The discovery of 5-formylcytosine in embryonic stem cell DNA

A disposable electrochemical magnetic immunosensor for the rapid and sensitive detection of 5-formylcytosine and 5-carboxylcytosine in DNA

5-formylcytosine (5 fC) and 5-carboxylcytosine (5caC) serve as key intermediates in DNA demethylation process with significant implications for gene regulation and disease progression. In this study, we introduce a novel electrochemical sensing platform specifically designed for the sensitive and selective detection of 5 fC and 5caC in DNA. Protein A-modified magnetic beads (ProtA-MBs) coupled with specific antibodies facilitate the immunorecognition and enrichment of these modified bases. Signal amplification is achieved through several chemical reactions involving the interaction between N3-kethonaxl and guanine, copper-free click chemistry for the attachment of dibenzocyclooctyne (DBCO)-Biotin, and the subsequent recognition by streptavidin-conjugated horseradish peroxidase (SA-HRP). The assay's readout is performed on a disposable laser-induced graphene (LIG) electrode, modified with the bead-antibody-DNA complex in a magnetic field, and analyzed using differential pulse voltammetry in a system employing hydroquinone (HQ) as the redox mediator and H2O2 as the substrate. This immunosensor displayed excellent sensitivity, with detection limits of 14.8 fM for 5 fC across a 0.1-1000 pM linear range and 87.4 fM for 5caC across a 0.5-5000 pM linear range, and maintained high selectivity even in the presence of interferences from other DNA modifications. Successful application in quantifying 5 fC and 5caC in genomic DNA from cell extracts, with recovery rates between 97.7% to 102.9%, underscores its potential for clinical diagnostics. N3-kethoxal was used for the first time in an electrochemical sensor. This work not only broadens the toolkit for detecting DNA modifications but also provides a fresh impetus for the development of point-of-care testing (POCT) technologies.

Quantification of modified nucleotides and nucleosides by isotope dilution mass spectrometry

Epigenetic modifications are closely related to certain disorders of the organism, including the development of tumors. One of the main epigenetic modifications is the methylation of DNA cytosines, 5-methyl-2'-deoxycycytidine. Furthermore, 5-mdC can be oxidized to form three new modifications, 5-(hydroxymethyl)-2'-deoxycytidine, 5-formyl-2'-deoxycytidine, and 5-carboxy-2'-deoxycytidine. The coupling of liquid chromatography with tandem mass spectrometry has been widely used for the total determination of methylated DNA cytosines in samples of biological and clinical interest. These methods are based on the measurement of the free compounds (e.g., urine) or after complete hydrolysis of the DNA (e.g., tissues) followed by a preconcentration, derivatization, and/or clean-up step. This review highlights the main advances in the quantification of modified nucleotides and nucleosides by isotope dilution using isotopically labeled analogs combined with liquid or gas chromatography coupled to mass spectrometry reported in the last 20 years. The different possible sources of labeled compounds are indicated. Special emphasis has been placed on the different types of chromatography commonly used (reverse phase and hydrophilic interaction liquid chromatography) and the derivatization methods developed to enhance chromatographic resolution and ionization efficiency. We have also revised the application of bidimensional chromatography and indicated significant biological and clinical applications of these determinations.

Non-canonical bases differentially represented in the sex chromosomes of the dioecious plant Silene latifolia

The oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), known as oxi-mCs, garners significant interest in plants as potential epigenetic marks. While research in mammals has established a role in cell reprogramming, carcinogenesis, and gene regulation, their functions in plants remain unclear. In rice, 5hmC has been associated with transposable elements (TEs) and heterochromatin. This study utilizes Silene latifolia, a dioecious plant with heteromorphic sex chromosomes and a genome with a large proportion of TEs, which provides a favourable environment for the study of oxi-mCs in individual sexes. Notably, we detected surprisingly high levels of oxi-mCs in S. latifolia comparable with mammals. Nuclei showed enrichment in heterochromatic regions, except for 5hmC whose signal was homogeneously distributed. Intriguingly, the same X chromosome in females displayed overall enrichment of 5hmC and 5fC compared with its counterpart. This fact is shared with 5mC, resembling dosage compensation. Co-localization showed higher correlation between 5mC and 5fC than with 5hmC, indicating no potential relationship between 5hmC and 5fC. Additionally, the promoter of several sex-linked genes and sex-biased TEs clustered in a clear sex-dependent way. Together, these findings unveil a hypothetical role for oxi-mCs in S. latifolia sex chromosome development, warranting further exploration.

Nanozyme-Enhanced Electrochemical Biosensors: Mechanisms and Applications

Nanozymes, as innovative materials, have demonstrated remarkable potential in the field of electrochemical biosensors. This article provides an overview of the mechanisms and extensive practical applications of nanozymes in electrochemical biosensors. First, the definition and characteristics of nanozymes are introduced, emphasizing their significant role in constructing efficient sensors. Subsequently, several common categories of nanozyme materials are delved into, including metal-based, carbon-based, metal-organic framework, and layered double hydroxide nanostructures, discussing their applications in electrochemical biosensors. Regarding their mechanisms, two key roles of nanozymes are particularly focused in electrochemical biosensors: selective enhancement and signal amplification, which crucially support the enhancement of sensor performance. In terms of practical applications, the widespread use of nanozyme-based electrochemical biosensors are showcased in various domains. From detecting biomolecules, pollutants, nucleic acids, proteins, to cells, providing robust means for high-sensitivity detection. Furthermore, insights into the future development of nanozyme-based electrochemical biosensors is provided, encompassing improvements and optimizations of nanozyme materials, innovative sensor design and integration, and the expansion of application fields through interdisciplinary collaboration. In conclusion, this article systematically presents the mechanisms and applications of nanozymes in electrochemical biosensors, offering valuable references and prospects for research and development in this field.

Whole-Genome Mapping of Epigenetic Modification of 5-Formylcytosine at Single-Base Resolution by Chemical Labeling Enrichment and Deamination Sequencing

DNA cytosine methylation (5-methylcytosine, 5mC) is a predominant epigenetic modification that plays a critical role in a variety of biological and pathological processes in mammals. In active DNA demethylation, the 10-11 translocation (TET) dioxygenases can sequentially oxidize 5mC to generate three modified forms of cytosine, 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Beyond being a demethylation intermediate, recent studies have shown that 5fC has regulatory functions in gene expression and chromatin organization. While some methods have been developed to detect 5fC, genome-wide mapping of 5fC at base resolution is still highly desirable. Herein, we propose a chemical labeling enrichment and deamination sequencing (CLED-seq) method for detecting 5fC in genomic DNA at single-base resolution. The CLED-seq method utilizes selective labeling and enrichment of 5fC-containing DNA fragments, followed by deamination mediated by apolipoprotein B mRNA-editing catalytic polypeptide-like 3A (APOBEC3A or A3A) and sequencing. In the CLED-seq process, while all C, 5mC, and 5hmC are interpreted as T during sequencing, 5fC is still read as C, enabling the precise detection of 5fC in DNA. Using the proposed CLED-seq method, we accomplished genome-wide mapping of 5fC in mouse embryonic stem cells. The mapping study revealed that promoter regions enriched with 5fC overlapped with H3K4me1, H3K4me3, and H3K27ac marks. These findings suggest a correlation between 5fC marks and active gene expression in mESCs. In conclusion, CLED-seq is a straightforward, bisulfite-free method that offers a valuable tool for detecting 5fC in genomes at a single-base resolution.

An Overview of Global, Local, and Base-Resolution Methods for the Detection of 5-Hydroxymethylcytosine in Genomic DNA

The discovery of 5-hydroxymethylcytosine (5hmC) as a common DNA modification in mammalian genomes has ushered in new areas of inquiry regarding the dynamic epigenome. The balance between 5hmC and its precursor, 5-methylcytosine (5mC), has emerged as a determinant of key processes including cell fate specification, and alterations involving these bases have been implicated in the pathogenesis of various diseases. The identification of 5hmC separately from 5mC initially posed a challenge given that legacy epigenetic sequencing technologies could not discriminate between these two most abundant modifications, a significant blind spot considering their potentially functionally opposing roles. The growing interest in 5hmC, as well as in the Ten-Eleven Translocation (TET) family enzymes that catalyze its generation and further oxidation to 5-formylcytosine (5fC) and 5-carboxycytosine (5caC), has spurred the development of versatile methods for 5hmC detection. These methods enable the quantification and localization of 5hmC in diverse biological samples and, in some cases, at the resolution of individual nucleotides. However, navigating this growing toolbox of methods for 5hmC detection can be challenging. Here, we detail existing and emerging methods for the detection, quantification, and localization of 5hmC at global, locus-specific, and base resolution levels. These methods are discussed in the context of their advantages and limitations, with the goal of providing a framework to help guide researchers in choosing the level of resolution and the associated method that could be most suitable for specific needs.

Genome-Wide 5-Formylcytosine Redistribution in KCl-Stimulated Mouse Primary Cortical Neurons is Associated with Neuronal Activity

An abundant accumulation of DNA demethylation intermediates has been identified in mammalian neurons. While the roles of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in neuronal function have been extensively studied, little is known about 5-formylcytosine (5fC) in neurons. Therefore, this study was to investigate the genome-wide distribution and potential functions of 5fC in neurons. In an in vitro culture model of mouse primary cortical neurons, we observed a dynamic increase in the total 5fC level in the neuronal genome after potassium chloride (KCl) stimulation. Subsequently, we employed chemical-labeling-enabled C-to-T conversion sequencing (CLEVER-seq) to examine the 5fC distribution at a single-base resolution. Bioinformatic analysis revealed that 5fC was enriched in promoter regions, and gene ontology (GO) analysis indicated that the differential formylation positions (DFP) were correlated with neuronal activities. Additionally, integration with previously published nascent RNA-seq data revealed a positive correlation between gene formylation and mRNA expression levels. As well, 6 neuro-activity-related genes with a positive correlation were validated. Furthermore, we observed higher chromatin accessibility and RNA pol II binding signals near the 5fC sites through multiomics analysis. Motif analysis identified potential reader proteins for 5fC. In conclusion, our work provides a valuable resource for studying the dynamic changes and functional roles of 5fC in activated mammalian neurons.

Dual chemical labeling enables nucleotide-resolution mapping of DNA abasic sites and common alkylation damage in human mitochondrial DNA

Mitochondrial DNA (mtDNA) modifications play an emerging role in innate immunity and inflammatory diseases. Nonetheless, relatively little is known regarding the locations of mtDNA modifications. Such information is critically important for deciphering their roles in mtDNA instability, mtDNA-mediated immune and inflammatory responses, and mitochondrial disorders. The affinity probe-based enrichment of lesion-containing DNA represents a key strategy for sequencing DNA modifications. Existing methods are limited in the enrichment specificity of abasic (AP) sites, a prevalent DNA modification and repair intermediate. Herein, we devise a novel approach, termed dual chemical labeling-assisted sequencing (DCL-seq), for mapping AP sites. DCL-seq features two designer compounds for enriching and mapping AP sites specifically at single-nucleotide resolution. For proof of principle, we mapped AP sites in mtDNA from HeLa cells under different biological conditions. The resulting AP site maps coincide with mtDNA regions with low TFAM (mitochondrial transcription factor A) coverage and with potential G-quadruplex-forming sequences. In addition, we demonstrated the broader applicability of the method in sequencing other DNA modifications in mtDNA, such as N7-methyl-2'-deoxyguanosine and N3-methyl-2'-deoxyadenosine, when coupled with a lesion-specific repair enzyme. Together, DCL-seq holds the promise to sequence multiple DNA modifications in various biological samples.

Chemical Conversion of 5-Fluoromethyl- and 5-Difluoromethyl-Uracil Bases in Oligonucleotides Using Postsynthetic Modification Strategy

This article describes the postsynthetic modification of oligonucleotides (ONs) containing 2'-deoxy-5-fluoromethyluridine (dU^CH2F ) and 2'-deoxy-5-difluoromethyluridine (dU^CHF2 ). Reactions of fully protected and controlled pore glass (CPG)-attached ONs containing dU^CH2F and dU^CHF2 in basic solutions result in deprotection of all protecting groups except for the 4,4'-dimethoxytrityl group, cleavage from CPG, and conversion of the fluoromethyl or difluoromethyl groups to afford the corresponding ONs containing 5-substituted 2'-deoxyuridines. Moreover, the difluoromethyl group can be converted to formyl, oxime, or hydrazone via the postsynthetic conversion of protection- and CPG-free ON containing dU^CHF2 . © 2023 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of fully protected and CPG-attached oligonucleotides containing 2'-deoxy-5-fluoromethyluridine and 2'-deoxy-5-difluoromethyluridine Basic Protocol 2: Postsynthetic modification of fully protected and CPG-attached oligonucleotides containing 2'-deoxy-5-fluoromethyluridine Basic Protocol 3: Postsynthetic modification of fully protected and CPG-attached oligonucleotide containing 2'-deoxy-5-difluoromethyluridine Basic Protocol 4: Postsynthetic modification of protection- and CPG-free oligonucleotide containing 2'-deoxy-5-difluoromethyluridine Support Protocol: Synthesis of 2'-deoxy-5-fluoromethyluridine and 2'-deoxy-5-difluoromethyluridine phosphoramidites.

Exploring the crop epigenome: a comparison of DNA methylation profiling techniques

Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.

The Epigenesis of Salivary Glands Carcinoma: From Field Cancerization to Carcinogenesis

Salivary gland carcinomas (SGCs) are a diverse collection of malignant tumors with marked differences in biological activity, clinical presentation and microscopic appearance. Although the etiology is varied, secondary radiation, oncogenic viruses as well as chromosomal rearrangements have all been linked to the formation of SGCs. Epigenetic modifications may also contribute to the genesis and progression of SGCs. Epigenetic modifications are any heritable changes in gene expression that are not caused by changes in DNA sequence. It is now widely accepted that epigenetics plays an important role in SGCs development. A basic epigenetic process that has been linked to a variety of pathological as well as physiological conditions including cancer formation, is DNA methylation. Transcriptional repression is caused by CpG islands hypermethylation at gene promoters, whereas hypomethylation causes overexpression of a gene. Epigenetic changes in SGCs have been identified, and they have been linked to the genesis, progression as well as prognosis of these neoplasms. Thus, we conduct a thorough evaluation of the currently known evidence on the involvement of epigenetic processes in SGCs.

Third-Generation Sequencing of Epigenetic DNA

The discovery of epigenetic bases has revolutionised the understanding of disease and development. Among the most studied epigenetic marks are cytosines covalently modified at the 5 position. In order to gain insight into their biological significance, the ability to determine their spatiotemporal distribution within the genome is essential. Techniques for sequencing on "next-generation" platforms often involve harsh chemical treatments leading to sample degradation. Third-generation sequencing promises to further revolutionise the field by providing long reads, enabling coverage of highly repetitive regions of the genome or structural variants considered unmappable by next generation sequencing technology. While the ability of third-generation platforms to directly detect epigenetic modifications is continuously improving, at present chemical or enzymatic derivatisation presents the most convenient means of enhancing reliability. This Review presents techniques available for the detection of cytosine modifications on third-generation platforms.

Role of DNA De-methylation intermediate '5-hydroxymethylcytosine' in ovarian cancer management: A comprehensive review

Ovarian cancer remains the most eminent silent killer, with high morbidity and mortality among all gynaecological cancers. The advanced-stage patient's diagnosis has a low survival rate caused by its asymptomatic progression and diverse histopathological sub-types, wherefore in poor prognosis and highly recurring malignancy with multidrug resistance towards chemotherapy. Epigenetic biomarkers open promising avenues of intriguing research to combat OC malignancy, furthermore a tool for its early diagnosis. 5-hydroxymethycytosine (5-hmC), alias the sixth base of the genome, is an intermediate formed during the recently established DNA demethylation process and catalysed via ten-eleven translocation (TET) family of enzymes. It plays a significant role in regulating gene expression and has sparked interest in various cancer types. This review summarizes the role of active DNA demethylation process, its enzymes and intermediate 5-hmC in epigenetic landscape of ovarian cancer as a potent biomarker for clinical translation in identification of therapeutic targets, diagnostic and prognostic evaluation.

Harnessing Nature's Molecular Recognition Capabilities to Map and Study RNA Modifications

RNA editing or "epitranscriptomic modification" refers to the processing of RNA that occurs after transcription to alter the sequence or structure of the nucleic acid. These chemical alterations can be found on either the ribose sugar or the nucleobase, and although many are "silent" and do not change the Watson-Crick-Franklin code of the RNA, others result in recoding events. More than 170 RNA modifications have been identified so far, each having a specific biological purpose. Additionally, dysregulated RNA editing has been linked to several types of diseases and disorders. As new modifications are discovered and our understanding of their functional impact grows, so does the need for selective methods of identifying and mapping editing sites in the transcriptome.The most common methods for studying RNA modifications rely on antibodies as affinity reagents; however, antibodies can be difficult to generate and often have undesirable off-target binding. More recently, selective chemical labeling has advanced the field by offering techniques that can be used for the detection, enrichment, and quantification of RNA modifications. In our method using acrylamide for inosine labeling, we demonstrated the versatility with which this approach enables pull-down or downstream functionalization with other tags or affinity handles. Although this method did enable the quantitative analysis of A-to-I editing levels, we found that selectivity posed a significant limitation, likely because of the similar reactivity profiles of inosine and pseudouridine or other nucleobases.Seeking to overcome the inherent limitations of antibodies and chemical labeling methods, a more recent approach to studying the epitranscriptome is through the repurposing of proteins and enzymes that recognize modified RNA. Our laboratory has used Endonuclease V, a repair enzyme that cleaves inosine-containing RNAs, and reprogrammed it to instead bind inosine. We first harnessed EndoV to develop a preparative technique for RNA sequencing that we termed EndoVIPER-seq. This method uses EndoV to enrich inosine-edited RNAs, providing better coverage in RNA sequencing and leading to the discovery of previously undetected A-to-I editing sites. We also leveraged EndoV to create a plate-based immunoassay (EndoVLISA) to quantify inosine in cellular RNA. This approach can detect differential A-to-I editing levels across tissue types or disease states while being independent of RNA sequencing, making it cost-effective and high-throughput. By harnessing the molecular recognition capabilities of this enzyme, we show that EndoV can be repurposed as an "anti-inosine antibody" to develop new methods of detecting and enriching inosine from cellular RNA.Nature has evolved a plethora of proteins and enzymes that selectively recognize and act on RNA modifications, and exploiting the affinity of these biomolecules offers a promising new direction for the field of epitranscriptomics.

Investigation of the effect of antibiotics on 5-formylcytosine content in mazie seedling tissues based on photoelectrochemical biosensor

Given the improved photoactivity of Bi₂S₃ by MXene, an article photoelectrochemical biosensor was designed for 5-formyl-2'-deoxycytidine (5fdCTP) detection, where Bi₂S₃: MXene was selected as photoactive material, polydopamine was used as solid electron donor and 5fdCTP capture reagent, calcined ZIF-8(C-ZIF-8) was chosen as the artificial enzyme. With the catalyzed by C-ZIF-8, 4-chloro-1-naphthol was allegro oxidized by H₂O₂ to form the insoluble benzo-4-chlorohexadienone, and then deposited on the surface of the electrode, Resulting in a decrease of the PEC response. Under the optimum conditions, the sensor has a linear range of 0.001-200 nM and a detection limit of 0.51 pM (3σ). The suitability of the developed method was appraised by investigating the effect of antibiotics on 5fdCTP content in the genomic DNA of the roots of maize seedlings. As a new detection platform, the application of this approach can be expanded to investigative the impact of other pollutants on the content of 5fdCTP in plant or animal tissues, explore the feasibility of 5fdCTP as a new indicator for the ecotoxicological effect of pollutants, and the photoelectrochemical method as a new assessment technique for the ecotoxicological effects of pollutants.

TET1 regulates gene expression and repression of endogenous retroviruses independent of DNA demethylation

DNA methylation (5-methylcytosine (5mC)) is critical for genome stability and transcriptional regulation in mammals. The discovery that ten-eleven translocation (TET) proteins catalyze the oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) revolutionized our perspective on the complexity and regulation of DNA modifications. However, to what extent the regulatory functions of TET1 can be attributed to its catalytic activity remains unclear. Here, we use genome engineering and quantitative multi-omics approaches to dissect the precise catalytic vs. non-catalytic functions of TET1 in murine embryonic stem cells (mESCs). Our study identifies TET1 as an essential interaction hub for multiple chromatin modifying complexes and a global regulator of histone modifications. Strikingly, we find that the majority of transcriptional regulation depends on non-catalytic functions of TET1. In particular, we show that TET1 is critical for the establishment of H3K9me3 and H4K20me3 at endogenous retroviral elements (ERVs) and their silencing that is independent of its canonical role in DNA demethylation. Furthermore, we provide evidence that this repression of ERVs depends on the interaction between TET1 and SIN3A. In summary, we demonstrate that the non-catalytic functions of TET1 are critical for regulation of gene expression and the silencing of endogenous retroviruses in mESCs.

DNA Hydroxymethylation in Smoking-Associated Cancers

5-hydroxymethylcytosine (5-hmC) was first detected in mammalian DNA five decades ago. However, it did not take center stage in the field of epigenetics until 2009, when ten-eleven translocation 1 (TET1) was found to oxidize 5-methylcytosine to 5-hmC, thus offering a long-awaited mechanism for active DNA demethylation. Since then, a remarkable body of research has implicated DNA hydroxymethylation in pluripotency, differentiation, neural system development, aging, and pathogenesis of numerous diseases, especially cancer. Here, we focus on DNA hydroxymethylation in smoking-associated carcinogenesis to highlight the diagnostic, therapeutic, and prognostic potentials of this epigenetic mark. We describe the significance of 5-hmC in DNA demethylation, the importance of substrates and cofactors in TET-mediated DNA hydroxymethylation, the regulation of TETs and related genes (isocitrate dehydrogenases, fumarate hydratase, and succinate dehydrogenase), the cell-type dependency and genomic distribution of 5-hmC, and the functional role of 5-hmC in the epigenetic regulation of transcription. We showcase examples of studies on three major smoking-associated cancers, including lung, bladder, and colorectal cancers, to summarize the current state of knowledge, outstanding questions, and future direction in the field.

Synthesis of Nucleobase-Modified Oligonucleotides by Post-Synthetic Modification in Solution

Oligonucleotides containing modified nucleobases have applications in various technologies. In general, to synthesize oligonucleotides with different nucleobase structures, each modified phosphoramidite monomer needs to be prepared over multiple steps and then introduced onto the oligonucleotides, which is time-consuming and inefficient. Post-synthetic modification is a powerful strategy for preparing many types of modified oligonucleotides, especially nucleobase-modified ones. Depending on the stage of modification, post-synthetic modification can be divided into two stages: "solid-phase modification," wherein an oligonucleotide attaches to the resin, and "solution-phase modification," wherein an oligonucleotide detaches itself from the resin. In this review, we focus on post-synthetic modification in solution for the synthesis of nucleobase-modified oligonucleotides, except the modifications to linkers for conjugation. Moreover, the reactions are summarized for each modified position of the nucleobases.

The pH-Dependence of the Hydration of 5-Formylcytosine - an Experimental and Theoretical Study

5-Formylcytosine is an important nucleobase in epigenetic regulation, whose hydrate form has been implicated in the formation of 5-carboxycytosine as well as oligonucleotide binding events. The hydrate content of 5-formylcytosine and its uracil derivative has now been quantified using a combination of NMR and mass spectroscopic measurements as well as theoretical studies. Small amounts of hydrate can be identified for the protonated form of 5-formylcytosine and for neutral 5-formyluracil. For neutral 5-formylcytosine, however, direct detection of the hydrate was not possible due to its very low abundance. This is in full agreement with theoretical estimates.

Modified cytosines versus cytosine in a DNA polymerase: retrieving thermodynamic and kinetic constants at the single molecule level

DNA methylation plays key roles in various areas, such as gene expression, regulation, epigenetics, and cancers. Since 5-methylcytosine (5mC) is commonly present in methylated DNA, characterizing the binding kinetics and thermodynamics of the nucleotide to the enzymatic pocket can help to understand the DNA replication process. Furthermore, 5-carboxycytosine (5caC) is a form that appears through the iterative oxidation of 5mC, and its effect on the DNA replication process is still not well known. Here, we immobilized a DNA polymerase (DNAP) with an orientation control on a tip of an atomic force microscope (AFM), and observed the interaction between the immobilized deoxyguanosine triphosphate (dGTP) on the surface and the DNAP in the presence of a DNA duplex. The interaction probability increased as the concentration of the DNA strand, and the affinity constant between the DNAP and DNA was obtained by fitting the change. Increasing the concentration of dGTP in solution diminished the interaction probability, and a fitting allowed us to retrieve the affinity constant between dGTP and the DNAP holding the DNA in the reaction pocket. Because the dissociation constant could be obtained through the loading rate dependence of the unbinding force value, both affinity and kinetic constants for cytosine (C), 5mC, and 5caC in the DNAP were compared in the light of the steric and electronic effect of the substituents at 5-position of cytosine.

Highly Selective Electrochemical Detection of 5-Formyluracil Relying on (2-Benzimidazolyl) Acetonitrile Labeling

The identification of formylpyrimidines in DNA is crucial for a better understanding of epigenetics. Although many techniques have been explored to detect their content, more accurate methods of formylpyrimidine determination are still required due to the relatively lower sensitivity or lack of selectivity in current methods. Herein, an electrochemical method based on the covalent bonding of the azido derivative of (2-benzimidazolyl) acetonitrile (azi-BIAN) and the aldehyde group of 5-formyluracil (5fU) was proposed for the selective detection of 5fU in the presence of 5-formylcytosine (5fC) and apyrimidinic (AP) sites. Target DNA containing 5fU was first treated with azi-BIAN and then incubated with DBCO-PEG4-Biotin to introduce a biotin group by copper-free click chemistry. Next, the sulfhydryl group was attached to the 5' end of above DNA through T4 polynucleotide kinase-catalyzed reaction. Subsequently, the labeled DNA was assembled onto the AuNPs-modified glassy carbon electrode (AuNPs/GCE) through Au-S bonds, and the streptavidin-horseradish peroxidase conjugate (SA-HRP) was further immobilized onto the surface of the above electrode by specific recognition between biotin and streptavidin. Finally, HRP catalyzed hydroquinone oxidation to benzoquinone to enhance the current signal, which was related to the amount of 5fU in nucleic acids. This method demonstrated a good linear relationship with 5fU concentrations ranging from 0.1 to 10 nM. Moreover, the level of 5fU in γ-irradiated nucleic acids was also successfully detected, indicating that the combination of molecule-depended chemical recognition and electrochemical sensing is a promising method for the selective and sensitive detection of 5fU.

Unified Description of Ultrafast Excited State Decay Processes in Epigenetic Deoxycytidine Derivatives

Epigenetic DNA modifications play a fundamental role in modulating gene expression and regulating cellular and developmental biological processes, thereby forming a second layer of information in DNA. The epigenetic 2'-deoxycytidine modification 5-methyl-2'-deoxycytidine, together with its enzymatic oxidation products (5-hydroxymethyl-2'-deoxycytidine, 5-formyl-2'-deoxycytidine, and 5-carboxyl-2'-deoxycytidine), are closely related to deactivation and reactivation of DNA transcription. Here, we combine sub-30-fs transient absorption spectroscopy with high-level correlated multiconfigurational CASPT2/MM computational methods, explicitly including the solvent, to obtain a unified picture of the photophysics of deoxycytidine-derived epigenetic DNA nucleosides. We assign all the observed time constants and identify the excited state relaxation pathways, including the competition of intersystem crossing and internal conversion for 5-formyl-2'-deoxycytidine and ballistic decay to the ground state for 5-carboxy-2'-deoxycytidine. Our work contributes to shed light on the role of epigenetic derivatives in DNA photodamage as well as on their possible therapeutic use.

The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function

We present a comprehensive, experimental and theoretical study of the impact of 5-hydroxymethylation of DNA cytosine. Using molecular dynamics, biophysical experiments and NMR spectroscopy, we found that Ten-Eleven translocation (TET) dioxygenases generate an epigenetic variant with structural and physical properties similar to those of 5-methylcytosine. Experiments and simulations demonstrate that 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC) generally lead to stiffer DNA than normal cytosine, with poorer circularization efficiencies and lower ability to form nucleosomes. In particular, we can rule out the hypothesis that hydroxymethylation reverts to unmodified cytosine physical properties, as hmC is even more rigid than mC. Thus, we do not expect dramatic changes in the chromatin structure induced by differences in physical properties between d(mCpG) and d(hmCpG). Conversely, our simulations suggest that methylated-DNA binding domains (MBDs), associated with repression activities, are sensitive to the substitution d(mCpG) ➔ d(hmCpG), while MBD3 which has a dual activation/repression activity is not sensitive to the d(mCpG) d(hmCpG) change. Overall, while gene activity changes due to cytosine methylation are the result of the combination of stiffness-related chromatin reorganization and MBD binding, those associated to 5-hydroxylation of methylcytosine could be explained by a change in the balance of repression/activation pathways related to differential MBD binding.

In Eukaryotic cells, DNA epigenetic modifications play an important role in gene expression and regulation, and protein recognition. In this work we investigate the physical implications of cytosine 5-hydroxymethylation on DNA, its structural and flexibility differences with methylated and unmodified cytosine using molecular dynamics, biophysical experiments and NMR spectroscopy.

In particular the effect of hydroxyl group on free energy of nucleosome and Methyl binding Protein (MBD) binding, comparing in silico and experimental data to shed light on the effect of the reduced flexibility and the direct protein-DNA recognition.

Enabling the Facile Synthesis of Arenes by Transition Metal Catalyzed Decarbonylation Methodology

Transition metal-catalyzed decarbonylation is an essential paradigm of synthetic organic chemistry. Decarbonylation offers a unique pathway to decoding the skeletal structure of arenes and enabling easy synthesis of structurally complicated molecules. Due to the omnipresence of carbonyl groups in a wide array of synthetically important complex molecules, the variety and scope of these transformations are enormous. As a result, the development of transition metal catalysts in such a simple decarbonylation reaction ranks among one of the most important topics in synthetic organic chemistry. Transition metals that have been employed range from 3d metals like V to second-row transition metals like Pd. The growing potential of this methodology has driven the pioneers of synthetic organic chemistry into delving into the details of this transition metal-catalyzed decarbonylation pathways. This review aims to take the readers through the employment of transition metals in various decarbonylation processes developed by our group, sticking not only to the scope and diversification of synthetically complex molecules, but also enabling the readers to understand the mechanistic insights, through computational and kinetic studies put forward in such reaction protocol, hoping to pave the way for future organic chemists to delve and hopefully solve the unique problems associated with this protocol.

Direct and Base Excision Repair-Mediated Regulation of a GC-Rich cis-Element in Response to 5-Formylcytosine and 5-Carboxycytosine

Stepwise oxidation of the epigenetic mark 5-methylcytosine and base excision repair (BER) of the resulting 5-formylcytosine (5-fC) and 5-carboxycytosine (5-caC) may provide a mechanism for reactivation of epigenetically silenced genes; however, the functions of 5-fC and 5-caC at defined gene elements are scarcely explored. We analyzed the expression of reporter constructs containing either 2′-deoxy-(5-fC/5-caC) or their BER-resistant 2′-fluorinated analogs, asymmetrically incorporated into CG-dinucleotide of the GC box cis-element (5′-TGGGCGGAGC) upstream from the RNA polymerase II core promoter. In the absence of BER, 5-caC caused a strong inhibition of the promoter activity, whereas 5-fC had almost no effect, similar to 5-methylcytosine or 5-hydroxymethylcytosine. BER of 5-caC caused a transient but significant promoter reactivation, succeeded by silencing during the following hours. Both responses strictly required thymine DNA glycosylase (TDG); however, the silencing phase additionally demanded a 5′-endonuclease (likely APE1) activity and was also induced by 5-fC or an apurinic/apyrimidinic site. We propose that 5-caC may act as a repressory mark to prevent premature activation of promoters undergoing the final stages of DNA demethylation, when the symmetric CpG methylation has already been lost. Remarkably, the downstream promoter activation or repression responses are regulated by two separate BER steps, where TDG and APE1 act as potential switches.

DNA Demethylation in the Processes of Repair and Epigenetic Regulation Performed by 2-Ketoglutarate-Dependent DNA Dioxygenases

Site-specific DNA methylation plays an important role in epigenetic regulation of gene expression. Chemical methylation of DNA, including the formation of various methylated nitrogenous bases, leads to the formation of genotoxic modifications that impair DNA functions. Despite the fact that different pathways give rise to methyl groups in DNA, the main pathway for their removal is oxidative demethylation, which is catalyzed by nonheme Fe(II)/α-ketoglutarate–dependent DNA dioxygenases. DNA dioxygenases share a common catalytic mechanism of the oxidation of the alkyl groups on nitrogenous bases in nucleic acids. This review presents generalized data on the catalytic mechanism of action of DNA dioxygenases and on the participation of typical representatives of this superfamily, such as prokaryotic enzyme AlkB and eukaryotic enzymes ALKBH1–8 and TET1–3, in both processes of direct repair of alkylated DNA adducts and in the removal of an epigenetic mark (5-methylcytosine).

Metabolic enzymes function as epigenetic modulators: A Trojan Horse for chromatin regulation and gene expression

Epigenetic modification is a fundamental biological process in living organisms, which has significant impact on health and behavior. Metabolism refers to a set of life-sustaining chemical reactions, including the uptake of nutrients, the subsequent conversion of nutrients into energy or building blocks for organism growth, and finally the clearance of redundant or toxic substances. It is well established that epigenetic modifications govern the metabolic profile of a cell by modulating the expression of metabolic enzymes. Strikingly, almost all the epigenetic modifications require substrates produced by cellular metabolism, and a large proportion of metabolic enzymes can transfer into nucleus to locally produce substrates for epigenetic modification, thereby providing an alternative link between metabolism, epigenetic modification and gene expression. Here, we summarize the recent literature pertinent to metabolic enzymes functioning as epigenetic modulators in the regulation of chromatin architecture and gene expression.

Quantification and mapping of DNA modifications

Apart from the four canonical nucleobases, DNA molecules carry a number of natural modifications. Substantial evidence shows that DNA modifications can regulate diverse biological processes. Dynamic and reversible modifications of DNA are critical for cell differentiation and development. Dysregulation of DNA modifications is closely related to many human diseases. The research of DNA modifications is a rapidly expanding area and has been significantly stimulated by the innovations of analytical methods. With the recent advances in methods and techniques, a series of new DNA modifications have been discovered in the genomes of prokaryotes and eukaryotes. Deciphering the biological roles of DNA modifications depends on the sensitive detection, accurate quantification, and genome-wide mapping of modifications in genomic DNA. This review provides an overview of the recent advances in analytical methods and techniques for both the quantification and genome-wide mapping of natural DNA modifications. We discuss the principles, advantages, and limitations of these developed methods. It is anticipated that new methods and techniques will resolve the current challenges in this burgeoning research field and expedite the elucidation of the functions of DNA modifications.

Comparative Nucleosomal Reactivity of 5-Formyl-Uridine and 5-Formyl-Cytidine

5‐Formyl‐deoxyuridine (fdU) and 5‐formyl‐deoxycytidine (fdC) are formyl‐containing nucleosides that are created by oxidative stress in differentiated cells. While fdU is almost exclusively an oxidative stress lesion formed from deoxythymidine (T), the situation for fdC is more complex. Next to formation as an oxidative lesion, it is particularly abundant in stem cells, where it is more frequently formed in an epigenetically important oxidation reaction performed by α‐ketoglutarate dependent TET enzymes from 5‐methyl‐deoxycytidine (mdC). Recently, it was shown that genomic fdC and fdU can react with the ϵ‐aminogroups of nucleosomal lysines to give Schiff base adducts that covalently link nucleosomes to genomic DNA. Here, we show that fdU features a significantly higher reactivity towards lysine side chains compared with fdC. This result shows that depending on the amounts of fdC and fdU, oxidative stress may have a bigger impact on nucleosome binding than epigenetics.

Deformylation of 5-Formylcytidine in Different Cell Types

Epigenetic programming of cells requires methylation of deoxycytidines (dC) to 5-methyl-dC (mdC) followed by oxidation to 5-hydroxymethyl-dC (hmdC), 5-formyl-dC (fdC), and 5-carboxy-dC (cadC). Subsequent transformation of fdC and cadC back to dC by various pathways establishes a chemical intra-genetic control circle. One of the discussed pathways involves the Tdg-independent deformylation of fdC directly to dC. Here we report the synthesis of a fluorinated fdC feeding probe (F-fdC) to study direct deformylation to F-dC. The synthesis was performed along a novel pathway that circumvents any F-dC as a reaction intermediate to avoid contamination interference. Feeding of F-fdC and observation of F-dC formation in vivo allowed us to gain insights into the Tdg-independent removal process. While deformylation was shown to occur in stem cells, we here provide data that prove deformylation also in different somatic cell types. We also investigated active demethylation in a non-dividing neurogenin-inducible system of iPS cells that differentiate into bipolar neurons.

Investigation of the inhibited biotoxicity of heavy metals towards 5- formylcytosine in rice by hydrochar based on photoelectrochemical biosensor

A photoelectrochemical (PEC) biosensor was constructed for 5-formylcytosine (5fC) nucleotide detection based on Ag₂S@WS₂ photoactive material and FeVO₄ catalytic signal quenching. After Ag₂S@WS₂ was modified onto the ITO substrate surface, 5fC recognition reagent of Au@4-amino3hydrazino5mercapto-1,2,4-triazol (Au@AHMT) was further modified through electrostatic adsorption. Afterwards, based on the specific chemical reaction between -NH₂ and -CHO, 5fC can be selectively recognized and captured. Subsequently, the nanoenzyme of FeVO₄ was recognized based on the specific reaction between the phosphate group of 5fC nucleotide and Fe³⁺. Under the catalysis of FeVO₄, the 4-chloro-1-naphthol in the detection solution can be oxidized to generate a precipitate, which will be retained on the electrode surface to inhibit the PEC signal. The developed method presented a widely dynamic range from 0.1 to 400 nM. The detection limit was 0.062 nM (3σ). This method also showed good detection selectivity, reproducibility and stability. The applicability was verified by investigating 5fC content change in genomic DNA of rice tissues after incubated with heavy metals. Moreover, the inhibited influence of hydrochar towards heavy metals was also assessed.

Contribution of Epigenetic Mechanisms in the Regulation of Environmentally-Induced Polyphenism in Insects

Simple Summary

Polyphenism is a widespread phenomenon in insects that allows organisms to produce alternative and discrete phenotypes in response to environmental conditions. Epigenetic mechanisms, including histone post-translational modifications, DNA methylation and non-coding RNAs, are essential mechanisms that can promote rapid and flexible changes in the expression of transcriptional programs associated with the production of alternative phenotypes. This review summarizes knowledge regarding the contribution of those mechanisms in the regulation of the most-studied examples of polyphenism in insects.

Abstract

Many insect species display a remarkable ability to produce discrete phenotypes in response to changes in environmental conditions. Such phenotypic plasticity is referred to as polyphenism. Seasonal, dispersal and caste polyphenisms correspond to the most-studied examples that are environmentally-induced in insects. Cues that induce such dramatic phenotypic changes are very diverse, ranging from seasonal cues, habitat quality changes or differential larval nutrition. Once these signals are perceived, they are transduced by the neuroendocrine system towards their target tissues where gene expression reprogramming underlying phenotypic changes occur. Epigenetic mechanisms are key regulators that allow for genome expression plasticity associated with such developmental switches. These mechanisms include DNA methylation, chromatin remodelling and histone post-transcriptional modifications (PTMs) as well as non-coding RNAs and have been studied to various extents in insect polyphenism. Differential patterns of DNA methylation between phenotypes are usually correlated with changes in gene expression and alternative splicing events, especially in the cases of dispersal and caste polyphenism. Combinatorial patterns of histone PTMs provide phenotype-specific epigenomic landscape associated with the expression of specific transcriptional programs, as revealed during caste determination in honeybees and ants. Alternative phenotypes are also usually associated with specific non-coding RNA profiles. This review will provide a summary of the current knowledge of the epigenetic changes associated with polyphenism in insects and highlights the potential for these mechanisms to be key regulators of developmental transitions triggered by environmental cues.

Enhanced photoactivity of ZnPc@WS2 heterojunction by CuBi2O4 and its application for photoelectrochemical detection of 5-formyl-2'-deoxycytidine

The endogenous epigenetic marker 5-formylcytosine (5 fC) is introduced by 5-methylcytosine (5 mC) oxidation under action of enzyme oxidation, and plays an important role in many life activities. Since the content of 5 fC in mammalian tissues and cells is very low, it is necessary to exploit a sensitive and specific detection method to further understand the function of 5 fC. In this work, a sensitively and selectively photoelectrochemical (PEC) biosensor was developed for 5-formyl-2'-deoxycytidine (5fdC) detection. CuBi₂O₄/ZnPc@WS₂ was used as photoactive material, where the formed ternary heterojunction structure greatly enhanced the PEC response and increased the detection sensitivity. Positively charged polyethyleneimine (PEI) was employed as 5fdC recognition and capture unit, where the amine group on PEI specifically reacted with aldehyde group of 5fdC to form stable amide bond. 4-Carboxyphenylboronic acid (4-CPBA) was adopted as crosslinker for 5fdC and amino functionalized CuBi₂O₄ based on the covalent interaction between 1,3-diol bond on 5fdC and boric acid structure on 4-CPBA, and the covalent interaction between -COOH on 4-CPBA and -NH₂ on amino functionalized CuBi₂O₄. On the basis of the positive synergistic effect of ZnPc and CuBi₂O₄ on improving the photoelectric performance of WS₂, the separation of photo-generated electron-hole pairs in semiconductors were promoted, and the examination range was expanded from 0.1 to 500 nM, and the detection limit was 0.0483 nM (3σ). Based on the unique covalent reaction between -NH₂ and -CHO, the PEC biosensor has excellent detection sensitivity, and can even separate 5fdC from 5-methylcytosine deoxyribonucleoside and 5-hydroxymethylcytosine deoxyribonucleoside. The effect of antibiotics and heavy metals on the 5fdC content in wheat tissue genome has also been further investigated using this sensor.

Molecular Epigenetics: Chemical Biology Tools Come of Age

The field of epigenetics has exploded over the last two decades, revealing an astonishing level of complexity in the way genetic information is stored and accessed in eukaryotes. This expansion of knowledge, which is very much ongoing, has been made possible by the availability of evermore sensitive and precise molecular tools. This review focuses on the increasingly important role that chemistry plays in this burgeoning field. In an effort to make these contributions more accessible to the nonspecialist, we group available chemical approaches into those that allow the covalent structure of the protein and DNA components of chromatin to be manipulated, those that allow the activity of myriad factors that act on chromatin to be controlled, and those that allow the covalent structure and folding of chromatin to be characterized. The application of these tools is illustrated through a series of case studies that highlight how the molecular precision afforded by chemistry is being used to establish causal biochemical relationships at the heart of epigenetic regulation.

Mechanistic Study on Oxidative DNA Damage and Modifications by Haloquinoid Carcinogenic Intermediates and Disinfection Byproducts

Haloquinones (XQs) are a group of carcinogenic intermediates of the haloaromatic environmental pollutants and newly identified chlorination disinfection byproducts (DBPs) in drinking water. The highly reactive hydroxyl radicals/alkoxyl radicals and quinone enoxy/ketoxy radicals were found to arise in XQs and H₂O₂ or organic hydroperoxides system, independent of transition-metal ions. However, it was not clear whether these haloquinoid carcinogens and hydroperoxides can cause oxidative DNA damage and modifications, and if so, what are the underlying molecular mechanisms. We found that 8-oxodeoxyguanosine (8-oxodG), DNA strand breaks, and three methyl oxidation products could arise when DNA was treated with tetrachloro-1,4-benzoquinone and H₂O₂ via a metal-independent and intercalation-enhanced oxidation mechanism. Similar effects were observed with other XQs, which are generally more efficient than the typical Fenton system. We further extended our studies from isolated DNA to genomic DNA in living cells. We also found that potent oxidation of DNA to the more mutagenic imidazolone dIz could be induced by XQs and organic hydroperoxides such as t-butylhydroperoxide or the physiologically relevant hydroperoxide 13S-hydroperoxy-9Z,11E-octadecadienoic acid via an unprecedented quinone-enoxy radical-mediated mechanism. These findings should provide new perspectives to explain the potential genotoxicity, mutagenesis, and carcinogenicity for the ubiquitous haloquinoid carcinogenic intermediates and DBPs.

Reduced Bisulfite Sequencing: Quantitative Base-Resolution Sequencing of 5-Formylcytosine

The generation of tools to study mammalian epigenetics is vital to understanding normal biological function and to identify how it is dysregulated in disease. The well-studied epigenetic DNA modification 5-methylcytosine can be enzymatically oxidized to 5-formylcytosine (5fC) in vivo. 5fC has been demonstrated to be an intermediate in demethylation, but recent evidence suggests that 5fC may have an epigenetic function of its own. We have developed reduced bisulfite sequencing (redBS-seq), which can quantitatively locate 5fC bases at single-base resolution in genomic DNA. In bisulfite sequencing (BS-seq), 5fC is converted to uracil, as happens to unmodified cytosine (C), and thus cannot be discriminated from C. However, in redBS-seq, a specific reduction of 5fC to 5-hydroxymethylcytosine (5hmC) stops this conversion, allowing its discrimination from C. 5fC levels are inferred by comparison of a redBS-Seq run with a BS-seq run.

[Roles of ten eleven translocation proteins family and 5-hydroxymethylcytosine in epigenetic regulation of stem cells and regenerative medicine]

The methylation of cytosine is one of the most fundamental epigenetic modifications in mammalian genomes, and is involved in multiple crucial processes including gene expression, cell differentiation, embryo development and oncogenesis. In the past, DNA methylation was thought to be an irreversible process, which could only be diluted passively through DNA replication. It is now becoming increa-singly obvious that DNA demethylation can be an active process and plays a crucial role in biological processes. Ten eleven translocation (TET) proteins are the key factors modulating DNA demethylation. This family contains three members: TET1, TET2 and TET3. Although three TET proteins have relatively conserved catalytic domains, their roles in organisms are not repeated, and their expression has significant cell/organ specificity. TET1 is mainly expressed in embryonic stem cells, TET2 is mainly expressed in hematopoietic system, and TET3 is widely expressed in cerebellum, cortex and hippocampus. This family catalyzes 5-methylcytosine to 5-hydroxymethylcytosine and other oxidative products, reactivates silenced-gene expression, in turn maintains stem cell pluripotency and regulates lineage specification. With the development of tissue engineering, organ transplantation, autologous tissue transplantation and artificial prosthesis have been widely used in clinical treatment, but these technologies have limitations. Regenerative medicine, which uses stem cells and stem cell related factors for treatment, may provide alternative therapeutic strategies for multiple diseases. Among all kinds of human stem cells, adipose-derived stem cells (ADSCs) are the most prospective stem cell lineage since they have no ethical issues and can be easily obtained with large quantities. To date, ADSCs have been shown to have strong proli-feration capacity, secrete numerous soluble factors and have multipotent differentiation ability. However, the underlying mechanism of the proliferation, secretion, acquired pluripotency, and lineage specific differentiation of ADSCs are still largely unknown. Some studies have explored the role of epigenetic regulation and TET protein in embryonic stem cells, but little is known about its role in ADSCs. By studying the roles of TET proteins and 5-hydroxymethylcytosine in ADSCs, we could provide new theoretical foundation for the clinical application of ADSCs and the stem cell-based therapy. In the future, combined with bioprinting technology, ADSCs may be used in tissue and organ regeneration, plastic surgery reconstruction and other broader fields.

TET-TDG Active DNA Demethylation at CpG and Non-CpG Sites

In mammalian genomes, cytosine methylation occurs predominantly at CG (or CpG) dinucleotide contexts. As part of dynamic epigenetic regulation, 5-methylcytosine (mC) can be erased by active DNA demethylation, whereby ten-eleven translocation (TET) enzymes catalyze the stepwise oxidation of mC to 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxycytosine (caC), thymine DNA glycosylase (TDG) excises fC or caC, and base excision repair yields unmodified cytosine. In certain cell types, mC is also enriched at some non-CG (or CH) dinucleotides, however hmC is not. To provide biochemical context for the distribution of modified cytosines observed in biological systems, we systematically analyzed the activity of human TET2 and TDG for substrates in CG and CH contexts. We find that while TET2 oxidizes mC more efficiently in CG versus CH sites, this context preference can be diminished for hmC oxidation. Remarkably, TDG excision of fC and caC is only modestly dependent on CG context, contrasting its strong context dependence for thymine excision. We show that collaborative TET-TDG oxidation-excision activity is only marginally reduced for CA versus CG contexts. Our findings demonstrate that the TET-TDG-mediated demethylation pathway is not limited to CG sites and suggest a rationale for the depletion of hmCH in genomes rich in mCH.

Cellular response to endogenous DNA damage: DNA base modifications in gene expression regulation

The integrity of the genetic information is continuously challenged by numerous genotoxic insults, most frequently in the form of oxidation, alkylation or deamination of the bases that result in DNA damage. These damages compromise the fidelity of the replication, and interfere with the progression and function of the transcription machineries. The DNA damage response (DDR) comprises a series of strategies to deal with DNA damage, including transient transcriptional inhibition, activation of DNA repair pathways and chromatin remodeling. Coordinated control of transcription and DNA repair is required to safeguardi cellular functions and identities. Here, we address the cellular responses to endogenous DNA damage, with a particular focus on the role of DNA glycosylases and the Base Excision Repair (BER) pathway, in conjunction with the DDR factors, in responding to DNA damage during the transcription process. We will also discuss functions of newly identified epigenetic and regulatory marks, such as 5-hydroxymethylcytosine and its oxidative products and 8-oxoguanine, that were previously considered only as DNA damages. In light of these resultsthe classical perception of DNA damage as detrimental for cellular processes are changing. and a picture emerges whereDNA glycosylases act as dynamic regulators of transcription, placing them at the intersection of DNA repair and gene expression modulation.

The Enzymatic Decarboxylation Mechanism of 5-Carboxy Uracil: A Comprehensive Quantum Chemical Study

Dynamic regulation of DNA methylation is an important process for the control of gene expression in mammals. It is believed that in the demethylation pathway of 5-methyl cytosine, the intermediate 5-carboxy cytosine (5caC) can be actively decarboxylated alongside the substitution in the base excision repair. For the active decarboxylation of 5caC, a decarboxylase has not been identified so far. Due to the similar chemistry of the decarboxylation of 5-carboxy uracil (5caU) to uracil (U) in the pyrimidine salvage pathway catalyzed by the iso-orotate decarboxylase (IDCase), the study of this reaction might give valuable insights into the active 5caC decarboxylation process. In this work, we employ quantum chemical and molecular mechanic calculations and find that the catalytic mechanism of IDCase proceeds via a direct decarboxylation mechanism. Detailed investigations on the reaction coordinate reveal that it is a one-step mechanism with concerted proton transfer and C-C bond opening.

Epigenetic regulation of satellite cell fate during skeletal muscle regeneration

In response to muscle injury, muscle stem cells integrate environmental cues in the damaged tissue to mediate regeneration. These environmental cues are tightly regulated to ensure expansion of muscle stem cell population to repair the damaged myofibers while allowing repopulation of the stem cell niche. These changes in muscle stem cell fate result from changes in gene expression that occur in response to cell signaling from the muscle environment.

Integration of signals from the muscle environment leads to changes in gene expression through epigenetic mechanisms. Such mechanisms, including post-translational modification of chromatin and nucleosome repositioning, act to make specific gene loci more, or less, accessible to the transcriptional machinery. In youth, the muscle environment is ideally structured to allow for coordinated signaling that mediates efficient regeneration. Both age and disease alter the muscle environment such that the signaling pathways that shape the healthy muscle stem cell epigenome are altered. Altered epigenome reduces the efficiency of cell fate transitions required for muscle repair and contributes to muscle pathology. However, the reversible nature of epigenetic changes holds out potential for restoring cell fate potential to improve muscle repair in myopathies.

In this review, we will describe the current knowledge of the mechanisms allowing muscle stem cell fate transitions during regeneration and how it is altered in muscle disease. In addition, we provide some examples of how epigenetics could be harnessed therapeutically to improve regeneration in various muscle pathologies.

Liquid Chromatography-Mass Spectrometry Analysis of Cytosine Modifications

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely used technique in the global analysis of epigenetic DNA modifications. The high-resolution chromatographic separation along with sensitive MS detection permits the identification and quantification of deoxyribonucleosides with precision and reliability. Although there have been tremendous advances in LC and MS instrumentation in recent years, sample preparation has not experienced a similar rate of development and is often a bottleneck to chemical analysis. Here we present a protocol for identification and quantification of cytosine modifications that combines a robust and efficient method to generate single nucleosides from genomic DNA samples followed by direct LC-MS/MS analysis.

Mapping the epigenetic modifications of DNA and RNA

Over 17 and 160 types of chemical modifications have been identified in DNA and RNA, respectively. The interest in understanding the various biological functions of DNA and RNA modifications has lead to the cutting-edged fields of epigenomics and epitranscriptomics. Developing chemical and biological tools to detect specific modifications in the genome or transcriptome has greatly facilitated their study. Here, we review the recent technological advances in this rapidly evolving field. We focus on high-throughput detection methods and biological findings for these modifications, and discuss questions to be addressed as well. We also summarize third-generation sequencing methods, which enable long-read and single-molecule sequencing of DNA and RNA modification.

DNA methylation methods: Global DNA methylation and methylomic analyses

DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has significant involvement for numerous biological processes in health and disease. The function of methylation of cytosine bases in DNA was originally proposed as a "silencing" epigenetic marker and focused on promoter regions of genes for decades. Improved technologies and accumulating studies have been extending our understanding of the roles of DNA methylation to various genomic contexts including gene bodies, repeat sequences and transcriptional start sites. The demand for comprehensively describing DNA methylation patterns spawns a diversity of DNA methylation profiling technologies that target its genomic distribution. These approaches have enabled the measurement of cytosine methylation from specific loci at restricted regions to single-base-pair resolution on a genome-scale level. In this review, we discuss the different DNA methylation analysis technologies primarily based on the initial treatments of DNA samples: bisulfite conversion, endonuclease digestion and affinity enrichment, involving methodology evolution, principles, applications, and their relative merits. This review may offer referable information for the selection of various platforms for genome-wide analysis of DNA methylation.

Retracted Article: Divergent synthesis of 5-substituted pyrimidine 2'-deoxynucleosides and their incorporation into oligodeoxynucleotides for the survey of uracil DNA glycosylases

Recent studies have indicated that 5-methylcytosine (5mC) residues in DNA can be oxidized and potentially deaminated to the corresponding thymine analogs. Some of these oxidative DNA damages have been implicated as new epigenetic markers that could have profound influences on chromatin function as well as disease pathology. In response to oxidative damage, the cells have a complex network of repair systems that recognize, remove and rebuild the lesions. However, how the modified nucleobases are detected and repaired remains elusive, largely due to the limited availability of synthetic oligodeoxynucleotides (ODNs) containing these novel DNA modifications. A concise and divergent synthetic strategy to 5mC derivatives has been developed. These derivatives were further elaborated to the corresponding phosphoramidites to enable the site-specific incorporation of modified nucleobases into ODNs using standard solid-phase DNA synthesis. The synthetic methodology, along with the panel of ODNs, is of great value to investigate the biological functions of epigenetically important nucleobases, and to elucidate the diversity in chemical lesion repair.