Facile synthesis of hydroxymethylcytosine-containing oligonucleotides and their reactivity upon osmium oxidation

Chemistry of installing epitranscriptomic 5-modified cytidines in RNA oligomers

Studies of 5-hydroxymethylcytidine (hm5C), 5-formylcytidine (f5C) and 5-carboxycytidine (ca5C) modifications as products of the 5-methylcytidine (m5C) oxidative demethylation pathway in cellular mRNAs constitute an important element of the new epitranscriptomic field of research. The dynamic process of m5C conversion and final turnover to the parent cytidine is considered a post-transcriptional layer of gene-expression regulation. However, the regulatory mechanism associated with epitranscriptomic cytidine modifications remains largely unknown. Therefore, oligonucleotides containing m5C oxidation products are of great value for the next generation of biochemical, biophysical, and structural studies on their function, metabolism, and contribution to human diseases. Herein, we summarize the synthetic strategies developed for the incorporation of hm5C, f5C and ca5C into RNA oligomers by phosphoramidite chemistry, including post-synthetic C5-cytidine functionalization and enzymatic methods.

Programmable tools for targeted analysis of epigenetic DNA modifications

Modifications of the cytosine 5-position are dynamic epigenetic marks of mammalian DNA with important regulatory roles in development and disease. Unraveling biological functions of such modified nucleobases is tightly connected with the potential of available methods for their analysis. Whereas genome-wide nucleobase quantification and mapping are first-line analyses, targeted analyses move into focus the more genomic sites with high biological significance are identified. We here review recent developments in an emerging field that addresses such targeted analyses via probes that combine a programmable, sequence-specific DNA-binding domain with the ability to directly recognize or cross-link an epigenetically modified nucleobase of interest. We highlight how such probes offer simple, high-resolution nucleobase analyses in vitro and enable in situ correlations between a nucleobase and other chromatin regulatory elements at user-defined loci on the single-cell level by imaging.

Whole-mount MeFISH: a novel technique for simultaneous visualization of specific DNA methylation and protein/RNA expression

To understand the spatiotemporal changes in cellular status that occur during embryonic development, it is desirable to detect simultaneously the expression of genes, proteins, and epigenetic modifications in individual embryonic cells. A technique termed methylation-specific fluorescence in situ hybridization (MeFISH) was developed recently that can visualize the methylation status of specific DNA sequences in cells fixed on a glass slide. Here, we adapted this glass slide-based MeFISH to the study of intact embryos, and established a method called whole-mount MeFISH. This method can be applied to any DNA sequences in theory and, as a proof-of-concept experiment, we examined the DNA methylation status of satellite repeats in developing mouse primordial germ cells, in which global DNA demethylation is known to take place, and obtained a result that was consistent with previous findings, thus validating the MeFISH method. We also succeeded in combining whole-mount MeFISH with immunostaining or RNA fluorescence in situ hybridization (RNA-FISH) techniques by adopting steps to retain signals of RNA-FISH or immunostaining after harsh denaturation step of MeFISH. The combined methods enabled the simultaneous visualization of DNA methylation and protein or RNA expression at single-cell resolution without destroying embryonic and nuclear structures. This whole-mount MeFISH technique should facilitate the study of the dynamics of DNA methylation status during embryonic development with unprecedented resolution.

Sequence-specific microscopic visualization of DNA methylation status at satellite repeats in individual cell nuclei and chromosomes

Methylation-specific fluorescence in situ hybridization (MeFISH) was developed for microscopic visualization of DNA methylation status at specific repeat sequences in individual cells. MeFISH is based on the differential reactivity of 5-methylcytosine and cytosine in target DNA for interstrand complex formation with osmium and bipyridine-containing nucleic acids (ICON). Cell nuclei and chromosomes hybridized with fluorescence-labeled ICON probes for mouse major and minor satellite repeats were treated with osmium for crosslinking. After denaturation, fluorescent signals were retained specifically at satellite repeats in wild-type, but not in DNA methyltransferase triple-knockout (negative control) mouse embryonic stem cells. Moreover, using MeFISH, we successfully detected hypomethylated satellite repeats in cells from patients with immunodeficiency, centromeric instability and facial anomalies syndrome and 5-hydroxymethylated satellite repeats in male germ cells, the latter of which had been considered to be unmethylated based on anti-5-methylcytosine antibody staining. MeFISH will be suitable for a wide range of applications in epigenetics research and medical diagnosis.

Discrimination between 5-hydroxymethylcytosine and 5-methylcytosine by a chemically designed peptide

An artificial phosphopeptide recognized the difference between methylated and hydroxymethylated cytosines in DNA. The Sp1 zinc finger peptide substituted by phosphotyrosine effectively discriminated between 5-methylcytosine, 5-hydroxymethylcytosine ((hm)C) and unmethylated cytosine. The DNA recognition properties of the peptide differ from those of other chemicals that detect (hm)C.