scholarly journals Live imaging of chromatin distribution reveals novel principles of nuclear architecture and chromatin compartmentalization

2021 ◽  
Vol 7 (23) ◽  
pp. eabf6251
Author(s):  
Daria Amiad-Pavlov ◽  
Dana Lorber ◽  
Gaurav Bajpai ◽  
Adriana Reuveny ◽  
Francesco Roncato ◽  
...  
Keyword(s):  
T Lymphocytes ◽  
Physical Modeling ◽  
Transcriptional Control ◽  
Three Dimensional ◽  
Nuclear Architecture ◽  
Nuclear Lamina ◽  
Nuclear Volume ◽  
Current View ◽  
Active Chromatin ◽  
Nuclear Interior

The three-dimensional organization of chromatin contributes to transcriptional control, but information about native chromatin distribution is limited. Imaging chromatin in live Drosophila larvae, with preserved nuclear volume, revealed that active and repressed chromatin separates from the nuclear interior and forms a peripheral layer underneath the nuclear lamina. This is in contrast to the current view that chromatin distributes throughout the nucleus. Furthermore, peripheral chromatin organization was observed in distinct Drosophila tissues, as well as in live human effector T lymphocytes and neutrophils. Lamin A/C up-regulation resulted in chromatin collapse toward the nuclear center and correlated with a significant reduction in the levels of active chromatin. Physical modeling suggests that binding of lamina-associated domains combined with chromatin self-attractive interactions recapitulate the experimental chromatin distribution profiles. Together, our findings reveal a novel mode of mesoscale organization of peripheral chromatin sensitive to lamina composition, which is evolutionary conserved.

scholarly journals Live imaging of chromatin distribution in muscle nuclei reveals novel principles of nuclear architecture and chromatin compartmentalization

2020 ◽  
Author(s):  
Daria Amiad-Pavlov ◽  
Dana Lorber ◽  
Gaurav Bajpai ◽  
Samuel Safran ◽  
Talila Volk
Keyword(s):  
Nuclear Architecture ◽  
Nuclear Lamina ◽  
Nuclear Volume ◽  
Common View ◽  
Over Expression ◽  
Peripheral Layer ◽  
Differentiated Cells ◽  
Fold Reduction ◽  
Transcriptional Output ◽  
Nuclear Compartmentalization

AbstractPackaging of the chromatin within the nucleus serves as an important factor in the regulation of transcriptional output. However, information on chromatin architecture on nuclear scale in fully differentiated cells, under physiological conditions and in live organisms, is largely unavailable. Here, we imaged nuclei and chromatin in muscle fibers of live, intact Drosophila larvae. In contrast to the common view that chromatin is distributed throughout the nuclear volume, we show that the entire chromatin, including active and repressed regions, forms a peripheral layer underneath the nuclear lamina, leaving a chromatin-devoid compartment at the nucleus center. Importantly, visualization of nuclear compartmentalization required imaging of un-fixed nuclei embedded within their intrinsic tissue environment, with preserved nuclear volume. Upon fixation of similar muscle nuclei, we observed an average of three-fold reduction in nuclear volume caused by dehydration and evidenced by nuclear flattening. In these conditions, the peripheral chromatin layer was not detected anymore, demonstrating the importance of preserving native biophysical tissue environment. We further show that nuclear compartmentalization is sensitive to the levels of lamin C, since over-expression of lamin C-GFP in muscle nuclei resulted in detachment of the peripheral chromatin layer from the lamina and its collapse into the nuclear center. Computer simulations of chromatin distribution recapitulated the peripheral chromatin organization observed experimentally, when binding of lamina associated domains (LADs) was incorporated with chromatin self-attractive interactions. Reducing the number of LADs led to collapse of the chromatin, similarly to our observations following lamin C over-expression. Taken together, our findings reveal a novel mode of mesoscale organization of chromatin within the nucleus in a live organism, in which the chromatin forms a peripheral layer separated from the nuclear interior. This architecture may be essential for robust transcriptional regulation in fully differentiated cells.

scholarly journals Condensins Exert Force on Chromatin-Nuclear Envelope Tethers to Mediate Nucleoplasmic Reticulum Formation in Drosophila melanogaster

2015 ◽  
Vol 5 (3) ◽  
pp. 341-352 ◽  
Author(s):  
Julianna Bozler ◽  
Huy Q Nguyen ◽  
Gregory C Rogers ◽  
Giovanni Bosco
Keyword(s):  
Nuclear Envelope ◽  
Chromatin Condensation ◽  
Three Dimensional ◽  
Nuclear Architecture ◽  
Nuclear Lamina ◽  
Dimensional Structure ◽  
Interphase Chromosome ◽  
Chromatin Compaction ◽  
Three Dimensional Structure ◽  
Nucleoplasmic Reticulum

Abstract Although the nuclear envelope is known primarily for its role as a boundary between the nucleus and cytoplasm in eukaryotes, it plays a vital and dynamic role in many cellular processes. Studies of nuclear structure have revealed tissue-specific changes in nuclear envelope architecture, suggesting that its three-dimensional structure contributes to its functionality. Despite the importance of the nuclear envelope, the factors that regulate and maintain nuclear envelope shape remain largely unexplored. The nuclear envelope makes extensive and dynamic interactions with the underlying chromatin. Given this inexorable link between chromatin and the nuclear envelope, it is possible that local and global chromatin organization reciprocally impact nuclear envelope form and function. In this study, we use Drosophila salivary glands to show that the three-dimensional structure of the nuclear envelope can be altered with condensin II-mediated chromatin condensation. Both naturally occurring and engineered chromatin-envelope interactions are sufficient to allow chromatin compaction forces to drive distortions of the nuclear envelope. Weakening of the nuclear lamina further enhanced envelope remodeling, suggesting that envelope structure is capable of counterbalancing chromatin compaction forces. Our experiments reveal that the nucleoplasmic reticulum is born of the nuclear envelope and remains dynamic in that they can be reabsorbed into the nuclear envelope. We propose a model where inner nuclear envelope-chromatin tethers allow interphase chromosome movements to change nuclear envelope morphology. Therefore, interphase chromatin compaction may be a normal mechanism that reorganizes nuclear architecture, while under pathological conditions, such as laminopathies, compaction forces may contribute to defects in nuclear morphology.

67 CORRELATION OF ARCHITECTURAL AND FUNCTIONAL REPROGRAMMING OF NUCLEI DURING EMBRYONIC GENOME ACTIVATION OF EARLY BOVINE EMBRYOS GENERATED BY IVF AND SCNT

2014 ◽  
Vol 26 (1) ◽  
pp. 147
Author(s):  
J. Popken ◽  
D. Koehler ◽  
A. Brero ◽  
A. Wuensch ◽  
T. Thormeyer ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Nuclear Architecture ◽  
Nuclear Space ◽  
Structured Illumination ◽  
Bovine Embryos ◽  
Structured Illumination Microscopy ◽  
Nuclear Compartment ◽  
Nuclear Interior ◽  
Embryonic Genome ◽  
Genome Activation

Development of mammalian pre-implantation embryos provides an excellent model to explore interactions of nuclear organisation and nuclear functions. Based on light optical sectioning with confocal laser scanning microscopy and structured illumination microscopy, we performed a quantitative three-dimensional image analysis of nuclei in early bovine embryos generated by in vitro fertilization (IVF) and somatic cell nuclear transfer (SCNT) of bovine fibroblast nuclei. The same sequence of changes was observed in nuclei of both IVF and SCNT embryos during embryonic genome activation (EGA) is that typically achieved in embryos between 8 and 16 cells. In both pre-EGA IVF and SCNT embryos, chromosome territories (CT) were assembled as spatially distinct entities at the nuclear periphery, whereas the nuclear interior was typically occupied by a mostly chromatin free lacuna enriched with splicing factors. Detection of H3K4m3 demonstrates the presence of transcriptionally competent chromatin before EGA, which was correlated with large-scale movements of CT into the nuclear interior and a several-fold decrease of nuclear volumes. Post-EGA nuclei are characterised by a conventional nuclear architecture with chromatin distributed throughout the nuclear space, heterochromatin enriched with histone markers for transcriptionally silent chromatin beneath the nuclear lamina and around nucleoli, as well as heterochromatin clusters and chromocenters throughout the nuclear interior. Pre- and post-EGA nuclei were recorded with the superior resolution of structured illumination microscopy to allow a quantitative analysis of the nuclear topography of H3K4me3 and RNAP II signals. These signals were highly significantly enriched in the perichromatin region (PR) surrounding the compact, transcriptionally silent interior of megabase-sized chromatin domains, which form the basic structural units of CT. The PR is in direct contact with interchromatin compartment (IC) channels starting at nuclear pores, permeating the nuclear space and harboring nuclear bodies in IC lacunas. Our findings support a model for the functional nuclear architecture based on spatially distinct, but co-aligned three-dimensional networks of an active and an inactive nuclear compartment. The active nuclear compartment is built up from the structurally and functionally interacting IC and PR, whereas the inactive nuclear compartment consists of the compact, transcriptionally silent core of chromatin domain clusters. This work is supported by the DFG (ZA 425/1-3, CR 59/29-2).

Transcriptional control within the three-dimensional context of nuclear architecture: Requirements for boundaries and direction

1999 ◽  
Vol 75 (S32) ◽  
pp. 24-31 ◽  
Author(s):  
Gary S. Stein ◽  
Andr� J. van Wijnen ◽  
Janet L. Stein ◽  
Jane B. Lian ◽  
Sandra McNeil ◽  
...  
Keyword(s):  
Transcriptional Control ◽  
Three Dimensional ◽  
Nuclear Architecture

scholarly journals Three-dimensional organization of Drosophila melanogaster interphase nuclei. I. Tissue-specific aspects of polytene nuclear architecture.

1987 ◽  
Vol 104 (6) ◽  
pp. 1455-1470 ◽  
Author(s):  
M Hochstrasser ◽  
J W Sedat
Keyword(s):  
Drosophila Melanogaster ◽  
Three Dimensional ◽  
Nuclear Architecture ◽  
Close Packing ◽  
Prothoracic Gland ◽  
Cell Type ◽  
Interphase Chromosome ◽  
Tissue Specific ◽  
Spatial Domains ◽  
Four Levels

Interphase chromosome organization in four different Drosophila melanogaster tissues, covering three to four levels of polyteny, has been analyzed. The results are based primarily on three-dimensional reconstructions from unfixed tissues using a computer-based data collection and modeling system. A characteristic organization of chromosomes in each cell type is observed, independent of polyteny, with some packing motifs common to several or all tissues and others tissue-specific. All chromosomes display a right-handed coiling chirality, despite large differences in size and degree of coiling. Conversely, in each cell type, the heterochromatic centromeric regions have a unique structure, tendency to associate, and intranuclear location. The organization of condensed nucleolar chromatin is also tissue-specific. The tightly coiled prothoracic gland chromosomes are arrayed in a similar fashion to the much larger salivary gland chromosomes described previously, having polarized orientations, nonintertwined spatial domains, and close packing of the arms of each autosome, whereas hindgut and especially the unusually straight midgut chromosomes display striking departures from these regularities. Surprisingly, gut chromosomes often appear to be broken in the centric heterochromatin. Severe deformations of midgut nuclei observed during gut contractions in living larvae may account for their unusual properties. Finally, morphometric measurements of chromosome and nuclear dimensions provide insights into chromosome growth and substructure and also suggest an unexpected parallel with diploid chromatin organization.

scholarly journals THE DEVELOPMENT OF A THREE-DIMENSIONAL MODEL OF WWER-1000 CORE USING THE MONTE CARLO SERPENT CODE FOR NEUTRON-PHYSICAL MODELING

2019 ◽  
pp. 58-61
Author(s):  
V.I. Gulik ◽  
O.R. Trofymenko ◽  
V.V. Galchenko ◽  
D.V. Budik
Keyword(s):  
Monte Carlo ◽  
3D Modeling ◽  
Physical Modeling ◽  
Three Dimensional ◽  
Reactor Core ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Fuel Assemblies

The article presents the use of the new Monte Carlo Serpent code for 3D modeling of the WWER-1000 reactor core. Core models for the first loading of RNPP4 and the 28th loading of SUNPP3, the fuel assemblies’ models of different manufacturers were developed and presented. Considerable attention was paid to the detailed modeling of the upper, lower and side reflectors. Validation calculations of the Monte Carlo Serpent code for the WWER-1000 reactor were performed on the basis of the first RNPP4 loading. For the 28th loading of SUNPP3, albedo coefficients for radial and axial reflectors were obtained.

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.

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