Structure-driven homology pairing of chromatin fibers: the role of electrostatics and protein-induced bridging

Unwrapping of Nucleosomal DNA Ends: A Multiscale Molecular Dynamics Study

(2012) Karine Voltz et al.   BIOPHYSICAL JOURNAL

Self-Assembly of Thin Plates from Micrococcal Nuclease-Digested Chromatin of Metaphase Chromosomes

(2012) Maria Milla et al.   BIOPHYSICAL JOURNAL

Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations

(2012) Yu Zhang et al.   CELL

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Higher-order chromatin structure: bridging physics and biology

(2012) Geoffrey Fudenberg et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Modelling chromatin structure and dynamics: status and prospects

(2012) Nikolay Korolev et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Human mitotic chromosomes consist predominantly of irregularly folded nucleosome fibres without a 30-nm chromatin structure

(2012) Yoshinori Nishino et al.   EMBO JOURNAL

Out of register: How DNA determines the chromatin fiber geometry

(2012) G. Lanzani et al.   EPL

A solution to the subdiffusion-efficiency paradox: Inactive states enhance reaction efficiency at subdiffusion conditions in living cells

(2012) L. E. Sereshki et al.   EPL

A model for the 3D chromatin architecture of pro and eukaryotes

(2012) Dieter W. Heermann et al.   METHODS

Genome-wide nucleosome positioning during embryonic stem cell development

(2012) Vladimir B Teif et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The mechanics behind DNA sequence-dependent properties of the nucleosome

(2012) Eugene Y. D. Chua et al.   NUCLEIC ACIDS RESEARCH

Strange kinetics of single molecules in living cells

(2012) Eli Barkai et al.   PHYSICS TODAY

Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation

(2012) D. A. Potoyan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complexity of chromatin folding is captured by the strings and binders switch model

(2012) M. Barbieri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Electrostatics of DNA compaction in viruses, bacteria and eukaryotes: functional insights and evolutionary perspective

(2012) Pascal Carrivain et al.   Soft Matter

The polyelectrolyte properties of chromatin

(2012) Nikolay Korolev et al.   Soft Matter

Chromosomes without a 30-nm chromatin fiber

(2012) Yasumasa Joti et al.   Nucleus

Nucleosome Structure(s) and Stability: Variations on a Theme

(2011) Andrew J. Andrews et al.   Annual Review of Biophysics

Electrostatic Braiding and Homologous Pairing of DNA Double Helices

(2011) Ruggero Cortini et al.   BIOPHYSICAL JOURNAL

Chromatin higher-order structures and gene regulation

(2011) Guohong Li et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Salt-modulated structure of polyelectrolyte-macroion complex fibers

(2011) Hoda Boroudjerdi et al.   EUROPEAN PHYSICAL JOURNAL E

Chromatin under mechanical stress: from single 30 nm fibers to single nucleosomes

(2011) Jan Bednar et al.   FEBS Journal

Toward Convergence of Experimental Studies and Theoretical Modeling of the Chromatin Fiber

(2011) Tamar Schlick et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Influence of mobile DNA-protein-DNA bridges on DNA configurations: Coarse-grained Monte-Carlo simulations

(2011) Renko de Vries   JOURNAL OF CHEMICAL PHYSICS

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

(2011) Eitan Yaffe et al.   NATURE GENETICS

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes

(2011) David Martin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Electrostatic interactions in biological DNA-related systems

(2011) A. G. Cherstvy   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Evidence for short-range helical order in the 30-nm chromatin fibers of erythrocyte nuclei

(2011) M. P. Scheffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Electrostatic Origin of Salt-Induced Nucleosome Array Compaction

(2010) Nikolay Korolev et al.   BIOPHYSICAL JOURNAL

Recombination Proteins Mediate Meiotic Spatial Chromosome Organization and Pairing

(2010) Aurora Storlazzi et al.   CELL

Diffusion-based DNA target colocalization by thermodynamic mechanisms

(2010) A. Scialdone et al.   DEVELOPMENT

DNA-DNA sequence homology recognition: physical mechanisms and open questions

(2010) A. G. Cherstvy   JOURNAL OF MOLECULAR RECOGNITION

Undulations Enhance the Effect of Helical Structure on DNA Interactions

(2010) D. J. Lee et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae

(2010) Alexandra B Lantermann et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ICM Web: the interactive chromatin modeling web server

(2010) Richard C. Stolz et al.   NUCLEIC ACIDS RESEARCH

Physics of DNA: unravelling hidden abilities encoded in the structure of ‘the most important molecule’

(2010) Alexei A. Kornyshev   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Condensed DNA: Condensing the concepts

(2010) Vladimir B. Teif et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Does CTCF mediate between nuclear organization and gene expression?

(2009) Rolf Ohlsson et al.   BIOESSAYS

Multiscale Analysis of Dynamics and Interactions of Heterochromatin Protein 1 by Fluorescence Fluctuation Microscopy

(2009) Katharina P. Müller et al.   BIOPHYSICAL JOURNAL

Nucleosome Shape Dictates Chromatin Fiber Structure

(2009) Martin Depken et al.   BIOPHYSICAL JOURNAL

Protein-Mediated Molecular Bridging: A Key Mechanism in Biopolymer Organization

(2009) Paul A. Wiggins et al.   BIOPHYSICAL JOURNAL

Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin

(2009) Aurélien Bancaud et al.   EMBO JOURNAL

Probing DNA−DNA Electrostatic Friction in Tight Superhelical DNA Plies

(2009) A. G. Cherstvy   JOURNAL OF PHYSICAL CHEMISTRY B

Positively Charged Residues in DNA-Binding Domains of Structural Proteins Follow Sequence-specific Positions of DNA Phosphate Groups

(2009) A. G. Cherstvy   JOURNAL OF PHYSICAL CHEMISTRY B

Dynamics and function of compact nucleosome arrays

(2009) Michael G Poirier et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mesoscale simulations of two nucleosome-repeat length oligonucleosomes

(2009) Tamar Schlick et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Single molecule detection of direct, homologous, DNA/DNA pairing

(2009) C. Danilowicz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

(2009) S. A. Grigoryev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Macromolecular Crowding and Confinement: Biochemical, Biophysical, and Potential Physiological Consequences

(2008) Huan-Xiang Zhou et al.   Annual Review of Biophysics

Nucleosome Geometry and Internucleosomal Interactions Control the Chromatin Fiber Conformation

(2008) Nick Kepper et al.   BIOPHYSICAL JOURNAL

A Thermodynamic Switch for Chromosome Colocalization

(2008) M. Nicodemi et al.   GENETICS

Protein−DNA Interactions:  Reaching and Recognizing the Targets

(2008) A. G. Cherstvy et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DNA Cholesteric Phases: The Role of DNA Molecular Chirality and DNA−DNA Electrostatic Interactions

(2008) A. G. Cherstvy   JOURNAL OF PHYSICAL CHEMISTRY B

DNA Double Helices Recognize Mutual Sequence Homology in a Protein Free Environment

(2008) Geoff S. Baldwin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure

(2008) Andrew Routh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome

(2008) Yutao Fu et al.   PLoS Genetics

Finding a match: how do homologous sequences get together for recombination?

(2007) Adi Barzel et al.   NATURE REVIEWS GENETICS