5-Hydroxymethylcytosine: the many faces of the sixth base of mammalian DNA

Accurate Mapping of 5-Glyceryl-methylcytosine Using Nanopore Sequencing

5-Glyceryl-methylcytosine (5gmC) is an epigenetic modification recently discovered in the genome of Chlamydomonas reinhardtii. It is formed by attaching a glyceryl group of vitamin C to the methyl moiety of 5mC, a process catalyzed by the CMD1 protein. 5gmC has been shown to play a role in promoting active DNA demethylation and photoacclimation. However, the precise localization of 5gmC and its role in gene transcription remain largely unexplored. To efficiently and economically map the distribution of 5gmC across the genome, we investigated the feasibility of nanopore sequencing for identifying this DNA modification. By introducing 5gmC into a set of model strands, significant current decreases associated with 5gmC were consistently observed during nanopore sequencing. This characteristic current signal enables direct identification of multiple 5gmC sites as well as 5gmC across various sequence contexts with reliable accuracy and single-molecule sensitivity. Moreover, we were able to discriminate between 5gmC and 5mC, as 5mC unambiguously increases the ionic current. These results demonstrate the feasibility of nanopore sequencing for mapping 5gmC at the genomic level and provide new insights into the exploration of the roles of 5gmC as a stable epigenetic mark.

Advancing TET Inhibitor Development: From Structural Insights to Biological Evaluation

Ten-eleven translocation (TET) methylcytosine dioxygenases are part of the epigenetic regulatory machinery that erases DNA methylation. Aberrant TET activities are frequently found in hematopoietic malignancies, where loss of TET2 function leads to DNA hypermethylation. A comprehensive understanding of the biological role of TETs is essential to elucidate disease pathogenesis and identify novel therapeutic strategies. We present a robust pipeline integrating protein X-ray crystallography, molecular modeling, and pharmacophore analysis to advance the current TET inhibitor development. In addition, we have synthesized and evaluated a series of 8-hydroxyquinoline (8-HQ) derivatives, demonstrating their potential as chemical tools to explore TET function further. These findings lay the groundwork for a TET-centered therapeutic approach.

Type-2 diabetes epigenetic biomarkers: present status and future directions for global and Indigenous health

Type-2 diabetes is a systemic condition with rising global prevalence, disproportionately affecting Indigenous communities worldwide. Recent advances in epigenomics methods, particularly in DNA methylation detection, have enabled the discovery of associations between epigenetic changes and Type-2 diabetes. In this review, we summarise DNA methylation profiling methods, and discuss how these technologies can facilitate the discovery of epigenomic biomarkers for Type-2 diabetes. We critically evaluate previous DNA methylation biomarker studies, particularly those using microarray platforms, and advocate for a shift towards sequencing-based approaches to improve genome-wide coverage. Furthermore, we emphasise the need for biomarker studies that include genetically diverse populations, especially Indigenous communities who are significantly impacted by Type-2 diabetes. We discuss research approaches and ethical considerations that can better facilitate Type-2 diabetes biomarker development to ensure that future genomics-based precision medicine efforts deliver equitable health outcomes. We propose that by addressing these gaps, future research can better capture the genetic and environmental complexities of Type-2 diabetes among populations at disproportionate levels of risk, ultimately leading to more effective diagnostic and therapeutic strategies.

Glycosidase-Enabled Locus-Specific Detection of 8-Oxo-7,8-dihydroguanine in Genomes under Oxidative Stress

Oxidative DNA damage is closely linked to the onset of various age-related diseases. A significant oxidation product, 8-oxo-7,8-dihydroguanine (8OG), has been considered an important epigenetic-like marker in regulating gene expression. Accurately quantifying the locus-specific 8OG levels is crucial for understanding its functional roles in disease induction and gene regulation. In this study, we developed a glycosylase cleavage-mediated extension stalling (GCES) method for the locus-specific detection and quantification of 8OG in genomic DNA. This method utilizes the 8OG-DNA glycosylase Pab-AGOG, which induces single-strand breaks in DNA containing 8OG. The resulting cleavage is then assessed and quantified by using quantitative real-time PCR (qPCR). We successfully applied this strategy to evaluate locus-specific 8OG in synthesized DNA and genomic DNA from HEK293T, HeLa, and HepG2 cell lines under oxidative stress or triclosan treatment. The results demonstrate that the GCES method is accurate and suitable for the site-specific quantification of 8OG in both synthesized and genomic DNA from biological samples. We observed an increased level of 8OG in genomic DNA from biological samples treated with H2O2 or triclosan, indicating that both agents can elevate 8OG level in DNA. Overall, the GCES method provides a valuable, straightforward, and cost-effective tool for the quantitative detection of 8OG in DNA at base resolution, which facilitates the investigation of its functional roles as an epigenetic-like or DNA damage marker.

Causes and consequences of DNA double-stranded breaks in cardiovascular disease

The genome, whose stability is essential for survival, is incessantly exposed to internal and external stressors, which introduce an estimated 104 to 105 lesions, such as oxidation, in the nuclear genome of each mammalian cell each day. A delicate homeostatic balance between the generation and repair of DNA lesions maintains genomic stability. To initiate transcription, DNA strands unwind to form a transcription bubble and provide a template for the RNA polymerase II (RNAPII) complex to synthesize nascent RNA. The process generates DNA supercoils and introduces torsional stress. To enable RNAPII processing, the supercoils are released by topoisomerases by introducing strand breaks, including double-stranded breaks (DSBs). Thus, DSBs are intrinsic genomic features of gene expression. The breaks are quickly repaired upon processing of the transcription. DNA lesions and damaged proteins involved in transcription could impede the integrity and efficiency of RNAPII processing. The impediment, which is referred to as transcription stress, not only could lead to the generation of aberrant RNA species but also the accumulation of DSBs. The latter is particularly the case when topoisomerase processing and/or the repair mechanisms are compromised. The DSBs activate the DNA damage response (DDR) pathways to repair the damaged DNA and/or impose cell cycle arrest and cell death. In addition, the release of DSBs into the cytosol activates the cytosolic DNA-sensing proteins (CDSPs), which along with the nuclear DDR pathways induce the expression of senescence-associated secretory phenotype (SASP), cell cycle arrest, senescence, cell death, inflammation, and aging. The primary stimulus in hereditary cardiomyopathies is a mutation(s) in genes encoding the protein constituents of cardiac myocytes; however, the phenotype is the consequence of intertwined complex interactions among numerous stressors and the causal mutation(s). Increased internal DNA stressors, such as oxidation, alkylation, and cross-linking, are expected to be common in pathological conditions, including in hereditary cardiomyopathies. In addition, dysregulation of gene expression also imposes transcriptional stress and collectively with other stressors provokes the generation of DSBs. In addition, the depletion of nicotinamide adenine dinucleotide (NAD), which occurs in pathological conditions, impairs the repair mechanism and further facilitates the accumulation of DSBs. Because DSBs activate the DDR pathways, they are expected to contribute to the pathogenesis of cardiomyopathies. Thus, interventions to reduce the generation of DSBs, enhance their repair, and block the deleterious DDR pathways would be expected to impart salubrious effects not only in pathological states, as in hereditary cardiomyopathies but also aging.

Chronic Inflammation to Cancer: The Impact of Oxidative Stress on DNA Methylation

The genomic landscape of cancer cells is complex and heterogeneous, with aberrant DNA methylation being a common observation. Growing evidence indicates that oxidants produced from immune cells may interact with epigenetic processes, and this may represent a mechanism for the initiation of altered epigenetic patterns observed in both precancerous and cancerous cells. Around 20% of cancers are linked to chronic inflammatory conditions, yet the precise mechanisms connecting inflammation with cancer progression remain unclear. During chronic inflammation, immune cells release oxidants in response to stimuli, which, in high concentrations, can cause cytotoxic effects. Oxidants are known to damage DNA and proteins and disrupt normal signalling pathways, potentially initiating a sequence of events that drives carcinogenesis. While research on the impact of immune cell-derived oxidants on DNA methylation remains limited, this mechanism may represent a crucial link between chronic inflammation and cancer development. This review examines current evidence on inflammation-associated DNA methylation changes in cancers related to chronic inflammation.

Orthologous mammalian A3A-mediated single-nucleotide resolution sequencing of DNA epigenetic modification 5-hydroxymethylcytosine

Epigenetic modifications in genomes play a crucial role in regulating gene expression in mammals. Among these modifications, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are recognized as the fifth and sixth nucleobases in genomes, respectively, and are the two most significant epigenetic marks in mammals. 5hmC serves as both an intermediate in active DNA demethylation and a stable epigenetic modification involved in various biological processes. Analyzing the location of 5hmC is essential for understanding its functions. In this study, we introduce an orthologous mammalian A3A-mediated sequencing (OMA-seq) method for the quantitative detection of 5hmC in genomic DNA at single-nucleotide resolution. OMA-seq relies on the deamination properties of two naturally occurring mammalian A3A proteins: green monkey A3A (gmA3A) and dog A3A (dogA3A). The combined use of gmA3A and dogA3A effectively deaminates cytosine (C) and 5mC, but not 5hmC. As a result, the original C and 5mC in DNA are deaminated and read as thymine (T) during sequencing, while the original 5hmC remains unchanged and is read as C. Consequently, the remaining C in the sequence indicates the presence of original 5hmC. Using OMA-seq, we successfully quantified 5hmC in genomic DNA from lung cancer tissue and corresponding normal tissue. OMA-seq enables accurate and quantitative mapping of 5hmC at single-nucleotide resolution, utilizing a pioneering single-step deamination protocol that leverages the high specificity of natural deaminases. This approach eliminates the need for bisulfite conversion, DNA glycosylation, chemical oxidation, or screening of engineered protein variants, thereby streamlining the analysis of 5hmC. The utilization of orthologous enzymes for 5hmC detection expands the toolkit for epigenetic research, enabling the precise mapping of modified nucleosides and uncovering new insights into epigenetic regulation.

TET2-mediated 5-hydroxymethylcytosine of TXNIP promotes cell cycle arrest in systemic anaplastic large cell lymphoma

BACKGROUND

5-Hydroxymethylcytosine (5hmC) modification represents a significant epigenetic modification within DNA, playing a pivotal role in a range of biological processes associated with various types of cancer. The role of 5hmC in systemic anaplastic large cell lymphoma (ALCL) has not been thoroughly investigated. This study aims to examine the function of 5hmC in the advancement of ALCL.

METHODS

Formalin-fixed, paraffin-embedded (FFPE) tumor tissues (n = 46) were obtained from ALCL patients. GEO dataset was used to analyze the expression 5hmC-relative enzymes. Immunohistochemistry was conducted to assess the level of 5hmC and Ten-eleven translocation 2 (TET2) on FFPE samples. The ALK-positive cell line, Su-DHL-1, and the ALK-negative cell line, DL-40, were utilized as in vitro experimental models. RNA-sequencing and hMeDIP-sequencing assays were performed to explore the potential functions of TET2 in cell cycle regulation.

RESULTS

Our study identified a reduction of 5hmC levels in patients with ALCL, which exhibited a positive correlation with TET2 expression. Downregulation TET2 resulted in decreased 5hmC levels and facilitated the progression of the cell cycle in ALCL cell lines. hMeDIP-seq and subsequent functional analyses demonstrated the involvement of thioredoxin interacting protein (TXNIP) in the regulation of ALCL cells. Further mechanistic studies revealed that 5hmC levels influenced TXNIP expression.

CONCLUSIONS

Our study underscores the pivotal roles of 5hmC and TET2 in the regulation of cell cycle progression in ALCL. Therapeutic strategies aimed at targeting 5hmC modification or TET2 may offer a novel approach for the management of ALCL.

"Aging Clocks" Based on Cell-Free DNA

Aging is associated with systemic changes in the physiological and molecular parameters of the body. These changes are referred to as biomarkers of aging. Statistical models that link changes in individual biomarkers to biological age are called aging clocks. These tools facilitate a comprehensive evaluation of bodily health and permit the quantitative determination of the rate of aging. A particularly promising area for the development of aging clocks is the analysis of cell-free DNA (cfDNA), which is present in the blood and contains numerous potential biomarkers. This review explores in detail the fragmentomics, topology, and epigenetic landscape of cfDNA as possible biomarkers of aging. The review further underscores the potential of leveraging single-molecule sequencing of cfDNA in conjunction with long-read technologies to simultaneously profile multiple biomarkers, a strategy that could lead to the development of more precise aging clocks.

Effect of DNA methylation on the osteogenic differentiation of mesenchymal stem cells: concise review

Mesenchymal stem cells (MSCs) have promising potential for bone tissue engineering in bone healing and regeneration. They are regarded as such due to their capacity for self-renewal, multiple differentiation, and their ability to modulate the immune response. However, changes in the molecular pathways and transcription factors of MSCs in osteogenesis can lead to bone defects and metabolic bone diseases. DNA methylation is an epigenetic process that plays an important role in the osteogenic differentiation of MSCs by regulating gene expression. An increasing number of studies have demonstrated the significance of DNA methyltransferases (DNMTs), Ten-eleven translocation family proteins (TETs), and MSCs signaling pathways about osteogenic differentiation in MSCs. This review focuses on the progress of research in these areas.

DNA Methylation Machinery in Gastropod Mollusks

The role of DNA methylation in mollusks is just beginning to be understood. This review synthesizes current knowledge on this potent molecular hallmark of epigenetic control in gastropods-the largest class of mollusks and ubiquitous inhabitants of diverse habitats. Their DNA methylation machinery shows a high degree of conservation in CG maintenance methylation mechanisms, driven mainly by DNMT1 homologues, and the presence of MBD2 and MBD2/3 proteins as DNA methylation readers. The mosaic-like DNA methylation landscape occurs mainly in a CG context and is primarily confined to gene bodies and housekeeping genes. DNA methylation emerges as a critical regulator of reproduction, development, and adaptation, with tissue-specific patterns being observed in gonadal structures. Its dynamics also serve as an important regulatory mechanism underlying learning and memory processes. DNA methylation can be affected by various environmental stimuli, including as pathogens and abiotic stresses, potentially impacting phenotypic variation and population diversity. Overall, the features of DNA methylation in gastropods are complex, being an essential part of their epigenome. However, comprehensive studies integrating developmental stages, tissues, and environmental conditions, functional annotation of methylated regions, and integrated genomic-epigenomic analyses are lacking. Addressing these knowledge gaps will advance our understanding of gastropod biology, ecology, and evolution.