Non-specific (entropic) forces as major determinants of the structure of mammalian chromosomes

Finan, Kieran; Cook, Peter R.; Marenduzzo, Davide

doi:10.1007/s10577-010-9150-y

Cited by 34 publications

(29 citation statements)

References 44 publications

(62 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, simulations have also shown that other factors may be involved in addition to the dominant role played by entropic forces. In one study, this entropic effect has been shown to depend on the presence of chromosome loops, which may also arise due to non-specific forces 57 . Our simulations suggest that chromosomes are largely territorial regardless of Chr-NE attachments.…”

Section: Chromosomes With More Numerous Ne Attachments Are More Terrimentioning

confidence: 99%

“…Chromosome territories have become a focus of a number of experiments 2, 35, 52-56 and computational simulations [57][58][59] . Recently, simulations that addressed the question of territory formation demonstrated that non-specific entropic forces may play a significant role in establishing and maintaining chromosome territories [57][58][59] .…”

Section: Chromosomes With More Numerous Ne Attachments Are More Terrimentioning

confidence: 99%

“…Recently, simulations that addressed the question of territory formation demonstrated that non-specific entropic forces may play a significant role in establishing and maintaining chromosome territories [57][58][59] . However, simulations have also shown that other factors may be involved in addition to the dominant role played by entropic forces.…”

Section: Chromosomes With More Numerous Ne Attachments Are More Terrimentioning

confidence: 99%

See 2 more Smart Citations

Quantified effects of chromosome-nuclear envelope attachments on 3D organization of chromosomes

Kinney

Onufriev

Sharakhov

2015

Nucleus

View full text Add to dashboard Cite

We use a combined experimental and computational approach to study the effects of chromosome-nuclear envelope (Chr-NE) attachments on the 3D genome organization of Drosophila melanogaster (fruit fly) salivary gland nuclei. We consider 3 distinct models: a Null model - without specific Chr-NE attachments, a 15-attachment model - with 15 previously known Chr-NE attachments, and a 48-attachment model - with 15 original and 33 recently identified Chr-NE attachments. The radial densities of chromosomes in the models are compared to the densities observed in 100 experimental images of optically sectioned salivary gland nuclei forming "z-stacks." Most of the experimental z-stacks support the Chr-NE 48-attachment model suggesting that as many as 48 chromosome loci with appreciable affinity for the NE are necessary to reproduce the experimentally observed distribution of chromosome density in fruit fly nuclei. Next, we investigate if and how the presence and the number of Chr-NE attachments affect several key characteristics of 3D genome organization: chromosome territories and gene-gene contacts. This analysis leads to novel insight about the possible role of Chr-NE attachments in regulating the genome architecture. Specifically, we find that model nuclei with more numerous Chr-NE attachments form more distinct chromosome territories and their chromosomes intertwine less frequently. Intra-chromosome and intra-arm contacts are more common in model nuclei with Chr-NE attachments compared to the Null model (no specific attachments), while inter-chromosome and inter-arm contacts are less common in nuclei with Chr-NE attachments. We demonstrate that Chr-NE attachments increase the specificity of long-range inter-chromosome and inter-arm contacts. The predicted effects of Chr-NE attachments are rationalized by intuitive volume vs. surface accessibility arguments.

show abstract

Section: Chromosomes With More Numerous Ne Attachments Are More Terrimentioning

confidence: 99%

Section: Chromosomes With More Numerous Ne Attachments Are More Terrimentioning

confidence: 99%

Section: Chromosomes With More Numerous Ne Attachments Are More Terrimentioning

confidence: 99%

See 1 more Smart Citation

Quantified effects of chromosome-nuclear envelope attachments on 3D organization of chromosomes

Kinney

Onufriev

Sharakhov

2015

Nucleus

View full text Add to dashboard Cite

show abstract

“…Some groups even doubt the existence of regular chromatin fibers in vivo. 320 On higher levels of eukaryotic chromatin compaction, [321][322][323][324] the fiber structure becomes even less certain. 325 Fiber organization in condensed metaphase chromosomes for instance involves a variety of different proteins.…”

Section: Ncp-ncp Es Interactions and 30 Nm Chromatin Fibersmentioning

confidence: 99%

Electrostatic interactions in biological DNA-related systems

Cherstvy

2011

Phys. Chem. Chem. Phys.

155

148

View full text Add to dashboard Cite

In this perspective article, we focus on recent developments in the theory of charge effects in biological DNA-related systems. The electrostatic effects on different levels of DNA organization are considered, including the DNA-DNA interactions, DNA complexation with cationic lipid membranes, DNA condensates and DNA-dense cholesteric phases, protein-DNA recognition, DNA wrapping in nucleosomes, and inter-nucleosomal interactions. For these systems, we develop a theoretical framework to describe the physical-chemical mechanisms of structure formation and anticipate some biological consequences. General biophysical principles of DNA compaction in chromatin fibers and DNA spooling inside viral capsids are discussed in the end, with emphasis on electrostatic aspects.

show abstract

“…With this realization came also the insight that loop formation and the possible colocalization of genes feature prominently in the organization. Of equal importance is the realization that entropy [9][10][11][12] drives much of the spatial organization.…”

Section: Introductionmentioning

confidence: 99%