Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modeling

Inner workings of gene folding

(2019) Michele Di Pierro   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub

(2019) Gavin D. Bascom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unraveling the multiplex folding of nucleosome chains in higher order chromatin

(2019) Sergei A. Grigoryev et al.   Essays in Biochemistry

Sensitive effect of linker histone binding mode and subtype on chromatin condensation

(2019) Ognjen Perišić et al.   NUCLEIC ACIDS RESEARCH

Dependence of Chromatosome Structure on Linker Histone Sequence and Posttranslational Modification

(2018) Mehmet Ali Öztürk et al.   BIOPHYSICAL JOURNAL

Chromatin Fiber Folding Directed by Cooperative Histone Tail Acetylation and Linker Histone Binding

(2018) Gavin D. Bascom et al.   BIOPHYSICAL JOURNAL

Chromatin Higher-Order Folding: A Perspective with Linker DNA Angles

(2018) Sergei A. Grigoryev   BIOPHYSICAL JOURNAL

Molecular Dynamics simulations of the Strings and Binders Switch model of chromatin

(2018) Carlo Annunziatella et al.   METHODS

Toward an Ensemble View of Chromatosome Structure: A Paradigm Shift from One to Many

(2018) Mehmet Ali Öztürk et al.   STRUCTURE

Modifying Chromatin by Histone Tail Clipping

(2018) Gajendra Kumar Azad et al.   JOURNAL OF MOLECULAR BIOLOGY

Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis

(2018) Bjørt K. Kragesteen et al.   NATURE GENETICS

Structure of an H1-Bound 6-Nucleosome Array Reveals an Untwisted Two-Start Chromatin Fiber Conformation

(2018) Isabel Garcia-Saez et al.   MOLECULAR CELL

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

Are TADs supercoiled?

(2018) Dusan Racko et al.   NUCLEIC ACIDS RESEARCH

Bottom–up modeling of chromatin segregation due to epigenetic modifications

(2018) Quinn MacPherson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of Nucleosome Stacking and Chromatin Compaction by the Histone H4 N-Terminal Tail–H2A Acidic Patch Interaction

(2017) Qinming Chen et al.   JOURNAL OF MOLECULAR BIOLOGY

Kilobase Pair Chromatin Fiber Contacts Promoted by Living-System-Like DNA Linker Length Distributions and Nucleosome Depletion

(2017) Gavin D Bascom et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1

(2017) Jan Bednar et al.   MOLECULAR CELL

Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging

(2017) Tadasu Nozaki et al.   MOLECULAR CELL

How best to identify chromosomal interactions: a comparison of approaches

(2017) James O J Davies et al.   NATURE METHODS

Emerging roles of linker histones in regulating chromatin structure and function

(2017) Dmitry V. Fyodorov et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Polymer physics of nuclear organization and function

(2017) A. Amitai et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture

(2017) Michele Di Pierro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells

(2017) Horng D. Ou et al.   SCIENCE

Multiscale coarse-grained modelling of chromatin components: DNA and the nucleosome

(2016) Nikolay Korolev et al.   ADVANCES IN COLLOID AND INTERFACE SCIENCE

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

(2016) Antoni Luque et al.   BIOPHYSICAL JOURNAL

Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping

(2016) Lilien N. Voong et al.   CELL

Multiscale simulation of DNA

(2016) Pablo D Dans et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The second decade of 3C technologies: detailed insights into nuclear organization

(2016) Annette Denker et al.   GENES & DEVELOPMENT

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

(2016) Gavin D. Bascom et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Capturing native interactions: intrinsic methods to study chromatin conformation

(2016) M Jordan Rowley et al.   Molecular Systems Biology

Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping

(2016) Viviana I. Risca et al.   NATURE

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

Insights into newly discovered marks and readers of epigenetic information

(2016) Forest H Andrews et al.   Nature Chemical Biology

Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome

(2016) Tsung-Han S Hsieh et al.   NATURE METHODS

Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome

(2016) Mehmet Ali Öztürk et al.   NUCLEIC ACIDS RESEARCH

Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes

(2016) Sergei A. Grigoryev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Visualizing the molecular sociology at the HeLa cell nuclear periphery

(2016) J. Mahamid et al.   SCIENCE

Advances in electron microscopy: A qualitative view of instrumentation development for macromolecular imaging and tomography

(2015) Rasmus R. Schröder   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

(2015) Tsung-Han S. Hsieh et al.   CELL

Chromatin Fibers Are Formed by Heterogeneous Groups of Nucleosomes In Vivo

(2015) Maria Aurelia Ricci et al.   CELL

The chromatin fiber: multiscale problems and approaches

(2015) Gungor Ozer et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study

(2015) Rosana Collepardo-Guevara et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

An Overview of Genome Organization and How We Got There: from FISH to Hi-C

(2015) James Fraser et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Structural Mechanisms of Nucleosome Recognition by Linker Histones

(2015) Bing-Rui Zhou et al.   MOLECULAR CELL

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

(2015) James O J Davies et al.   NATURE METHODS

Increasing Nucleosome Occupancy Is Correlated with an Increasing Mutation Rate so Long as DNA Repair Machinery Is Intact

(2015) Puya G. Yazdi et al.   PLoS One

Long-Range Chromatin Interactions

(2015) Job Dekker et al.   Cold Spring Harbor Perspectives in Biology

Stacked thin layers of metaphase chromatin explain the geometry of chromosome rearrangements and banding

(2015) Joan-Ramon Daban   Scientific Reports

Nanotechnology: from the ancient time to nowadays

(2015) Delphine Schaming et al.   Foundations of Chemistry

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Post-Translational Modifications of Histones That Influence Nucleosome Dynamics

(2014) Gregory D. Bowman et al.   CHEMICAL REVIEWS

Chromatin as dynamic 10-nm fibers

(2014) Kazuhiro Maeshima et al.   CHROMOSOMA

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

(2014) Jim R Hughes et al.   NATURE GENETICS

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

(2014) Wenxiu Ma et al.   NATURE METHODS

Dynamic condensation of linker histone C-terminal domain regulates chromatin structure

(2014) Antoni Luque et al.   NUCLEIC ACIDS RESEARCH

Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains

(2014) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

Chromatin fiber polymorphism triggered by variations of DNA linker lengths

(2014) R. Collepardo-Guevara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cryo-EM Study of the Chromatin Fiber Reveals a Double Helix Twisted by Tetranucleosomal Units

(2014) F. Song et al.   SCIENCE

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

The genome folding mechanism in yeast

(2013) Hajime Kimura et al.   JOURNAL OF BIOCHEMISTRY

Developmentally Regulated Linker Histone H1c Promotes Heterochromatin Condensation and Mediates Structural Integrity of Rod Photoreceptors in Mouse Retina

(2013) Evgenya Y. Popova et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Chromatin Insulators: Linking Genome Organization to Cellular Function

(2013) Jennifer E. Phillips-Cremins et al.   MOLECULAR CELL

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

An Advanced Coarse-Grained Nucleosome Core Particle Model for Computer Simulations of Nucleosome-Nucleosome Interactions under Varying Ionic Conditions

(2013) Yanping Fan et al.   PLoS One

Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning

(2013) G. Moyle-Heyrman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs

(2013) G. Andrey et al.   SCIENCE

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

High-Resolution Mapping of H1 Linker Histone Variants in Embryonic Stem Cells

(2013) Kaixiang Cao et al.   PLoS Genetics

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

Histone H4 K16Q Mutation, an Acetylation Mimic, Causes Structural Disorder of Its N-Terminal Basic Patch in the Nucleosome

(2012) Bing-Rui Zhou et al.   JOURNAL OF MOLECULAR BIOLOGY

A map of nucleosome positions in yeast at base-pair resolution

(2012) Kristin Brogaard et al.   NATURE

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Crucial role of dynamic linker histone binding and divalent ions for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes

(2012) Rosana Collepardo-Guevara et al.   NUCLEIC ACIDS RESEARCH

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

The Effect of Linker Histone's Nucleosome Binding Affinity on Chromatin Unfolding Mechanisms

(2011) Rosana Collepardo-Guevara et al.   BIOPHYSICAL JOURNAL

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

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

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

Chromatin folding - from biology to polymer models and back

(2011) M. Tark-Dame et al.   JOURNAL OF CELL SCIENCE

Energy Landscape Analyses of Disordered Histone Tails Reveal Special Organization of Their Conformational Dynamics

(2011) Davit A. Potoyan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

DNA and nucleosomes direct distinct folding of a linker histone H1 C-terminal domain

(2011) He Fang et al.   NUCLEIC ACIDS RESEARCH

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

Histone fold modifications control nucleosome unwrapping and disassembly

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

The impact of histone post-translational modifications on developmental gene regulation

(2010) Mark N. Cruickshank et al.   AMINO ACIDS

Modeling Studies of Chromatin Fiber Structure as a Function of DNA Linker Length

(2010) Ognjen Perišić et al.   JOURNAL OF MOLECULAR BIOLOGY

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

Histone H1 null vertebrate cells exhibit altered nucleosome architecture

(2010) Hideharu Hashimoto et al.   NUCLEIC ACIDS RESEARCH

Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation

(2010) Hideki Tanizawa et al.   NUCLEIC ACIDS RESEARCH

Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization

(2010) Manfred Bohn et al.   PLoS One

Living without 30nm chromatin fibers

(2010) Eden Fussner et al.   TRENDS IN BIOCHEMICAL SCIENCES

Gene regulation by nucleosome positioning

(2010) Lu Bai et al.   TRENDS IN GENETICS

Chromatin Higher-order Structure and Dynamics

(2010) C. L. Woodcock et al.   Cold Spring Harbor Perspectives in Biology

Super-Resolution Fluorescence Microscopy

(2009) Bo Huang et al.   Annual Review of Biochemistry

Entropic organization of interphase chromosomes

(2009) Peter R. Cook et al.   JOURNAL OF CELL BIOLOGY

ChIP-based methods for the identification of long-range chromatin interactions

(2009) Melissa J. Fullwood et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

A Tale of Tails: How Histone Tails Mediate Chromatin Compaction in Different Salt and Linker Histone Environments†

(2009) Gaurav Arya et al.   JOURNAL OF PHYSICAL CHEMISTRY A

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Spatially confined folding of chromatin in the interphase nucleus

(2009) J. Mateos-Langerak 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

Chromatin loops in gene regulation

(2008) Stephan Kadauke et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Analysis of cryo-electron microscopy images does not support the existence of 30-nm chromatin fibers in mitotic chromosomes in situ

(2008) M. Eltsov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CTCF-dependent enhancer-blocking by alternative chromatin loop formation

(2008) C. Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping

(2008) Vijay K Tiwari et al.   PLOS BIOLOGY