Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements.

No abstract is available for this paper.

• Publication year

  2016

• Venue

  Journal of Physical Chemistry B

• Publication date

  2016-06-16

• Fields of study

  Biology, Materials Science, Physics, Chemistry, Medicine

• Identifiers
  DOI 10.1021/acs.jpcb.6b03197PMID 27218881PMCID PMC6268121
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Correlation among DNA Linker Length, Linker Histone Concentration, and Histone Tails in Chromatin.

  2016cited by this paper
• Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes

  2016cited by this paper
• Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

  2015cited by this paper
• Chromatin fibers are formed by heterogeneous groups of nucleosomes in vivo.

  2015cited by this paper
• Structural Mechanisms of Nucleosome Recognition by Linker Histones.

  2015cited by this paper
• Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study.

  2015cited by this paper
• Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

  2015cited by this paper
• Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells

  2015cited by this paper
• Histone exchange, chromatin structure and the regulation of transcription

  2015cited by this paper
• The chromatin fiber: multiscale problems and approaches.

  2015cited by this paper
• Role of DNA sequence based structural features of promoters in transcription initiation and gene expression.

  2014cited by this paper
• Chromatin fiber polymorphism triggered by variations of DNA linker lengths

  2014cited by this paper
• Dynamic condensation of linker histone C-terminal domain regulates chromatin structure

  2014cited by this paper
• A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

  2014cited by this paper
• Master transcription factors and mediator establish super-enhancers at key cell identity genes.

  2013cited by this paper
• XPG and XPF endonucleases trigger chromatin looping and DNA demethylation for accurate expression of activated genes.

  2012cited by this paper
• A Role for Snf2-Related Nucleosome-Spacing Enzymes in Genome-Wide Nucleosome Organization

  2011cited by this paper
• Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations

  2011cited by this paper
• Chromatin folding – from biology to polymer models and back

  2011cited by this paper
• The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

  2011cited by this paper
• The fractal globule as a model of chromatin architecture in the cell

  2011cited by this paper
• Toward Convergence of Experimental Studies and Theoretical Modeling of the Chromatin Fiber*

  2011cited by this paper
• Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization

  2010cited by this paper
• Modeling studies of chromatin fiber structure as a function of DNA linker length.

  2010cited by this paper
• A Structural Perspective on the Where, How, Why, and What of Nucleosome Positioning

  2010cited by this paper
• Transcriptional silencing of {gamma}-globin by BCL11A involves long-range interactions and cooperation with SOX6.

  2010cited by this paper
• Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus

  2009cited by this paper
• Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

  2009cited by this paper
• The physics behind the larger scale organization of DNA in eukaryotes

  2009cited by this paper
• A tale of tails: how histone tails mediate chromatin compaction in different salt and linker histone environments.

  2009cited by this paper
• Mapping cis- and trans- chromatin interaction networks using chromosome conformation capture (3C).

  2009cited by this paper
• Tissue- and Expression Level–Specific Chromatin Looping at Maize b1 Epialleles[W]

  2009cited by this paper
• Genomic interactions: chromatin loops and gene meeting points in transcriptional regulation.

  2009cited by this paper
• Mesoscale simulations of two nucleosome-repeat length oligonucleosomes.

  2009cited by this paper
• Exchange of GATA factors mediates transitions in looped chromatin organization at a developmentally regulated gene locus.

  2008cited by this paper
• PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping

  2008cited by this paper
• Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure

  2008cited by this paper
• Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo.

  2007cited by this paper
• Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex

  2007cited by this paper
• Functional interaction between PML and SATB1 regulates chromatin-loop architecture and transcription of the MHC class I locus

  2007cited by this paper
• Higher-order structures of chromatin: the elusive 30 nm fiber.

  2007cited by this paper
• Regulation of magnesium homeostasis and transport in mammalian cells.

  2007cited by this paper
• Chromatin modifications and their function.

  2007cited by this paper
• Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model

  2006cited by this paper
• Flexible histone tails in a new mesoscopic oligonucleosome model.

  2006cited by this paper
• CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2.

  2006cited by this paper
• SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes

  2006cited by this paper
• Nucleosome positions predicted through comparative genomics

  2006cited by this paper
• Long-Range Interactions between Three Transcriptional Enhancers, Active Vκ Gene Promoters, and a 3′ Boundary Sequence Spanning 46 Kilobases

  2005cited by this paper
• Three-Dimensional Maps of All Chromosomes in Human Male Fibroblast Nuclei and Prometaphase Rosettes

  2005cited by this paper
• Long-range control of gene expression: emerging mechanisms and disruption in disease.

  2005cited by this paper
• Genome-Scale Identification of Nucleosome Positions in S. cerevisiae

  2005cited by this paper
• IL-13受体α2降低血吸虫病肉芽肿的炎症反应并延长宿主存活时间[英]/Mentink-Kane MM,Cheever AW，Thompson RW，et al//Proc Natl Acad Sci U S A

  2005cited by this paper
• Evidence for nucleosome depletion at active regulatory regions genome-wide

  2004cited by this paper
• Chromatin Compaction by a Polycomb Group Protein Complex

  2004cited by this paper
• The active spatial organization of the beta-globin locus requires the transcription factor EKLF.

  2004cited by this paper
• Identification of Specific Functional Subdomains within the Linker Histone H10 C-terminal Domain*

  2004cited by this paper
• GATA-4 and GATA-5 Transcription Factor Genes and Potential Downstream Antitumor Target Genes Are Epigenetically Silenced in Colorectal and Gastric Cancer

  2003cited by this paper
• Molecular biology. Chromatin higher order folding--wrapping up transcription.

  2002cited by this paper
• Looping and interaction between hypersensitive sites in the active beta-globin locus.

  2002cited by this paper
• Computer simulation of the 30-nanometer chromatin fiber.

  2002cited by this paper
• Chromatin Higher Order Folding--Wrapping up Transcription

  2002cited by this paper
• Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution.

  2002cited by this paper
• Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome.

  2001cited by this paper
• Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain

  2001cited by this paper
• DNA persistence length revisited.

  2001cited by this paper
• Linker histone binding and displacement: versatile mechanism for transcriptional regulation

  2000cited by this paper
• Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin.

  1998cited by this paper
• Helical wormlike chains in polymer solutions

  1997cited by this paper
• DNA bending and its relation to nucleosome positioning.

  1985cited by this paper
• 6 – Chromosome Structure and Levels of Chromosome Organization

  1979cited by this paper
• Interactions of highly charged colloidal cylinders with applications to double-stranded.

  1977cited by this paper
• Higher order coiling of DNA in chromatin.

  1977cited by this paper
• Interactions of highly charged colloidal cylinders with applications to double‐stranded DNA

  1977cited by this paper
• MONTE CARLO CALCULATION OF THE AVERAGE EXTENSION OF MOLECULAR CHAINS

  1955cited by this paper
• The Monte Carlo method.

  1949cited by this paper
• THE JOURNAL OF PHYSICAL CHEMISTRY B

  year unknowncited by this paper
• Chromatin Modifications and Their Function

  year unknowncited by this paper

• Nucleosome Linker Length and Distribution as Major Players in Epigenetic Regulation: Insights from Cryo-Electron Microscopy and Modeling of Retina Cell Maturation

  2025cites this paper
• Regulation of Genome Architecture in Huntington’s Disease

  2025cites this paper
• Predicting gene expression changes from chromatin structure modification

  2025cites this paper
• Regulation of chromatin architecture by protein binding: insights from molecular modeling

  2024cites this paper
• True-to-scale DNA-density maps correlate with major accessibility differences between active and inactive chromatin.

  2023cites this paper
• Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics

  2023cites this paper
• True-to-scale DNA-density maps correlate with major accessibility 1 differences between active and inactive chromatin Localization and constrained movements of microinjected nanobeads within the cycle Interchromatin and Matrix: An Integrated View of the Architecture. Critical

  2022cites this paper
• Genome modeling: From chromatin fibers to genes.

  2022cites this paper
• An associative memory Hamiltonian model for DNA and nucleosomes

  2022cites this paper
• Brownian Dynamics Simulations of Mesoscale Chromatin Fibers.

  2022cites this paper
• True-to-scale DNA-density maps correlate with major accessibility differences between active and inactive chromatin

  2022cites this paper
• Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface

  2021cites this paper
• Four-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome

  2021cites this paper
• Is the H4 histone tail intrinsically disordered or intrinsically multifunctional?

  2021cites this paper
• 4D chromosome reconstruction elucidates the spatial reorganization of the mammalian X-chromosome

  2021cites this paper
• Mesoscale Modeling and Single-Nucleosome Tracking Reveal Remodeling of Clutch Folding and Dynamics in Stem Cell Differentiation

  2021cites this paper
• Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment

  2020cites this paper
• Mesoscale Modeling of Nucleosome-Binding Antibody PL2-6: Mono- versus Bivalent Chromatin Complexes.

  2020cites this paper
• Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry

  2020cites this paper
• Mechanistic modeling of chromatin folding to understand function

  2020cites this paper
• Mechanistic Modelling of Chromatin Folding to Understand Function.

  2020cites this paper
• Genome organization: experiments and modelling

  2020cites this paper
• 1CPN: A coarse-grained multi-scale model of chromatin.

  2019cites this paper
• Ion counting demonstrates a high electrostatic field generated by the nucleosome

  2019cites this paper
• Nucleosome Crowding in Chromatin Slows the Diffusion but Can Promote Target Search of Proteins.

  2019cites this paper
• Biophysics and the Genomic Sciences.

  2019cites this paper
• Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modeling

  2019cites this paper
• Data formats for modelling the spatial structure of chromatin based on experimental positions of nucleosomes

  2019cites this paper
• Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR.

  2019cites this paper
• Mesoscale Modeling of a Nucleosome-Binding Antibody (PL2-6): Mono- vs. Bivalent Chromatin Complexes

  2019cites this paper
• Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations

  2019cites this paper
• Dynamic chromatin organization in the cell.

  2019cites this paper
• Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub

  2019influential citation
• Major Determinants of Nucleosome Positioning.

  2018cites this paper
• Chromatin Fiber Folding Directed by Cooperative Histone Tail Acetylation and Linker Histone Binding.

  2018cites this paper
• The 10-nm chromatin fiber and its relationship to interphase chromosome organization

  2017cites this paper
• Dependence of the Linker Histone and Chromatin Condensation on the Nucleosome Environment.

  2017cites this paper
• Genomic Energy Landscapes.

  2017cites this paper
• Genome organization: experiments and modeling

  2017cites this paper
• Linking Chromatin Fibers to Gene Folding by Hierarchical Looping.

  2017cites this paper
• Kilobase Pair Chromatin Fiber Contacts Promoted by Living-System-Like DNA Linker Length Distributions and Nucleosome Depletion.

  2017cites this paper
• Transferable model for chromosome architecture

  2016cites this paper