization is an essential feature of three-dimensional genome organization, no genomic method exists for measuring chromosome distances to defined nuclear structures. In this study, we describe TSA-Seq, a new mapping method capable of providing a “cytological ruler” for estimating mean chromosomal distances from nuclear speckles genome-wide and for predicting several Mbp chromosome trajectories between nuclear compartments without sophisticated computational modeling. Ensemble-averaged results in K562 cells reveal a clear nuclear lamina to speckle axis correlated with a striking spatial gradient in genome activity. This gradient represents a convolution of multiple spatially separated nuclear domains including two types of transcription “hot zones.” Transcription hot zones protruding furthest into the nuclear interior and positioning deterministically very close to nuclear speckles have higher numbers of total genes, the most highly expressed genes, housekeeping genes, genes with low transcriptional pausing, and super-enhancers. Our results demonstrate the capability of TSA-Seq for genome-wide mapping of nuclear structure and suggest a new model for spatial organization of transcription and gene expression.

Translocation of zinc from vacuole to nucleus during yeast meiosis

1983 ◽  
Vol 25 (5) ◽  
pp. 415-419 ◽  
Author(s):  
Carl A. Bilinski ◽  
John J. Miller
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Staining Procedure ◽  
Vegetative Cells ◽  
Nuclear Compartments ◽  
Polyphosphate Bodies ◽  
Yeast Meiosis ◽  
Zinc Translocation

A novel staining procedure employing the UV fluorochrome DAPI (4′,6-diamidino-2-phenylindole∙2HCl) and dithizone (diphenylthiocarbazone) was developed for microcytochemical determination of sites of zinc localization in Saccharomyces cerevisiae Hansen. In vegetative cells vacuolar polyphosphate bodies stained with dithizone, whereas in sporulating cells nucleoli and centriolar plaques were dithizone-positive. Hence, dithizone not only permitted localization of zinc but also indicated zinc translocation from vacuolar to nuclear compartments during differentiation from the vegetative to sporulated state.

scholarly journals Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Minchul Kim ◽  
Vedran Franke ◽  
Bettina Brandt ◽  
Elijah D. Lowenstein ◽  
Verena Schöwel ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Mouse Model ◽  
Fiber Type ◽  
Muscle Cells ◽  
Skeletal Muscle Cells ◽  
Isolated Nuclei ◽  
Nuclear Compartments ◽  
Transcriptional Dynamics ◽  
Single Nucleus ◽  
Functional Analyses

AbstractSyncytial skeletal muscle cells contain hundreds of nuclei in a shared cytoplasm. We investigated nuclear heterogeneity and transcriptional dynamics in the uninjured and regenerating muscle using single-nucleus RNA-sequencing (snRNAseq) of isolated nuclei from muscle fibers. This revealed distinct nuclear subtypes unrelated to fiber type diversity, previously unknown subtypes as well as the expected ones at the neuromuscular and myotendinous junctions. In fibers of the Mdx dystrophy mouse model, distinct subtypes emerged, among them nuclei expressing a repair signature that were also abundant in the muscle of dystrophy patients, and a nuclear population associated with necrotic fibers. Finally, modifications of our approach revealed the compartmentalization in the rare and specialized muscle spindle. Our data identifies nuclear compartments of the myofiber and defines a molecular roadmap for their functional analyses; the data can be freely explored on the MyoExplorer server (https://shiny.mdc-berlin.de/MyoExplorer/).

scholarly journals Publisher Correction: Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments

2019 ◽  
Vol 51 (2) ◽  
pp. 364-364
Author(s):  
Stephanie Fanucchi ◽  
Ezio T. Fok ◽  
Emiliano Dalla ◽  
Youtaro Shibayama ◽  
Kathleen Börner ◽  
...  
Keyword(s):  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Immune Genes ◽  
Nuclear Compartments

scholarly journals Modification of Nuclear Compartments and the 3D Genome in the Course of a Viral Infection

Acta Naturae ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 34-46
Author(s):  
S. V. Razin ◽  
A. A. Gavrilov ◽  
O. V. Iarovaia
Keyword(s):  
Viral Infection ◽  
Cell Nucleus ◽  
Genome Structure ◽  
Antiviral Defense ◽  
3D Genome ◽  
Nuclear Compartments ◽  
Defense Systems ◽  
3D Genome Structure ◽  
Cellular Genome

The review addresses the question of how the structural and functional compartmentalization of the cell nucleus and the 3D organization of the cellular genome are modified during the infection of cells with various viruses. Particular attention is paid to the role of the introduced changes in the implementation of the viral strategy to evade the antiviral defense systems and provide conditions for viral replication. The discussion focuses on viruses replicating in the cell nucleus. Cytoplasmic viruses are mentioned in cases when a significant reorganization of the nuclear compartments or the 3D genome structure occurs during an infection with these viruses.

scholarly journals Ultrastructural immunocytochemistry shows impairment of RNA pathways in skeletal muscle nuclei of old mice: A link to sarcopenia?

2021 ◽  
Vol 65 (2) ◽  
Author(s):  
Maria Assunta Lacavalla ◽  
Barbara Cisterna ◽  
Carlo Zancanaro ◽  
Manuela Malatesta
Keyword(s):  
Skeletal Muscle ◽  
Ribonuclease A ◽  
Rrna Genes ◽  
Nuclear Actin ◽  
Ultrastructural Immunocytochemistry ◽  
Nuclear Compartments ◽  
Age Related ◽  
Methyl Cytosine ◽  
Rna Pathways ◽  
Old Mice

During aging, skeletal muscle is affected by sarcopenia, a progressive decline in muscle mass, strength and endurance that leads to loss of function and disability. Cell nucleus dysfunction is a possible factor contributing to sarcopenia because aging-associated alterations in mRNA and rRNA transcription/maturation machinery have been shown in several cell types including muscle cells. In this study, the distribution and density of key molecular factors involved in RNA pathways namely, nuclear actin (a motor protein and regulator of RNA transcription), 5-methyl cytosine (an epigenetic regulator of gene transcription), and ribonuclease A (an RNA degrading enzyme) were compared in different nuclear compartments of late adult and old mice myonuclei by means of ultrastructural immunocytochemistry. In all nuclear compartments, an age-related decrease of nuclear actin suggested altered chromatin structuring and impaired nucleus-to-cytoplasm transport of both mRNA and ribosomal subunits, while a decrease of 5-methyl cytosine and ribonuclease A in the nucleoli of old mice indicated an age-dependent loss of rRNA genes. These findings provide novel experimental evidence that, in the aging skeletal muscle, nuclear RNA pathways undergo impairment, likely hindering protein synthesis and contributing to the onset and progression of sarcopenia.

scholarly journals RNA promotes the formation of spatial compartments in the nucleus

2020 ◽  
Author(s):  
Sofia A. Quinodoz ◽  
Prashant Bhat ◽  
Noah Ollikainen ◽  
Joanna W. Jachowicz ◽  
Abhik K. Banerjee ◽  
...  
Keyword(s):  
Nuclear Structure ◽  
Ribosome Biogenesis ◽  
Three Dimensional ◽  
Spatial Proximity ◽  
High Concentration ◽  
3D Structures ◽  
Nuclear Compartments ◽  
Regulatory Processes ◽  
Wide Range ◽  
Heterochromatin Assembly

SUMMARYThe nucleus is a highly organized arrangement of RNA, DNA, and protein molecules that are compartmentalized within three-dimensional (3D) structures involved in shared functional and regulatory processes. Although RNA has long been proposed to play a global role in organizing nuclear structure, exploring the role of RNA in shaping nuclear structure has remained a challenge because no existing methods can simultaneously measure RNA-RNA, RNA-DNA, and DNA-DNA contacts within 3D structures. To address this, we developed RNA & DNA SPRITE (RD-SPRITE) to comprehensively map the location of all RNAs relative to DNA and other RNAs. Using this approach, we identify many RNAs that are localized near their transcriptional loci (RNA-DNA) together with other diffusible ncRNAs (RNA-RNA) within higher-order DNA structures (DNA-DNA). These RNA-chromatin compartments span three major classes of nuclear functions: RNA processing (including ribosome biogenesis, mRNA splicing, snRNA biogenesis, and histone mRNA processing), heterochromatin assembly, and gene regulation. More generally, we identify hundreds of ncRNAs that form stable nuclear compartments in spatial proximity to their transcriptional loci. We find that dozens of nuclear compartments require RNA to guide protein regulators into these 3D structures, and focusing on several ncRNAs, we show that these ncRNAs specifically regulate heterochromatin assembly and the expression of genes contained within these compartments. Together, our results demonstrate a unique mechanism by which RNA acts to shape nuclear structure by forming high concentration territories immediately upon transcription, binding to diffusible regulators, and guiding them into spatial compartments to regulate a wide range of essential nuclear functions.

scholarly journals Hi-C-LSTM: Learning representations of chromatin contacts using a recurrent neural network identifies genomic drivers of 3D genome conformation

2021 ◽  
Author(s):  
Kevin Dsouza ◽  
Alexandra Maslova ◽  
Ediem Al-Jibury ◽  
Matthias Merkenschlager ◽  
Vijay Bhargava ◽  
...  
Keyword(s):  
Neural Network ◽  
Short Term Memory ◽  
Regulatory Elements ◽  
Short Term ◽  
3D Genome ◽  
Nuclear Compartments ◽  
Long Short Term Memory ◽  
Latent Representations ◽  
Low Dimensional ◽  
The Relationship

Abstract Despite the availability of chromatin conformation capture experiments, discerning the relationship between the 1D genome and 3D conformation remains a challenge, which limits our understanding of their affect on gene expression and disease. We propose Hi-C-LSTM, a method that produces low-dimensional latent representations that summarize intra-chromosomal Hi-C contacts via a recurrent long short-term memory (LSTM) neural network model. We find that these representations contain all the information needed to recreate the original Hi-C matrix with high accuracy, outperforming existing methods. These representations enable the identification of a variety of conformation-defining genomic elements, including nuclear compartments and conformation-related transcription factors. They furthermore enable in-silico perturbation experiments that measure the influence of cis-regulatory elements on conformation.

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