Organization and function of the 3D genome

@article{Bonev2016OrganizationAF,
  title={Organization and function of the 3D genome},
  author={Boyan B. Bonev and Giacomo Cavalli},
  journal={Nature Reviews Genetics},
  year={2016},
  volume={17},
  pages={661-678}
}
Understanding how chromatin is organized within the nucleus and how this 3D architecture influences gene regulation, cell fate decisions and evolution are major questions in cell biology. Despite spectacular progress in this field, we still know remarkably little about the mechanisms underlying chromatin structure and how it can be established, reset and maintained. In this Review, we discuss the insights into chromatin architecture that have been gained through recent technological… 
Plant 3D genomics: the exploration and application of chromatin organization
TLDR
Recent advances in 3D genome mapping approaches are reviewed, the understanding of the sophisticated organization of spatial structures is understood, and the application of 3D genomic principles in plants are discussed.
Understanding the 3D genome: Emerging impacts on human disease.
Understanding 3D genome organization by multidisciplinary methods.
TLDR
The most commonly used techniques of 3D genome organization analysis are described and their contribution to current knowledge of nuclear architecture is described and a perspective on up-and-coming methods that open possibilities for future major discoveries is provided.
Advances in higher-order chromatin architecture: the move towards 4D genome
TLDR
Recent advances in the understanding of principles of higher-order chromosome conformation and technologies to investigate 4D chromatin interactions are discussed.
Polymer models are a versatile tool to study chromatin 3D organization.
TLDR
How Polymer Physics, combined with numerical Molecular Dynamics simulation and Machine Learning based inference, can capture important aspects of genome organization, including the description of tissue-specific structural rearrangements, the detection of novel, regulatory-linked architectural elements and the structural variability of chromatin at the single-cell level is discussed.
Three-dimensional chromatin packing and positioning of plant genomes
TLDR
This Review summarizes the understanding of plant chromatin organization and positioning beyond the nucleosomal level, advanced by up-to-date chromatin conformation capture methods and visualization techniques, as well as discusses future directions.
Chromatin Organization and Function in Drosophila
TLDR
This work reviews here how the genome of Drosophila melanogaster is organized into the cell nucleus, from small scale histone–DNA interactions to chromosome and lamina interactions in the nuclear space.
...
...

References

SHOWING 1-10 OF 152 REFERENCES
Three-dimensional genome architecture: players and mechanisms
TLDR
Sophisticated methods for mapping chromatin contacts are generating genome-wide data that provide deep insights into the formation of chromatin interactions, and into their roles in the organization and function of the eukaryotic cell nucleus.
The Role of Chromosome Domains in Shaping the Functional Genome
CTCF: an architectural protein bridging genome topology and function
TLDR
Although CTCF has been assigned various roles that are often contradictory, new results now help to draw a unifying model to explain the many functions of this protein.
Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions
TLDR
It is found that the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs and short interspersed element (SINE) retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome.
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
TLDR
It is shown that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair at CTCF sites, and it is found that the observed contact domains are inconsistent with the equilibrium state for an ordinary condensed polymer.
...
...