Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning

Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions

(2016) Alexey K. Shaytan et al.   JOURNAL OF MOLECULAR BIOLOGY

HistoneDB 2.0: a histone database with variants—an integrated resource to explore histones and their variants

(2016) Eli J. Draizen et al.   Database-The Journal of Biological Databases and Curation

Rapid Deamination of Cyclobutane Pyrimidine Dimer Photoproducts at TCG Sites in a Translationally and Rotationally Positioned Nucleosomein Vivo

(2015) Vincent J. Cannistraro et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural analysis of nucleosomal barrier to transcription

(2015) Daria A. Gaykalova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome

(2015) David Winogradoff et al.   Scientific Reports

Pioneer transcription factors in cell reprogramming

(2014) Makiko Iwafuchi-Doi et al.   GENES & DEVELOPMENT

DNA Damage by Histone Radicals in Nucleosome Core Particles

(2014) Chuanzheng Zhou et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Rotational positioning of nucleosomes facilitates selective binding of p53 to response elements associated with cell cycle arrest

(2013) F. Cui et al.   NUCLEIC ACIDS RESEARCH

Nucleosome Remodeling and Epigenetics

(2013) P. B. Becker et al.   Cold Spring Harbor Perspectives in Biology

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?

(2012) Karolin Luger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A Map of Minor Groove Shape and Electrostatic Potential from Hydroxyl Radical Cleavage Patterns of DNA

(2011) Eric P. Bishop et al.   ACS Chemical Biology

OPERating ON Chromatin, a Colorful Language where Context Matters

(2011) Kathryn E. Gardner et al.   JOURNAL OF MOLECULAR BIOLOGY

Nonhistone Scm3 Binds to AT-Rich DNA to Organize Atypical Centromeric Nucleosome of Budding Yeast

(2011) Hua Xiao et al.   MOLECULAR CELL

Crystal structure of the human centromeric nucleosome containing CENP-A

(2011) Hiroaki Tachiwana et al.   NATURE

The centromeric nucleosome of budding yeast is perfectly positioned and covers the entire centromere

(2011) H. A. Cole et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleosome structural studies

(2010) Song Tan et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Crystal Structures of Nucleosome Core Particles Containing the ‘601’ Strong Positioning Sequence

(2010) Dileep Vasudevan et al.   JOURNAL OF MOLECULAR BIOLOGY

Single-base resolution mapping of H1-nucleosome interactions and 3D organization of the nucleosome

(2010) S. H. Syed et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Insight into the Sequence Dependence of Nucleosome Positioning

(2010) Bin Wu et al.   STRUCTURE

Major Evolutionary Transitions in Centromere Complexity

(2009) Harmit S. Malik et al.   CELL

Using DNA mechanics to predict in vitro nucleosome positions and formation energies

(2009) Alexandre V. Morozov et al.   NUCLEIC ACIDS RESEARCH

The unique structure of A-tracts and intrinsic DNA bending

(2009) Tali E. Haran et al.   QUARTERLY REVIEWS OF BIOPHYSICS

A 1,2-d(GpG) Cisplatin Intrastrand Cross-Link Influences the Rotational and Translational Setting of DNA in Nucleosomes

(2008) Matthias Ober et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Footprinting protein–DNA complexes using the hydroxyl radical

(2008) Swapan S Jain et al.   Nature Protocols

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

(2008) Xiang-Jun Lu et al.   Nature Protocols