Search Results (52)

The enzyme ABH2, one of nine human DNA dioxygenases of the AlkB family, belongs to the superfamily of Fe(II)/α-ketoglutarate-dependent dioxygenases and plays a crucial role in the direct reversal repair of nonbulky alkyl lesions in DNA nucleobases. ABH2 has broad substrate specificity, directly oxidizing DNA damages such as N¹-methyladenine, N³-methylcytosine, 1,N⁶-ethenoadenine, 3,N⁴-ethenocytosine, and a number of others. In our investigation, we sought to uncover the subtleties of the mechanisms governing substrate specificity in ABH2 by focusing on several critical amino acid residues situated in its active site. To gain insight into the function of this enzyme, we performed a functional mapping of its active site region, concentrating on pivotal residues, participating in forming a damaged binding pocket of the enzyme (Val99 and Ser125), as well as the residues directly involved in interactions with damaged bases, namely Arg110, Phe124, Arg172, and Glu175. To support our experimental data, we conducted a series of molecular dynamics simulations, exploring the interactions between the ABH2 mutant forms, bearing corresponding substitutions and DNA substrates, and harboring various types of methylated bases, specifically N¹-methyladenine or N³-methylcytosine. The comparative studies revealed compelling data indicating that alterations in most of the studied amino acid residues significantly influence both the binding affinity of the enzyme for DNA and its catalytic efficiency. Intriguingly, the findings suggest that the mutations impact the catalytic activity of ABH2 to a greater extent than its ability to associate with DNA strands. Collectively, these results show how changes to the active site affect molecular dynamics and reaction kinetics, improving our understanding of the substrate recognition process in this pivotal enzyme. Full article

Methylation is a biochemical process involving the addition of methyl groups to proteins, lipids, and nucleic acids (both DNA and RNA). DNA methylation predominantly occurs on cytosine and adenine nucleobases, and the resulting products—most frequently 5-methylcytosine and N⁶-methyladenine epigenetic marks—can significantly influence gene activity at the affected genomic sites without modifying the DNA sequence called nucleotide order. Various environmental factors can alter the DNA methylation pattern. Among these, methyl donor micronutrients, such as specific amino acids, choline, and several B vitamins (including folate, pyridoxine, thiamine, riboflavin, niacin, and cobalamin), primarily regulate one-carbon metabolism. This molecular pathway stimulates glutathione synthesis and recycles intracellular methionine. Glutathione plays a pivotal role during oocyte activation by protecting against oxidative stress, whereas methionine is crucial for the production of S-adenosyl-L-methionine, which serves as the universal direct methyl donor for cellular methylation reactions. Because local DNA methylation patterns at genes regulating fertility can be inherited by progeny for multiple generations even in the absence of the original disrupting factors to which the parent was exposed, and DNA methylation levels at specific genomic sites highly correlate with age and can also be passed to offspring, nutrition can influence reproduction and life span in a transgenerational manner. Full article

Drought stress is a predominant abiotic constraint adversely affecting global rice (Oryza sativa) production and threatening food security. While the transcriptional and post-transcriptional regulation of drought-responsive pathways has been widely investigated, the emerging field of epitranscriptomics, particularly RNA chemical modifications such as N6-methyladenosine (m⁶A), adds a new dimension to gene regulation under stress. The most prevalent internal modification in eukaryotic messenger RNA influences RNA metabolism by interacting dynamically with enzymes that add, remove, or recognize the modification. Recent studies in rice reveal that m⁶A deposition is not static but dynamically regulated in response to water-deficit conditions, influencing transcript stability, splicing, nuclear export, and translation efficiency of key drought-responsive genes. This review critically synthesizes current findings on the distribution and functional implications of m⁶A and other epitranscriptomic marks (e.g., 5-methylcytosine [m⁵C], pseudouridine [Ψ]) in modulating rice responses to drought. We discuss the regulatory circuitry involving m⁶A effectors such as OsMTA, OsFIP37, and YTH domain proteins and their integration with known drought-signaling pathways including ABA and reactive oxygen species (ROS) cascades. We also highlight emerging high-resolution technologies such as m⁶A-seq, direct RNA sequencing, and nanopore-based detection that facilitate epitranscriptomic profiling in rice. Finally, we propose future directions for translating epitranscriptomic knowledge into crop improvement, including CRISPR/Cas-based modulation of RNA modification machinery to enhance drought tolerance. Full article

The synthesis of various heterocyclic base modifications of nucleic acids has been thoroughly investigated; however, much less is known about their catabolism. Also, little is known about the transport of such compounds across the microbial cell membranes. Using the Saccharomyces cerevisiae single-gene deletion library, we performed genome-wide screening for genes affecting the growth of yeast in minimal media supplemented with N⁴-acetylcytosine as a source of uracil. We found that Fcy1, Fcy21, Bud16, Gnd1, and Fur4 proteins are required for efficient growth in the tested medium. Additionally, we used several heterocyclic pyrimidine bases and Fcy homolog mutants to test their growth in respective minimal media. We found that tested permeases differently affect the growth of yeast that is dependent on the heterocyclic pyrimidine bases used as a source of uracil. The most pronounced effect was observed for the ∆fur4 mutant, which was growing much slower than the corresponding wild-type strain in the media supplemented with N⁴-acetylcytosine, 4-methylthiouracil, N⁴-methylcytosine, N⁴,N⁴-dimethylcytosine, 2-thiouracil, or 4-thiouracil. We suggest that Fur4 protein is the major yeast transporter of modified heterocyclic pyrimidine bases. Our observations might be helpful when investigating the actions of various heterocyclic base-based antifungal, anticancer, and antiviral drugs. Full article

The diverse methylation modifications of DNA, histones and RNA have emerged as pivotal regulatory mechanisms of gene expression in multiple biological processes at the epigenetic level. They function by coordinating gene expression through impacting gene transcription, mRNA processing and maturation, protein translation and metabolism. Changes in methylation profiles of nucleic acids and histones have been observed in many different types neural injuries in both the central nervous system and the peripheral nervous system, such as 5-methylcytosine in DNA, N6-methyladenosine in RNA and methylation of lysine residues in various histones. Importantly, altering these modifications plays key roles in regulation of neural injury and repair. In this review, we highlight recent research advances of the methylation-related epigenetic modifications in multiple aspects of neural injury and regeneration, including neural protection, axon regeneration, microenvironment modulation and neural functional recovery. We also discuss the current unsolved problems in the field and propose potential future research directions. Full article

Osteoarthritis (OA) is a chronic joint disorder characterized by progressive degeneration of articular cartilage, pain, synovial inflammation, and bone remodeling. Post-transcriptional RNA modifications, known as epitranscriptome, are a group of biochemical alterations in the primary RNA transcript that might influence RNA structure, stability, and function. Different kinds of RNA modifications have been recognized, such as methylation, acetylation, pseudouridylation, and phosphorylation. N6-methyladenosine (m6A), 5-methylcytosine (m5C), N7-methylguanosine (m7G), 2′-O-ribose methylation (2′-O-Me), and pseudouridylation (Ψ) are the most prevalent RNA modifications. Recent studies have shown that disruption in these modifications can interfere with gene expression and protein function. Here, we will review all types of RNA modifications and how they contribute to the onset and progression of OA. To the best of our knowledge, this is the first review comprehensively addressing all epitranscriptomic modifications in OA. Full article

RNA methylation, characterized by modifications such as N⁶-methyladenosine, 5-methylcytosine, and N¹-methyladenosine plays a crucial role in post-transcriptional gene regulation across diverse biological systems. While research on RNA methylation has predominantly focused on mammals, particularly its roles in epigenetic regulation and cancer biology, recent studies in insects have begun to explore their extensive functions in insect physiology. This review examines the mechanisms by which RNA methylation regulates growth, development, reproduction, environmental adaptation, and immune response in insects, providing insights into the biological characteristics of these organisms without prematurely speculating on pest control strategies. It aims to offer valuable insights into the role of RNA methylation in insect biology and resistance. Full article

DNA methylation, a cornerstone of epigenetic regulation, governs critical biological processes including transcriptional modulation, genomic imprinting, and transposon suppression through chromatin architecture remodeling. Recent advances have revealed that aberrant methylation patterns—characterized by spatial-temporal dysregulation and stochastic molecular noise—serve as key drivers of diverse pathological conditions, from oncogenesis to neurodegenerative disorders. However, the field faces dual challenges: (1) current understanding remains fragmented due to the inherent spatiotemporal heterogeneity of methylation landscapes across tissues and developmental stages, and (2) mechanistic insights into non-canonical methylation pathways (particularly 6mA) in non-mammalian systems are conspicuously underdeveloped. This review systematically synthesizes the evolutionary-conserved versus species-specific features of 5-methylcytosine (5mC) and N6-methyladenine (6mA) regulatory networks across three biological kingdoms. Through comparative analysis of methylation/demethylation enzymatic cascades (DNMTs/TETs in mammals, CMTs/ROS1 in plants, and DIM-2/DNMTA in fungi), we propose a unified framework for targeting methylation-associated diseases through precision epigenome editing, while identifying critical knowledge gaps in fungal methylome engineering that demand urgent investigation. Full article

N⁴-methylcytosine is a modified heterocyclic base present both in RNA and DNA. The biosynthesis and function of this derivative are widely investigated. However, how the demethylation of this base occurs is not known. Here, we have investigated the growth of an Escherichia coli uracil auxotroph strain in minimal M9 medium supplemented with N⁴-methylcytosine. We have found that this compound, but not the related N⁴,N⁴-dimethylcytosine, well supports growth with a generation time of the bacterium being 3 h compared to 1.5 h for media supplemented with cytosine or uracil. Using high-performance liquid chromatography (HPLC), we have demonstrated that the concentration of N⁴-methylcytosine in the growth medium decreases by 12% after 24 h of growth. We have shown that N⁴-methylcytosine is not directly converted into uracil by E. coli CodA cytosine deaminase. Instead, we propose the enzymatic pathway in which N⁴-methylcytosine is converted into cytosine by yet unknown demethylase, whereas CodA converts the resulting cytosine to uracil, thereby supporting the growth. Full article

Degenerative retinal diseases can lead to blindness if left untreated. At present, there are no curative therapies for retinal diseases. Therefore, effective treatment strategies for slowing the progression of retinal diseases and thus improving patients’ life standards are urgently needed. The present study aimed to assess the effect of sinusoidal electromagnetic field (EMF) (50 Hz, 1.3 mT) treatment for 15 and 30 min on spontaneously arising retinal pigment epithelial cells (ARPE-19) and retinal ganglion cells (RGC-5) and its short-term post-treatment significance. Our study indicated the beneficial impact of EMF treatment on the proliferative and migratory capacity of the tested cells. ARPE-19 and RGC-5 cells exposed to an EMF exhibited elevated levels of HO-1, increased N6-methyladenosine (m⁶A) and N5-methylcytosine (m⁵C) status mediated by METTL3 and NSUN2, respectively, and changes in levels of DNA damage repair factors, which may contribute to the regenerative properties of ARPE-19 and RGC-5 cells. Overall, this analysis showed that EMF (sinusoidal, 50 Hz, 1.3 mT) treatment may serve as a potential therapeutic strategy for retinal diseases. Full article

RNA modification is a key posttranscriptional process playing various biological roles, and one which has been reported to exist extensively in cellular RNAs. Interestingly, recent studies have shown that viral RNAs also contain a variety of RNA modifications, which are regulated dynamically by host modification machinery and play critical roles in different stages of the viral life cycle. In this review, we summarize the reports of four typical modifications reported on viral RNAs, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N4-acetylcytosine (ac4C), and N1-methyladenosine (m1A), describe the molecular mechanisms of these modification processes, and illustrate their impacts on viral replication, pathogenicity, and innate immune responses. Notably, we find that RNA modifications in different viruses share some common features and mechanisms in their generation, regulation, and function, highlighting the potential for viral RNA modifications and the related host machinery to serve as the targets or bases for the development of antiviral therapeutics and vaccines. Full article

The regulation of gene expression is crucial for maintaining cellular activities and responding to environmental stimuli. RNA molecules are central to this regulatory network, influencing transcription, post-transcriptional processing, and translation. Recent advancements have expanded our understanding of RNA modifications beyond the nucleus, highlighting their impact on chloroplast function and photosynthesis efficiency. Chloroplasts, essential for photosynthesis, rely on precise genetic regulation to adapt to environmental changes. RNA modifications, such as methylation and pseudouridylation, are critical in regulating chloroplast RNA stability, processing, and translation. This review summarizes current knowledge of how RNA modifications affect chloroplast function and photosynthesis. It discusses the roles of specific RNA modifications occurring in chloroplast RNA, including N6-methyladenosine (m⁶A), 5-methylcytosine (m⁵C), and pseudouridylation, as well as the enzymes which are known to be involved in these processes. This review also explores extrachloroplastic RNA modifications that influence chloroplast function, emphasizing the importance of m⁶A and m⁵C modifications and their associated enzymes. Full article

Both DNA 5-methylcytosine (5mC) and RNA N6-methyladenosine (m⁶A) modifications are reported to participate in cellular stress responses including inflammation. Phosphoenolpyruvate carboxykinase 2 (PCK2) is upregulated in Kupffer cells (KCs) to facilitate the proinflammatory phosphorylation signaling cascades upon LPS stimulation, yet the role of 5mC and m⁶A in PCK2 upregulation remain elusive. Here, we report that the significantly augmented PCK2 mRNA and protein levels are associated with global 5mC demethylation coupled with m⁶A hypermethylation in LPS-activated KCs. The suppression of 5mC demethylation or m⁶A hypermethylation significantly alleviates the upregulation of PCK2 and proinflammatory cytokines in LPS-challenged KCs. Further reciprocal tests indicate 5mC demethylation is upstream of m⁶A hypermethylation. Specifically, CpG islands in the promoters of PCK2 and RNA methyltransferase (METTL3 and METTL14) genes are demethylated, while the 3′UTR of PCK2 mRNA is m6A hypermethylated, in LPS-stimulated KCs. These modifications contribute to the transactivation of the PCK2 gene as well as increased PCK2 mRNA stability and protein production via a m⁶A-mediated mechanism with IGF2BP1 as the reader protein. These results indicate that DNA 5mC and RNA m6A collaborate to upregulate PCK2 expression, respectively, at the transcriptional and post-transcriptional levels during KC activation. Full article

N4-methylcytosine (4mC) is a critical epigenetic modification that plays a pivotal role in the regulation of a multitude of biological processes, including gene expression, DNA replication, and cellular differentiation. Traditional experimental methods for detecting DNA N4-methylcytosine sites are time-consuming, labor-intensive, and costly, making them unsuitable for large-scale or high-throughput research. Computational methods for identifying DNA N4-methylcytosine sites enable the rapid and cost-effective analysis of DNA 4mC sites across entire genomes. In this study, we focus on the identification of DNA 4mC sites in the mouse genome. Although there are already some computational methods that can predict DNA 4mC sites in the mouse genome, there is still significant room for improvement in accurately predicting them due to their inability to fully capture the multifaceted characteristics of DNA sequences. To address this issue, we propose a new deep learning predictor called Mus4mCPred, which utilizes multi-view feature learning and deep hybrid networks for accurately predicting DNA 4mC sites in the mouse genome. The predictor Mus4mCPred firstly employed different encoding methods to extract the feature vectors of DNA sequences, then input these features generated by different encoding methods into various hybrid deep learning models for the learning and extraction of more sophisticated representations of these features, and finally fused the extracted multi-view features to serve as the final features for DNA 4mC site prediction in the mouse genome. Multi-view features enabled the more comprehensive capture of data characteristics, enhancing the feature representation of DNA sequences. The independent test results showed that the sensitivity (Sn), specificity (Sp), accuracy (Acc), and Matthews’ correlation coefficient (MCC) were 0.7688, 0.9375, 0.8531, and 0.7165, respectively. The predictor Mus4mCPred outperformed other state-of-the-art methods, achieving the accurate identification of 4mC sites in the mouse genome. Full article

Many contaminated soils contain several toxic elements (TEs) in elevated contents, and plant–TE interactions can differ from single TE contamination. Therefore, this study investigated the impact of combined contamination (As, Cd, Pb, Zn) on the physiological and metabolic processes of lettuce. After 45 days of exposure, TE excess in soil resulted in the inhibition of root and leaf biomass by 40 and 48%, respectively. Oxidative stress by TE accumulation was indicated by markers—malondialdehyde and 5-methylcytosine—and visible symptoms of toxicity (leaf chlorosis, root browning) and morpho-anatomical changes, which were related to the change in water regime (water potential decrease). An analysis of free amino acids (AAs) indicated that TEs disturbed N and C metabolism, especially in leaves, increasing the total content of free AAs and their families. Stress-induced senescence by TEs suggested changes in gas exchange parameters (increase in transpiration rate, stomatal conductance, and intercellular CO₂ concentration), photosynthetic pigments (decrease in chlorophylls and carotenoids), a decrease in water use efficiency, and the maximum quantum yield of photosystem II. These results confirmed that the toxicity of combined contamination significantly affected the processes of lettuce by damaging the antioxidant system and expressing higher leaf sensitivity to TE multicontamination. Full article