The 4D nucleome: Evidence for a dynamic nuclear landscape based on co‐aligned active and inactive nuclear compartments

  title={The 4D nucleome: Evidence for a dynamic nuclear landscape based on co‐aligned active and inactive nuclear compartments},
  author={Thomas Cremer and Marion Cremer and Barbara H{\"u}bner and Hilmar Strickfaden and Daniel Smeets and Jens Popken and Michael Sterr and Yolanda Markaki and Karsten Rippe and Christoph Cremer},
  journal={FEBS Letters},

The Interchromatin Compartment Participates in the Structural and Functional Organization of the Cell Nucleus

The role of the interchromatin compartment (IC) in shaping nuclear landscapes is focused on and it is postulated that it provides routes for imported transcription factors to target sites, for export routes of mRNA as ribonucleoproteins toward NPCs, as well as for the intranuclear passage of regulatory RNAs from sites of transcription to remote functional sites.

Nuclear compartmentalization, dynamics, and function of regulatory DNA sequences

A multilayered shell‐like chromatin organization of chromatin domain clusters with increasing chromatin compaction levels from the periphery toward the interior with a decondensed transcriptionally active peripheral layer and compact repressed chromatin typically located in the interior is suggested.

Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters

The finding of a structural organization of CDCs based on radially arranged layers of different chromatin compaction levels indicates a complex higher-order chromatin organization beyond a dichotomic classification of chromatin into an ‘open,” active and ‘closed,’ inactive state.

Remodeling of nuclear landscapes during human myelopoietic cell differentiation maintains co-aligned active and inactive nuclear compartments

The findings substantiate the conservation of the recently published ANC-INC network model of mammalian nuclear organization during human myelopoiesis irrespective of profound changes of the global nuclear architecture observed during this differentiation process.

Cohesin depleted cells rebuild functional nuclear compartments after endomitosis

Using live-cell and super-resolved 3D microscopy, it is demonstrated that cohesin depleted cells pass through an endomitosis and rebuild a single multilobulated nucleus (MLN) with chromosome territories (CTs) pervaded by interchromatin channels.

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

Physical modeling suggests that binding of lamina-associated domains combined with chromatin self-attractive interactions recapitulate the experimental chromatin distribution profiles and reveals a novel mode of mesoscale organization of peripheral chromatin sensitive to lamina composition, which is evolutionary conserved.

DNA sequence-dependent chromatin architecture and nuclear hubs formation

It is conjecture that dynamic DNA binding affinity and flexibility underlay the emergence of chromatin condensates, their growth is likely promoted in mechanically soft regions (GC-rich) of the lowest chromatin and nucleosome densities.

The 4D Nucleome: Genome Compartmentalization in an Evolutionary Context

The conservation of fundamental features of higher order chromatin arrangements throughout the evolution of metazoan animals suggests the existence of conserved, but still unknown mechanism(s) controlling this architecture.

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

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, may be essential for robust transcriptional regulation in fully differentiated cells.



Functional nuclear organization of transcription and DNA replication: a topographical marriage between chromatin domains and the interchromatin compartment.

The nuclear topography of RNA transcription and DNA replication in mammalian cell types is studied with super-resolution fluorescence microscopy, which offers a resolution beyond the classical Abbe/Raleigh limit and confirms the presence of RNA Pol II clusters indicative of transcription factories.

Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci

3D-SIM provides experimental evidence for profound differences between the functional architecture of transcriptionally active CTs and the Barr body, and proposes that the PR and macromolecular complexes in IC channels together form the transcriptionally permissive active nuclear compartment (ANC).

Chromosome territories, nuclear matrix filaments and inter-chromatin channels: a topological view on nuclear architecture and function

In this essay, the possible role of in vivo networks of nuclear matrix filaments and interchromatin channels in nuclear compartmentalization with spezial reference to the question of their topological relationships with chromosomal domains and non-chromatin domains is considered.

Chromosome territories, interchromatin domain compartment, and nuclear matrix: an integrated view of the functional nuclear architecture.

A model of a modular and dynamic chromosome territory (CT) organization is presented that basically three nuclear compartments exist, an "open" higher-order chromatin compartment with chromatin domains containing active genes, a "closed" Chromatin compartment comprising inactive genes, and an interchromatin domain (ICD) compartment that contains macromolecular complexes for transcription, splicing, DNA replication, and repair.

Chromatin domains and the interchromatin compartment form structurally defined and functionally interacting nuclear networks

It is demonstrated that most chromatin exists in the form of higher-order chromatin domains with a compaction level at least 10 times above the level of extended 30 nm chromatin fibers, which demonstrates the existence of the IC as a dynamic, structurally distinct nuclear compartment, which is functionally linked with the chromatin compartment.

Specificity, propagation, and memory of pericentric heterochromatin

A predictive mathematical model is developed that explains how chromatin‐bound SUV39H1/2 complexes act as nucleation sites and propagate a spatially confined PCH domain with elevated histone H3 lysine 9 trimethylation levels via chromatin dynamics, which makes it an attractive model for establishing functional epigenetic domains throughout the genome.

In Vivo Chromatin Organization of Mouse Rod Photoreceptors Correlates with Histone Modifications

Transcription is located in the most decondensed and highly acetylated chromatin regions, but since acetylation is found associated with compact chromatin it is not sufficient to decondense chromatin in vivo, and it is shown that a combination of histone marks defines distinct concentric heterochromatin domains.

Revealing the high-resolution three-dimensional network of chromatin and interchromatin space: A novel electron-microscopic approach to reconstructing nuclear architecture

A novel approach associating a pre-embedding selective visualization of nuclear components with a method making use of ultramicrotomy combined with scanning electron microscopy is applied to the study of DNA distribution within the nuclear volume and reconstruction of 3D chromatin arrangement in nuclei of rat hepatocytes and endothelial cells.

4D Chromatin dynamics in cycling cells

It is suggested that long-range DNA-DNA interactions in cell nuclei may depend on a combination of rotational CT movements and locally constrained chromatin movements.

Polymer models of chromatin organization

The exploration of the spatial organiza-tion of chromosomes in the cell nucleushas been greatly enhanced by genome-scale technologies such as Hi-C methods, and it is emerging that chromosomes tend to form 1Mb sized domains with increased levels of intra-interactions.