Epigenetic Marks Research Articles

Genetic and epigenetic control of dormancy transitions throughout the year in the monoecious cork oak.

Bud dormancy plays a vital role in flowering regulation and fruit production, being highly regulated by endogenous and environmental cues. Deployment of epigenetic modifications and differential gene expression control bud dormancy/break cycles. Information on how these genetic and epigenetic mechanisms are regulated throughout the year is still scarce for temperate trees such as Quercus suber. Here, the expression levels of CENTRORADIALIS-LIKE (CENL) and DORMANCY-ASSOCIATED PROTEIN 1 (QsDYL1) during seasonal cycles of bud development, suggesting that QsCENL may be implicated in growth cessation in Q. suber and that QsDYL1 is a good dormancy marker. As gene expression can be regulated by the activity of chromatin modifiers, we have analysed the expression of these genes and the deposition of epigenetic marks in dormant versus non-dormant bud meristems. The DNA methyl transferases CHROMOMEHTYLASE 3 (QsCMT3) and METHYLTRANSFERASE 1 (QsMET1) were more expressed in the transition between dormancy to bud swelling. QsCMT3 was also highly expressed during the late stages of active bud formation. Conversely, the HISTONE ACETYLTRANSFERASE 1 (QsHAC1) was up-regulated during growth cessation and dormancy when compared to bud swelling. These results indicate that epigenetic regulation is implicated in how bud development progresses in Q. suber, which can be observed in the different profile deposition of the repressive and active marks, 5mC and H3K18Ac/H3K4me, respectively. The identification of bud-specific genetic and epigenetic profiling opens new possibilities to predict the relative rate of dormancy/growth of the bud stages, providing tools to understand how trees respond to the current challenges posed by climate change.

The inflammatory and oxidative phenotype of gestational diabetes is epigenetically transmitted to the offspring: role of methyltransferase MLL1-induced H3K4me3.

Hyperglycaemia during gestational diabetes (GD) predisposes women and their offspring to later cardiometabolic disease. The hyperglycaemia-mediated epigenetic changes remain to be elucidated. Methyltransferase MLL1-induced trimethylation of histone 3 at lysine 4 (H3K4me3) activates inflammatory and oxidative phenotype. This epigenetic mark in GD women and its transmission to the offspring were investigated. Peripheral blood mononuclear cells (PBMC) were collected from GD and control (C) women and also from adolescents born to women of both groups. Endothelial human umbilical vein endothelial cells (HUVEC) and cord blood mononuclear cells (CBMC) were from umbilical cords. The NF-κBp65 and NOX4 expressions were investigated by reverse transcription quantitative polymerase chain reaction and immunofluorescence (IF). MLL1 and H3K4me3 were investigated by immunoblotting and IF. H3K4me3 on NF-κBp65 and NOX4 promoters was studied by chromatin immunoprecipitation. Superoxide anion generation was measured by electron spin resonance spectroscopy. Plasma cytokines were measured by enzyme-linked immunosorbent assay. To investigate the role of MLL1, HUVEC were exposed to inhibitor MM102 or siRNA transfection. PBMC, CBMC, and HUVEC showed an increase of NF-κBp65, IL-6, ICAM-1, MCP-1, and VCAM-1 mRNAs. These findings were associated with H3K4me3 enrichment in the promoter of NF-κBp65. Elevated H3K4me3 and cytokine levels were observed in GD adolescents. MLL1 drives H3K4me3 not only on NF-kB p65, but also on NOX4 promoter. Inhibition of MLL1 blunted NF-κBp65 and NOX4 by modulating inflammatory and oxidative phenotype. Such proof-of-concept study shows persistence of MLL1-dependent H3K4me3 in offspring born to GD women, suggesting an epigenetic-driven transmission of maternal phenotype. These findings may pave the way for pharmacological reprogramming of adverse histone modifications to mitigate abnormal phenotypes underlying early ASCVD.

Multiplexed Methylated DNA Immunoprecipitation Sequencing (Mx-MeDIP-Seq) to Study DNA Methylation Using Low Amounts of DNA

Background/Objectives: DNA methylation is a key epigenetic mark involved in regulating gene expression. Aberrant DNA methylation contributes to various human diseases, including cancer, autoimmune disorders, atherosclerosis, and cardiovascular diseases. While whole-genome bisulfite sequencing and methylated DNA immunoprecipitation (MeDIP) are standard techniques for studying DNA methylation, they are typically limited to a few samples per run, making them expensive and low-throughput. Therefore, an automation-friendly method is needed to increase throughput and reduce costs without compromising data quality. Methods and Results: We developed a novel method called Multiplexed Methylated DNA Immunoprecipitation Sequencing (Mx-MeDIP-Seq), which can be used to analyze many DNA samples in parallel, requiring only small amounts of input DNA. In this method, 10 different DNA samples were fragmented, purified, barcoded, and pooled prior to immunoprecipitation. In a head-to-head comparison, we observed a 99% correlation between MeDIP-Seq performed individually or combined as Mx-MeDIP-Seq. Moreover, multiplexed MeDIP led to more than 95% normalized percent recovery and a 25-fold enrichment ratio by qPCR, like the enrichment of the conventional method. This technique was successfully performed with as little as 25 ng of DNA, equivalent to 3400 to 6200 cells. Up to 10 different samples were processed simultaneously in a single run. Overall, the Mx-MeDIP-Seq method is cost-effective with faster processing to analyze DNA methylome, making this technique more suitable for high-throughput DNA methylome analysis. Conclusions: Mx-MeDIP-Seq is a cost-effective and efficient method for high-throughput DNA methylation analysis, offering faster processing and reduced sample requirements. This technique makes DNA methylome analysis more accessible for large-scale studies.

Genomic insights into genes expressed specifically during infancy highlight their dominant influence on the neuronal system

BackgroundElucidating the dynamics of gene expression across developmental stages, including the genomic characteristics of brain expression during infancy, is pivotal in deciphering human psychiatric and neurological disorders and providing insights into developmental disorders.ResultsLeveraging comprehensive human GWAS associations with temporal and spatial brain expression data, we discovered a distinctive co-expression cluster comprising 897 genes highly expressed specifically during infancy, enriched in functions related to the neuronal system. This gene cluster notably harbors the highest ratio of genes linked to psychiatric and neurological disorders. Through computational analysis, MYT1L emerged as a potential central transcription factor governing these genes. Remarkably, the infancy-specific expressed genes, including SYT1, exhibit prominent colocalization within human accelerated regions. Additionally, chromatin state analysis unveiled prevalent epigenetic markers associated with enhancer-specific modifications. In addition, this cluster of genes has demonstrated to be specifically highly expressed in cell-types including excitatory neurons, medial ganglionic eminence and caudal ganglionic eminence.ConclusionsThis study comprehensively characterizes the genomics and epigenomics of genes specifically expressed during infancy, identifying crucial hub genes and transcription factors. These findings offer valuable insights into early detection strategies and interventions for psychiatric and neurological disorders.

DNA Hypomethylation Activates the RpMYB2-Centred Gene Network to Enhance Regeneration of Adventitious Roots.

Plants, being immobile, are exposed to environmental adversities such as wind, snow and animals that damage their structure, making regeneration essential for their survival. The adventitious roots (ARs) primarily emerge from a detached explant to uptake nutrients; therefore, the molecular network involved in their regeneration needs to be explored. DNA methylation, a key epigenetic mark, influences molecular pathways, and recent studies suggested its role in regeneration. In our research, the application of 5-azacytidine (5-azaC), an inhibitor of DNA methylation, caused the earlier initiation and development of root primordia and consequently enhanced the AR regeneration rate in Robinia psuedoacacia L (black locust). The whole-genome bisulfite sequencing (WGBS) revealed a decrease in global methylation and an increase in hypomethylated cytosine sites and regions across all contexts including CHH, CHG and mergedCG caused transcriptional variations in 5-azaC-treated sample. The yeast two-hybrid (Y2H) assay revealed a RpMYB2-centred network of transcriptionally activated transcription factors (TFs) including RpWRKY23, RpGATA23, RpSPL16 and other genes like RpSDP, RpSS1, RpBEN1, RpGULL05 and RpCUV with nuclear localization suggesting their potential co-localization. Additionally, yeast one-hybrid (Y1H) assay showed the interaction of RpMYB2 interactors, RpGATA23 and RpWRKY23, with promoters of RpSK6 and RpCDC48, and luciferase reporting assay (LRA) validated their binding with RpSK6. Our results revealed that hypomethylation-mediated transcriptomic modifications activated the RpMYB2-centred gene network to enhance AR regeneration in black locust hypocotyl cuttings. These findings pave the way for genetic modification to improve plant regeneration ability and increase wood production while withstanding environmental damage.

Heavy Metals in Umbilical Cord Blood: Effects on Epigenetics and Child Development.

Heavy metals like arsenic, mercury, cadmium, and lead are harmful pollutants that can change how our genes are regulated without altering the DNA sequence, specifically through a process called DNA methylation (DNAm) at 5-methylcytosine, an epigenetic mark that we will focus on in this review. These changes in DNAm are most sensitive during pregnancy, a critical time for development when these modifications can affect how traits are expressed. Historically, most research on these environmental effects has focused on adults, but now there is more emphasis on studying the impacts during early development and childhood. The placenta acts as a protective barrier between the mother and the baby, and by examining it, scientists can identify changes in key genes that might affect long-term health. This review looks at how exposure to heavy metals during pregnancy can cause changes in the gene regulation by DNAm in newborns, as seen in their umbilical cord blood. These changes reflect the baby's genetic state during pregnancy and can be influenced by the mother's environment and genetics, as well as the baby's own genetics.

The Roles of H3K9me3 Writers, Readers, and Erasers in Cancer Immunotherapy.

The interplay between cancer and the immune system has captivated researchers for a long time. Recent developments in cancer immunotherapy have substantiated this interest with a significant benefit to cancer patients. Tumor and immune cells are regulated via a wide range of molecular mechanisms involving intricate transcriptional and epigenetic networks. Epigenetic processes influence chromatin structure and accessibility, thus governing gene expression, replication, and DNA damage repair. However, aberrations within epigenetic signatures are frequently observed in cancer. One of the key epigenetic marks is the trimethylation of histone 3 at lysine 9 (H3K9me3), confined mainly within constitutive heterochromatin to suppress DNA accessibility. It is deposited at repetitive elements, centromeric and telomeric loci, as well as at the promoters of various genes. Dysregulated H3K9me3 deposition disrupts multiple pathways, including immune signaling. Consequently, altered H3K9me3 dynamics may modify the efficacy of immunotherapy. Indeed, growing evidence highlights the pivotal roles of various proteins mediating H3K9me3 deposition (SETDB1/2, SUV39H1/2), erasure (KDM3, KDM4 families, KDM7B, LSD1) and interpretation (HP1 proteins, KAP1, CHD4, CDYL, UHRF1) in modulating immunotherapy effectiveness. Here, we review the existing literature to synthesize the available information on the influence of these H3K9me3 writers, erasers, and readers on the response to immunotherapy.

The epigenetic impact of daily diet food choices on human health and chronic diseases

Nutrition, certain lifestyle behaviors (smoking, drug, alcohol addictions, etc.) and environment all contribute to cancer and other lines development. Similarly, epigenetic pathways are known to occur at the intersection between the generally reversible effects of lifestyle or ecological factors and the irreversible alterations that explain numerous diseases. Chemoprevention is the process of intervening in the epigenome to mitigate the detrimental effects of environmental factors or certain lifestyles before they lead to significant consequences. DNA is permanently exposed to various substances modifying both its genetic and epigenetic configuration. It’s controlled by various agents (methyl donors, sophisticated enzymes, etc.). Pesticides, artificial food additives, drugs and environmental toxins penetrating the placenta, can result in developmental program alterations and epigenetic changes in a fetus. In nutrition context, the research revealed that several foods can alter epigenetic markers. Some vitamins may alter DNA methylation patterns and histone alterations, possibly influencing gene expression and disease risk. Thus, dietary treatments may provide an epigenetic regulation, emphasizing nutrition role in preserving health and preventing illness via epigenetics Keywords: human epigenetics, epigenetic regulation of diseases, daily food ration, healthy food

Using human disease mutations to understand de novo DNA methyltransferase function.

DNA methylation is a repressive epigenetic mark that is pervasive in mammalian genomes. It is deposited by DNA methyltransferase enzymes (DNMTs) that are canonically classified as having de novo (DNMT3A and DNMT3B) or maintenance (DNMT1) function. Mutations in DNMT3A and DNMT3B cause rare Mendelian diseases in humans and are cancer drivers. Mammalian DNMT3 methyltransferase activity is regulated by the non-catalytic region of the proteins which contain multiple chromatin reading domains responsible for DNMT3A and DNMT3B recruitment to the genome. Characterising disease-causing missense mutations has been central in dissecting the function and regulation of DNMT3A and DNMT3B. These observations have also motivated biochemical studies that provide the molecular details as to how human DNMT3A and DNMT3B mutations drive disorders. Here, we review progress in this area highlighting recent work that has begun dissecting the function of the disordered N-terminal regions of DNMT3A and DNMT3B. These studies have elucidated that the N-terminal regions of both proteins mediate novel chromatin recruitment pathways that are central in our understanding of human disease mechanisms. We also discuss how disease mutations affect DNMT3A and DNMT3B oligomerisation, a process that is poorly understood in the context of whole proteins in cells. This dissection of de novo DNMT function using disease-causing mutations provides a paradigm of how genetics and biochemistry can synergise to drive our understanding of the mechanisms through which chromatin misregulation causes human disease.

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.

Histone Methylation-Mediated Reproductive Toxicity to Consumer Product Chemicals in Caenorhabditis elegans: An Epigenetic Adverse Outcome Pathway (AOP).

The significance of histone methylation in epigenetic inheritance underscores its relevance to disease and the chronic effects of environmental chemicals. However, limited evidence of the causal relationships between chemically induced epigenetic changes and organismal-level effects hinders the application of epigenetic markers in ecotoxicological assessments. This study explored the contribution of repressive histone marks to reproductive toxicity induced by chemicals in consumer products in Caenorhabditis elegans, applying the adverse outcome pathway (AOP) framework. Triclosan (TCS) and tetrabromobisphenol A (TBBPA) exposures caused reproductive toxicity and altered histone methyltransferase (HMT) and histone demethylase (HDM) activities, increasing the level of trimethylation of H3K9 and H3K27. Notably, treatment with an H3K27-specific HMT inhibitor alleviated reproductive defects and the transcriptional response of genes related to vitellogenin, xenobiotic metabolism, and oxidative stress. Comparison of points of departure (PODs) based on calculated benchmark concentrations (BMCs) revealed the sensitivity of histone-modifying enzyme activities to these chemicals. Our findings suggest that the 'disturbance of HMT and HDM' can serve as the molecular initiating event (MIE) leading to reproductive toxicity in the epigenetic AOP for TCS and TBBPA. The study extended the biological applicability of these enzymes by identifying model species with analogous protein sequences and functions. This combined approach enhances the essentiality, empirical support, and taxonomic domain of applicability (tDOA), which are crucial considerations for ecotoxicological AOPs. Given the widespread use and environmental distribution of chemicals in consumer products, this study proposes histone-modifying enzyme activity as an effective screening tool for reproductive toxicants and emphasizes the integration of epigenetic mechanisms into a prospective ERA.

Dissecting the role of transcription factor AP2-M in Babesia asexual replication.

Babesia spp. are obligate intracellular parasites that invade host cells to complete their asexual development and transmission. Here, we identified a transcription factor AP2-M (BXIN_0799) in Babesia sp. Xinjiang (Bxj), a member of the Apicomplexan AP2 family, which regulates gene expression related to red blood cell (RBC) invasion and cell cycle progression. Our genome-wide analysis of (Cut-Tag) data shows that AP2-M specifically recognized DNA motifs in the promoters of target genes. AP2-M target genes included other AP2 gene family members and epigenetic markers, which could modulate gene expression involved in RBC invasion, merozoite morphology, and cell cycle phases, as indicated by RNA sequencing, proteomics, and single-cell RNA sequencing (scRNA-seq) data from an ap2-m gene disrupted strain (AP2-M (-)). We conclude that AP2-M appeared to contribute to the process of red blood cell invasion, maintain merozoite morphology, and cell cycle progression through GS and MS phases.

Regulation of m6A (N6-Methyladenosine) methylation modifiers in solid cancers.

Solid cancers constitute a tremendous burden on global healthcare, requiring a deeper understanding of the molecular mechanisms underlying cancer development and progression. Epigenetic changes, notably N6-methyladenosine (m6A) RNA methylation, have emerged as important contributors to the biology of solid tumors in recent years. This epigenetic mark dynamically affects gene expression at the post-transcriptional level and modulates a variety of cellular processes, making it a focus of research in the context of solid tumors. m6A modification patterns are dysregulated in a variety of solid cancers, including ovarian, breast, lung, colorectal, pancreatic, and others. This dysregulated m6A landscape has been shown to induce significant changes in the expression of oncogenes, tumor suppressors, and genes involved in cancer stem cells, metastasis, and treatment resistance. In solid tumors, the interaction of m6A "writers" (e.g., METTL3, METTL14, and others), "erasers" (e.g., ALKBH5, FTO), and "readers" (e.g., members of YTHDF proteins and others) delicately changes the m6A methylome. Targeting m6A regulators as a potential therapeutic method to control gene expression and prevent tumor development seems a novel strategy. To enhance treatment results, advances in this area of research have led to the development of targeted treatments aiming at restoring or altering m6A alteration patterns in solid tumors.

Targeting Sepsis: Disease Tolerance, Immune Resilience, and Compartmentalized Immunity

Introduction: Sepsis remains a major contributor to critical care mortality and morbidity worldwide. Despite advances in understanding its complex immunopathology, the compartmentalized nature of immune responses across different organs has yet to be fully translated into targeted therapies. This review explores the burden of sepsis on organ-specific immune dysregulation, immune resilience, and epigenetic reprogramming, emphasizing translational challenges and opportunities. Methods: We implemented a systematic literature search strategy, incorporating data from studies published between 2010 and 2024, to evaluate the role of molecular profiling techniques, including transcriptomics and epigenetic markers, in assessing the feasibility of targeted therapies. Results: Sepsis-induced immune dysregulation manifests differently in various organs, with lung, heart, liver, and kidney responses driven by unique local immune environments. Organ-specific biomarkers, such as the Spns2/S1P axis in lung macrophages, mitochondrial dysfunction in the heart, proenkephalin for early acute kidney injury (AKI), and adrenomedullin for predicting multi-organ failure, offer promising avenues for timely intervention. Furthermore, immune resilience, particularly through regulatory T-cell modulation and cytokine targeting (e.g., IL-18), is crucial for long-term recovery. Epigenetic mechanisms, including histone modification and trained immunity, present opportunities for reprogramming immune responses but require more precision to avoid unintended inflammatory sequelae. Conclusions: A deeper understanding of compartmentalized immune responses and the dynamic immune landscape in sepsis is critical for developing precision therapies. Real-time immune monitoring and organ-targeted interventions could revolutionize sepsis management, although significant barriers remain in clinical translation. Further research is required to establish biomarkers and treatment timing that optimize therapeutic efficacy while minimizing systemic risks.

Quercetin ameliorates senescence and promotes osteogenesis of BMSCs by suppressing the repetitive element‑triggered RNA sensing pathway.

Cell senescence impedes the self‑renewal and osteogenic capacity of bone marrow mesenchymal stem cells (BMSCs), thus limiting their application in tissue regeneration. The present study aimed to elucidate the role and mechanism of repetitive element (RE) activation in BMSC senescence and osteogenesis, as well as the intervention effect of quercetin. In an H2O2‑induced BMSC senescence model, quercetin treatment alleviated senescence as shown by a decrease in senescence‑associated β‑galactosidase (SA‑β‑gal)‑positive cell ratio, increased colony formation ability and decreased mRNA expression of p21 and senescence‑associated secretory phenotype genes. DNA damage response marker γ‑H2AX increased in senescent BMSCs, while expression of epigenetic markers methylation histone H3 Lys9, heterochromatin protein 1α and heterochromatin‑related nuclear membrane protein lamina‑associated polypeptide 2 decreased. Quercetin rescued these alterations, indicating its ability to ameliorate senescence by stabilizing heterochromatin structure where REs are primarily suppressed. Transcriptional activation of REs accompanied by accumulation of cytoplasmic double‑stranded (ds)RNA, as well as triggering of the RNA sensor retinoic acid‑inducible gene I (RIG‑I) receptor pathway in H2O2‑induced senescent BMSCs were shown. Similarly, quercetin treatment inhibited these responses. Additionally, RIG‑I knockdown led to a decreased number of SA‑β‑gal‑positive cells, confirming its functional impact on senescence. Induction of senescence or administration of dsRNA analogue significantly hindered the osteogenic capacity of BMSCs, while quercetin treatment or RIG‑I knockdown reversed the decline in osteogenic function. The findings of the current study demonstrated that quercetin inhibited the activation of REs and the RIG‑I RNA sensing pathway via epigenetic regulation, thereby alleviating the senescence of BMSCs and promoting osteogenesis.

A new opportunity for N-acetylcysteine. An outline of its classic antioxidant effects and its pharmacological potential as an epigenetic modulator in liver diseases treatment.

Liver diseases represent a worldwide health problem accountable for two million deaths per year. Oxidative stress is critical for the development of these diseases. N-acetyl cysteine (NAC) is effective in preventing liver damage, both in experimental and clinical studies, and evidence has shown that the pharmacodynamic mechanisms of NAC are related to its antioxidant nature and ability to modulate key signaling pathways. Here, we provide a comprehensive description of the beneficial effects of NAC in the treatment of liver diseases, addressing the first evidence of its role as a scavenger and precursor of reduced glutathione, along with studies showing its immunomodulatory action, as well as the ability of NAC to modulate epigenetic hallmarks. We searched the PubMed database using the following keywords: oxidative stress, liver disease, epigenetics, antioxidants, NAC, and antioxidant therapies. There was no time limit to gather all available information on the subject. NAC has shown efficacy in treating liver damage, exerting mechanisms of action different from those of free radical scavengers. Like different antioxidant therapies, its effectiveness and safety are related to the administered dose; therefore, designing new pharmacological formulations for this drug is imperative to achieve an adequate response. Finally, there is still much to explore regarding its effect on epigenetic marker characteristics of liver damage, turning it into a drug with broad therapeutic potential. According to the literature reviewed, NAC could be an appropriate option in clinical studies related to hepatic injury and, in the future, a repurposing alternative for treating liver diseases.

Understanding the Etiopathogenesis of Cardiomyopathies: New Insights

Background Cardiomyopathy, a rare heart disease, is characterized by abnormalities in cardiac wall thickness and chamber size, leading to impaired contraction, relaxation, conduction, rhythm, and reduced pumping ability. Aim This review aims to provide a comprehensive understanding of cardiomyopathy by examining its various aspects Method A literature survey was conducted using online databases such as PubMed, Google Scholar, and Web of Science, covering publications from January 1995 to July 2023. Result Genetic mutations in key muscle contraction genes (MYH7, MYL2, MYL3, MYBPC3, TNNT2, TPM1, TNNI3, ACTC) contribute to cardiomyopathy. Additionally, epigenetic markers in genes like FKBP5, TBX5, HAND1, POLA2, PLAAT3, and CCDC88B, along with environmental factors such as alcohol addiction, smoking, and stress, significantly influence disease risk. Genetic testing, including whole exome/genome sequencing, has revolutionized diagnosis, enabling early detection and intervention. Familial genetic testing facilitates personalized management. Conclusion Cardiomyopathy is a complex disease with genetic and environmental influences. Various techniques, including genetic testing, aid in its identification and management. Furthermore, machine learning (ML) techniques have emerged as valuable tools in understanding and predicting cardiomyopathy outcomes.

Expanding the Role of Molecular Genetic Expertise in Crime Detection and Investigation

Molecular genetic testing using DNA plays a crucial role in the field of justice. Beyond the analysis of genomic DNA sequences, advanced methods such as mitochondrial DNA analysis, epigenetic marker identification, and RNA profiling are being developed. A particularly promising approach is forensic phenotyping, which involves predicting human characteristics from DNA samples, including appearance, biogeographic origin, and age.

Ultrasensitive Amplification-Free Quantification of a Methyl CpG-Rich Cancer Biomarker by Single-Molecule Kinetic Fingerprinting.

The most well-studied epigenetic marker in humans is the 5-methyl modification of cytosine in DNA, which has great potential as a disease biomarker. Currently, quantification of DNA methylation relies heavily on bisulfite conversion followed by PCR amplification and NGS or microarray analysis. PCR is subject to potential bias in differential amplification of bisulfite-converted methylated versus unmethylated sequences. Here, we combine bisulfite conversion with single-molecule kinetic fingerprinting to develop an amplification-free assay for DNA methylation at the branched-chain amino acid transaminase 1 (BCAT1) promoter. Our assay selectively responds to methylated sequences with a limit of detection below 1 fM and a specificity of 99.9999%. Evaluating complex genomic DNA matrices, we reliably distinguish <5% DNA methylation at the BCAT1 promoter in whole blood DNA from completely unmethylated whole-genome amplified DNA. Taken together, these results demonstrate the feasibility and sensitivity of our amplification-free, single-molecule quantification approach to improve the early detection of methylated cancer DNA biomarkers.

MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylated regions from whole-genome datasets.

DNA methylation is an epigenetic mark involved in the regulation of gene expression, and patterns of DNA methylation anticorrelate with chromatin accessibility and transcription factor binding. DNA methylation can be profiled at the single cytosine resolution in the whole genome and has been performed in many cell types and conditions. Computational approaches are then essential to study DNA methylation patterns in a single condition or capture dynamic changes of DNA methylation levels across conditions. Toward this goal, we developed MethyLasso, a new approach to segment DNA methylation data. We use it as an all-in-one tool to perform the identification of low-methylated regions, unmethylated regions, DNA methylation valleys and partially methylated domains in a single condition as well as differentially methylated regions between two conditions. We performed a rigorous benchmarking comparing existing approaches by evaluating the agreement of the regions across tools, their number, size, level of DNA methylation, boundaries, cytosine-guanine content and coverage using several real datasets as well as the sensitivity and precision of the approaches using simulated data and show that MethyLasso performs best overall. MethyLasso is freely available at https://github.com/bardetlab/methylasso.