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Mechanism of methylation leading to the formation of het-CH 3 and C-CH 3 connectivities in RNA and DNA.
Source publication
Chemical modification of nucleobases plays an important role for the control of gene expression on different levels. That includes the modulation of translation by modified tRNA-bases or silencing and reactivation of genes by methylation and demethylation of cytosine in promoter regions. Especially dynamic methylation of adenine and cytosine is ess...
Contexts in source publication
Context 1
... addition of the methyl-group to DNA and RNA bases (Fig. 2) is catalyzed by DNA-and RNA-methyltransferases that use S-adenosyL-methionine (SAM) as an active methyl-group donor. [21][22][23] While the methyltransferases that methylate RNA bases are now under extensive investigations, the enzymes that catalyze the methylation of dC in DNA are well characterized. In mammalian cells, 3 active ...
Context 2
... pairs compared with the bulk genomic DNA and found in 40% of promoter regions in the mammalian genome, with even higher levels (60%) in the human genome. 38,39 Symmetric methylation of CpG:GpC islands is consequently a hallmark of silenced genes. 40,41 The enzymatic mechanism of how methyltransferases meth- ylate DNA and RNA bases is shown in Fig. 2. Centers with a cer- tain nucleophilicity like the amino group of the RNA base A can attack the SAM coenzyme directly leading to immediate methyl- ation. This type of direct methylation is certainly operating for the formation of 6m 2 A, 4mC or m6Am. SAM as nature's "methyl iodide" is hence reactive enough to methylate even weak ...
Context 3
... contrast to the formation of het-CH 3 connections, meth- ylation of the dC base in DNA at position C5 is far more com- plex. The C5-center features no nucleophilicity at all, making direct methylation impossible. Nature solves this problem by exploiting a helper nucleophile (R-SH, Fig. 2). The DNMT enzymes attack the dC base first with a nucleophilic thiol in a 1,6 addition reaction. This establishes a nucleophilic enamine substructure (green in Fig. 2), which can subsequently be meth- ylated with the SAM cofactor. Importantly, the helper nucleo- phile is subsequently eliminated, thereby re-establishing the aromatic ...
Context 4
... is far more com- plex. The C5-center features no nucleophilicity at all, making direct methylation impossible. Nature solves this problem by exploiting a helper nucleophile (R-SH, Fig. 2). The DNMT enzymes attack the dC base first with a nucleophilic thiol in a 1,6 addition reaction. This establishes a nucleophilic enamine substructure (green in Fig. 2), which can subsequently be meth- ylated with the SAM cofactor. Importantly, the helper nucleo- phile is subsequently eliminated, thereby re-establishing the aromatic system. This more complex enzymatic transformation allows nature to methylate non-nucleophilic carbon atoms to create C-CH 3 connectivities which feature a strong and ...
Context 5
... is feasi- ble. There is currently no evidence that this type of chemistry occurs in vivo but we could show that stem cell lysates feature a decarboxylating activity. 68 Interesting is the observation that deformylation and decarboxylation of 5fdC and 5cadC after reaction with a thiol nucleophile leads to a reaction intermedi- ate (boxed in Fig. 2 and 4) that is the key intermediate observed already during methylation of dC to 5mdC by the DNMTs. It is therefore tempting to speculate that DNMT enzymes are involved in the deformylation and decarboxylation maybe fol- lowed by immediate re-methylation. Although this reaction sequence would follow chemical logic, it needs to clarified in ...
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Citations
... The current TNM classi cation system is inadequate in predicting prognosis for ACC [24], highlighting the need to understand the molecular mechanisms of tumorigenesis. Methylation, a well-studied mechanism of epigenetic regulation, has been extensively explored as a factor in tumorigenesis [25,26]. One speci c area of interest is m7G methylation, which has been identi ed as a critical player in RNA modi cation and is involved in dysregulation of mRNA, tRNA, and rRNA [27]. ...
N7-methylguanosine (M7G) is a prevalent modification of mRNA in biological systems, and plays a role in various biological processes. Previous research has demonstrated that expression of m7G RNA modification is correlated with cancer and a range of other pathological conditions. The study aimed to explore the potential of m7G as a prognostic biomarker and therapeutic target for Adrenocortical Carcinoma (ACC). A comprehensive analysis was conducted to identify m7G-related genes in ACC by first compiling a list of 26 critical regulators through previous research and Gene Set Enrichment Analysis (GSEA). Subsequently, LASSO Cox regression analysis was performed on RNA-seq data from The Cancer Genome Atlas (TCGA) and accompanying clinical data, resulting in the identification of nine m7G prognostic signatures (GEMIN5, DCPS, AGO2, EIF4E2, NCBP1, WDR4, EIF4A1, EIF4E3, NUDT16) to create a predictive signature. Patients with ACC were then classified into high- and low-risk groups based on the predictive signature, with the results showing that patients in the high-risk group had a poorer prognosis. The m7G signature demonstrated high diagnostic sensitivity and robustness, as demonstrated by its diagnostic performance and external validation through the Gene Expression Omnibus (GEO). This study provides a comprehensive analysis of m7G RNA methylation in ACC and offers insight into the gene expression, function, interaction, and predictive value of m7G-related genes, which may provide valuable information for prognosis prediction and treatment guidance for ACC patients.
... The binding of 5-methylcytosine recruitment protein to the binding of transcription factors on the binding effect of space, promoter activity, and gene expression regulation. Incorrect cytosine methylation pattern is a risk factor for many cancers [13]. As essential regulators of DNA methylation, DNMT3A and DNMT3B play essential roles in de novo DNA methylation [14]. ...
Background
DNA methyltransferase 3A (DNMT3A) is essential for de-novo methylation and cell development. Recent studies have shown that dysregulation of methylation regulated by DNMT3A is highly implicated in cancer progression. However, the regulatory roles of DNMT3A in various cancers are not completely clear and need further investigation.
Methods
The RNA-seq data in The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression databases (GTEx) are the source of this study. Western blot assays were performed to exhibit the relative expression level of DNMT3A in clinical glioma samples. CBioportal was utilized to explore the genomic alternation of DNMT3A. The images of immunofluorescence downloaded from the Human Protein Atlas (HPA) help to show the subcellular distribution of DNMT3A proteins. ComPPI is a powerful tool for studying protein interactions. Single-cell sequencing cohorts from TISCH were used to reveal the DNMT3A expression levels in different cell types. Two types of survival algorithms were conducted to assess the prognostic value of DNMT3A in pan-cancer. Gene Set Enrichment Analysis (GSEA) was applied to explore various cellular pathways and hallmarks. Immune cells infiltration in pan-cancer was summarized using data available on TIMER 2.0 website.
Results
The expression level of DNMT3A is significantly up-regulated in tumor tissue compared with that in normal tissue in most cancers. DNMT3A is discovered to have great accordance with the immune-related hallmarks like immune response signaling. In addition, the infiltration of DNMT3A in various subtypes of immune cells showed obvious aggregation of Treg, MDSC, B cell, Neutrophil, and Monocyte. At last, the robust prognostic ability of DNMT3A was further enhanced in several independent immunotherapy cohorts.
... DNA methylation refers to the addition of a methyl group to 5′ position of cytosine residues (5mC) throughout the genome. DNA methylation is written by the family of enzymes known as DNA methyltransferases (DNMT1, DNMT2, and DNMT3) [108]. While DNA methylation can be dynamically regulated in response to various stimuli, it is generally stably maintained in many cases, particularly in differentiated cells where it plays a crucial role in determining cell identity and fate. ...
... While DNA methylation can be dynamically regulated in response to various stimuli, it is generally stably maintained in many cases, particularly in differentiated cells where it plays a crucial role in determining cell identity and fate. DNA demethylation is limited to only a few specific loci in differentiated cells, and occurs through specific mechanisms that involve the activity of TET (ten-eleven translocation) family of enzymes in conjunction with other factors [108]. However, the process of systematic TET-determined DNA demethylation is known to occur during early embryonic development, particularly after zygote formation, where it plays a critical role in erasing epigenetic marks and enabling the establishment of new gene expression patterns [108]. ...
... DNA demethylation is limited to only a few specific loci in differentiated cells, and occurs through specific mechanisms that involve the activity of TET (ten-eleven translocation) family of enzymes in conjunction with other factors [108]. However, the process of systematic TET-determined DNA demethylation is known to occur during early embryonic development, particularly after zygote formation, where it plays a critical role in erasing epigenetic marks and enabling the establishment of new gene expression patterns [108]. Additionally, DNA methylation may be passively lost through cellular replication cycles due to a basal inefficacy of the maintenance DNMT1, and this phenomenon has been utilized as a marker of biological aging of different tissues in mammals [47]. ...
The number of “omics” approaches is continuously growing. Among others, epigenetics has appeared as an attractive area of investigation by the cardiovascular research community, notably considering its association with disease development. Complex diseases such as cardiovascular diseases have to be tackled using methods integrating different omics levels, so called “multi-omics” approaches. These approaches combine and co-analyze different levels of disease regulation. In this review, we present and discuss the role of epigenetic mechanisms in regulating gene expression and provide an integrated view of how these mechanisms are interlinked and regulate the development of cardiac disease, with a particular attention to heart failure. We focus on DNA, histone, and RNA modifications, and discuss the current methods and tools used for data integration and analysis. Enhancing the knowledge of these regulatory mechanisms may lead to novel therapeutic approaches and biomarkers for precision healthcare and improved clinical outcomes.
... The human UCP1 gene structure is notable for a high degree of methylation ("CG islands") in its promoter region. Methylation of CG islands within gene promoters can lead to their silencing [54]. The human lysine (K)-specific demethylase 3A (KDM3A) is critically important in regulating the expression of metabolic genes and obesity resistance [55]. ...
We present here an innovative modular and outsourced model of drug research and development for microRNA oligonucleotide therapeutics (miRNA ONTs). This model is being implemented by a biotechnology company, namely AptamiR Therapeutics, in collaboration with Centers of Excellence in Academic Institutions. Our aim is to develop safe, effective and convenient active targeting miRNA ONT agents for the metabolic pandemic of obesity and metabolic-associated fatty liver disease (MAFLD), as well as deadly ovarian cancer.
... There are two modes of methylation regulation under biomechanical stimulation in tumor: One is demethylation within regions of the genome, and another is methylation of special CpG sites [15], during which DNA methyltransferase (DNMT) plays a key role. The methylation changes induced by mechanical factors regulate the activity and proliferation of tumor cells. ...
The occurrence and development of tumors depend on a complex regulation by not only biochemical cues, but also biomechanical factors in tumor microenvironment. With the development of epigenetic theory, the regulation of biomechanical stimulation on tumor progress genetically is not enough to fully illustrate the mechanism of tumorigenesis. However, biomechanical regulation on tumor progress epigenetically is still in its infancy. Therefore, it is particularly important to integrate the existing relevant researches and develop the potential exploration. This work sorted out the existing researches on the regulation of tumor by biomechanical factors through epigenetic means, which contains summarizing the tumor epigenetic regulatory mode by biomechanical factors, exhibiting the influence of epigenetic regulation under mechanical stimulation, illustrating its existing applications, and prospecting the potential. This review aims to display the relevant knowledge through integrating the existing studies on epigenetic regulation in tumorigenesis under mechanical stimulation so as to provide theoretical basis and new ideas for potential follow-up research and clinical applications.
Graphical Abstract
Mechanical factors under physiological conditions stimulate the tumor progress through epigenetic ways, and new strategies are expected to be found with the development of epidrugs and related delivery systems.
... Furthermore, dynamic adenine methylation and demethylation are important for the biological behaviors of cells. Impaired methylation patterns interfere with cell growth and development, potentially leading to dysplasia or neoplasia [4]. The N 6 -methyladenosine (m 6 A) modification, catalyzed by an RNA methyltransferase complex comprising METTL3, METTL14, and WTAP, is the most common internal mRNA modification in eukaryotes and is present in over 50% of all methylated ribonucleotides [5]. ...
Background
METTL3, an mRNA m⁶A methyltransferase, has been implicated in various steps of mRNA metabolism, such as stabilization, splicing, nuclear transportation, translation, and degradation. However, whether METTL3 dysregulation is involved in Hirschsprung disease (HSCR) development remains unclear. In this study, we preliminarily elucidated the role of METTL3 in HSCR and sought to identify the associated molecular mechanism.
Methods
The gene expression levels of YAP and several methyltransferases, demethylases, and effectors were evaluated by RT-qPCR. Protein levels were evaluated by western blot and immunohistochemistry. Cell proliferation and migration were detected by CCK-8 and Transwell assays, respectively. The overall levels of m⁶A modification were determined by colorimetry.
Results
We found that m⁶A levels were reduced in the stenotic intestinal tissue of patients with HSCR. When METTL3 was knocked down in SH-SY5Y and HEK-293T cells, the proliferative and migratory abilities of the cells were inhibited, m⁶A modification levels were reduced, and YAP expression was increased. Importantly, YAP and METTL3 expression displayed a negative correlation in both cell lines as well as in HSCR tissue.
Conclusions
Our results provide evidence for an interaction between METTL3 and YAP in HSCR, and further suggest that METTL3 is involved in the pathogenesis of HSCR by regulating neural crest cell proliferation and migration upstream of YAP.
... Epitranscriptomics is an emerging biological research field, which has received extensive attention in the regulation of VEC damage in recent years [8,9]. RNA methylation is the most common type of RNA modification in eukaryotes, accounting for 60% of the total Ribonu-cleic Acid (RNA) modifications [10]. Among them, N6methyladenosine (m6A) modification is considered to be the most common, reversible and dynamic eukaryotic messenger RNA (mRNA) transcription modification among all RNA modification types, accounting for about half of all methylated ribonucleotides [11]. ...
Background:
Cardiovascular disease, one of the most common types of disease in clinical practice today, carries a very high risk of disability and death. This research aims to examine genome-wide changes in injured human dermal microvascular endothelial cells (HDMECs) using the Ribonucleic Acid sequencing (RNA-Seq) technique, and to search for key genes influencing N6-methyladenosine (m6A) methylation, thus gaining new insights into future clinical diagnosis and treatment of cardiovascular diseases (CVDs) and laying a foundation for follow-up research.
Methods:
Impaired HDMECs (injury group), established by endotoxin intervention, were analyzed by RNA-Seq for differentially expressed genes (DEGs) relative to normal HDMECs (control group). Then, DEGs that might be associated with m6A methylation were selected for expression blocking to observe m6A methylation alterations. The migration, angiogenesis, and inflammatory response of damaged HDMECs were detected by cell scratch assay, western blotting, and Enzyme-linked Immunosorbent Assay (ELISA) experiments, respectively.
Results:
In this study, 20 DEGs were screened out from the two groups by RNA-Seq, of which 17 were up-regulated and 3 were down-regulated. The C-C motif chemokine receptor 10 (CCR10) was selected for subsequent analysis. Real-Time Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) identified elevated CCR10 expression and reduced m6A methylation levels in the injury group (p < 0.05). After blocking CCR10 expression in damaged HDMECs by BI6901 (a CCR10 specific blocker) m6A methylation, cell activity, vascular endothelial growth factor A (VEGFA) and CD31 protein expression, as well as relative length and branches of tube formation were found to be increased compared with the injury group, while the levels of inflammatory factors interleukin-1 (IL-1), interleukin-1 (IL-6) and tumor necrosis factor-α (TNF-α) were decreased (p < 0.05).
Conclusions:
Blocking CCR10 expression can activate m6A methylation, promote cell activity, inhibit inflammatory reactions and alleviate HDMEC injury, which may become a breakthrough in future diagnosis and treatment of cardiovascular diseases.
... However, there is also a growing body of evidence indicating that the methylation of DNA is not only inherited and established during development, but it also constantly changes throughout individual's lifetime likely affecting physiological and pathological neuronal processes (Sharma, 2015;Szyf, 2015;Bierer et al., 2020;Daskalakis et al., 2021). It was shown that DNA methylation and demethylation are important in fully differentiated cells (Nabel et al., 2012;Traube and Carell, 2017). As an example, locus-specific DNA demethylation and de novo methylation are induced by neuronal activation arguing that DNA methylation is important for normal brain function (Traube and Carell, 2017). ...
... It was shown that DNA methylation and demethylation are important in fully differentiated cells (Nabel et al., 2012;Traube and Carell, 2017). As an example, locus-specific DNA demethylation and de novo methylation are induced by neuronal activation arguing that DNA methylation is important for normal brain function (Traube and Carell, 2017). The active demethylation at the gene promoter is a trigger for neural plasticity (Nabel et al., 2012). ...
... Furthermore, the abnormalities in DNA methylation were observed in several diseases (Rasmussen and Helin, 2016;Hwang et al., 2017;Wojdacz et al., 2019). For example, many cancer types are characterized by decreased global methylation levels, except for promoter regions of crucial regulatory and tumor suppressor genes which are hypermethylated and their expression is therefore silenced (Traube and Carell, 2017). Moreover, several neuroepigenetic changes have been recently described in neurodevelopmental, psychiatric and neurodegenerative disorders (Cholewa-Waclaw et al., 2016), such as: autism (Aspra et al., 2022), schizophrenia (Song et al., 2022), posttraumatic stress disorder (Montalvo-Ortiz et al., 2022), heroin addiction (Kozlenkov et al., 2017), and Parkinson's disease (Kaut et al., 2022). ...
Alcohol use disorder (AUD) is a worldwide problem. Unfortunately, the molecular mechanisms of alcohol misuse are still poorly understood, therefore successful therapeutic approaches are limited. Accumulating data indicate that the tendency for compulsive alcohol use is inherited, suggesting a genetic background as an important factor. However, the probability to develop AUD is also affected by life experience and environmental factors. Therefore, the epigenetic modifications that are altered over lifetime likely contribute to increased risk of alcohol misuse. Here, we review the literature looking for the link between DNA methylation in the brain, a common epigenetic modification, and AUD-related behaviors in humans, mice and rats. We sum up the main findings, identify the existing gaps in our knowledge and indicate future directions of the research.
... Abnormal methylation of gene promoter cg sites could induce their aberrant expression to affect some crucial biological processes, such as cell proliferation, tumor invasion, and metastasis. 27,28 We evaluated the methylation status of promoter cg sites and found that the EIF5A2 levels in HNSCC was significantly inversely correlated with the EIF5A2 promoter methylation status, suggesting that aberrant methylation may be associated with abnormal EIF5A2 expression. ...
Background
This study attempted to investigate the significance of eukaryotic initiation factor 5A2 (EIF5A2) in the prognosis and regulatory network of head and neck squamous cell carcinoma (HNSCC).
Methods
EIF5A2 expression, prognostic information, and methylation levels of HNSCC were collected from the Cancer Genome Atlas (TCGA) database. Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) and Western blot analyses were performed to determine EIF5A2 levels in HNSCC and normal tissue samples. R software was employed for expression analysis and prognosis assessment of EIF5A2 in HNSCC. A competing endogenous RNA (ceRNA) network was generated with the starBase database. Gene set enrichment analysis (GSEA) was used to determine the enriched physiological functions and network related to high expression of EIF5A2 in HNSCC. Immune infiltration-related outcomes were acquired from the CIBERSORT and Tumor Immune Estimation Resource (TIMER) database.
Results
EIF5A2 overexpression was observed in HNSCC and linked to poor progression-free survival and overall survival time. Cox regression analyses showed that EIF5A2 level was a stand-alone indicator of HNSCC patients' prognosis. A ceRNA network analysis highlighted the SNHG16/miR-10b-5p/EIF5A2 axis in EIF5A2 regulation. The GSEA results indicated that EIF5A2 was involved in complex signaling pathways. The CIBERSORT and TIMER databases revealed significant associations between EIF5A2 expression and immune cell infiltration.
Conclusion
EIF5A2 overexpression may be a risk factor for prognosis in HNSCC and may be regulated by the SNHG16/miR-10b-5p/EIF5A2 axis.
... Furthermore, dynamic adenine methylation and demethylation are important for the biological behaviors of cells. Impaired methylation patterns interfere with cell growth and development, potentially leading to dysplasia or neoplasia [4]. The N 6 -methyladenosine (m 6 A) modi cation, catalyzed by a RNA methyltransferase complex comprising METTL3, METTL14, and WTAP, is the most common internal mRNA modi cation in eukaryotes and is present in over 50% of all methylated ribonucleotides [5]. ...
Background METTL3, a mRNA m⁶A methyltransferase, has been implicated in various steps of mRNA metabolism, such as stabilization, splicing, nuclear transportation, translation, and degradation. However, whether METTL3 dysregulation is involved in Hirschsprung disease (HSCR) development remains unclear. In this study, we preliminarily elucidated the role of METTL3 in HSCR and sought to identify the associated molecular mechanism.
Methods The gene expression levels of YAP and several methyltransferases, demethylases, and effectors were evaluated by RT-qPCR. Protein levels were evaluated by western blot and immunohistochemistry. Cell proliferation and migration were detected by CCK-8 and Transwell assays, respectively. The overall levels of m⁶A modification were determined by colorimetry.
Results We found that m⁶A levels were reduced in stenotic intestinal tissue of patients with HSCR. When METTL3 was knocked down in SH-SY5Y and HEK-293T cells, the proliferative and migratory abilities of the cells were inhibited, m⁶A modification levels were reduced, and YAP expression was increased. Importantly, YAP and METTL3 expression displayed a negative correlation in both cell lines as well as in HSCR tissue.
Conclusions Our results provide evidence for an interaction between METTL3 and YAP in HSCR, and further suggest that METTL3 is involved in the pathogenesis of HSCR by regulating neural crest cell proliferation and migration upstream of YAP.
