Ligand‐Incorporation Site in 5‐Methylcytosine‐Detection Probe Modulating the Site of Osmium Complexation with the Target DNA

Sugizaki, Kaori; Nakamura, Akiko; Yanagisawa, Hiroki; Okamoto, Akimitsu

doi:10.1002/cbdv.201100425

Cited by 7 publications

(4 citation statements)

References 16 publications

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“…The latter possibility is significant because CpG dinucleotides are well-known mutation hotspots and often changed to TpG. Although osmium can react with thymine (42), base pairing between thymine and bipyridine-attached adenine prevents complex formation as long as the modified adenine is located in the middle of the ICON probe (43). Nevertheless, increased signal gain is required to obtain good MeFISH images.…”

Section: Discussionmentioning

confidence: 99%

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

Miyanari

Shirane

et al. 2013

Nucleic Acids Research

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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.

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Section: Discussionmentioning

confidence: 99%

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

Miyanari

Shirane

et al. 2013

Nucleic Acids Research

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“…196 Fluorimetric detection has also been used in combination with crosslinking by bipyridine ligands. 197 Methylation-specific fluorescence in situ hybridisation (MeFISH) uses ICON probes for in vivo visualisation of cytosine modifications.…”

Section: Detection Of Cacmentioning

confidence: 99%

Methods for detection of cytosine and thymine modifications in DNA

Berney

McGouran

2018

Nat Rev Chem

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Methylation of cytosine at the 5-position is a common epigenetic marker in mammalian DNA, and plays an important role in regulating gene expression. Oxidised derivatives of 5-methylcytosine have recently been discovered. As well as being intermediates in an active demethylation pathway, some of these oxidised derivatives may function as epigenetic markers in their own right. Oxidised derivatives of thymine are also known as products of DNA damage. There is evidence however that one such derivative, 5-hydroxymethyluracil, may play an epigenetic role. There is a pressing need to learn more about these modifications, due to the role epigenetic markers play in development, and diseases such as cancer. This emerging area of research requires methods for detecting cytosine and thymine modifications in DNA with a high degree of accuracy and sequence specificity. This review will introduce the biochemistry of cytosine and thymine modifications, and discuss new and established detection methods which have been developed to overcome the high degree of difficulty associated with studying these modifications in DNA. Introduction: Cytosine and Thymine Modifications DNA codes for all the proteins necessary for life, but the DNA sequence is not the sole determinant of all the phenotypic traits of cells and organisms. Transcription of DNA is tightly regulated by epigenetic modifications, which play an important role in controlling when and where specific genes are expressed. 1,2 Epigenetic modifications regulate important processes such as cellular differentiation, and are also implicated in various diseases including cancer, autism spectrum disorder, and other developmental diseases such as Rett syndrome. 3-5 Epigenetic control of gene expression is often mediated through covalent modification of DNA itself, or of the histone proteins which pack DNA in the nucleus. These modifications do not result in changes to the DNA sequence, but can affect the binding of certain proteins to the DNA, including transcription factors and proteins which regulate chromatin structure. 6-8 In mammals and many other eukaryotes, the most common epigenetic covalent modification of DNA is methylation of cytosine (C) at the 5-position. Such modifications can be inherited, but can also be enzymatically introduced and removed in response to stimuli. 9 5-Methylcytosine (mC) is introduced by the methylation of cytosine residues by DNA-methyltransferases (DNMTs) with an S-adenosylmethionine cofactor. 5-Methylcytosine is most often found in the context of 5'-cytosinephosphate-guanine-3' (CpG) dinucleotides. Regions containing a high density of CpG sequences are found in about 72% of promoters in the human genome. 10 Methylation of these regions causes

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“…Therefore, the double bond has been the major target of 5mC and subjected to several reactions, such as oxidation by potassium osmate(VI), vanadium(V) oxide/lithium bromide, and sodium periodate/lithium bromide (Figure a). By introducing a 5mC double bond‐selective conjugation chemistry using potassium osmate(VI), our group developed an artificial DNA probe, interstrand complexes formed by osmium and nucleic acids (ICON) probe (Figure ), which enables detection of 5mC in a sequence‐specific manner,, even in fixed cells . This is the first demonstration of 5mC‐specific visualization in genome DNA by combining fluorescence in situ hybridization (FISH) technology.…”

Section: Modification‐selective Chemical Reactions That Advance Reseamentioning

confidence: 99%

Chemistry‐Driven Epigenetic Investigation of Histone and DNA Modifications

Sueoka

Koyama

Hayashi

et al. 2018

The Chemical Record

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In the regulation processes of gene expression, genomic DNA and nuclear proteins, including histone proteins, cooperate with each other, leading to the distinctive functions of eukaryotic cells such as pluripotency and differentiation. Chemical modification of histone proteins and DNA has been revealed as one of the major driving forces in the complicated epigenetic regulation system. However, understanding of the precise molecular mechanisms is still limited. To address this issue, researchers have proposed both biological and chemical strategies for the preparation and detection of modified proteins and nucleic acids. In this review, we focus on chemical methods around the field of epigenetics. Chemical protein synthesis has enabled the preparation of site-specifically modified histones and their successful application to various in vitro assays, which have emphasized the significance of posttranslational modifications of interest. We also review the modification-specific chemical reactions against synthetic and genomic DNA, which enabled discrimination of several modified bases at single-base resolution.

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Ligand‐Incorporation Site in 5‐Methylcytosine‐Detection Probe Modulating the Site of Osmium Complexation with the Target DNA

Cited by 7 publications

References 16 publications

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

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

Methods for detection of cytosine and thymine modifications in DNA

Chemistry‐Driven Epigenetic Investigation of Histone and DNA Modifications

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