5-Methylcytosine is Oxidized to the Natural Metabolites of TET Enzymes by a Biomimetic Iron(IV)-Oxo Complex

Ten-eleven-translocation (TET) methyl cytosine dioxygenases play a key role in epigenetics by oxidizing the epigenetic marker 5-methyl cytosine (5mC) to 5-hydroxymethyl cytosine (5hmC), 5-formyl cytosine (5fC), and 5-carboxy cytosine (5cC). Although much of the metabolism of 5mC has been studied closely, certain aspects—such as discrepancies among the observed catalytic activity of TET enzymes and calculated bond dissociation energies of the different cytosine substrates—remain elusive. Here, it is reported that the DNA base 5mC is oxidized to 5hmC, 5fC, and 5cC by a biomimetic iron(IV)-oxo complex, reminiscent of the activity of TET enzymes. Studies show that 5hmC is preferentially turned over compared with 5mC and 5fC and that this is in line with the calculated bond dissociation energies. The optimized syntheses of d₃-5mC and d₂-5hmC are also reported and in the reaction with the biomimetic iron(IV)-oxo complex these deuterated substrates showed large kinetic isotope effects, confirming the hydrogen abstraction as the rate-limiting step. Taken together, these results shed light on the intrinsic reactivity of the C−H bonds of epigenetic markers and the contribution of the second coordination sphere in TET enzymes.     

Quantification of 5-methylcytosine, 5-hydroxymethylcytosine and 5-carboxylcytosine from the blood of cancer patients by an enzyme-based immunoassay

Background

Genome-wide aberrations of the classic epigenetic modification 5-methylcytosine (5mC), considered the hallmark of gene silencing, has been implicated to play a pivotal role in mediating carcinogenic transformation of healthy cells. Recently, three epigenetic marks derived from enzymatic oxidization of 5mC namely 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), have been discovered in the mammalian genome. Growing evidence suggests that these novel bases possess unique regulatory functions and may play critical roles in carcinogenesis.

Methods

To provide a quantitative basis for these rare epigenetic marks, we have designed a biotin–avidin mediated enzyme-based immunoassay (EIA) and evaluated its performance in genomic DNA isolated from blood of patients diagnosed with metastatic forms of lung, pancreatic and bladder cancer, as well as healthy controls. The proposed EIA incorporates spatially optimized biotinylated antibody and a high degree of horseradish-peroxidase (HRP) labeled streptavidin, facilitating signal amplification and sensitive detection.

Results

We report that the percentages of 5mC, 5hmC and 5caC present in the genomic DNA of blood in healthy controls as 1.025 ± 0.081, 0.023 ± 0.006 and 0.001 ± 0.0002, respectively. We observed a significant (p < 0.05) decrease in the mean global percentage of 5hmC in blood of patients with malignant lung cancer (0.013 ± 0.003%) in comparison to healthy controls.

Conclusion

The precise biological roles of these epigenetic modifications in cancers are still unknown but in the past two years it has become evident that the global 5hmC content is drastically reduced in a variety of cancers. To the best of our knowledge, this is the first report of decreased 5hmC content in the blood of metastatic lung cancer patients and the clinical utility of this observation needs to be further validated in larger sample datasets.     

Quantification of DNA methylation and hydroxymethylation in Alzheimer's disease mouse model using LC‐MS/MS

Ambiguous alteration patterns of 5‐methylcytosine (5mC) and 5‐hydroxymethylcytosine (5hmC) involved in Alzheimer's disease (AD) obstructed the mechanism investigation of this neurological disorder from epigenetic view. Here, we applied a fully quantitative and validated LC‐MS/MS method to determine genomic 5mC and 5hmC in the brain cortex of 3 month‐aged (12, 15, and 18 month) AD model mouse and found significant increases of 5mC and 5hmC levels in different months of AD mouse when compared with age‐matched wild‐type control and exhibited rising trend from 12‐month to 18‐month AD mouse, thereby supporting genomic DNA methylation and hydroxymethylation were positively correlated with developing AD.     

Discrimination of methylcytosine from hydroxymethylcytosine in DNA molecules

Modified DNA bases are widespread in biology. 5-Methylcytosine (mC) is a predominant epigenetic marker in higher eukaryotes involved in gene regulation, development, aging, cancer, and disease. Recently, 5-hydroxymethylcytosine (hmC) was identified in mammalian brain tissue and stem cells. However, most of the currently available assays cannot distinguish mC from hmC in DNA fragments. We investigate here the physical properties of DNA with modified cytosines, in efforts to develop a physical tool that distinguishes mC from hmC in DNA fragments. Molecular dynamics simulations reveal that polar cytosine modifications affect internal base pair dynamics, while experimental evidence suggest a correlation between the modified cytosine's polarity, DNA flexibility, and duplex stability. On the basis of these physical differences, solid-state nanopores can rapidly discriminate among DNA fragments with mC or hmC modification by sampling a few hundred molecules in the solution. Further, the relative proportion of hmC in the sample can be determined from the electronic signature of the intact DNA fragment.     

Nucleobase Modifiers Identify TET Enzymes as Bifunctional DNA Dioxygenases Capable of Direct N-Demethylation

TET family enzymes are known for oxidation of the 5-methyl substituent on 5-methylcytosine (5mC) in DNA. 5mC oxidation generates the stable base 5-hydroxymethylcytosine (5hmC), starting an indirect, multi-step process that ends with reversion of 5mC to unmodified cytosine. While probing the nucleobase determinants of 5mC recognition, we discovered that TET enzymes are also proficient as direct N-demethylases of cytosine bases. We find that N-demethylase activity can be readily observed on substrates lacking a 5-methyl group and, remarkably, TET enzymes can be similarly proficient in either oxidation of 5mC or demethylation of N4-methyl substituents. Our results indicate that TET enzymes can act as both direct and indirect demethylases, highlight the active-site plasticity of these Fe^II/α-ketoglutarate-dependent dioxygenases, and suggest activity on unexplored substrates that could reveal new TET biology.     

Site-specific quantification of 5-carboxylcytosine in DNA by chemical conversion coupled with ligation-based PCR

5-Methylcytosine (5mC) is the most important epigenetic modification in mammals. The active DNA demethylation could be achieved through the ten-eleven translocation (TET) protein-mediated oxidization of 5mC with the generation of 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). It has been known that 5mC, 5hmC and 5fC play critical roles in modulating gene expression. However, unlike the 5mC, 5hmC, and 5fC, the functions of 5caC are still underexplored. Investigation of the functions of 5caC relies on the accurate quantification and localization analysis of 5caC in DNA. In the current study, we developed a method by chemical conversion in conjugation with ligation-based real-time quantitative PCR (qPCR) for the site-specific quantification of 5caC in DNA. This method depends on the selective conversion of 5caC to form dihydrouracil (DHU) by pyridine borane treatment. DHU behaves like thymine and pairs with adenine (DHU-A). Thus, the chemical conversion by pyridine borane leads to the transformation of base paring from 5caC-G to DHU-A, which is utilized to achieve the site-specific detection and quantification of 5caC in DNA. As a proof-of-concept, the developed method was successfully applied in the site-specific quantification of 5caC in synthesized DNA spiked in complex biological samples. The method is rapid, straightforward and cost-effective, and shows promising in promoting the investigation of the functional roles of 5caC in future study.     

Identification of epigenetic DNA modifications with a protein nanopore

Two DNA bases, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (hmC), marks of epigenetic modification, are recognized in immobilized DNA strands and distinguished from G, A, T and C by nanopore current recording. Therefore, if further aspects of nanopore sequencing can be addressed, the approach will provide a means to locate epigenetic modifications in unamplified genomic DNA.     

Nucleobase Modifiers Identify TET Enzymes as Bifunctional DNA Dioxygenases Capable of Direct N‐Demethylation

TET family enzymes are known for oxidation of the 5‐methyl substituent on 5‐methylcytosine (5mC) in DNA. 5mC oxidation generates the stable base 5‐hydroxymethylcytosine (5hmC), starting an indirect, multi‐step process that ends with reversion of 5mC to unmodified cytosine. While probing the nucleobase determinants of 5mC recognition, we discovered that TET enzymes are also proficient as direct N‐demethylases of cytosine bases. We find that N‐demethylase activity can be readily observed on substrates lacking a 5‐methyl group and, remarkably, TET enzymes can be similarly proficient in either oxidation of 5mC or demethylation of N4‐methyl substituents. Our results indicate that TET enzymes can act as both direct and indirect demethylases, highlight the active‐site plasticity of these Fe^II/α‐ketoglutarate‐dependent dioxygenases, and suggest activity on unexplored substrates that could reveal new TET biology.     

Improved synthesis and mutagenicity of oligonucleotides containing 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine

5-Formylcytosine (fC or (5-CHO)dC) and 5-carboxylcytosine (caC or (5-COOH)dC) have recently been identified as constituents of mammalian DNA. The nucleosides are formed from 5-methylcytosine (mC or (5-Me)dC) via 5-hydroxymethylcytosine (hmC or (5-HOMe)dC) and are possible intermediates of an active DNA demethylation process. Here we show efficient syntheses of phosphoramidites which enable the synthesis of DNA strands containing these cytosine modifications based on Pd(0)-catalyzed functionalization of 5-iododeoxycytidine. The first crystal structure of fC reveals the existence of an intramolecular H-bond between the exocyclic amine and the formyl group, which controls the conformation of the formyl substituent. Using a newly designed in vitro mutagenicity assay we show that fC and caC are only marginally mutagenic, which is a prerequisite for the bases to function as epigenetic control units.     

Direct decarboxylation of ten-eleven translocation-produced 5-carboxylcytosine in mammalian genomes forms a new mechanism for active DNA demethylation

DNA cytosine methylation (5-methylcytosine, 5mC) is the most important epigenetic mark in higher eukaryotes. 5mC in genomes is dynamically controlled by writers and erasers. DNA (cytosine-5)-methyltransferases (DNMTs) are responsible for the generation and maintenance of 5mC in genomes. Active demethylation of 5-methylcytosine (5mC) is achieved by ten-eleven translocation (TET) dioxygenase-mediated oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC are further processed by thymine DNA glycosylase (TDG)-initiated base excision repair (BER) to restore unmodified cytosines. The TET-TDG-BER pathway could cause the production of DNA strand breaks and therefore jeopardize the integrity of genomes. Here, we investigated the direct decarboxylation of 5caC in mammalian genomes by using metabolic labeling with 2′-fluorinated 5caC (F-5caC) and mass spectrometry analysis. Our results clearly demonstrated the decarboxylation of 5caC occurring in mammalian genomes, which unveiled that, in addition to the TET-TDG-BER pathway, the direct decarboxylation of TET-produced 5caC constituted a new pathway for active demethylation of 5mC in mammalian genomes.

We demonstrated that the ten-eleven translocation (TET) dioxygenase-mediated oxidation of 5-methylcytosine followed by direct decarboxylation of 5-carboxylcytosine constitutes a novel pathway for active DNA demethylation in mammalian genomes.     

Novel Photodynamic Effect of a Psoralen‐Conjugated Oligonucleotide for the Discrimination of the Methylation of Cytosine in DNA

DNA methylation and demethylation significantly affect the deactivation and activation processes of gene expression significantly. In particular, C‐5‐methylation of cytosine in the CpG islands is important for the epigenetic modification in genes, which plays a key role in regulating gene expression. The determination of the location and frequency of DNA methylation is important for the elucidation of the mechanisms of cell differentiation and carcinogenesis. Here we designed a psoralen‐conjugated oligonucleotide (PS‐oligo) for the discrimination of 5‐methylcytosine (5‐mC) in DNA. The cross‐linking behavior of psoralen derivatives with pyrimidine bases, such as thymine, uracil and cytosine has been well discussed, but there are no reports which have examined whether cross‐linking efficiency of psoralen with cytosine would be changed with or without C‐5 methylation. We found that the cross‐linking efficiency of PS‐oligo with target‐DNA containing 5‐mC was greatly increased compared to the case of target‐DNA without 5‐mC, approximately seven‐fold higher. Here we report a new aspect of the photocross‐linking behavior of psoralen with 5‐mC that is applicable to a simple, sequence‐specific and quantitative analysis for the discrimination of 5‐mC in DNA, which can be applicable to study the epigenetic behavior of gene expressions.     

Amperometric biosensor for 5-hydroxymethylcytosine based on enzymatic catalysis and using spherical poly(acrylic acid) brushes

5-Hydroxymethylcytosine in DNA (5hmC-DNA) plays an important biological role in sculpting the epigenetic landscape. Its presence is linked to diseases, especially cancers. The authors describe an amperometric biosensor for the determination of 5hmC. It is based on a chemical modification of the hydroxy group of 5hmC in the DNA sequence. Enzymatic signal amplification is accomplished by using DNA methyltransferase (M.HhaI-DNA-cytosine-5-methyltransferase) to achieve chemical modification. A graphene-perylenetetracarboxylic acid nanocomposite was used to modify a glassy carbon electrode (GCE) that acts as a substrate electrode. A composite consisting of horseradish peroxidase on silica/poly(acrylic acid) brushes is employed as the signal amplification unit. Under the optimized conditions, there is a linear response to the logarithm of the 5hmC-DNA concentration in the range from 0.5 to 30 nM, with a 0.23 nM detection limit (at an S/N ratio of 3) in the potential range from ?0.3 V to -0.8 V at 100 mV/s. The bioassay has excellent specificity and can even discriminate the similar base 5mC.

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Graphical abstract An amperometric biosensor is fabricated for 5-hydroxymethylcytosine (5hmC) determination, where DNA methyltransferase was used to achieve chemical modification of 5hmC, and spherical poly(acrylic acid) brushes conjugated horseradish peroxidase was used as the signal amplification unit. The biosensor showed high sensitivity and specificity.

     

Modified Nucleotides for Discrimination between Cytosine and the Epigenetic Marker 5‐Methylcytosine

5‐Methyl‐2′‐deoxycytosine, the most common epigenetic marker of DNA in eukaryotic cells, plays a key role in gene regulation and affects various cellular processes such as development and carcinogenesis. Therefore, the detection of 5mC can serve as an important biomarker for diagnostics. Here we describe that modified dGTP analogues as well as modified primers are able to sense the presence or absence of a single methylation of C, even though this modification does not interfere directly with Watson–Crick nucleobase pairing. By screening several modified nucleotide scaffolds, O⁶‐modified 2′‐deoxyguanosine analogues were identified as discriminating between C and 5mC. These modified nucleotides might find application in site‐specific 5mC detection, for example, through real‐time PCR approaches.     

Direct Sensing of 5‐Methylcytosine by Polymerase Chain Reaction

The epigenetic control of genes by the methylation of cytosine resulting in 5‐methylcytosine (5mC) has fundamental implications for human development and disease. Analysis of alterations in DNA methylation patterns is an emerging tool for cancer diagnostics and prognostics. Here we report that two thermostable DNA polymerases, namely the DNA polymerase KlenTaq derived from Thermus aquaticus and the KOD DNA polymerase from Thermococcus kodakaraensis, are able to extend 3′‐mismatched primer strands more efficiently from 5 mC than from unmethylated C. This feature was advanced by generating a DNA polymerase mutant with further improved 5mC/C discrimination properties and its successful application in a novel methylation‐specific PCR approach directly from untreated human genomic DNA.     

Preferential 5‐Methylcytosine Oxidation in the Linker Region of Reconstituted Positioned Nucleosomes by Tet1 Protein

Tet (ten–eleven translocation) family proteins oxidize 5‐methylcytosine (mC) to 5‐hydroxymethylcytosine (hmC), 5‐formylcytosine (fC), and 5‐carboxycytosine (caC), and are suggested to be involved in the active DNA demethylation pathway. In this study, we reconstituted positioned mononucleosomes using CpG‐methylated 382 bp DNA containing the Widom 601 sequence and recombinant histone octamer, and subjected the nucleosome to treatment with Tet1 protein. The sites of oxidized methylcytosine were identified by bisulfite sequencing. We found that, for the oxidation reaction, Tet1 protein prefers mCs located in the linker region of the nucleosome compared with those located in the core region.     

Pyrene‐Based Quantitative Detection of the 5‐Formylcytosine Loci Symmetry in the CpG Duplex Content during TET‐Dependent Demethylation

Methylcytosine (5mC) is mostly symmetrically distributed in CpG sites. Ten‐eleven‐translocation (TET) proteins are the key enzymes involved in active DNA demethylation through stepwise oxidation of 5mC. However, oxidation pathways of TET enzymes in the symmetrically methylated CpG context are still elusive. Employing the unique fluorescence properties of pyrene group, we designed and synthesized a sensitive fluorescence‐based probe not only to target 5‐formylcytosine (5fC) sites, but also to distinguish symmetric from asymmetric 5fC sites in the double stranded DNA context during TET‐dependent 5mC oxidation process. Using this novel probe, we revealed dominant levels of symmetric 5fC among total 5fC sites during in vitro TET‐dependent 5mC oxidation and novel mechanistic insights into the TET‐dependent 5mC oxidation in the mCpG context.     

A primer-initiated strand displacement amplification strategy for sensitive detection of 5-Hydroxymethylcytosine in genomic DNA

5-Hydroxymethylcytosine (5hmC), an intermediate product of DNA demethylation, is important for the regulation of gene expression during development and even tumorigenesis. The challenges associated with determination of 5hmC level include its extremely low abundance and high structural similarity with other cytosine derivatives, which resulted in sophisticated treatment with large amount of sample input. Herein, we developed a primer-initiated strand displacement amplification (PISDA) strategy to quantify the global 5hmC in genomic DNA from mammalian tissues with high sensitivity/selectivity, low input and simple operation. This sensitive fluorescence method is based on 5hmC-specific glucosylation, primer ligation and DNA amplification. After the primer was labeled on 5hmC site, DNA polymerase and nicking enzyme will repeatedly act on each primer, causing a significant increase of fluorescence signal to magnify the minor difference of 5hmC content from other cytosine derivatives. This method enables highly sensitive analysis of 5hmC with a detection limit of 0.003% in DNA (13.6 fmol, S/N = 3) from sample input of only 150 ng, which takes less than 15 min for determination. Further determination of 5hmC in different tissues not only confirms the widespread presence of 5hmC but also indicates its significant variation in different tissues and ages. Importantly, this PISDA strategy exhibits distinct advantages of bisulfite-free treatment, mild conditions and simple operation without the involvement of either expensive equipment or large amount of DNA sample. This method can be easily performed in almost all research and medical laboratories, and would provide a promising prospect to detect global 5hmC in mammalian tissues.