Towards a robust algorithm to determine topological domains from colocalization data

@article{Moscalets2015TowardsAR,
  title={Towards a robust algorithm to determine topological domains from colocalization data},
  author={Alexander P. Moscalets and Leonid Nazarov and Mikhail V. Tamm},
  journal={arXiv: Biological Physics},
  year={2015},
  volume={2},
  pages={503-516}
}
One of the most important tasks in understanding the complex spatial organization of the genome consists in extracting information about this spatial organization, the function and structure of chromatin topological domains from existing experimental data, in particular, from genome colocalization (Hi-C) matrices. Here we present an algorithm allowing to reveal the underlying hierarchical domain structure of a polymer conformation from analyzing the modularity of colocalization matrices. We… 

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References

SHOWING 1-10 OF 52 REFERENCES

Capturing Chromosome Conformation

Using the yeast Saccharomyces cerevisiae, this work could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis and found that chromatin is highly flexible throughout.

The fractal globule as a model of chromatin architecture in the cell

The concept of the fractal globule is presented, comparing it to other states of a polymer and focusing on its properties relevant for the biophysics of chromatin, which make it an attractive model for chromatin organization inside a cell.

Spatially confined folding of chromatin in the interphase nucleus

A polymer model able to describe key properties of chromatin over length scales ranging from 0.5 to 75 Mb is presented and can explain the observed data and suggests that on the tens-of-megabases length scale P is small, i.e., 10–30 loops per 100 Mb, sufficient to enforce folding inside the confined space of a chromosome territory.

Complexity of chromatin folding is captured by the strings and binders switch model

The strings and binders switch model reproduces the recently proposed “fractal–globule” model, but only as one of many possible transient conformations.

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Hi-C is described, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing and demonstrates the power of Hi-C to map the dynamic conformations of entire genomes.

From a melt of rings to chromosome territories: the role of topological constraints in genome folding

Pro and contra of the hypothesis that generic polymer properties of topological constraints are behind many aspects of chromatin folding in eukaryotic cells are reviewed, as well as recent experimental discoveries related to genome folding.

Structure and Dynamics of Interphase Chromosomes

Computer simulations are used to show that the experimentally observed territory shapes and spatial distances between marked chromosome sites for human, Drosophila, and budding yeast chromosomes can be reproduced by a parameter-free minimal model of decondensing chromosomes.

A statistical model of intra-chromosome contact maps.

It is shown that the existence of a quenched primary structure coupled with hierarchical folding induces a full range of features observed in experimental Hi-C maps: hierarchical elements, chess-board intermittency and large-scale compartmentalization.

Analysis of the structure of complex networks at different resolution levels

The proposed method allows for multiple resolution screening of the modular structure, and its application to two real social networks allows us to find the exact splits reported in the literature, as well as the substructure beyond the actual split.

Crumpled globule model of the three-dimensional structure of DNA

We argue that in order to maintain the biological function of DNA confined inside the cell nucleus, its spatial structure has to be unknotted, of the so-called crumpled globule type. The fixation of
...