Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution

TET-mediated 5hmC in breast cancer: mechanism and clinical potential

Breast cancer is the most common cancer among women, with differences in clinical features due to its distinct molecular subtypes. Current studies have demonstrated that epigenetic modifications play a crucial role in regulating the progression of breast cancer. Among these mechanisms, DNA demethylation and its reverse process have been studied extensively for their roles in activating or silencing cancer related gene expression. Specifically, Ten-Eleven Translocation (TET) enzymes are involved in the conversion process from 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), which results in a significant difference in the global level of 5hmC in breast cancer compared with normal tissues. In this review, we summarize the functions of TET proteins and the regulated 5hmC levels in the pathogenesis of breast cancer. Discussions on the clinical values of 5hmC in early diagnosis and the prediction of prognosis are also mentioned.

Target-initiated autocatalytic and concatenated DNAzyme/CHA amplification cascades for highly sensitive fluorescent detection of TET1 dioxygenase

The sensitive detection of the dysregulated expression of ten-eleven translocation 1 (TET1) dioxygenase, a key DNA 5-methylcytosine (5 mC) oxidation regulator in the expression of developmental genes, is of significant importance for the diagnosis of various genetic diseases and cancers. This study describes the establishment of a highly sensitive fluorescent TET1 bioassay based on the 5 mC-modified/Zn2+-dependent DNAzyme-containing hairpin probe and the autocatalytic and concatenated DNAzyme/catalytic hairpin assembly (CHA) signal amplification cascades. TET1 target molecules specifically recognize and cut the 5 mC sites in the hairpin probes to release active DNAzyme sequences, which bind and cleave the double-stem-loop substrate strands to trigger multiple concatenated signal amplification recycling cycles with the presence of the fuel strands and two fluorescently quenched signal hairpins. These DNA reaction cascades thus result in the unfolding of lots of signal hairpins to substantially recover fluorescence for highly sensitive TET1 assay with a calculated detection limit of 6.9 fM. Additionally, such bioassay shows high selectivity toward TET1 and its real applicability has been successfully demonstrated for cancer cell lysate and human serum samples.

Gene editing using CRISPR-Cas9 technology: potential implications in assisted reproduction

PURPOSE OF REVIEW

This article reviews the mechanisms, advancements, and potential implications of clustered regularly interspaced short palindromic repeats-associated (CRISPR-Cas) gene editing technology, with a specific focus on its applications in reproductive biology and assisted reproduction. It aims to explore the benefits and challenges of integrating this revolutionary technology into clinical and research settings.

RECENT FINDINGS

CRISPR-Cas9 is a transformative tool for precise genome editing, enabling targeted modifications through mechanisms like nonhomologous end joining (NHEJ) and homology-directed repair (HDR). Innovations such as Cas9 nickase and dCas9 systems have improved specificity and expanded applications, including gene activation, repression, and epigenetic modifications. In reproductive research, CRISPR has facilitated gene function studies, corrected genetic mutations in animal models, and demonstrated potential in addressing human infertility and hereditary disorders. Emerging applications include mitochondrial genome editing, population control of disease vectors via gene drives, and detailed analyses of epigenetic mechanisms.

SUMMARY

CRISPR-Cas9 technology has revolutionized genetic engineering by enabling precise genome modifications. This article discusses its mechanisms, focusing on the repair pathways (NHEJ and HDR) and methods to mitigate off-target effects. In reproductive biology, CRISPR has advanced our understanding of fertility genes, allowed corrections of hereditary mutations, and opened avenues for novel therapeutic strategies. While its clinical application in human-assisted reproduction faces ethical and safety challenges, ongoing innovations hold promise for broader biomedical applications.

Highly Sensitive and Diversified Electrochemiluminescence DNA Methylation Biosensing Platform Based on Self-Assembly of Nanotags

This work proposes a highly sensitive, simple, and reliable electrochemiluminescence (ECL) DNA methylation biosensing platform by employing DNA-functionalized magnetic beads (DNA-MBs) for target capture and nanotag self-assembly aggregation for signal amplification. The target methylated DNA was first captured on DNA-MBs through base pairing recognition, and then its methylation sites were recognized by antibody-5mC (Ab-5mC). Afterward, a pair of antibodies functionalized [Ru(byp)3]2+-doped silica nanoparticles (Ab2-Ru@SiO2 and Ab3-Ru@SiO2) was layer-by-layer assembled on Ab-5mC for amplified signal transduction. The sensing beads could be transferred to screen-printed carbon electrodes (SPCEs) for ECL curve detection via photomultiplier tube or to gold-coated indium tin oxide (Au/ITO) arrays for high-throughput imaging detection. As the nanotag assembly layers increased from 1 to 3, the detection sensitivities of SPCE-based curve detection and Au/ITO-based imaging detection were enhanced 7-fold and 3-fold, achieving detection limits down to 0.8 pM and 0.9 fM, respectively. The nanotags showed good stability, with storage times of 300 days for Ru@SiO2 and 60 days for Ab-Ru@SiO2, respectively. This method is universal and could be applied to detect different methylated DNAs by using their corresponding DNA-MBs. The proposed ECL biosensing platform possessed advantages of high sensitivity, good diversity, and practicality, showing potential for high-throughput DNA methylation detection in clinical diagnosis.

Novel Tet3 enzymes for next-generation epigenetic sequencing

Epigenetic regulation of gene expression is essential for cellular development and differentiation processes in higher eukaryotes. Modifications of cytosine, in particular 5-methylcytosine (5mdC), in DNA play a central role through impacting chromatin structure, repressing transposons, and regulating transcription. DNA methylation is actively installed by DNA methyltransferases and reversed through Tet-dioxygenase-mediated oxidation of 5mdC to 5-hydroxylmethylcytosine (5hmdC), 5-formylcytosine (5fdC), and 5-carboxycytosine (5cadC). It is crucial to understand the role of these epigenetic DNA modifications in cellular differentiation and developmental processes, as well as in disease state mapping and tracing of 5mdC and its oxidized forms. In bisulfite sequencing, which has been the benchmark for mapping 5mdC for the last few decades, degradation of the majority of genetic material occurs through harsh chemical treatment. Alternative sequencing methods often utilize Tet-enzyme-mediated oxidation of 5mdC to locate 5mdC and 5hmdC in genomic DNA. Herein, we report the development of novel Tet3-variants for oxidation-based bisulfite-free 5mdC- sequencing.

Reliable investigation of DNA methylation using Oxford nanopore technologies

Oxford Nanopore Technologies (ONT) offers an efficient and effective solution for studying DNA methylation. Both R9.4.1 and R10.4.1 ONT chemistries have been widely used to generate numerous DNA methylation data, making it inevitable to conduct cross-ONT-chemistry methylation analysis. However, the two ONT chemistries have unique designs and may cause potential bias in methylation detection, complicating cross-chemistry methylation investigation. In this study, we sequenced two pairs of wild-type and their knockout samples using R9.4.1 and R10.4.1 chemistries and investigated the concordance and bias of the two pairs of ONT methylation data. Although we confirmed high concordances of methylation data generated by the two ONT chemistries and the improvement of R10 chemistry in repeat regions, we found that both chemistries possess detection bias for methylation. Thus, cross-ONT-chemistry methylation studies identified hundreds of thousands of differential methylation sites caused by chemistry variabilities. We also explored different methods to calculate coverage and methylation percentages. Our evaluations provide valuable recommendations for cross-ONT-chemistry methylation analysis and suggest better practices for robust methylation investigation.

Genomic and fragmentomic landscapes of cell-free DNA for early cancer detection

Genomic analyses of cell-free DNA (cfDNA) in plasma are enabling noninvasive blood-based biomarker approaches to cancer detection and disease monitoring. Current approaches for identification of circulating tumour DNA typically use targeted tumour-specific mutations or methylation analyses. An emerging approach is based on the recognition of altered genome-wide cfDNA fragmentation in patients with cancer. Recent studies have revealed a multitude of characteristics that can affect the compendium of cfDNA fragments across the genome, collectively called the 'cfDNA fragmentome'. These changes result from genomic, epigenomic, transcriptomic and chromatin states of an individual and affect the size, position, coverage, mutation, structural and methylation characteristics of cfDNA. Identifying and monitoring these changes has the potential to improve early detection of cancer, especially using highly sensitive multi-feature machine learning approaches that would be amenable to broad use in populations at increased risk. This Review highlights the rapidly evolving field of genome-wide analyses of cfDNA characteristics, their comparison to existing cfDNA methods, and recent related innovations at the intersection of large-scale sequencing and artificial intelligence. As the breadth of clinical applications of cfDNA fragmentome methods have enormous public health implications for cancer screening and personalized approaches for clinical management of patients with cancer, we outline the challenges and opportunities ahead.

DNA methylation in breast cancer: early detection and biomarker discovery through current and emerging approaches

Breast cancer remains one of the most common cancers in women worldwide. Early detection is critical for improving patient outcomes, yet current screening methods have limitations. Therefore, there is a pressing need for more sensitive and specific approaches to detect breast cancer in its earliest stages. Liquid biopsy has emerged as a promising non-invasive method for early cancer detection and management. DNA methylation, an epigenetic alteration that often precedes genetic changes, has been observed in precancerous or early cancer stages, making it a valuable biomarker. This review explores the role of DNA methylation in breast cancer and its potential for developing blood-based tests. We discuss advancements in DNA methylation detection methods, recent discoveries of potential DNA methylation biomarkers from both single-omics and multi-omics integration studies, and the role of machine learning in enhancing diagnostic accuracy. Challenges and future directions are also addressed. Although challenges remain, advances in multi-omics integration and machine learning continue to enhance the clinical potential of methylation-based biomarkers. Ongoing research is crucial to further refine these approaches and improve early detection and patient outcomes.

Dynamic Regulation of 5-Formylcytidine on tRNA

Post-transcriptional modifications on RNA play an important role in biological processes, but we lack an understanding of the molecular mechanisms underlying the function of many modifications. Here we characterize the distribution and dynamic regulation of 5-formylcytidine (f5C), a modification primarily found on tRNAs, across different cell lines, mouse tissues, and in response to environmental stress. We identify perturbation in bulk f5C levels using nucleoside LC-MS and quantify individual modification stoichiometry at the wobble base of mt-tRNA-Met and tRNA-Leu-CAA using nucleotide resolution f5C sequencing technology. Our studies show that f5C modifications on tRNAs are dynamic, and responsive to fluctuations in cellular iron levels and O2 concentration. Further, we show using a translation reporter assay that decoding of Leu UUA codons is impaired in cells lacking f5C, implicating f5C(m)34 on tRNA-Leu-CAA in wobble decoding. Together, our work illuminates dynamic epitranscriptomic mechanisms regulating protein translation in response to environment.

Direct single-nucleotide resolution sequencing of DNA 5-methylcytosine using engineered DNA methyltransferase-mediated CMD-seq

5-Methylcytosine (5mC) is a crucial epigenetic modification in the mammalian genome, primarily occurring at CG dinucleotides. Accurate localization of 5mC is essential for understanding its functional significance. In this study, we discovered a novel DNA methyltransferase, designated M.MedI, from the bacterium Mycoplasmopsis edwardii. M.MedI exhibits carboxymethylation activity towards cytosines in CG sites in DNA. We further engineered a variant of M.MedI by mutating its critical active site residue 377 asparagine (N) to lysine (K), resulting in M.MedI-N377K. This engineered M.MedI-N377K enzyme demonstrated superior carboxymethylation activity towards cytosines in CG sites in both unmethylated and hemi-methylated DNA. Utilizing the newly identified M.MedI-N377K methyltransferase, we developed a novel method, engineered DNA methyltransferase-mediated carboxymethylation deamination sequencing (CMD-seq), for the stoichiometric detection of 5mC in DNA at single-nucleotide resolution. In CMD-seq, M.MedI-N377K efficiently transfers a carboxymethyl group to cytosines in CG sites in the presence of carboxy-S-adenosyl-l-methionine (caSAM), generating 5-carboxymethylcytosine (5camC). Subsequent treatment with the deaminase A3A deaminates 5mC to form thymine (T), which pairs with adenine (A) and is read as T, while 5camC remains unchanged, pairing with guanine (G) and being read as cytosine (C) during sequencing. We successfully applied CMD-seq to quantify 5mC sites in the promoters of tumor suppressor genes RASSF1A and SHOX2 in human lung cancer tissue and adjacent normal tissue. The quantification results were highly comparable to those obtained using traditional bisulfite sequencing. Overall, CMD-seq provides a valuable tool for bisulfite-free, single-nucleotide resolution, and quantitative detection of 5mC in limited DNA samples.

Joint analysis of chromatin accessibility and gene expression in the same single cells reveals cancer-specific regulatory programs

Biological analyses conducted at the single-cell scale have revealed profound impacts of heterogeneity and plasticity of chromatin states and gene expression on physiology and cancer. Here, we developed Parallel-seq, a technology for simultaneously measuring chromatin accessibility and gene expression in the same single cells. By combining combinatorial cell indexing and droplet overloading, Parallel-seq generates high-quality data in an ultra-high-throughput fashion and at a cost two orders of magnitude lower than alternative technologies (10× Multiome and ISSAAC-seq). We applied Parallel-seq to 40 lung tumor and tumor-adjacent clinical samples and obtained over 200,000 high-quality joint scATAC-and-scRNA profiles. Leveraging this large dataset, we characterized copy-number variations (CNVs) and extrachromosomal circular DNA (eccDNA) heterogeneity in tumor cells, predicted hundreds of thousands of cell-type-specific regulatory events, and identified enhancer mutations affecting tumor progression. Our analyses highlight Parallel-seq's power in investigating epigenetic and genetic factors driving cancer development at the cell-type-specific level and its utility for revealing vulnerable therapeutic targets.

Evolution of genome-wide methylation profiling technologies

In this mini-review, we explore the advancements in genome-wide DNA methylation profiling, tracing the evolution from traditional methods such as methylation arrays and whole-genome bisulfite sequencing to the cutting-edge single-molecule profiling enabled by long-read sequencing (LRS) technologies. We highlight how LRS is transforming clinical and translational research, particularly by its ability to simultaneously measure genetic and epigenetic information, providing a more comprehensive understanding of complex disease mechanisms. We discuss current challenges and future directions in the field, emphasizing the need for innovative computational tools and robust, reproducible approaches to fully harness the capabilities of LRS in molecular diagnostics.

Assessing the virological response to direct-acting antiviral therapies in the HBV cure programme

Hepatitis B virus (HBV) is a global health problem with over 250 million people affected worldwide. Nucleos(t)ide analogues remain the standard of care and suppress production of progeny virions; however, they have limited effect on the viral transcriptome and long-term treatment is associated with off-target toxicities. Promising results are emerging from clinical trials and several drug classes have been evaluated, including capsid assembly modulators and RNA interfering agents. Whilst peripheral biomarkers are used to monitor responses and define treatment endpoints, they fail to reflect the full reservoir of infected hepatocytes. Given these limitations, consideration should be given to the merits of sampling liver tissue, especially in the context of clinical trials. In this review article, we will discuss methods for profiling HBV in liver tissue and their value to the HBV cure programme.

Chemical Modification Coupled with Isothermal CRISPR-Based Assay for Sensitive Detection of DNA Hydroxymethylation

5-Hydroxymethylcytosine (5hmC) plays a key role in the DNA demethylation process and serves as a stable epigenetic marker in the human genome which is closely associated with disease progression, particularly in diabetes, colorectal cancer, and liver cancer. However, convenient and sensitive methods for detecting and quantifying 5hmC in the genome are scarce, especially in complex biological environments. Herein, a novel attempt at hypersensitive quantitative detection of 5hmC was presented. A multifunctional photosensitive probe was therefore introduced for specific labeling, enrichment, and elution of 5hmC-DNA. Combining with isothermal assay leveraging rolling circle amplification and Cas12a for accurate recognition, we achieved quantitative detection of 5hmC DNA in trace amounts at a level of 11 fM. Global 5hmC was measured in various biological samples using as little as 10 ng of input DNA by a real-time PCR instrument. The reported approach imposed no sequence restrictions, demonstrating promising potential for detecting modified bases in trace amounts of nucleic acids within complex environments, such as blood, urine, and saliva samples.

NAT10 and N4-acetylcytidine restrain R-loop levels and related inflammatory responses

N4-acetylcytidine (ac4C) is deposited on diverse RNAs by N-acetyltransferase 10 (NAT10), a protein with high biological relevance for aging and cancer. We performed a comprehensive survey of ac4C using metabolic labeling, sodium cyanoborohydride chemical treatment coupled to next-generation sequencing (NGS), and ac4C antibody-based cell and molecular biology techniques. Our analysis shows that NAT10-dependent ac4C-acetylation is robust in rRNA and specific tRNAs but low/spurious in mRNA. It also revealed an inflammatory signature and mutagenesis at transcriptionally active sites in NAT10-KO cells. This finding led us to explore the role of NAT10 in R-loops, which were recently linked to APOBEC3B-mediated mutagenesis. Our analysis showed that R-loops are ac4C-acetylated in a NAT10-dependent manner. Furthermore, NAT10 restrains the levels of R-loops at a subset of differentially expressed genes in a catalytic activity-dependent manner. Together with cellular biology data showing ac4C-modified RNA in endosomal structures, we propose that increased levels of ac4C-unmodified RNAs, likely derived from R-loops, in endosomal structures induce inflammatory responses.

Computational analysis of DNA methylation from long-read sequencing

DNA methylation is a critical epigenetic mechanism in numerous biological processes, including gene regulation, development, ageing and the onset of various diseases such as cancer. Studies of methylation are increasingly using single-molecule long-read sequencing technologies to simultaneously measure epigenetic states such as DNA methylation with genomic variation. These long-read data sets have spurred the continuous development of advanced computational methods to gain insights into the roles of methylation in regulating chromatin structure and gene regulation. In this Review, we discuss the computational methods for calling methylation signals, contrasting methylation between samples, analysing cell-type diversity and gaining additional genomic insights, and then further discuss the challenges and future perspectives of tool development for DNA methylation research.

Comparative analysis of pyrosequencing and next-generation sequencing for assessing MGMT methylation in glioma patients

BACKGROUND

The methylation status of the O6-methylguanine-DNA methyltransferase (MGMT) gene promoter is pivotal in clinical decision-making for glioma patients. Pyrosequencing (PSQ) has been regarded as the gold standard for determining the MGMT promoter status. Nevertheless, PSQ is limited by its low throughput, high costs, and intricate protocols. In this study, we present a comparative analysis of the performance of PSQ and next-generation sequencing (NGS) in evaluating MGMT methylation in glioma patients.

METHODS

Initially, we developed an amplicon-based NGS method for quantifying MGMT methylation. Subsequently, a comparative assessment was carried out to evaluate the MGMT promoter methylation levels in 50 formalin-fixed paraffin-embedded (FFPE) glioma samples using both PSQ and NGS. Finally, a consistency analysis was performed to compare the results obtained from PSQ and NGS.

RESULTS

The results revealed a significant correlation between PSQ and NGS (R2 = 0.88). Moreover, the consistency rate of the test results among the 50 samples was 94% (47/50), with one negative sample and two positive samples showing inconsistency. These three samples were verified using MethyLight technology, and the results were consistent with those obtained from NGS.

CONCLUSIONS

This study indicates that, although PSQ is the gold standard, the quantitative detection of MGMT methylation by NGS is more accurate than that by PSQ. NGS is characterized by high throughput and cost-effectiveness, while also yielding accurate and stable results. Therefore, NGS provides a viable alternative to the PSQ method for detecting MGMT methylation.

Chemical Strategies to Modulate and Manipulate RNA Epigenetic Modifications

ConspectusRNA epigenetics has rapidly emerged as a key frontier in chemical biology, revealing that modifications to RNA bases and riboses can fine-tune essential cellular processes such as gene expression, translation, and metabolic homeostasis. Traditionally, researchers have relied on manipulating the "writers," "erasers," and "readers" of RNA modifications─i.e., protein cofactors─to alter and study these marks. Those enzyme-centric strategies, including small molecule inhibitors and CRISPR/Cas-based genetic perturbations, have been highly effective and are advancing in clinical applications. However, purely chemical approaches for installing, removing, or transforming RNA modifications without enzyme disturbance have offered distinct advantages, such as temporal control, reversibility, and bypassing compensatory biological feedback mechanisms that often arise with genetic or enzymatic inhibition. Every chemist should be concerned about RNA modifications, because they represent a striking intersection of molecular recognition, organic transformation, and cellular function. The ability to direct chemical reactivity at specific nucleosides in RNA can illuminate how individual modifications impact the overall gene regulation. Further, since improper RNA modification and damage patterns are implicated in cancer, metabolic disorders, and neurodegeneration, these chemical repair tools have potential as diagnostic and therapeutic interventions. Beyond medicine, agriculture also stands to benefit from chemical control of nucleoside-based plant hormones, possibly leading to improved crop productivity and resilience.In this Account, we outline several innovative chemical strategies tailored to different classes of RNA modifications. Flavin-based bioorthogonal chemistry has enabled demethylation of N6-methyladenosine (m6A) independent of endogenous demethylases, while oxidative bioorthogonal reactions can convert 5-methylcytidine (m5C) into distinct formyl derivatives for labeling and sequencing. Nitrogen-oxide and photochemical routes provided access for the selective removal of the side chain of N6-isopentenyladenosine (i6A), offering insights for both cell biology and plant hormone research. We also showcase how rationally designed small molecules can rewire complex RNA damage repair pathways, facilitating selective correction of vinyl-adduct lesions otherwise resistant to enzymatic repair. These purely chemical methods bypass the constraints of enzyme dependence, affording temporal precision (e.g., via light activation) and site-selective modification or labeling of RNA. By strategically engineering reactivity, we have uncovered new epitranscriptomic phenomena, such as in situ generation of non-native RNA modification, that offer fresh capabilities for cell imaging or targeted manipulation of plant callus development. Together, these discoveries signal a paradigm shift: chemical tools can complement or even surpass conventional enzyme-based methods for investigating, editing, and repairing RNA modifications. The ramifications are broad. Chemists can leverage these new reactivities to dissect the molecular underpinnings of diseases linked to epitranscriptomic dysregulation and to engineer next-generation therapeutic, diagnostic, and sequencing platforms. Plant biologists can apply the same chemical strategies to hone agronomic traits, from seed vigor to stress resilience. Ultimately, as we have deepened the mechanistic insights and refined reaction design for increased biocompatibility, purely chemical control of the RNA epigenome is poised to become one of the mainstream approaches across fields spanning chemistry, biology, and medicine─fostering deeper understanding of RNA's role in health and disease and opening new avenues for precise interventions.

Investigating Single-Molecule Molecular Inversion Probes for Medium-Scale Targeted DNA Methylation Analysis

BACKGROUND

Epigenetic biomarkers, particularly CpG methylation, are increasingly employed in clinical and forensic settings. However, we still lack a cost-effective, sensitive, medium-scale method for the analysis of hundreds to thousands of user-defined CpGs suitable for minute DNA input amounts (<10 ng). In this study, motivated by promising results in the genetics field, we investigated single-molecule molecular inversion probes (smMIPs) for simultaneous analysis of hundreds of CpGs by using an example set of 514 age-associated CpGs (Zhang model).

METHODS

First, we developed a novel smMIP design tool to suit bisulfite-converted DNA (Locksmith). Then, to optimize the capture process, we performed single-probe capture for ten selected, representative smMIPs. Based on this pilot, the full smMIP panel was tested under varying capture conditions, including hybridization and elongation temperature, smMIP and template DNA amounts, dNTP concentration and elongation time.

RESULTS

Overall, we found that the capture efficiency was highly probe-(and hence, sequence-) dependent, with a heterogeneous coverage distribution across CpGs higher than the 1000-fold range. Considering CpGs with at least 20X coverage, we yielded robust methylation detection with levels comparable to those obtained from the gold standard EPIC microarray analysis (Pearsons's r: 0.96).

CONCLUSIONS

The observed low specificity and uniformity indicate that smMIPs in their current form are not compatible with the lowered complexity of bisulfite-converted DNA.

Independent evaluation of an 11-CpG panel for age estimation in blood

DNA methylation patterns have emerged as reliable markers for age estimation, offering potential applications in forensic investigations, namely, in cases where there is no information about a possible suspect, in the identification of victims of mass disasters, or in immigration cases when assessing the age of individuals seeking asylum. This study aimed to evaluate the 11-CpG panel proposed by Aliferi et al. (2022) for age estimation. During the implementation phase, the ELOVL2 amplicon from the original work was replaced with a shorter fragment, and the two PCR multiplexes were optimized by changing the amplicons and primer conditions of each multiplex. The technical performance of the optimised assay was assessed using artificially methylated DNA standards. Robust quantification of the methylation levels at the 11 CpG sites was observed. Sensitivity tests demonstrated that DNA inputs down to 10 ng could produce reliable methylation quantification. Using the optimised panel, 148 Danish blood samples (18 - 68 years of age) were typed for their methylation status at the 11 CpG sites. Results showed that the DNA methylation at the 11 CpG loci was significantly correlated with age (0.68 ≤ r ≤ 0.88) in the Danish sample set, confirming the potential of the 11 CpGs in age prediction. A Danish age prediction model was constructed using 108 of the Danish blood samples and a support vector machine with polynomial function (SVMp). The performances of the new model and the original model based on UK individuals were compared using the remaining 40 Danish blood samples. Comparing the published model to the one developed in this study gave similar results with mean absolute errors (MAE) of 3.28 and 3.35, respectively. However, the original model showed a bias in the age predictions, underestimating the age by an average of 1.53 years in the Danish samples. This bias towards underestimation was not observed in the newly developed age prediction model based on Danish individuals. In summary, this assay provides a reasonably accurate age estimation of a single-source donor, if the sample material is blood and more than 10 ng of nuclear DNA can be extracted from the sample.

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.

Double and single stranded detection of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore sequencing

5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are modified versions of cytosine in DNA with roles in regulating gene expression. Using whole genomic DNA from mouse cerebellum, we benchmark 5mC and 5hmC detection by Oxford Nanopore Technologies sequencing against other standard techniques. In addition, we assess the ability of duplex base-calling to study strand asymmetric modification. Nanopore detection of 5mC and 5hmC is accurate relative to compared techniques and opens means of studying these modifications. Strand asymmetric modification is widespread across the genome but reduced at imprinting control regions and CTCF binding sites in mouse cerebellum. Here we demonstrate the unique ability of nanopore sequencing to improve the resolution and detail of cytosine modification mapping.

Strategic base modifications refine RNA function and reduce CRISPR-Cas9 off-targets

In contrast to traditional RNA regulatory approaches that modify the 2'-OH group, this study explores strategic base modifications using 5-carboxylcytosine (ca5C). We developed a technique where ca5C is transformed into dihydrouracil via treatment with borane-pyridine complex or 2-picoline borane complex, leading to base mutations that directly impact RNA functionality. This innovative strategy effectively manages CRISPR-Cas9 system activities, significantly minimizing off-target effects. Our approach not only demonstrates a significant advancement in RNA manipulation but also offers a new method for the precise control of gene editing technologies, showcasing its potential for broad application in chemical biology.

Fragment-specific Quantification of 5hmC by qPCR via a Combination of Enzymatic Digestion and Deamination: Extreme Specificity, High Sensitivity, and Clinical Applicability

Accurate identification and quantification of 5-hydroxymethylcytosine (5hmC) can help elucidate its function in gene expression and disease pathogenesis. Current 5hmC analysis methods still present challenges, especially for clinical applications, such as having a risk of false-positive results and a lack of sufficient sensitivity. Herein, a 5hmC quantification method for fragment-specific DNA sequences with extreme specificity, high sensitivity, and clinical applicability was established using a quantitative real-time PCR (qPCR)-based workflow through the combination of enzymatic digestion and biological deamination strategy (EDD-5hmC assay). The EDD-5hmC approach enriched glycosylated 5hmC via enzyme digestion and then APOBEC (apolipoprotein B mRNA editing catalytic polypeptide-like)-mediated deamination to efficiently differentiate between various cytosine(C) modification states, resulting in 5hmC quantification with extreme specificity such that nonspecific amplification is reduced over eight million-fold. Moreover, the nondestructive biological treatment process of the EDD-5hmC assay exhibits high sensitivity, yielding the limit of detection of 30 aM. For the first time, we measured 5hmC levels in colorectal cancer tissues and matched paracancerous tissues to evaluate the ability to differentiate colorectal cancer, with the area under the receiver operating characteristic curve of up to 82.8% for the single gene of Septin9 and 83.6% for the combinations of Septin9 and Syndecan-2 (SDC2), demonstrating the EDD-5hmC assay is a promising method with clinical applicability for accurately quantifying the 5hmC level.

Significant roles of RNA 5-methylcytosine methylation in cancer

Cancer stands as a leading cause of mortality and poses an escalating threat to global health. Epigenetic dysregulation is pivotal in the onset and advancement of cancer. Recent research on RNA 5-methylcytosine (m5C) methylation has underscored its significant role in cancer. RNA m5C methylation is a key component in gene expression regulation and is intricately linked to cancer development, offering valuable insights for cancer diagnosis, treatment, and prognosis. This review provides an in-depth examination of the three types of regulators associated with RNA m5C methylation and their biological functions. It further investigates the expression and impact of RNA m5C methylation and its regulators in cancer, focusing on their mechanisms in cancer progression and clinical relevance. The current research on inhibitors targeting RNA m5C methylation-related regulators remains underdeveloped, necessitating further exploration and discovery.

Leveraging epigenetic alterations in pancreatic ductal adenocarcinoma for clinical applications

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy characterized by late detection and poor prognosis. Recent research highlights the pivotal role of epigenetic alterations in driving PDAC development and progression. These changes, in conjunction with genetic mutations, contribute to the intricate molecular landscape of the disease. Specific modifications in DNA methylation, histone marks, and non-coding RNAs are emerging as robust predictors of disease progression and patient survival, offering the potential for more precise prognostic tools compared to conventional clinical staging. Moreover, the detection of epigenetic alterations in blood and other non-invasive samples holds promise for earlier diagnosis and improved management of PDAC. This review comprehensively summarises current epigenetic research in PDAC and identifies persisting challenges. These include the complex nature of epigenetic profiles, tumour heterogeneity, limited access to early-stage samples, and the need for highly sensitive liquid biopsy technologies. Addressing these challenges requires the standardisation of methodologies, integration of multi-omics data, and leveraging advanced computational tools such as machine learning and artificial intelligence. While resource-intensive, these efforts are essential for unravelling the functional consequences of epigenetic changes and translating this knowledge into clinical applications. By overcoming these hurdles, epigenetic research has the potential to revolutionise the management of PDAC and improve patient outcomes.

BASAL: a universal mapping algorithm for nucleotide base-conversion sequencing

Utilizing base-conversion (BC) techniques, single-base resolution profiling of RNA and DNA modifications has significantly advanced. BC strategies range from one-way conversions (e.g. cytosine-to-thymine for 5-methylcytosine, adenine-to-guanine for N6-methyladenosine), to multi-way conversions (e.g. adenine to cytosine/guanine/thymine for N1-methyladenosine) and deletion-induced conversions (e.g. pseudouridine-to-deletion). Existing sequence aligners struggle with these diverse conversions, often leading to misaligning or inefficiency. We introduce BASAL (BAse-conversion Sequencing ALigner), which leverages bit-masking technology to accurately calculate mismatch penalties and supports all BC strategies. BASAL outperforms state-of-the-art tools in both mapping accuracy and efficiency. Through simulated and real data testing, along with experimental validation, we demonstrate that BASAL excels at identifying reliable modification sites. Moreover, BASAL enhances single-cell m6A analysis, revealing cell subpopulations and a cell evolutionary direction that align with biological functions, which other aligners fall short. BASAL's versatility establishes it as a universal aligner for RNA and DNA modification sequencing, facilitating groundbreaking discoveries in epigenomics and epitranscriptomics.

Multimodal cell-free DNA whole-genome TAPS is sensitive and reveals specific cancer signals

The analysis of circulating tumour DNA (ctDNA) through minimally invasive liquid biopsies is promising for early multi-cancer detection and monitoring minimal residual disease. Most existing methods focus on targeted deep sequencing, but few integrate multiple data modalities. Here, we develop a methodology for ctDNA detection using deep (80x) whole-genome TET-Assisted Pyridine Borane Sequencing (TAPS), a less destructive approach than bisulphite sequencing, which permits the simultaneous analysis of genomic and methylomic data. We conduct a diagnostic accuracy study across multiple cancer types in symptomatic patients, achieving 94.9% sensitivity and 88.8% specificity. Matched tumour biopsies are used for validation, not for guiding the analysis, imitating an early detection scenario. Furthermore, in silico validation demonstrates strong discrimination (86% AUC) at ctDNA fractions as low as 0.7%. Additionally, we successfully track tumour burden and ctDNA shedding from precancerous lesions post-treatment without requiring matched tumour biopsies. This pipeline is ready for further clinical evaluation to extend cancer screening and improve patient triage and monitoring.

Selective Photocatalytic C-H Oxidation of 5-Methylcytosine in DNA

Selective C-H activation on complex biological macromolecules is a key goal in the field of organic chemistry. It requires thermodynamically challenging chemical transformations to be delivered under mild, aqueous conditions. 5-Methylcytosine (5mC) is a fundamentally important epigenetic modification in DNA that has major implications for biology and has emerged as a vital biomarker. Selective functionalisation of 5mC would enable new chemical approaches to tag, detect and map DNA methylation to enhance the study and exploitation of this epigenetic feature. We demonstrate the first example of direct and selective chemical oxidation of 5mC to 5-formylcytosine (5fC) in DNA, employing a photocatalytic system. This transformation was used to selectively tag 5mC. We also provide proof-of-concept for deploying this chemistry for single-base resolution sequencing of 5mC and genetic bases adenine (A), cytosine (C), guanine (G), thymine (T) in DNA on a next-generation sequencing system. This work exemplifies how photocatalysis has the potential to transform the analysis of DNA.

Simultaneous single-cell analysis of 5mC and 5hmC with SIMPLE-seq

Dynamic 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) modifications to DNA regulate gene expression in a cell-type-specific manner and are associated with various biological processes, but the two modalities have not yet been measured simultaneously from the same genome at the single-cell level. Here we present SIMPLE-seq, a scalable, base resolution method for joint analysis of 5mC and 5hmC from thousands of single cells. Based on orthogonal labeling and recording of 'C-to-T' mutational signals from 5mC and 5hmC sites, SIMPLE-seq detects these two modifications from the same molecules in single cells and enables unbiased DNA methylation dynamics analysis of heterogeneous biological samples. We applied this method to mouse embryonic stem cells, human peripheral blood mononuclear cells and mouse brain to give joint epigenome maps at single-cell and single-molecule resolution. Integrated analysis of these two cytosine modifications reveals distinct epigenetic patterns associated with divergent regulatory programs in different cell types as well as cell states.

Mapping epigenetic modifications by sequencing technologies

The "epigenetics" concept was first described in 1942. Thus far, chemical modifications on histones, DNA, and RNA have emerged as three important building blocks of epigenetic modifications. Many epigenetic modifications have been intensively studied and found to be involved in most essential biological processes as well as human diseases, including cancer. Precisely and quantitatively mapping over 100 [1], 17 [2], and 160 [3] different known types of epigenetic modifications in histone, DNA, and RNA is the key to understanding the role of epigenetic modifications in gene regulation in diverse biological processes. With the rapid development of sequencing technologies, scientists are able to detect specific epigenetic modifications with various quantitative, high-resolution, whole-genome/transcriptome approaches. Here, we summarize recent advances in epigenetic modification sequencing technologies, focusing on major histone, DNA, and RNA modifications in mammalian cells.

Profiling the epigenome using long-read sequencing

The advent of single-molecule, long-read sequencing (LRS) technologies by Oxford Nanopore Technologies and Pacific Biosciences has revolutionized genomics, transcriptomics and, more recently, epigenomics research. These technologies offer distinct advantages, including the direct detection of methylated DNA and simultaneous assessment of DNA sequences spanning multiple kilobases along with their modifications at the single-molecule level. This has enabled the development of new assays for analyzing chromatin states and made it possible to integrate data for DNA methylation, chromatin accessibility, transcription factor binding and histone modifications, thereby facilitating comprehensive epigenomic profiling. Owing to recent advancements, alternative, nascent and translating transcripts can be detected using LRS approaches. This Review discusses LRS-based experimental and computational strategies for characterizing chromatin states and highlights their advantages over short-read sequencing methods. Furthermore, we demonstrate how various long-read methods can be integrated to design multi-omics studies to investigate the relationship between chromatin states and transcriptional dynamics.

DNA methylation in mammalian development and disease

The DNA methylation field has matured from a phase of discovery and genomic characterization to one seeking deeper functional understanding of how this modification contributes to development, ageing and disease. In particular, the past decade has seen many exciting mechanistic discoveries that have substantially expanded our appreciation for how this generic, evolutionarily ancient modification can be incorporated into robust epigenetic codes. Here, we summarize the current understanding of the distinct DNA methylation landscapes that emerge over the mammalian lifespan and discuss how they interact with other regulatory layers to support diverse genomic functions. We then review the rising interest in alternative patterns found during senescence and the somatic transition to cancer. Alongside advancements in single-cell and long-read sequencing technologies, the collective insights made across these fields offer new opportunities to connect the biochemical and genetic features of DNA methylation to cell physiology, developmental potential and phenotype.

Bisulfite-Free and Quantitative Detection of DNA Methylation at Single-Base Resolution by eROS1-seq

5-Methylcytosine (5mC) is the most significant DNA modification present in mammalian genomes. Understanding the roles of 5mC in diverse biological processes requires quantitative detection at single-base resolution. In this study, we engineered the repressor of the silencing 1 (ROS1) protein derived from Arabidopsis thaliana to enhance its 5mC glycosylase/lyase activity, resulting in the creation of the engineered ROS1 (eROS1) protein. Leveraging the unique properties of eROS1, we introduced a method termed engineered ROS1 sequencing (eROS1-seq) for bisulfite-free and quantitative detection of 5mC in DNA at single-base resolution. In eROS1-seq, the eROS1 protein selectively cleaves 5mC while leaving unmodified cytosine (C) intact, followed by the incorporation of dTTP, which subsequently results in sequencing as thymine (T). This method effectively differentiates between C and 5mC. Unlike conventional bisulfite sequencing (BS-seq), which predominantly converts cytosines, eROS1-seq specifically transforms 5mC into T, thereby avoiding potential imbalances in the nucleobase composition of the sequencing library. Using eROS1-seq, we successfully achieved quantitative and site-specific detection of 5mC in the genomic DNA of lung cancer tissue. Overall, the eROS1-seq approach is bisulfite-free and straightforward, making it a valuable tool for the quantitative detection of 5mC at single-base resolution.

Robust Bisulfite-Free Single-Molecule Real-Time Sequencing of Methyldeoxycytidine Based on a Novel hpTet3 Enzyme

In addition to the four canonical nucleosides dA, dG, dC and T, genomic DNA contains the additional base 5-methyldeoxycytidine (mdC). The presence of this methylated cytidine nucleoside in promoter regions or gene bodies significantly affects the transcriptional activity of the corresponding gene. Consequently, the methylation patterns of genes are crucial for either silencing or activating genes. Sequencing the positions of mdC in the genome is therefore of paramount importance for early cancer diagnostics as it helps determine incorrect gene expression. Currently, the bisulfite method is the gold standard for mdC-sequencing. However, this method has the drawback that the majority of the input DNA is degraded during the bisulfite treatment. Additionally, bisulfite sequencing is prone to errors. Here, we report a benign, bisulfite-free mdC sequencing method termed EMox-seq, which is based on third-generation single-molecule SMRT sequencing. The foundation of this technology is a new Tet3 enzyme that efficiently oxidizes mdCs to 5-carboxycytidine (cadC). In turn, cadC provides an excellent readout by SMRT sequencing using specially trained AI-based algorithms.

Role of epigenetic mechanisms in the pathogenesis of chronic respiratory diseases and response to inhaled exposures: From basic concepts to clinical applications

Epigenetic modifications are chemical groups in our DNA (and chromatin) that determine which genes are active and which are shut off. Importantly, they integrate environmental signals to direct cellular function. Upon chronic environmental exposures, the epigenetic signature of lung cells gets altered, triggering aberrant gene expression programs that can lead to the development of chronic lung diseases. In addition to driving disease, epigenetic marks can serve as attractive lung disease biomarkers, due to early onset, disease specificity, and stability, warranting the need for more epigenetic research in the lung field. Despite substantial progress in mapping epigenetic alterations (mostly DNA methylation) in chronic lung diseases, the molecular mechanisms leading to their establishment are largely unknown. This review is meant as a guide for clinicians and lung researchers interested in epigenetic regulation with a focus on DNA methylation. It provides a short introduction to the main epigenetic mechanisms (DNA methylation, histone modifications and non-coding RNA) and the machinery responsible for their establishment and removal. It presents examples of epigenetic dysregulation across a spectrum of chronic lung diseases and discusses the current state of epigenetic therapies. Finally, it introduces the concept of epigenetic editing, an exciting novel approach to dissecting the functional role of epigenetic modifications. The promise of this emerging technology for the functional study of epigenetic mechanisms in cells and its potential future use in the clinic is further discussed.

Enriched Methylomes of Low-input and Fragmented DNA Using Fragment Ligation EXclusive Methylation Sequencing (FLEXseq)

Methylome profiling is an emerging clinical tool for tumor classification and liquid biopsies. Here, we developed FLEXseq, a genome-wide methylation profiler that enriches and sequences the fragments of DNA flanking the CCGG motif. FLEXseq strongly correlates (Pearson's r = 0.97) with whole genome bisulfite sequencing (WGBS) while enriching 18-fold. To demonstrate the broad applicability of FLEXseq, we verified its usage across cells, body fluids, and formalin-fixed paraffin-embedded (FFPE) tissues. DNA dilutions down to 250 pg decreased CpG coverage, but bias in methylation remained low (Pearson's r ≥ 0.90) compared to a 10 ng input. FLEXseq offers a cost-efficient, base-pair resolution methylome with potential as a diagnostic tool for tissue and liquid biopsies.

A promising application of kidney-specific cell-free DNA methylation markers in real-time monitoring sepsis-induced acute kidney injury

Sepsis-induced acute kidney injury (SI-AKI) is a common clinical syndrome that is associated with high mortality and morbidity. Effective timely detection may improve the outcome of SI-AKI. Kidney-derived cell-free DNA (cfDNA) may provide new insight into understanding and identifying SI-AKI. Plasma cfDNA from 82 healthy individuals, 7 patients with sepsis non-acute kidney injury (SN-AKI), and 9 patients with SI-AKI was subjected to genomic methylation sequencing. We deconstructed the relative contribution of cfDNA from different cell types based on cell-specific methylation markers and focused on exploring the association between kidney-derived cfDNA and SI-AKI.Based on the deconvolution of the cfDNA methylome: SI-AKI patients displayed the elevated cfDNA concentrations with an increased contribution of kidney epithelial cells (kidney-Ep) DNA; kidney-Ep derived cfDNA achieved high accuracy in distinguishing SI-AKI from SN-AKI (AUC = 0.92, 95% CI 0.7801-1); the higher kidney-ep cfDNA concentrations tended to correlate with more advanced stages of SI-AKI; strikingly, SN-AKI patients with potential kidney damage unmet by SI-AKI criteria showed higher levels of kidney-Ep derived cfDNA than healthy individuals. The autonomous screening of kidney-Ep (n = 24) and kidney endothelial (kidney-Endo, n = 12) specific methylation markers indicated the unique identity of kidney-Ep/kidney-Endo compared with other cell types, and its targeted assessment reproduced the main findings of the deconvolution of the cfDNA methylome. Our study first demonstrates that kidney-Ep- and kidney-Endo-specific methylation markers can serve as a novel marker for SI-AKI emergence, supporting further exploration of the utility of kidney-specific cfDNA methylation markers in the study of SI-AKI.

Mice with NOP2/sun RNA methyltransferase 5 deficiency die before reaching puberty due to fatal kidney damage

BACKGROUND

NOP2/Sun RNA methyltransferase 5 (NSUN5) is an RNA methyltransferase that has a broad distribution and plays critical roles in various biological processes. However, our knowledge of the biological functions of NSUN5 in mammals is very limited. Therefore, in this study, we investigate the role of NSUN5 in mice.

METHODS

In the present research, we built a mouse model (Nsun5-/-) using the CRISPR/Cas9 system to investigated the specific role of NSUN5.

RESULTS

We observed that Nsun5-/- mice had a reduced body weight compared to wild-type mice. Additionally, their survival rate gradually decreased to 20% after postnatal day (PD) 21. Further examination revealed the Nsun5-/- mice had multiple organ damage, with the most severe damage occurring in the kidneys. Moreover, we observed glycogen deposition and fibrosis, along with a notable shorting of the primary foot processes of glomeruli in Nsun5-/- kidneys. Furthermore, we found that the kidneys of Nsun5-/- mice showed increased expression of the apoptotic signal Caspase-3 and accumulated stronger DNA damage at PD 21.

CONCLUSIONS

In our study, we found that mice lacking NSUN5 died before puberty due to kidney fatal damage caused by DNA damage and cell apoptosis. These results suggest that NSUN5 plays a vital role in preventing the accumulation of DNA damage and cell apoptosis in the kidney.

Domain-knowledge enabled ensemble learning of 5-formylcytosine (f5C) modification sites

5-formylcytidine (f5C) is a unique post-transcriptional RNA modification found in mRNA and tRNA at the wobble site, playing a crucial role in mitochondrial protein synthesis and potentially contributing to the regulation of translation. Recent studies have unveiled that the f5C modifications may drive mitochondrial mRNA translation to power cancer metastasis. Accurate identification of f5C sites is essential for further unraveling their molecular functions and regulatory mechanisms, but there are currently no computational methods available for predicting their locations. In this study, we introduce an innovative ensemble approach, successfully enabling the computational recognition of Saccharomyces cerevisiae f5C. We conducted a comprehensive model selection process that involved multiple basic machine learning and deep learning algorithms such as recurrent neural networks, convolutional neural networks and Transformer-based models. Initially trained only on sequence information, these individual models achieved an AUROC ranging from 0.7104 to 0.7492. Through the integration of 32 novel domain-derived genomic features, the performance of individual models has significantly improved to an AUROC between 0.7309 and 0.8076. To further enhance accuracy and robustness, we then constructed the ensembles of these individual models with different combinations. The best performance attained by our ensemble models reached an AUROC of 0.8391. Shapley additive explanations were conducted to explain the significant contributions of genomic features, providing insights into the putative distribution of f5C across various topological regions and potentially paving the way for revealing their functional relevance within distinct genomic contexts. A freely accessible web server that allows real-time analysis of user-uploaded sites can be accessed at: www.rnamd.org/Resf5C-Pred.

A DNA Polymerase Variant Senses the Epigenetic Marker 5-Methylcytosine by Increased Misincorporation

Dysregulation of DNA methylation is associated with human disease, particularly cancer, and the assessment of aberrant methylation patterns holds great promise for clinical diagnostics. However, DNA polymerases do not effectively discriminate between processing 5-methylcytosine (5 mC) and unmethylated cytosine, resulting in the silencing of methylation information during amplification or sequencing. As a result, current detection methods require multi-step DNA conversion treatments or careful analysis of sequencing data to decipher individual 5 mC bases. To overcome these challenges, we propose a novel DNA polymerase-mediated 5 mC detection approach. Here, we describe the engineering of a thermostable DNA polymerase variant derived from Thermus aquaticus with altered fidelity towards 5 mC. Using a screening-based evolutionary approach, we have identified a DNA polymerase that exhibits increased misincorporation towards 5 mC during DNA synthesis. This DNA polymerase generates mutation signatures at methylated CpG sites, allowing direct detection of 5 mC by reading an increased error rate after sequencing without prior treatment of the sample DNA.

Circulating tumor DNA methylation detection as biomarker and its application in tumor liquid biopsy: advances and challenges

Circulating tumor DNA (ctDNA) methylation, an innovative liquid biopsy biomarker, has emerged as a promising tool in early cancer diagnosis, monitoring, and prognosis prediction. As a noninvasive approach, liquid biopsy overcomes the limitations of traditional tissue biopsy. Among various biomarkers, ctDNA methylation has garnered significant attention due to its high specificity and early detection capability across diverse cancer types. Despite its immense potential, the clinical application of ctDNA methylation faces substantial challenges pertaining to sensitivity, specificity, and standardization. In this review, we begin by introducing the basic biology and common detection techniques of ctDNA methylation. We then explore recent advancements and the challenges faced in the clinical application of ctDNA methylation in liquid biopsies. This includes progress in early screening and diagnosis, identification of clinical molecular subtypes, monitoring of recurrence and minimal residual disease (MRD), prediction of treatment response and prognosis, assessment of tumor burden, and determination of tissue origin. Finally, we discuss the future perspectives and challenges of ctDNA methylation detection in clinical applications. This comprehensive overview underscores the vital role of ctDNA methylation in enhancing cancer diagnostic accuracy, personalizing treatments, and effectively monitoring disease progression, providing valuable insights for future research and clinical practice.

Unveiling DNA methylation in Alzheimer's disease: a review of array-based human brain studies

The intricacies of Alzheimer's disease pathogenesis are being increasingly illuminated by the exploration of epigenetic mechanisms, particularly DNA methylation. This review comprehensively surveys recent human-centered studies that investigate whole genome DNA methylation in Alzheimer's disease neuropathology. The examination of various brain regions reveals distinctive DNA methylation patterns that associate with the Braak stage and Alzheimer's disease progression. The entorhinal cortex emerges as a focal point due to its early histological alterations and subsequent impact on downstream regions like the hippocampus. Notably, ANK1 hypermethylation, a protein implicated in neurofibrillary tangle formation, was recurrently identified in the entorhinal cortex. Further, the middle temporal gyrus and prefrontal cortex were shown to exhibit significant hypermethylation of genes like HOXA3, RHBDF2, and MCF2L, potentially influencing neuroinflammatory processes. The complex role of BIN1 in late-onset Alzheimer's disease is underscored by its association with altered methylation patterns. Despite the disparities across studies, these findings highlight the intricate interplay between epigenetic modifications and Alzheimer's disease pathology. Future research efforts should address methodological variations, incorporate diverse cohorts, and consider environmental factors to unravel the nuanced epigenetic landscape underlying Alzheimer's disease progression.

Clinical validation of peripheral blood mononuclear cell DNA methylation markers for accurate early detection of hepatocellular carcinoma in Asian patients

BACKGROUND

Hepatocellular carcinoma (HCC), a leading cause of cancer-related deaths globally, poses significant challenges in early detection. Improved diagnostic accuracy can drastically influence patient outcomes, emphasizing the need for innovative, non-invasive biomarkers.

METHODS

This study utilized a cohort of 402 participants, including healthy controls, chronic hepatitis patients, and HCC patients from Bangladesh, to evaluate DNA methylation signatures in peripheral blood mononuclear cells (PBMC). We performed targeted next-generation sequencing on selected genes previously identified to assess their methylation dynamics. The development of M8 and M4 scores was based on these dynamics, using Receiver Operating Characteristic (ROC) analysis to determine their effectiveness in detecting early-stage HCC alongside existing markers such as epiLiver and alpha-fetoprotein (AFP).

RESULTS

Integration of M8 and M4 scores with epiLiver and AFP significantly enhances diagnostic sensitivity for early-stage HCC. The M4+epiLiver score achieves a sensitivity of 79.4% in Stage A HCC, while combining M4 with AFP increases sensitivity to 88.2-95.7% across all stages, indicating a superior diagnostic performance compared to each marker used alone.

CONCLUSIONS

Our study confirms that combining gene methylation profiles with established diagnostic markers substantially improves the sensitivity of detecting early-stage HCC. This integrated diagnostic approach holds promise for advancing non-invasive cancer diagnostics, potentially leading to earlier treatment interventions and improved survival rates for high-risk patients.

Methods for Detection and Mapping of Methylated and Hydroxymethylated Cytosine in DNA

The chemical modifications of DNA are of pivotal importance in the epigenetic regulation of cellular processes. Although the function of 5-methylcytosine (5mC) has been extensively investigated, the significance of 5-hydroxymethylcytosine (5hmC) has only recently been acknowledged. Conventional methods for the detection of DNA methylation frequently lack the capacity to distinguish between 5mC and 5hmC, resulting in the combined reporting of both. The growing importance of 5hmC has prompted the development of a multitude of methods for the qualitative and quantitative analysis of 5hmC in recent years, thereby facilitating researchers' understanding of the mechanisms underlying the onset and progression of numerous diseases. This review covers both established and novel methods for the detection of cytosine modifications, including 5mC, 5hmC, 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), with a particular focus on those that allow for accurate mapping and detection, particularly with third-generation sequencing. The review aims to help researchers choose the most appropriate methods based on their specific research goals and budget.

Ultrafast bisulfite sequencing detection of 5-methylcytosine in DNA and RNA

Bisulfite sequencing (BS-seq) to detect 5-methylcytosine (5mC) is limited by lengthy reaction times, severe DNA damage, overestimation of 5mC level and incomplete C-to-U conversion of certain DNA sequences. We present ultrafast BS-seq (UBS-seq), which uses highly concentrated bisulfite reagents and high reaction temperatures to accelerate the bisulfite reaction by ~13-fold, resulting in reduced DNA damage and lower background noise. UBS-seq allows library construction from small amounts of purified genomic DNA, such as from cell-free DNA or directly from 1 to 100 mouse embryonic stem cells, with less overestimation of 5mC level and higher genome coverage than conventional BS-seq. Additionally, UBS-seq quantitatively maps RNA 5-methylcytosine (m5C) from low inputs of mRNA and allows the detection of m5C stoichiometry in highly structured RNA sequences. Our UBS-seq results identify NSUN2 as the major 'writer' protein responsible for the deposition of ~90% of m5C sites in HeLa mRNA and reveal enriched m5C sites in 5'-regions of mammalian mRNA, which may have functional roles in mRNA translation regulation.

IMPRESS: Improved methylation profiling using restriction enzymes and smMIP sequencing, combined with a new biomarker panel, creating a multi-cancer detection assay

BACKGROUND

Despite the worldwide progress in cancer diagnostics, more sensitive diagnostic biomarkers are needed. The methylome has been extensively investigated in the last decades, but a low-cost, bisulfite-free detection method for multiplex analysis is still lacking.

METHODS

We developed a methylation detection technique called IMPRESS, which combines methylation-sensitive restriction enzymes and single-molecule Molecular Inversion Probes. We used this technique for the development of a multi-cancer detection assay for eight of the most lethal cancer types worldwide. We selected 1791 CpG sites that can distinguish tumor from normal tissue based on DNA methylation. These sites were analysed with IMPRESS in 35 blood, 111 tumor and 114 normal samples. Finally, a classifier model was built.

RESULTS

We present the successful development of IMPRESS and validated it with ddPCR. The final classifier model discriminating tumor from normal samples was built with 358 CpG target sites and reached a sensitivity of 0.95 and a specificity of 0.91. Moreover, we provide data that highlight IMPRESS's potential for liquid biopsies.

CONCLUSIONS

We successfully created an innovative DNA methylation detection technique. By combining this method with a new multi-cancer biomarker panel, we developed a sensitive and specific multi-cancer assay, with potential use in liquid biopsies.

RNA methylation in neurodevelopment and related diseases

Biological development and genetic information transfer are governed by genetic, epigenetic, transcriptional, and posttranscriptional mechanisms. RNA methylation, the attachment of methyl (-CH 3) groups to RNA molecules, is a posttranscriptional modification that has gained increasing attention in recent years because of its role in RNA epitranscriptomics. RNA modifications (RMs) influence various aspects of RNA metabolism and are involved in the regulation of diverse biological processes and diseases. Neural cell types emerge at specific stages of brain development, and recent studies have revealed that neurodevelopment, aging, and disease are tightly linked to transcriptome dysregulation. In this review, we discuss the roles of N6-methyladenine (m6A) and 5-methylcytidine (m5C) RNA modifications in neurodevelopment, physiological functions, and related diseases.

Whole-Genome Bisulfite Sequencing (WGBS) Analysis of Gossypium hirsutum under High-Temperature Stress Conditions

BACKGROUND

DNA methylation is an important part of epigenetic regulation and plays an important role in the response of plants to adverse stress.

METHODS

In this study, whole-genome bisulfite sequencing (WGBS) was performed on the high-temperature-resistant material Xinluzao 36 and the high-temperature-sensitive material Che 61-72 at 0 h and 12 h under high-temperature stress conditions.

RESULTS

The results revealed that the Gossypium hirsutum methylation levels of CG and CHG (H = A, C, or T) decreased after the high-temperature stress treatment, and the methylation level of the A subgenome was significantly greater than that of the D subgenome. The methylation level of CHH increased, and the methylation level of CHH in the D subgenome was significantly greater than that in the A subgenome after high-temperature stress treatment. The methylation density of CG is lower than that of CHG and CHH, and the methylation density of the middle region of chromosomes is greater than that of both ends, which is opposite to the distribution density of genes. There were 124 common differentially methylated genes in the CG, CHG, and CHH groups, and 5130 common DEGs and differentially methylated genes were found via joint analysis with RNA-seq; these genes were significantly enriched in the biosynthesis of plant hormones, thiamine metabolism, glutathione metabolism, and tyrosine metabolism pathways. DNA methylation did not affect the expression of many genes (accounting for 85.68% of the differentially methylated genes), DNA methylation-promoted gene expression was located mainly in the downstream region of the gene or gene body, and the expression of inhibitory genes was located mainly in the upstream region of the gene.

CONCLUSIONS

This study provides a theoretical basis for further exploration of the gene expression and functional regulatory mechanism of G. hirsutum DNA methylation under high-temperature stress conditions.

Mining nucleic acid "omics" to boost liquid biopsy in cancer

Treatments for cancer patients are becoming increasingly complex, and there is a growing desire from clinicians and patients for biomarkers that can account for this complexity to support informed decisions about clinical care. To achieve precision medicine, the new generation of biomarkers must reflect the spatial and temporal heterogeneity of cancer biology both between patients and within an individual patient. Mining the different layers of 'omics in a multi-modal way from a minimally invasive, easily repeatable, liquid biopsy has increasing potential in a range of clinical applications, and for improving our understanding of treatment response and resistance. Here, we detail the recent developments and methods allowing exploration of genomic, epigenomic, transcriptomic, and fragmentomic layers of 'omics from liquid biopsy, and their integration in a range of applications. We also consider the specific challenges that are posed by the clinical implementation of multi-omic liquid biopsies.