DNA-friendly Cu(<scp>ii</scp>)/TEMPO-catalyzed 5-hydroxymethylcytosine-specific oxidation

Matsushita, Taku; Moriyama, Yuya; Nagae, Genta; Aburatani, Hiroyuki; Okamoto, Akimitsu

doi:10.1039/c7cc02814h

Cited by 11 publications

(19 citation statements)

References 30 publications

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“…This can also be used to detect hmC by first oxidising hmC to fC. 61 While Maxam-Gilbert sequencing methods require gel electrophoresis which is time consuming and labour intensive, they provide robust sequence specific detection of mC and hmC.…”

Section: Chemical Detection Methodsmentioning

confidence: 99%

“…66 Cu(II) perchlorate, TEMPO and bipyridine also selectively oxidise hmC to fC. 61 Another derivatisation step that has been employed to detect hmC is the glucosylation of this residue using β-glucosyltransferase. Subsequent treatment of the DNA with TET1 oxidises all 5-modified cytosine residues to caC, except hmC which is now protected.…”

Section: Chemical Detection Methodsmentioning

confidence: 99%

“…28 Direct labelling of fC with biotin via an oxime or hydrazone linkage has also been used. 61,121 Selective labelling of fC has been achieved using a (Figure 4). 124 The adamantane can then be recognised by a macrocycle known as CB7 through a host-guest binding interaction.…”

Section: Detection Of Fcmentioning

confidence: 99%

“…Biotinylation via a hydrazone linkage 61 2-(Adamantyl)ethoxyamine 124 Trimethylindole derivative 125 2-Hydrazinyl-N-(pyren-1-yl)acetamide 128 fC-Seal 28 Biotinylation via an oxime linkage 121 1,3-Indandione derivative 122 CLEVER-seq 123 CBAN (single-base resolution detection demonstrated only in oligonucleotide models) 126 azi-BP 127 Exploiting DNA-Protein Interactions MBDs tethered to green fluorescent protein and zinc finger 135 (mC) Detection of caC using TALEs Nanopore sequencing methods [162][163][164][165][166][169][170][171] Zinc finger fused with luciferase in combination with an MBD 136 (mC) Precipitation of DNA fragments using an MBD 137 (mC) J-binding protein 1 138 (hmC) Artificial phosphopeptide 139 (mC) Detection of mC and hmC using TALEs [141][142][143][144] Use of DNMT to install a cleavable biotin 149 (unmodified C) TOP-seq 150 (unmodified C) Simultaneous detection of mC and hmC using DNMT1 151 Detection of hmC using DNMT1 152 Oxidation of mC to caC followed by SMRT sequencing 155,156 SMRT bisulfite sequencing 157 (mC) hMe-Seal followed by SMRT sequencing 158 Cytosine (C) residues in DNA can be methylated by DNAmethyltransferases (DNMTs). The resulting 5-methylcytosine (mC) residues are susceptible to oxidation by the ten-eleven translocation dioxygenase (TET) family of enzymes to produce 5-hydroxymethylcytosine (hmC), and subsequently 5-formylcytosine (fC) and 5-carboxylcytosine (caC).…”

Section: Detection Of Fcmentioning

confidence: 99%

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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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Section: Chemical Detection Methodsmentioning

confidence: 99%

Section: Chemical Detection Methodsmentioning

confidence: 99%

Section: Detection Of Fcmentioning

confidence: 99%

Section: Detection Of Fcmentioning

confidence: 99%

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Methods for detection of cytosine and thymine modifications in DNA

Berney

McGouran

2018

Nat Rev Chem

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“…However, using potassium perruthenate is less ideal due to the high reactivity and nonspecific damage to genomic DNA. Recently, we used a mixture of copper(II) perchlorate and 2,2,6,6‐tetramethylpiperidine‐1‐oxyl (Cu(II)/TEMPO) for the oxidation of 5hmC . The Cu(II)/TEMPO system showed no undesired damage to DNA because of its mild oxidation ability.…”

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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Chemical Methods to Identify Epigenetic Modifications in Cytosine Bases

Kumar,

Manna

2024

Chemistry An Asian Journal

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Chemical modifications to Cytosine bases are among the most studied epigenetic markers and their detection in the human genome plays a crucial role in gaining more insights about gene regulation, prognosis of genetic disorders and unraveling genetic inheritance patterns. The Cytosine methylated at the 5th position and oxidized derivatives thereof generated in the demethylation pathways, perform separate and unique epigenetic functions in an organism. As the presence of various Cytosine modifications is associated with diverse diseases, including cancer, there has been a strong focus on developing methods, both chemical and alternative approaches, capable of detecting these modifications at a single‐base resolution across the entire genome. In this comprehensive review, we aim to consolidate the various chemical methods and understanding their chemistry that have been established to date for the detection of various Cytosine modifications.

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DNA-friendly Cu(ii)/TEMPO-catalyzed 5-hydroxymethylcytosine-specific oxidation

Cited by 11 publications

References 30 publications

Methods for detection of cytosine and thymine modifications in DNA

Methods for detection of cytosine and thymine modifications in DNA

Chemistry‐Driven Epigenetic Investigation of Histone and DNA Modifications

Chemical Methods to Identify Epigenetic Modifications in Cytosine Bases

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