• Corpus ID: 245385123

Intra-Chromosomal Potentials from Nucleosomal Positioning Data

@inproceedings{Li2021IntraChromosomalPF,
  title={Intra-Chromosomal Potentials from Nucleosomal Positioning Data},
  author={Kunhe Li and Nestor Norio Oiwa and Sujeet Kumar Mishra and Dieter W. Heermann},
  year={2021}
}
No systematic method exists to derive intra-chromosomal potentials between nucleosomes along a chromosome consistently across a given genome. Such potentials can yield information on nucleosomal ordering, thermal as well as mechanical properties of chromosomes. Thus, indirectly, they shed light on a possible mechanical genomic code along a chromosome. To develop a method yielding effective intrachromosomal potentials between nucleosomes a generalized Lennard-Jones potential for the… 

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References

SHOWING 1-10 OF 40 REFERENCES

Superstructure Detection in Nucleosome Distribution Shows Common Pattern within a Chromosome and within the Genome

TLDR
A theoretical model to coarse-grain nucleosome positioning data is developed and a genome-wide clustering is obtained for Candida albicans, showing the existence beyond hetero- and eu-chromatin inside the chromosomes.

A genomic code for nucleosome positioning

TLDR
This work isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosom–DNA interaction model, and to predict the genome-wide organization of nucleosomes.

nucleR: a package for non-parametric nucleosome positioning

TLDR
NucleR is an R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments and allows for in situ visualization as well as to export results to common genome browser formats.

Ten principles of heterochromatin formation and function

Heterochromatin is a key architectural feature of eukaryotic chromosomes, which endows particular genomic domains with specific functional properties. The capacity of heterochromatin to restrain the

Modeling nucleosome position distributions from experimental nucleosome positioning maps

TLDR
This work presents a method for identifying non-overlapping nucleosome configurations that combines binary-variable analysis and a Monte Carlo approach with a simulated annealing scheme and applies the method to compare nucleosomes positioning at transcription factor binding sites in different mouse cell types.

Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation

TLDR
Polymer modeling is used to investigate the conformations of two 2Mb-wide DNA loci in normal and cohesin depleted cells, providing evidence that the architecture of the studied loci is controlled by a thermodynamics mechanism of polymer phase separation whereby chromatin self-assembles in segregated globules.

Improved nucleosome-positioning algorithm iNPS for accurate nucleosome positioning from sequencing data.

TLDR
An improved nucleosome-positioning algorithm-iNPS- is described, which achieves significantly better performance than the widely used NPS package and achieves higher significance and lower false positive rates than previously published methods.

Deciphering the mechanical code of genome and epigenome

TLDR
The genetic code and the mechanical code are linked: sequence-dependent mechanical properties of coding DNA constrains the amino acid sequence despite the degeneracy in the genetic code.

Physics behind the mechanical nucleosome positioning code.

TLDR
A simplified model of the nucleosomes where a coarse-grained DNA molecule is frozen into an idealized superhelical shape is introduced and it is found to reproduce qualitatively all the main features known to influence nucleosome positions.

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

TLDR
Systematic analysis of highly rearranged balancer chromosomes in Drosophila shows that extensive changes to chromatin topology affect the expression of only a subset of genes, and suggests that properties other than chromatinTopology ensure productive enhancer–promoter interactions.