A model for the 3D chromatin architecture of pro and eukaryotes.
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Summary
A model and a methodology that uses only very basic constituents to capture the relevant features of folding are shown to be capable to describe the folding of human chromosomes in inter- and metaphase as well as for the Escherichia coli circular chromosomes.
- Type
- article
- Published
- 2012-11-01
- Cited by
- 18
- References
- 41
- OpenAlex
- https://openalex.org/W2071214888
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:19356237
Keywords
Chromatin, Computational biology, Folding (DSP implementation), Biology, Metaphase
References
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- The physics behind the larger scale organization of DNA in eukaryotes
- Dynamic long‐range chromatin interactions control Myb proto‐oncogene transcription during erythroid development
- A decade of 3C technologies: insights into nuclear organization.
- A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation
- Mapping genomes in 3D
- Loops Determine the Mechanical Properties of Mitotic Chromosomes
- Chromosome structure predicted by a polymer model
- Crumpled globule model of the three-dimensional structure of DNA
- Physical nuclear organization: loops and entropy.
- Mean-field theory and critical exponents for a random resistor network
- Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements.
- A random-walk/giant-loop model for interphase chromosomes.
- A chromatin insulator driving three-dimensional Polycomb response element (PRE) contacts and Polycomb association with the chromatin fiber
- Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization
- The bond fluctuation method: a new effective algorithm for the dynamics of polymers in all spatial dimensions
- Estimating genomic distance from DNA sequence location in cell nuclei by a random walk model.
- Spatially confined folding of chromatin in the interphase nucleus
- Chromatin folding – from biology to polymer models and back
- Quantitative analysis of chromosome conformation capture assays (3C-qPCR)
Cited by
- Combined collapse by bridging and self-adhesion in a prototypical polymer model inspired by the bacterial nucleoid.
- Investigation of the Chromosome Regions with Significant Affinity for the Nuclear Envelope in Fruit Fly – A Model Based Approach
- Spatial confinement is a major determinant of the folding landscape of human chromosomes
- Depletion of the Chromatin Looping Proteins CTCF and Cohesin Causes Chromatin Compaction: Insight into Chromatin Folding by Polymer Modelling
- Structure-driven homology pairing of chromatin fibers: the role of electrostatics and protein-induced bridging
- Quantified effects of chromosome-nuclear envelope attachments on 3D organization of chromosomes
- Graphical and Topological Analysis of the Cell Nucleus
- Relevance and limitations of crowding, fractal, and polymer models to describe nuclear architecture.
- Encounter times of chromatin loci influenced by polymer decondensation.
- How Chromosome-Nuclear Envelope Attachments Affect 3D Genome Organization
- A First-principles Approach to Large-scale Nuclear Architecture
- Multiple transcription factors contribute to inter-chromosomal interaction in yeast
- Inferring the three-dimensional structures of the X-chromosome during X-inactivation
- Nonequilibrium Biophysical Processes Influence the Large-Scale Architecture of the Cell Nucleus.
- Chromatin as an active polymeric material.
- Systems-level chromosomal parameters represent a suprachromosomal basis for the non-random chromosomal arrangement in human interphase nuclei
- Systems-level chromosomal parameters represent the suprachromosomal basis for a non-random chromosomal arrangement in human interphase nuclei
- Correction: Depletion of the Chromatin Looping Proteins CTCF and Cohesin Causes Chromatin Compaction: Insight into Chromatin Folding by Polymer Modelling
- 3C-BASED TECHNOLOGIES TO STUDY THE SHAPE OF THE GENOME
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