Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability (Q36627544)

15 August 2017

Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability (English)

1 reference

15 August 2017

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31 May 2020

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31 May 2020

1 reference

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31 May 2020

1 reference

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31 May 2020

Qiucen Zhang

1 reference

31 May 2020

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26905257%20AND%20SRC:MED&resulttype=core&format=json

Thuy T M Ngo

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26905257%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

Chuan He

series ordinal

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31 May 2020

language of work or name

English

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publication date

24 February 2016

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15 August 2017

Nature Communications

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31 May 2020

volume

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31 May 2020

page(s)

10813

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Creative Commons Attribution 4.0 International

31 May 2020

start time

24 February 2016

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April 2022 Public Data File from Crossref

copyrighted

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cites work

5-Formylcytosine can be a stable DNA modification in mammals

1 reference

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Asymmetric unwrapping of nucleosomes under tension directed by DNA local flexibility

30 September 2017

1 reference

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Reversing DNA methylation: mechanisms, genomics, and biological functions

30 September 2017

1 reference

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TET enzymes, TDG and the dynamics of DNA demethylation.

30 September 2017

1 reference

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

30 September 2017

1 reference

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

30 September 2017

1 reference

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Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming

30 September 2017

1 reference

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DNA methylation: roles in mammalian development

30 September 2017

1 reference

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ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Regulation of the nucleosome unwrapping rate controls DNA accessibility.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Effects of DNA methylation on the structure of nucleosomes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

SSB functions as a sliding platform that migrates on DNA via reptation.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

The discovery of 5-formylcytosine in embryonic stem cell DNA.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Nascent transcript sequencing visualizes transcription at nucleotide resolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Nucleosome accessibility governed by the dimer/tetramer interface

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Single-pair FRET experiments on nucleosome conformational dynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Structure of RCC1 chromatin factor bound to the nucleosome core particle

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

3D-DART: a DNA structure modelling server

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Hidden Markov analysis of nucleosome unwrapping under force

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Structure and mechanism for DNA lesion recognition

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Effect of force on mononucleosomal dynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Scalable molecular dynamics with NAMD

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Rapid spontaneous accessibility of nucleosomal DNA.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Nucleosomes facilitate their own invasion

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Impact of CpG methylation on structure, dynamics and solvation of cAMP DNA responsive element

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Functional links between nuclear structure, gene expression, DNA replication, and methylation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Crystal structure of the nucleosome core particle at 2.8 Å resolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Effects of DNA methylation on DNA-binding proteins and gene expression.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

DNA flexibility studied by covalent closure of short fragments into circles

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

DNA methylation regulated nucleosome dynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Nucleosomal elements that control the topography of the barrier to transcription

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Impact of methylation on the physical properties of DNA.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Syntheses of 5-formyl- and 5-carboxyl-dC containing DNA oligos as potential oxidation products of 5-hydroxymethylcytosine in DNA.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Discrimination of Methylcytosine from Hydroxymethylcytosine in DNA Molecules

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

DNA methylation increases nucleosome compaction and rigidity

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Nanoelectromechanics of methylated DNA in a synthetic nanopore.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Sequence-Dependent Effects in the Cyclization of Short DNA.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

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

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Spontaneous sharp bending of double-stranded DNA.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4770088

Epigenetic reprogramming in mouse primordial germ cells

20 September 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS10813

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS10813

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS10813

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS10813

Demethylation of the zygotic paternal genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS10813

The dynamic impact of CpG methylation in DNA

21 January 2018

1 reference

12 December 2020

Mitochondria and the death of oocytes

1 reference

12 December 2020

Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II

1 reference

12 December 2020

Bending and flexibility of methylated and unmethylated EcoRI DNA

1 reference

12 December 2020

Identifiers

DOI

10.1038/NCOMMS10813

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26905257%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

31 May 2020

ADS bibcode

2016NatCo...710813N

0 references

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26905257%20AND%20SRC:MED&resulttype=core&format=json

31 May 2020

PubMed publication ID

26905257

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26905257%20AND%20SRC:MED&resulttype=core&format=json