Dynamics of a DNA Mismatch Site Held in Confinement Discriminate Epigenetic Modifications of Cytosine

Johnson, Robert P.; Fleming, Aaron M.; Perera, Rukshan T.; Burrows, Cynthia J.; White, Henry S.

doi:10.1021/jacs.6b12284

Cited by 33 publications

(41 citation statements)

References 46 publications

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“…Aldehydes in aqueous solution can undergo an acid/base catalyzed hydration reactions ( 59 ). Contrary to previous reports on different dsDNA sequences featuring 5fC in the context of X:C mismatches (where X is either 5mC, 5hmC, 5fC or 5caC) ( 60 ), we do not detect resonances compatible with such a hydrate form neither in 1 H nor in 13 C based experiments.…”

Section: Resultscontrasting

confidence: 99%

Impact of 5-formylcytosine on the melting kinetics of DNA by 1H NMR chemical exchange

Dubini

Schön

Müller

et al. 2020

Nucleic Acids Research

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Abstract 5-Formylcytosine (5fC) is a chemically edited, naturally occurring nucleobase which appears in the context of modified DNA strands. The understanding of the impact of 5fC on dsDNA physical properties is to date limited. In this work, we applied temperature-dependent 1H Chemical Exchange Saturation Transfer (CEST) NMR experiments to non-invasively and site-specifically measure the thermodynamic and kinetic influence of formylated cytosine nucleobase on the melting process involving dsDNA. Incorporation of 5fC within symmetrically positioned CpG sites destabilizes the whole dsDNA structure—as witnessed from the ∼2°C decrease in the melting temperature and 5–10 kJ mol−1 decrease in ΔG°—and affects the kinetic rates of association and dissociation. We observed an up to ∼5-fold enhancement of the dsDNA dissociation and an up to ∼3-fold reduction in ssDNA association rate constants, over multiple temperatures and for several proton reporters. Eyring and van’t Hoff analysis proved that the destabilization is not localized, instead all base-pairs are affected and the transition states resembles the single-stranded conformation. These results advance our knowledge about the role of 5fC as a semi-permanent epigenetic modification and assist in the understanding of its interactions with reader proteins.

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Section: Resultscontrasting

confidence: 99%

Impact of 5-formylcytosine on the melting kinetics of DNA by 1H NMR chemical exchange

Dubini

Schön

Müller

et al. 2020

Nucleic Acids Research

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“…Chemical modifications to nucleobases play important roles in mediating fundamental biological processes ( Booth et al., 2015 , Shu et al., 2018 , Suzuki and Bird, 2008 , Wu and Zhang, 2017 ) and are regarded as hallmarks of many diseases ( Chen et al., 2017 , Jackson and Bartek, 2009 , Johnson et al., 2017 ). Therefore, a detailed analysis of natural nucleobase modifications is essential for a complete understanding of genetic and epigenetic regulation ( Hong et al., 2018 , Iwan et al., 2017 , Liu et al., 2016 , Shen et al., 2014 ).…”

Section: Introductionmentioning

confidence: 99%

Highly Selective 5-Formyluracil Labeling and Genome-wide Mapping Using (2-Benzimidazolyl)Acetonitrile Probe

Wang

Liu

et al. 2018

iScience

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SummaryChemical modifications to nucleobases have a great influence on various cellular processes, by making gene regulation more complex, thus indicating their profound impact on aspects of heredity, growth, and disease. Here, we provide the first genome-wide map of 5-formyluracil (5fU) in living tissues and evaluate the potential roles for 5fU in genomics. We show that an azido derivative of (2-benzimidazolyl)acetonitrile has high selectivity for enriching 5fU-containing genomic DNA. The results have demonstrated the feasibility of using this method to determine the genome-wide distribution of 5fU. Intriguingly, most 5fU sites were found in intergenic regions and introns. Also, distribution of 5fU in human thyroid carcinoma tissues is positively correlated with binding sites of POLR2A protein, which indicates that 5fU may distributed around POLR2A-binding sites.

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“…162 Pores formed from α-hemolysin have also been used to detect cytosine modifications. 163 Chemical labelling of mC and hmC has been used to improve the detectability of these modifications using α-hemolysin pores. 164,165 Aerolysin pores have also been used, and have the advantage that they are stable under harsh conditions and can be used in serum, which is desirable for diagnostic applications.…”

Section: Detection Of Cacmentioning

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%

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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Dynamics of a DNA Mismatch Site Held in Confinement Discriminate Epigenetic Modifications of Cytosine

Cited by 33 publications

References 46 publications

Impact of 5-formylcytosine on the melting kinetics of DNA by 1H NMR chemical exchange

Impact of 5-formylcytosine on the melting kinetics of DNA by 1H NMR chemical exchange

Highly Selective 5-Formyluracil Labeling and Genome-wide Mapping Using (2-Benzimidazolyl)Acetonitrile Probe

Methods for detection of cytosine and thymine modifications in DNA

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