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Expert Reviews in Molecular Medicine Mar 2021Methylation at DNA, RNA and protein levels plays critical roles in many cellular processes and is associated with diverse differentiation events, physiological... (Review)
Review
Methylation at DNA, RNA and protein levels plays critical roles in many cellular processes and is associated with diverse differentiation events, physiological activities and human diseases. To aid in the diagnostic and therapeutic design for cancer treatment utilising methylation, this review provides a boutique yet comprehensive overview on methylation at different levels including the mechanisms, cross-talking and clinical implications with a particular focus on cancers. We conclude that DNA methylation is the sole type of methylation that has been largely translated into clinics and used for, mostly, early diagnosis. Translating the onco-therapeutic and prognostic values of RNA and protein methylations into clinical use deserves intensive efforts. Simultaneous examination of methylations at multiple levels or together with other forms of molecular markers represents an interesting research direction with profound clinical translational potential.
Topics: DNA Methylation; Humans; Neoplasms; Protein Processing, Post-Translational
PubMed: 33787478
DOI: 10.1017/erm.2021.4 -
Current Opinion in Structural Biology Dec 2020The amide bond with its planarity and lack of chemical reactivity is at the heart of protein structure. Chemical methylation of amides is known but was considered too... (Review)
Review
The amide bond with its planarity and lack of chemical reactivity is at the heart of protein structure. Chemical methylation of amides is known but was considered too harsh to be accessible to biology. Until last year there was no protein structure in the data bank with an enzymatically methylated amide. The discovery that the natural macrocyclic product, omphalotin is ribosomally synthesized, was not as had been assumed by non-ribosomal peptide synthesis. This was the first definitive evidence that an enzyme could methylate the amide bond. The enzyme, OphMA, iteratively self-hypermethylates its own C-terminus using SAM as cofactor. A second enzyme OphP, a prolyl oligopeptidase cleaves the core peptide from OphMA and cyclizes it into omphalotin. The molecular mechanism for OphMA was elucidated by mutagenesis, structural, biochemical and theoretical studies. This review highlights current progress in peptide N-methylating enzymes.
Topics: Amides; Cyclosporine; Methylation; Peptides, Cyclic; Protein Processing, Post-Translational; Proteins
PubMed: 32653730
DOI: 10.1016/j.sbi.2020.06.004 -
American Journal of Physiology. Cell... Oct 2019Compelling evidence indicates that epigenetic regulations orchestrate dynamic macrophage polarization. -methyladenosine (mA) methylation is the most abundant epigenetic...
Compelling evidence indicates that epigenetic regulations orchestrate dynamic macrophage polarization. -methyladenosine (mA) methylation is the most abundant epigenetic modification of mammalian mRNA, but its role in macrophage polarization is still completely unknown. Here, we show that the mA-catalytic enzyme methyltransferase like 3 (METTL3) is specifically upregulated following the M1 polarization of mouse macrophages. Furthermore, METTL3 knockdown through siRNA transfection markedly inhibited M1, but enhanced M2, macrophage polarization. Conversely, its overexpression via plasmid transfection greatly facilitated M1, but attenuated M2, macrophage polarization. Further methylated RNA immunoprecipitation and in vitro mA methylation assays suggested that METTL3 directly methylates mRNA encoding signal transducer and activator of transcription 1 (STAT1), a master transcription factor controlling M1 macrophage polarization, at its coding sequence and 3'-untranslated regions. In addition, METTL3-mediated mRNA methylation significantly increased mRNA stability and subsequently upregulated STAT1 expression. In conclusion, METTL3 drives M1 macrophage polarization by directly methylating mRNA, potentially serving as an anti-inflammatory target.
Topics: Adenosine; Animals; Anti-Inflammatory Agents; Gene Expression Regulation; Macrophage Activation; Macrophages; Male; Methylation; Methyltransferases; Mice, Inbred C57BL; RNA, Messenger; STAT1 Transcription Factor
PubMed: 31365297
DOI: 10.1152/ajpcell.00212.2019 -
Topics in Current Chemistry (Cham) May 2022Direct reductive N-methylation of inexpensive and readily available nitro compounds as raw material feedstocks is more attractive and straightforward compared with... (Review)
Review
Direct reductive N-methylation of inexpensive and readily available nitro compounds as raw material feedstocks is more attractive and straightforward compared with conventional N-methylation of amines to prepare biologically and pharmaceutically important N-methylated amine derivatives. This strategy for synthesis of N-methylamines avoids prepreparation of NH-free amines and therefore significantly shortens the separation and purification steps. In recent years, numerous methylating agents and catalytic systems have been reported for this appealing transformation. Thus, it is an appropriate time to summarize such advances. This review elaborates on the most important discoveries and advances in this research arena, with special emphasis on the mechanistic aspect of reactions that may provide new insights into catalyst improvement.
Topics: Amines; Catalysis; Methylation; Nitro Compounds
PubMed: 35606628
DOI: 10.1007/s41061-022-00382-w -
Journal of the History of Biology Dec 2022DNA methylation is a quintessential epigenetic mechanism. Widely considered a stable regulator of gene silencing, it represents a form of "molecular braille," chemically... (Review)
Review
DNA methylation is a quintessential epigenetic mechanism. Widely considered a stable regulator of gene silencing, it represents a form of "molecular braille," chemically printed on DNA to regulate its structure and the expression of genetic information. However, there was a time when methyl groups simply existed in cells, mysteriously speckled across the cytosine building blocks of DNA. Why was the code of life chemically modified, apparently by "no accident of enzyme action" (Wyatt 1951)? If all cells in a body share the same genome sequence, how do they adopt unique functions and maintain stable developmental states? Do cells remember? In this historical perspective, I review epigenetic history and principles and the tools, key scientists, and concepts that brought us the synthesis and discovery of prokaryotic and eukaryotic methylated DNA. Drawing heavily on Gerard Wyatt's observation of asymmetric levels of methylated DNA across species, as well as to a pair of visionary 1975 DNA methylation papers, 5-methylcytosine is connected to DNA methylating enzymes in bacteria, the maintenance of stable cellular states over development, and to the regulation of gene expression through protein-DNA binding. These works have not only shaped our views on heritability and gene regulation but also remind us that core epigenetic concepts emerged from the intrinsic requirement for epigenetic mechanisms to exist. Driven by observations across prokaryotic and eukaryotic worlds, epigenetic systems function to access and interpret genetic information across all forms of life. Collectively, these works offer many guiding principles for our epigenetic understanding for today, and for the next generation of epigenetic inquiry in a postgenomics world.
Topics: DNA Methylation; Epigenesis, Genetic; DNA; Gene Silencing; Eukaryota; Writing
PubMed: 36239862
DOI: 10.1007/s10739-022-09691-8 -
Bioorganic Chemistry Dec 2023Peptide-based drugs have garnered considerable attention in recent years owing to their increasingly crucial role in the treatment of diverse diseases. However, the... (Review)
Review
Peptide-based drugs have garnered considerable attention in recent years owing to their increasingly crucial role in the treatment of diverse diseases. However, the limited pharmacokinetic properties of peptides have hindered their full potential. One prominent strategy for enhancing the druggability of peptides is N-methylation, which involves the addition of a methyl group to the nitrogen atom of the peptide backbone. This modification significantly improves the stability, bioavailability, receptor binding affinity and selectivity of peptide drug candidates. In this review, we provide a comprehensive overview of the advancements in synthetic methods for N-methylated peptide synthesis, as well as the associated limitations. Moreover, we explore the versatile effects of N-methylation on various aspects of peptide properties. Furthermore, we emphasize the efforts dedicated to N-methylated peptide pharmaceuticals that have successfully obtained marketing approval.
Topics: Methylation; Peptides; Drug Development; Nitrogen; Pharmaceutical Preparations
PubMed: 37776681
DOI: 10.1016/j.bioorg.2023.106892 -
Environmental Science & Technology Jan 2019Methylmercury (MeHg) is an environmental contaminant of concern because it biomagnifies in aquatic food webs and poses a health hazard to aquatic biota, piscivorous... (Review)
Review
Methylmercury (MeHg) is an environmental contaminant of concern because it biomagnifies in aquatic food webs and poses a health hazard to aquatic biota, piscivorous wildlife and humans. The dominant source of MeHg to freshwater systems is the methylation of inorganic Hg (IHg) by anaerobic microorganisms; and it is widely agreed that in situ rates of Hg methylation depend on two general factors: the activity of Hg methylators and their uptake of IHg. A large body of research has focused on the biogeochemical processes that regulate these two factors in nature; and studies conducted within the past ten years have made substantial progress in identifying the genetic basis for intracellular methylation and defining the processes that govern the cellular uptake of IHg. Current evidence indicates that all Hg methylating anaerobes possess the gene pair hgcAB that encodes proteins essential for Hg methylation. These genes are found in a large variety of anaerobes, including iron reducers and methanogens; but sulfate reduction is the metabolic process most often reported to show strong links to MeHg production. The uptake of Hg substrate prior to methylation may occur by passive or active transport, or by a combination of both. Competitive inhibition of Hg uptake by Zn speaks in favor of active transport and suggests that essential metal transporters are involved. Shortly after its formation, MeHg is typically released from cells, but the efflux mechanisms are unknown. Although methylation facilitates Hg depuration from the cell, evidence suggests that the hgcAB genes are not induced or favored by Hg contamination. Instead, high MeHg production can be linked to high Hg bioavailability as a result of the formation of Hg(SH), HgS nanoparticles, and Hg-thiol complexes. It is also possible that sulfidic conditions require strong essential metal uptake systems that inadvertently bring Hg into the cytoplasm of Hg methylating microbes. In comparison with freshwaters, Hg methylation in open ocean waters appears less restricted to anoxic environments. It does seem to occur mainly in oxygen deficient zones (ODZs), and possibly within anaerobic microzones of settling organic matter, but MeHg (CHHg) and MeHg ((CH)Hg) have been shown to form also in surface water samples from the euphotic zone. Future studies may disclose whether several different pathways lead to Hg methylation in marine waters and explain why MeHg is a significant Hg species in oceans but seemingly not in most freshwaters.
Topics: Food Chain; Humans; Mercury; Methylation; Methylmercury Compounds; Sulfides; Water Pollutants, Chemical
PubMed: 30525497
DOI: 10.1021/acs.est.8b02709 -
Organic & Biomolecular Chemistry Jul 2022The clinically used DNA-alkylating drug streptozotocin (STZ) was investigated using a simple work-up as an -methylating agent to transform various carboxylic acids,...
The clinically used DNA-alkylating drug streptozotocin (STZ) was investigated using a simple work-up as an -methylating agent to transform various carboxylic acids, sulfonic acids and phosphorous acids into corresponding methyl esters, and did so with yields of up to 97% in 4 h at room temperature. Good substrate tolerance was observed, and benefited from the mild conditions and compatibility of the reaction with water.
Topics: Carboxylic Acids; DNA; Esters; Methylation; Streptozocin
PubMed: 35621003
DOI: 10.1039/d2ob00578f -
Open Biology Sep 2018RNA methylations play a significant regulatory role in diverse biological processes. Although the transcriptome-wide discovery of unknown RNA methylation sites is... (Review)
Review
RNA methylations play a significant regulatory role in diverse biological processes. Although the transcriptome-wide discovery of unknown RNA methylation sites is essential to elucidate their function, the development of a bigger variety of detection approaches is desirable for multiple reasons. Many established detection methods for RNA modifications heavily rely on the specificity of the respective antibodies. Thus, the development of antibody-independent transcriptome-wide methods is beneficial. Even the antibody-independent high-throughput sequencing-based methods are liable to produce false-positive or false-negative results. The development of an independent method for each modification could help validate the detected modification sites. Apart from the transcriptome-wide methods for methylation detection , methods for monitoring the presence of a single methylation at a determined site are also needed. In contrast to the transcriptome-wide detection methods, the techniques used for monitoring purposes need to be cheap, fast and easy to perform. This review considers modern approaches for site-specific detection of methylated nucleotides in RNA. We also discuss the potential of third-generation sequencing methods for direct detection of RNA methylations.
Topics: Humans; Methylation; RNA; Sequence Analysis, RNA; Exome Sequencing
PubMed: 30185602
DOI: 10.1098/rsob.180121 -
Wiley Interdisciplinary Reviews.... 2010DNA methylation plays a critical role in the regulation of gene expression. The ability to access the methylation status for a large number of genes or the entire genome... (Review)
Review
DNA methylation plays a critical role in the regulation of gene expression. The ability to access the methylation status for a large number of genes or the entire genome should greatly facilitate the understanding of the nature of gene regulation in cells, and epigenetic mechanism of interactions between cells and environment. Microarray and sequencing-based DNA methylation profiling technologies have been developed to meet this goal. These methods can be categorized into three main classes based on how the methylation status is interrogated: discrimination of bisulfite induced C to T transition; cleavage of genomic DNA by methylation-sensitive restriction enzymes; and immunoprecipitation with methyl-binding protein or antibodies against methylated cytosines. With the development of next-generation sequencing technologies, genome-wide bisulfite sequencing has become a reality. Either whole- or reduced-genome approaches have been used to get the most comprehensive DNA methylation profiles in organisms of various genome sizes.
Topics: Base Sequence; DNA; DNA Methylation; Epigenesis, Genetic; Gene Expression Profiling; Genome; Humans; Methylation; Oligonucleotide Array Sequence Analysis; Sulfites
PubMed: 20836023
DOI: 10.1002/wsbm.35