Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability

Asymmetric Unwrapping of Nucleosomes under Tension Directed by DNA Local Flexibility

(2015) Thuy T.M. Ngo et al.   CELL

Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics

(2015) Xingyu Lu et al.   CELL RESEARCH

5-Formylcytosine can be a stable DNA modification in mammals

(2015) Martin Bachman et al.   Nature Chemical Biology

Reversing DNA Methylation: Mechanisms, Genomics, and Biological Functions

(2014) Hao Wu et al.   CELL

ISWI Remodelers Slide Nucleosomes with Coordinated Multi-Base-Pair Entry Steps and Single-Base-Pair Exit Steps

(2013) Sebastian Deindl et al.   CELL

Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming

(2013) Chun-Xiao Song et al.   CELL

Intra- and inter-nucleosome interactions of the core histone tail domains in higher-order chromatin structure

(2013) Sharon Pepenella et al.   CHROMOSOMA

TET enzymes, TDG and the dynamics of DNA demethylation

(2013) Rahul M. Kohli et al.   NATURE

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

(2013) William A. Pastor et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

DNA Methylation Regulated Nucleosome Dynamics

(2013) Isabel Jimenez-Useche et al.   Scientific Reports

Impact of Methylation on the Physical Properties of DNA

(2012) Alberto Pérez et al.   BIOPHYSICAL JOURNAL

Nucleosomal Elements that Control the Topography of the Barrier to Transcription

(2012) Lacramioara Bintu et al.   CELL

Regulation of the nucleosome unwrapping rate controls DNA accessibility

(2012) Justin A. North et al.   NUCLEIC ACIDS RESEARCH

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

(2012) R. Vafabakhsh et al.   SCIENCE

The Discovery of 5-Formylcytosine in Embryonic Stem Cell DNA

(2011) Toni Pfaffeneder et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

SSB Functions as a Sliding Platform that Migrates on DNA via Reptation

(2011) Ruobo Zhou et al.   CELL

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells

(2011) H. Wu et al.   GENES & DEVELOPMENT

Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium

(2011) Katarina Hart et al.   Journal of Chemical Theory and Computation

Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems

(2011) Jejoong Yoo et al.   Journal of Physical Chemistry Letters

Effects of DNA Methylation on the Structure of Nucleosomes

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

Genome-wide Regulation of 5hmC, 5mC, and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells

(2011) Yufei Xu et al.   MOLECULAR CELL

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

(2011) William A. Pastor et al.   NATURE

The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes

(2011) Lacramioara Bintu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Syntheses of 5-Formyl- and 5-Carboxyl-dC Containing DNA Oligos as Potential Oxidation Products of 5-Hydroxymethylcytosine in DNA

(2011) Qing Dai et al.   ORGANIC LETTERS

Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

(2011) Y.-F. He et al.   SCIENCE

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

(2011) S. Ito et al.   SCIENCE

Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells

(2011) Keith E. Szulwach et al.   PLoS Genetics

Single-pair FRET experiments on nucleosome conformational dynamics

(2010) Ruth Buning et al.   BIOCHIMIE

DNA Methylation Increases Nucleosome Compaction and Rigidity

(2010) John S. Choy et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Discrimination of Methylcytosine from Hydroxymethylcytosine in DNA Molecules

(2010) Meni Wanunu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure of RCC1 chromatin factor bound to the nucleosome core particle

(2010) Ravindra D. Makde et al.   NATURE

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

Visualizing one-dimensional diffusion of eukaryotic DNA repair factors along a chromatin lattice

(2010) Jason Gorman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nucleosome accessibility governed by the dimer/tetramer interface

(2010) Vera Böhm et al.   NUCLEIC ACIDS RESEARCH

Nanoelectromechanics of Methylated DNA in a Synthetic Nanopore

(2009) U. Mirsaidov et al.   BIOPHYSICAL JOURNAL

Hidden Markov Analysis of Nucleosome Unwrapping Under Force

(2009) M. Kruithof et al.   BIOPHYSICAL JOURNAL

High-resolution dynamic mapping of histone-DNA interactions in a nucleosome

(2009) Michael A Hall et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

3D-DART: a DNA structure modelling server

(2009) M. van Dijk et al.   NUCLEIC ACIDS RESEARCH

Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II

(2009) C. Hodges et al.   SCIENCE

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE