The impact of the sequence-dependent physical properties of DNA on chromatin dynamics

DNAcycP: a deep learning tool for DNA cyclizability prediction

(2022) Keren Li et al.   NUCLEIC ACIDS RESEARCH

ATP binding facilitates target search of SWR1 chromatin remodeler by promoting one-dimensional diffusion on DNA

(2022) Claudia C Carcamo et al.   eLife

Deciphering the mechanical code of the genome and epigenome

(2022) Aakash Basu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural mechanism of extranucleosomal DNA readout by the INO80 complex

(2022) Franziska Kunert et al.   Science Advances

DNA mechanics and its biological impact

(2021) Aakash Basu et al.   JOURNAL OF MOLECULAR BIOLOGY

Impact of DNA methylation on 3D genome structure

(2021) Diana Buitrago et al.   Nature Communications

Genome information processing by the INO80 chromatin remodeler positions nucleosomes

(2021) Elisa Oberbeckmann et al.   Nature Communications

DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles

(2021) Jejoong Yoo et al.   NUCLEIC ACIDS RESEARCH

Primary Role of the Nucleosome

(2020) Roger D. Kornberg et al.   MOLECULAR CELL

DNA mismatches reveal conformational penalties in protein–DNA recognition

(2020) Ariel Afek et al.   NATURE

Measuring DNA mechanics on the genome scale

(2020) Aakash Basu et al.   NATURE

Sub-nucleosomal Genome Structure Reveals Distinct Nucleosome Folding Motifs

(2019) Masae Ohno et al.   CELL

Nucleosome Orientation Map Finds Two New Chromatin Folding Motifs

(2019) Viviana I. Risca   CELL

CTCF: a Swiss-army knife for genome organization and transcription regulation

(2019) Luca Braccioli et al.   Essays in Biochemistry

The diverse roles of DNA methylation in mammalian development and disease

(2019) Maxim V. C. Greenberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

DNA loop extrusion by human cohesin

(2019) Iain F. Davidson et al.   SCIENCE

Human cohesin compacts DNA by loop extrusion

(2019) Yoori Kim et al.   SCIENCE

DNA sequence encodes the position of DNA supercoils

(2018) Sung Hyun Kim et al.   eLife

Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes

(2017) Cedric R. Clapier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2016) Lilien N. Voong et al.   CELL

Genomic Nucleosome Organization Reconstituted with Pure Proteins

(2016) Nils Krietenstein et al.   CELL

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

(2016) Viviana I. Risca et al.   NATURE

Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability

(2016) Thuy T. M. Ngo et al.   Nature Communications

The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors

(2016) Nicola Wiechens et al.   PLoS Genetics

In vitro selection of DNAs with an increased propensity to form small circles

(2015) Gabriel Rosanio et al.   BIOPOLYMERS

Determinants of nucleosome positioning

(2013) Kevin Struhl et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Probing Allostery Through DNA

(2013) S. Kim et al.   SCIENCE

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

(2012) Kristin Brogaard et al.   NATURE

DNA Methylation and Its Basic Function

(2012) Lisa D Moore et al.   NEUROPSYCHOPHARMACOLOGY

Extreme Bendability of DNA Less than 100 Base Pairs Long Revealed by Single-Molecule Cyclization

(2012) R. Vafabakhsh et al.   SCIENCE

Effects of DNA Methylation on the Structure of Nucleosomes

(2011) Ju Yeon Lee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cytosine methylation alters DNA mechanical properties

(2011) Philip M. D. Severin et al.   NUCLEIC ACIDS RESEARCH

Sequence dependence of DNA bending rigidity

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

DNA Sequence-Directed Organization of Chromatin: Structure-Based Computational Analysis of Nucleosome-Binding Sequences

(2009) Sreekala Balasubramanian et al.   BIOPHYSICAL JOURNAL

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

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

Oscillations in supercoiling drive circadian gene expression in cyanobacteria

(2009) Vikram Vijayan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA