Effects of Cytosine Hydroxymethylation on DNA Strand Separation

Abstract

Cytosine hydroxymethylation is an epigenetic control factor in higher organisms. New discoveries of the biological roles of hydroxymethylation serve to raise questions about how this epigenetic modification exerts its functions and how organisms discriminate cytosine hydroxymethylation from methylation. Here, we report investigations that reveal an effect of cytosine hydroxymethylation on mechanical properties of DNA under load. The findings are based on molecular force assay measurements and steered molecular dynamics simulations. Molecular force assay experiments identified significant effects of hydroxymethylation on stretching-induced strand separation; the underlying physical mechanism has been revealed by steered molecular dynamics simulations. We find that hydroxymethylation can either upregulate or downregulate DNA's strand separation propensity, suggesting that hydroxymethylation can control gene expression by facilitating or obstructing the action of transcription machinery or the access to chromosomal DNA.

Understanding the structural and dynamic consequences of DNA epigenetic modifications: Computational insights into cytosine methylation and hydroxymethylation

“…One example of this is the work of Schulten and co-workers on DNA strand separation. 8,47 These authors combined single molecule force microscopy experiments with steered MD simulations and showed that cytosine methylation and hydroxymethylation alter the mechanical properties of DNA, thus facilitating strand separation. 8,47 However, although they identified this effect, they did not determine its underlying mechanism.…”

“…8,47 These authors combined single molecule force microscopy experiments with steered MD simulations and showed that cytosine methylation and hydroxymethylation alter the mechanical properties of DNA, thus facilitating strand separation. 8,47 However, although they identified this effect, they did not determine its underlying mechanism. Another important example is a recent study of methylation in CpG-rich sequences, which showed that methylation lowers the energy difference between the B-and Z-DNA conformations for these highly repetitive sequences.…”

“…3 Another interesting cytosine modification is hydroxymethylation, which was recently discovered to also be present in significant amounts in the genome. While its functions are still unclear, 8 it appears to be involved in gene regulation, and interference with hydroxymethylated cytosines can result in a variety of cancers, including myeloid cancers. 9 Even though no protein has been found to interact with hydroxymethylation sites on DNA, 10-11 translocation proteins (TET) have been identified as converters of methylcytosine to hydroxymethylcytosine.…”

Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores

“…Pulling only one of the termini (3′ or 5′) and constraining the corresponding termini on the opposite end can lead to strand separation. In fact, various types of SMD simulations have been employed to study the effects of methylation and hydroxymethylation on DNA strand separation [57, 58]. …”

Protein–DNA force assay in a microfluidic format

“…The binder is not labeled. MFA has been used for a variety of applications and alterations of the DNA, including mismatches, 18 methylation 19 or hydroxymethylation 20 have been shown to be detectable. Its measurement principle has been applied to the binding of transcription factors, nucleases and polyamides 21 and RNAprotein interactions.…”