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Spatial confinement is a major determinant of the folding landscape of human chromosomes.

Gürsoy G, Xu Y, Kenter AL, Liang J - Nucleic Acids Res. (2014)

Bottom Line: Here we describe a model called constrained self-avoiding chromatin (C-SAC) for studying spatial structures of chromosomes, as the available space is a key determinant of chromosome folding.We show that the equilibrium ensemble of randomly folded chromosomes in the confined nuclear volume gives rise to the experimentally observed higher-order architecture of human chromosomes, including average scaling properties of mean-square spatial distance, end-to-end distance, contact probability and their chromosome-to-chromosome variabilities.Our results indicate that the overall structure of a human chromosome is dictated by the spatial confinement of the nuclear space, which may undergo significant tissue- and developmental stage-specific size changes.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA.

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Scaling exponents α and ν when different fractions of C-SAC chromatin chains are covered by binding sites. The binding energy is assigned to 6kBT (12) for two relative temperatures (T in grey, 10T in black). Neither scaling exponents experiences significant changes as the binder coverage increases.
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Figure 4: Scaling exponents α and ν when different fractions of C-SAC chromatin chains are covered by binding sites. The binding energy is assigned to 6kBT (12) for two relative temperatures (T in grey, 10T in black). Neither scaling exponents experiences significant changes as the binder coverage increases.

Mentions: Our results showed that there is virtually no change in the scaling exponents α and ν in C-SAC chains after introducing binders compared to the original C-SAC chains, where the only constraint is the spatial confinement of the cell nucleus (Figure 4). These results indicate that random self-avoiding chromatin chains folded inside a confined space have an intrinsic propensity to form loops, without the explicit introduction of additional binders. Overall, our results indicate that the confinement at the scale D is the dominant factor in determining the average scaling behavior of chromatin structures.


Spatial confinement is a major determinant of the folding landscape of human chromosomes.

Gürsoy G, Xu Y, Kenter AL, Liang J - Nucleic Acids Res. (2014)

Scaling exponents α and ν when different fractions of C-SAC chromatin chains are covered by binding sites. The binding energy is assigned to 6kBT (12) for two relative temperatures (T in grey, 10T in black). Neither scaling exponents experiences significant changes as the binder coverage increases.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4117743&req=5

Figure 4: Scaling exponents α and ν when different fractions of C-SAC chromatin chains are covered by binding sites. The binding energy is assigned to 6kBT (12) for two relative temperatures (T in grey, 10T in black). Neither scaling exponents experiences significant changes as the binder coverage increases.
Mentions: Our results showed that there is virtually no change in the scaling exponents α and ν in C-SAC chains after introducing binders compared to the original C-SAC chains, where the only constraint is the spatial confinement of the cell nucleus (Figure 4). These results indicate that random self-avoiding chromatin chains folded inside a confined space have an intrinsic propensity to form loops, without the explicit introduction of additional binders. Overall, our results indicate that the confinement at the scale D is the dominant factor in determining the average scaling behavior of chromatin structures.

Bottom Line: Here we describe a model called constrained self-avoiding chromatin (C-SAC) for studying spatial structures of chromosomes, as the available space is a key determinant of chromosome folding.We show that the equilibrium ensemble of randomly folded chromosomes in the confined nuclear volume gives rise to the experimentally observed higher-order architecture of human chromosomes, including average scaling properties of mean-square spatial distance, end-to-end distance, contact probability and their chromosome-to-chromosome variabilities.Our results indicate that the overall structure of a human chromosome is dictated by the spatial confinement of the nuclear space, which may undergo significant tissue- and developmental stage-specific size changes.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA.

Show MeSH