scholarly journals Emerin modulates spatial organization of chromosome territories in cells on softer matrices

2018 ◽  
Vol 46 (11) ◽  
pp. 5561-5586 ◽  
Author(s):  
Roopali Pradhan ◽  
Devika Ranade ◽  
Kundan Sengupta
Keyword(s):  
Spatial Organization ◽  
Chromosome Territories ◽  
In Cells

Investigation of Spatial Organization of Chromosome Territories in Chromosome Exchange Aberrations After Ionizing Radiation Exposure

2018 ◽  
Vol 115 (1) ◽  
pp. 77-89 ◽  
Author(s):  
Adayabalam S. Balajee ◽  
Jacob T. Sanders ◽  
Rosela Golloshi ◽  
Igor Shuryak ◽  
Rachel Patton McCord ◽  
...  
Keyword(s):  
Ionizing Radiation ◽  
Radiation Exposure ◽  
Spatial Organization ◽  
Chromosome Territories ◽  
Ionizing Radiation Exposure

scholarly journals Gene density and transcription influence the localization of chromatin outside of chromosome territories detectable by FISH

2002 ◽  
Vol 159 (5) ◽  
pp. 753-763 ◽  
Author(s):  
Nicola L. Mahy ◽  
Paul E. Perry ◽  
Wendy A. Bickmore
Keyword(s):  
Spatial Organization ◽  
Cell Types ◽  
Gene Density ◽  
Epidermal Differentiation ◽  
Chromosome 1 ◽  
Chromosome Territories ◽  
Chromosome 11 ◽  
Epidermal Differentiation Complex ◽  
High Gene ◽  
Complex Locus

Genes can be transcribed from within chromosome territories; however, the major histocompatibilty complex locus has been reported extending away from chromosome territories, and the incidence of this correlates with transcription from the region. A similar result has been seen for the epidermal differentiation complex region of chromosome 1. These data suggested that chromatin decondensation away from the surface of chromosome territories may result from, and/or may facilitate, transcription of densely packed genes subject to coordinate regulation. To investigate whether localization outside of the visible confines of chromosome territories can also occur for regions that are not coordinately regulated, we have examined the spatial organization of human 11p15.5 and the syntenic region on mouse chromosome 7. This region is gene rich but its genes are not coordinately expressed, rather overall high levels of transcription occur in several cell types. We found that chromatin from 11p15.5 frequently extends away from the chromosome 11 territory. Localization outside of territories was also detected for other regions of high gene density and high levels of transcription. This is shown to be partly dependent on ongoing transcription. We suggest that local gene density and transcription, rather than the activity of individual genes, influences the organization of chromosomes in the nucleus.

scholarly journals Nuclear Organization of Mammalian Genomes

1999 ◽  
Vol 146 (6) ◽  
pp. 1211-1226 ◽  
Author(s):  
Nicolas Sadoni ◽  
Sabine Langer ◽  
Christine Fauth ◽  
Giorgio Bernardi ◽  
Thomas Cremer ◽  
...  
Keyword(s):  
Spatial Organization ◽  
Chromosome Structure ◽  
Nuclear Architecture ◽  
Replication Timing ◽  
Cell Types ◽  
Higher Order ◽  
Chromosome Territories ◽  
Mitotic Chromosomes ◽  
Organizational Principle ◽  
Mammalian Genomes

We investigated the nuclear higher order compartmentalization of chromatin according to its replication timing (Ferreira et al. 1997) and the relations of this compartmentalization to chromosome structure and the spatial organization of transcription. Our aim was to provide a comprehensive and integrated view on the relations between chromosome structure and functional nuclear architecture. Using different mammalian cell types, we show that distinct higher order compartments whose DNA displays a specific replication timing are stably maintained during all interphase stages. The organizational principle is clonally inherited. We directly demonstrate the presence of polar chromosome territories that align to build up higher order compartments, as previously suggested (Ferreira et al. 1997). Polar chromosome territories display a specific orientation of early and late replicating subregions that correspond to R- or G/C-bands of mitotic chromosomes. Higher order compartments containing G/C-bands replicating during the second half of the S phase display no transcriptional activity detectable by BrUTP pulse labeling and show no evidence of transcriptional competence. Transcriptionally competent and active chromatin is confined to a coherent compartment within the nuclear interior that comprises early replicating R-band sequences. As a whole, the data provide an integrated view on chromosome structure, nuclear higher order compartmentalization, and their relation to the spatial organization of functional nuclear processes.

Spatial Organization of the Chicken α-Globin Gene Domain in Cells of Different Origins

2005 ◽  
Vol 39 (6) ◽  
pp. 851-856
Author(s):  
E. S. Ioudinkova ◽  
A. V. Petrov ◽  
Y. S. Vassetzky ◽  
S. V. Razin
Keyword(s):  
Spatial Organization ◽  
Globin Gene ◽  
Different Origins ◽  
Globin Gene Domain ◽  
In Cells

Spatial organization of chromosome territories in the interphase nucleus of trisomy 21 cells

Chromosoma ◽  
2017 ◽  
Vol 127 (2) ◽  
pp. 247-259 ◽  
Author(s):  
Stephan Kemeny ◽  
Christophe Tatout ◽  
Gaelle Salaun ◽  
Céline Pebrel-Richard ◽  
Carole Goumy ◽  
...  
Keyword(s):  
Trisomy 21 ◽  
Interphase Nucleus ◽  
Spatial Organization ◽  
Chromosome Territories

scholarly journals Modular Spectral Imaging System for Discrimination of Pigments in Cells and Microbial Communities

2008 ◽  
Vol 75 (3) ◽  
pp. 758-771 ◽  
Author(s):  
Lubos Polerecky ◽  
Andrew Bissett ◽  
Mohammad Al-Najjar ◽  
Paul Faerber ◽  
Harald Osmers ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Spatial Organization ◽  
Microbial Mats ◽  
Imaging System ◽  
Spatial Scales ◽  
Spectral Imaging ◽  
Hyperspectral Data ◽  
Resolution Imaging ◽  
In Cells

ABSTRACT Here we describe a spectral imaging system for minimally invasive identification, localization, and relative quantification of pigments in cells and microbial communities. The modularity of the system allows pigment detection on spatial scales ranging from the single-cell level to regions whose areas are several tens of square centimeters. For pigment identification in vivo absorption and/or autofluorescence spectra are used as the analytical signals. Along with the hardware, which is easy to transport and simple to assemble and allows rapid measurement, we describe newly developed software that allows highly sensitive and pigment-specific analyses of the hyperspectral data. We also propose and describe a number of applications of the system for microbial ecology, including identification of pigments in living cells and high-spatial-resolution imaging of pigments and the associated phototrophic groups in complex microbial communities, such as photosynthetic endolithic biofilms, microbial mats, and intertidal sediments. This system provides new possibilities for studying the role of spatial organization of microorganisms in the ecological functioning of complex benthic microbial communities or for noninvasively monitoring changes in the spatial organization and/or composition of a microbial community in response to changing environmental factors.

scholarly journals Single-molecule imaging suggests compact and spliceosome dependent organization of long introns

2021 ◽  
Author(s):  
Srivathsan Adivarahan ◽  
A.M.S.Kalhara Abeykoon ◽  
Daniel Zenklusen
Keyword(s):  
Rna Polymerase Ii ◽  
Single Molecule ◽  
Splice Site ◽  
Spatial Organization ◽  
Spliceosome Assembly ◽  
U2 Snrnp ◽  
Rna In Situ Hybridization ◽  
Intron Removal ◽  
In Cells

Intron removal from pre-mRNAs is a critical step in the processing of RNA polymerase II transcripts, required to create translation competent mRNAs. In humans, introns account for large portions of the pre-mRNA, with intronic sequences representing about 95% of most pre-mRNA. Intron length varies considerably; introns can be as short as a few to hundreds of thousands of nucleotides in length. How nascent long intronic RNA is organized during transcription to facilitate the communication between 5′ and 3′ splice-sites required for spliceosome assembly however is still poorly understood. Here, we use single-molecule fluorescent RNA in situ hybridization (smFISH) to investigate the spatial organization of co- and post-transcriptional long introns in cells. Using two long introns within the POLA1 pre-mRNA as a model, we show that introns are packaged into compact assemblies, and when fully transcribed, are organized in a looped conformation with their ends in proximity. This organization is observed for nascent and nucleoplasmic pre-mRNAs and requires spliceosome assembly, as disruption of U2 snRNP binding results in introns with separated 5′ and 3′ ends. Moreover, interrogating the spatial organization of partially transcribed co-transcriptional POLA1 intron 35 indicates that the 5′ splice site is maintained proximal to the 3′ splice site during transcription, supporting a model that 5′ splice site tethering to the elongating polymerase might contribute to spliceosome assembly at long introns. Together, our study reveals details of intron and pre-mRNA organization in cells and provides a tool to investigate mechanisms of splicing for long introns.

Chromatin as an active polymeric material

2020 ◽  
Vol 4 (2) ◽  
pp. 111-118
Author(s):  
Gautam I. Menon
Keyword(s):  
Large Scale ◽  
Transcriptional Activity ◽  
Spatial Organization ◽  
Nuclear Architecture ◽  
Chromosome Territories ◽  
X Chromosomes ◽  
Equilibrium Processes ◽  
Territorial Organization ◽  
Differential Positioning ◽  
Radial Separation

The patterns of the large-scale spatial organization of chromatin in interphase human somatic cells are not random. Such patterns include the radial separation of euchromatin and heterochromatin, the territorial organization of individual chromosomes, the non-random locations of chromosome territories and the differential positioning of the two X chromosomes in female cells. These features of large-scale nuclear architecture follow naturally from the hypothesis that ATP-consuming non-equilibrium processes associated with highly transcribed regions of chromosomes are a source of ‘active’ forces. These forces are in excess of those that arise from Brownian motion. Simulations of model chromosomes that incorporate such activity recapitulate these features. In addition, they reproduce many other aspects of the spatial organization of chromatin at large scales that are known from experiments. Our results, reviewed here, suggest that the distribution of transcriptional activity across chromosomes underlies many aspects of large-scale nuclear architecture that were hitherto believed to be unrelated.

scholarly journals Two timescales control the creation of large protein aggregates in cells

2021 ◽  
Author(s):  
Ander Movilla Miangolarra ◽  
Aleria Duperray-Susini ◽  
Mathieu Coppey ◽  
Michele Castellana
Keyword(s):  
Protein Aggregation ◽  
Pore Size ◽  
Cell Biology ◽  
Spatial Organization ◽  
Aggregation Process ◽  
Large Protein ◽  
Random Forces ◽  
Small Clusters ◽  
Slow Timescale ◽  
In Cells

Protein aggregation is of particular interest due to its connection with many diseases and disorders. Many factors can alter the dynamics and result of this process, one of them being the diffusivity of the monomers and aggregates in the system. Here, we study experimentally and theoretically an aggregation process in cells, and we identify two distinct physical timescales that set the number and size of aggregates. The first timescale involves fast aggregation of small clusters freely diffusing in the cytoplasm, while, in the second one, the aggregates are larger than the pore size of the cytoplasm and thus barely diffuse, and the aggregation process is slowed down. However, the process is not entirely halted, potentially reflecting a myriad of active but random forces forces that stir the aggregates. Such slow timescale is essential to account for the experimental results of the aggregation process. These results could also have implications in other processes of spatial organization in cell biology, such as phase-separated droplets.

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