Figure 2 - available via license: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
Content may be subject to copyright.
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 ...
Similar publications
Alphaproteobacteria include bacteria with very different modes of life, from free‐living to host‐associated and pathogenic bacteria. Their genomes vary in size and organization from single circular chromosomes to multipartite genomes and are often methylated by one or more adenine or cytosine methyltransferases (MTases). These include MTases that a...
4-methylcytosine (4mC) is an important DNA modification in prokaryotes, but its relevance, and even presence in eukaryotes have been mysterious. Here we show that spermatogenesis in the liverwort Marchantia polymorpha involves two waves of extensive DNA methylation reprogramming. First, 5-methylcytosine (5mC), a well-known eukaryotic DNA modificati...
The review summarizes the data on pro- and eukaryotic RNA (C5-cytosine) methyltransferases. The structure, intracellular location, RNA targets, and catalytic mechanisms of these enzymes, as well as the functional role of methylated cytosine residues in RNA are presented. The functions of RNA (C5-cytosine) methyltransferases unassociated with their...
Chez Arabidopsis thaliana, le silencing transcriptionnel est associé notamment aux modifications post-traductionnelles des queues des histones et à la méthylation des cytosines en contexte CG, CHG et CHH (où H peut être indifféremment T, A ou C). Plusieurs voies indépendantes conduisent à la méthylation de l’ADN en tout contexte via les méthyltrans...
We report a new subgroup of Type III Restriction-Modification systems that use m4C methylation for host protection. Recognition specificities for six such systems, each recognizing a novel motif, have been determined using single molecule real-time DNA sequencing. In contrast to all previously characterized Type III systems which modify adenine to...
Citations
... It has emerged as a major area of research interest, encompassing several types, including m 6 A, m 1 A, m 5 C, m 7 G, among others. Specifically, RNA m 5 C applies to the methylation of cytosine at the fifth carbon position in RNA [10][11][12]. 5-Methylcytosine (m 5 C), which is present in RNA, is a common modifier in human RNAs [13]. Up to now, a total of 95,391 m 5 C peaks have been reported within the human metagenome [14]. ...
Traumatic brain injury (TBI) poses a major global health challenge, leading to serious repercussions for those affected and imposing considerable financial strains on families and healthcare systems. RNA methylation, especially 5-methylcytosine (m5C), plays a crucial role as an epigenetic modification in regulating RNA at the level of post-transcriptional regulation. However, the impact of TBI on the m5C methylation profile of long non-coding RNAs (lncRNAs) remains unexplored. In the present study, we conducted a thorough transcriptome-wide examination of m5C methylation in lncRNAs in a rat TBI model utilizing MeRIP-Seq. Our results revealed significant differences in the amount and distribution of m5C methylation in lncRNAs between TBI and control groups, indicating profound changes in m5C methylation following TBI. Bioinformatic analyses linked these specifically methylated transcripts to pathways involved in immune response, neural repair, and lipid metabolism, providing insight into possible mechanisms underlying TBI pathology. These findings offer novel perspectives on the post-transcriptional modifications in lncRNA m5C methylation following TBI, which may contribute to understanding the disease mechanisms and developing targeted therapeutic strategies.
... Here we describe the discovery, synthesis and evaluation of a structurally extended oligonucleotide backbone chemistry named extended nucleic acid (exNA), consisting of an extra methylene insertion between the 5′-C and 5′-OH of a nucleoside in the context of 2′-O-methyl (2′-OMe) and 2′-deoxy-fluoro (2′-F) ribose modifications ( Fig. 1) [38][39][40] . In contrast to naturally occurring methylation, which is reversible by cellular demethylases 41,42 , the exNA backbone is designed to be a permanent structural modification of the oligonucleotide. We demonstrate that the exNA backbone imparts substantial improvements in exonuclease stability, while minimally impacting the overall structure, charge and thermodynamic stability of the siRNA duplex. ...
Therapeutic small interfering RNA (siRNA) requires sugar and backbone modifications to inhibit nuclease degradation. However, metabolic stabilization by phosphorothioate (PS), the only backbone chemistry used clinically, may be insufficient for targeting extrahepatic tissues. To improve oligonucleotide stabilization, we report the discovery, synthesis and characterization of extended nucleic acid (exNA) consisting of a methylene insertion between the 5′-C and 5′-OH of a nucleoside. exNA incorporation is compatible with common oligonucleotide synthetic protocols and the PS backbone, provides stabilization against 3′ and 5′ exonucleases and is tolerated at multiple oligonucleotide positions. A combined exNA–PS backbone enhances resistance to 3′ exonuclease by ~32-fold over the conventional PS backbone and by >1,000-fold over the natural phosphodiester backbone, improving tissue exposure, tissue accumulation and efficacy in mice, both systemically and in the brain. The improved efficacy and durability imparted by exNA may enable therapeutic interventions in extrahepatic tissues, both with siRNA and with other oligonucleotides such as CRISPR guide RNA, antisense oligonucleotides, mRNA and tRNA.
... We found that the most predominant form of RPN1 mutation status in cancer was amplification, and amplification of the gene should be considered a hallmark of carcinogenesis [44]. In cancer cells, RPN1 promoter methylation tends to be reduced, which can lead to disturbed gene expression and genomic instability [45,46]. Interestingly, the mutation in RPN1 significantly increased the mutation rates of SULT1D1P, LRRTM4-AS1, LINC01851, SNAR-H, LINC01565, DNAJB8, PLXND1, DNAJB8-AS1, CFAP92, and PLXNA1. ...
... In this study, we proved that SiNPs induced hypermethylation in the promoter region of Crem by pyrosequencing assay. Cytosine methylation in the promoter region of DNA may silence the gene expression (Traube and Carell 2017), so Crem hypermethylation is consistent with the downregulation of Crem expression in vivo. We used the methylation inhibitor deoxyazacytidine (5-aza) in vitro to verify the results of in vivo experiments. ...
Exposure to silica nanoparticles (SiNPs) could causally contribute to malfunctioning of the spermatogenesis, but the underlying mechanism is rarely known. This study was designed to explore the mechanism of Crem hypermethylation in SiNP-induced reproductive toxicity. The male mice were exposure to SiNPs (0 and 20 mg/kg·bw) once every 5 days via intratracheal instillation for 35 days. After exposure stopped, half of each group was killed, and the rest were sacrificed after another 15-day feeding. GC-2 cells were treated with 0 and 20 μg/mL SiNPs. The results showed that SiNPs led to structure damage of spermatocyte and sperm, caused spermatocyte apoptosis, and decreased sperm quantity and quality. After 15 days of the withdrawal, the testicular tissue damage gradually recovered. Mechanistic study showed that SiNPs induced hypermethylation of the gene of cAMP responsive element modulator (Crem) in the promoter region. Downregulation of Crem inhibited the expression of outer dense fiber 1 (Odf1), resulting in abnormal sperm flagella structure; at the same time, Crem inhibited the expression of Bcl-xl, causing upregulation of cytochrome-C, cleaved-caspase-9/caspase-9, cleaved-caspase-3/caspase-3, resulting in mitochondrial dependent apoptotic pathway. However, 5-aza, DNA methylation inhibitor, could reverse the SiNP-induced downregulation of Crem and reverse the Crem/Bcl-xl-mediated mitochondrial dependent apoptotic pathway. These results suggested SiNPs could disrupt spermatogenesis by causing Crem hypermethylation to regulate the Odf1 and Bcl-xl in spermatocytes resulting in the sperm flagella structure and spermatocyte apoptosis. Our study provided new insights into the male reproductive toxicity mechanism of SiNPs; Crem demethylation may be a potential way to prevent reproductive dysfunction from SiNP exposure.
... Epigenetic processes involve molecular switches influenced by development, environmental factors, and experiences, regulating gene expression without altering DNA and impacting traits across generations (Jangid et al., 2018). A pivotal mechanism involves the addition or removal of methyl groups from DNA or RNA, orchestrated by methyltransferases and demethylases (Traube and Carell, 2017). Methyltransferase-like enzymes, such as METTL3, play a crucial role in depositing methyl groups specifically on the nitrogen atom at the sixth position of the adenine base in RNA, forming N6-methyladenosine (m6A; Masatoshi et al., 2018). ...
... DNA methylation exhibits a similar effect, and it is important to identify whether changes in gene DNA methylation drive alterations in gene expression. Genes whose expression levels are influenced by methylation changes are often referred to as methylation-driven genes (30). To ascertain whether the genes involved in our diagnostic model are methylation-driven, we analyzed the TCGA PCa dataset and GSE84749 dataset. ...
Background
Prostate cancer (PCa) is the most prevalent type of male genitourinary tumor, remains the second leading cause of deaths due to cancer in the United States in men. The aim of this study was to perform an integrative epigenetic analysis to explore the epigenetic abnormalities involved in the development and progression of PCa, and present advanced diagnostics and improved individual outcomes.
Methods
Genome-wide DNA methylation profiles obtained from The Cancer Genome Atlas (TCGA) were analyzed and a diagnostic model was constructed. For validation, we employed profiles from the Gene Expression Omnibus (GEO) and methylation data derived from clinical samples. Gene set enrichment analysis (GSEA) and the Tumor Immune Estimation Resource (TIMER) were employed for GSEA and to assess immune cell infiltration, respectively.
Results
An accurate diagnostic method for PCa was established based on the methylation level of Cyclin-D2 (CCND2) and glutathione S-transferase pi-1 (GSTP1), with an impressive area under the curve (AUC) value of 0.937. The model’s reliability was further confirmed through validation using four GEO datasets GSE76938 (AUC =0.930), GSE26126 (AUC =0.906), GSE112047 (AUC =1.000), GSE84749 (AUC =0.938) and clinical samples (AUC =0.980). Notably, the TIMER analysis indicated that hypermethylation of CCND2 and GSTP1 was associated with reduced immune cell infiltration, higher tumor purity, and an increased risk of tumor progression.
Conclusions
In conclusion, our study provides a robust and reliable methylation-based diagnostic model for PCa. This model holds promise as an improved approach for screening and diagnosing PCa, potentially enhancing early detection and patient outcomes, as well as for an advanced clinical management for PCa in the framework of predictive, preventive and personalised medicine.
... 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.
