Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability

Thuy Ngo, Jejoong Yoo, Qing Dai, Qiucen Zhang, Chuan He, Aleksei Aksimentiev, Taekjip Ha

Research output: Contribution to journalArticle

53 Citations (Scopus)

Abstract

Cytosine can undergo modifications, forming 5-methylcytosine (5-mC) and its oxidized products 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC). Despite their importance as epigenetic markers and as central players in cellular processes, it is not well understood how these modifications influence physical properties of DNA and chromatin. Here we report a comprehensive survey of the effect of cytosine modifications on DNA flexibility. We find that even a single copy of 5-fC increases DNA flexibility markedly. 5-mC reduces and 5-hmC enhances flexibility, and 5-caC does not have a measurable effect. Molecular dynamics simulations show that these modifications promote or dampen structural fluctuations, likely through competing effects of base polarity and steric hindrance, without changing the average structure. The increase in DNA flexibility increases the mechanical stability of the nucleosome and vice versa, suggesting a gene regulation mechanism where cytosine modifications change the accessibility of nucleosomal DNA through their effects on DNA flexibility.

Original languageEnglish (US)
Article number10813
JournalNature Communications
Volume7
DOIs
StatePublished - Feb 24 2016
Externally publishedYes

Fingerprint

Nucleosomes
Mechanical stability
Cytosine
flexibility
deoxyribonucleic acid
DNA
5-Methylcytosine
chromatin
gene expression
Molecular Dynamics Simulation
Epigenomics
Gene expression
markers
Chromatin
Molecular dynamics
polarity
Physical properties
physical properties
molecular dynamics
Computer simulation

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability. / Ngo, Thuy; Yoo, Jejoong; Dai, Qing; Zhang, Qiucen; He, Chuan; Aksimentiev, Aleksei; Ha, Taekjip.

In: Nature Communications, Vol. 7, 10813, 24.02.2016.

Research output: Contribution to journalArticle

Ngo, Thuy ; Yoo, Jejoong ; Dai, Qing ; Zhang, Qiucen ; He, Chuan ; Aksimentiev, Aleksei ; Ha, Taekjip. / Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability. In: Nature Communications. 2016 ; Vol. 7.
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AU - Ha, Taekjip

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