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Experimental & Molecular Medicine Apr 2017Histone modifications are key epigenetic regulatory features that have important roles in many cellular events. Lysine methylations mark various sites on the tail and... (Review)
Review
Histone modifications are key epigenetic regulatory features that have important roles in many cellular events. Lysine methylations mark various sites on the tail and globular domains of histones and their levels are precisely balanced by the action of methyltransferases ('writers') and demethylases ('erasers'). In addition, distinct effector proteins ('readers') recognize specific methyl-lysines in a manner that depends on the neighboring amino-acid sequence and methylation state. Misregulation of histone lysine methylation has been implicated in several cancers and developmental defects. Therefore, histone lysine methylation has been considered a potential therapeutic target, and clinical trials of several inhibitors of this process have shown promising results. A more detailed understanding of histone lysine methylation is necessary for elucidating complex biological processes and, ultimately, for developing and improving disease treatments. This review summarizes enzymes responsible for histone lysine methylation and demethylation and how histone lysine methylation contributes to various biological processes.
Topics: Animals; Histone Code; Histone Demethylases; Histone-Lysine N-Methyltransferase; Histones; Humans; Methylation; Protein Processing, Post-Translational
PubMed: 28450737
DOI: 10.1038/emm.2017.11 -
Analytical Methods : Advancing Methods... May 2023Methylation of cytosine to 5-methylcytosine on CpG dinucleotides is the most frequently studied epigenetic modification involved in the regulation of gene expression. In...
Methylation of cytosine to 5-methylcytosine on CpG dinucleotides is the most frequently studied epigenetic modification involved in the regulation of gene expression. In normal tissues, tissue-specific CpG methylation patterns are established during development. In contrast, alterations in methylation patterns have been observed in abnormal cells, such as cancer cells. Cancer type-specific CpG methylation patterns have been identified and used as biomarkers for cancer diagnosis. In this study, we developed a hybridization-based CpG methylation level sensing system using a methyl-CpG-binding domain (MBD)-fused fluorescent protein. In this system, the target DNA is captured by a complementary methylated probe DNA. When the target DNA is methylated, a symmetrically methylated CpG is formed in the double-stranded DNA. MBD specifically recognizes symmetrical methyl-CpG on double-stranded DNA; therefore, the methylation level is quantified by measuring the fluorescence intensity of the bound MBD-fused fluorescent protein. We prepared MBD-fused AcGFP1 and quantified the CpG methylation levels of the target DNA against , , and long interspersed nuclear element-1 (LINE-1) using MBD-AcGFP1. This detection principle can be applied to the simultaneous and genome-wide modified base detection systems using microarrays coupled with modified base binding proteins fused to fluorescent proteins.
Topics: DNA-Binding Proteins; CpG Islands; DNA Methylation; Cytosine; DNA
PubMed: 37010025
DOI: 10.1039/d3ay00227f -
Oncogene May 2001Recent findings suggest that lysine and arginine-specific methylation of histones may cooperate with other types of post-translational histone modification to regulate... (Review)
Review
Recent findings suggest that lysine and arginine-specific methylation of histones may cooperate with other types of post-translational histone modification to regulate chromatin structure and gene transcription. Proteins that methylate histones on arginine residues can collaborate with other coactivators to enhance the activity of specific transcriptional activators such as nuclear receptors. Lysine methylation of histones is associated with transcriptionally active nuclei, regulates other types of histone modifications, and is necessary for proper mitotic cell divisions. The fact that some transcription factors and proteins involved in RNA processing can also be methylated suggests that protein methylation may also contribute in other ways to regulation of transcription and post-transcriptional steps in gene regulation. In future work, it will be important to develop methods for evaluating the precise roles of protein methylation in the regulation of native genes in physiological settings, e.g. by using chromatin immunoprecipitation assays, differentiating cell culture systems, and genetically altered cells and animals. It will also be important to isolate additional protein methyltransferases by molecular cloning and to characterize new methyltransferase substrates, the regulation of methyltransferase activities, and the roles of new methyltransferases and substrates.
Topics: Animals; Chromatin; Gene Expression Regulation; Histones; Humans; Methylation; Proteins; Transcription, Genetic
PubMed: 11420716
DOI: 10.1038/sj.onc.1204325 -
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 -
Journal of Proteome Research Oct 2023Protein methylation is receiving more and more attention due to its essential role in diverse biological processes. Large-scale analysis of protein methylation requires...
Protein methylation is receiving more and more attention due to its essential role in diverse biological processes. Large-scale analysis of protein methylation requires the efficient identification of methylated peptides at the proteome level; unfortunately, a significant number of methylated peptides are highly hydrophilic and hardly retained during reversed-phase chromatography, making it difficult to be identified by conventional approaches. Herein, we report the development of a novel strategy by combining hydrophobic derivatization and high pH strong cation exchange enrichment, which significantly expands the identification coverage of the methylproteome. Noteworthily, the total number of identified methylated short peptides was improved by more than 2-fold. By this strategy, we identified 492 methylation sites from NCI-H460 cells compared to only 356 sites identified in native forms. The identification of methylation sites before and after derivatization was highly complementary. Approximately 2-fold the methylation sites were obtained by combining the results identified in both approaches (native and derivatized) as compared with the only analysis in native forms. Therefore, this novel chemical derivatization strategy is a promising approach for the comprehensive identification of protein methylation by improving the identification of methylated short peptides.
Topics: Methylation; Peptides; Protein Processing, Post-Translational; Chromatography, Reverse-Phase; Proteome
PubMed: 37738134
DOI: 10.1021/acs.jproteome.3c00318 -
Pharmacological Research Dec 2009Post-translational modifications are well-known effectors in DNA damage signaling and epigenetic gene expression. Protein arginine methylation is a covalent modification... (Review)
Review
Post-translational modifications are well-known effectors in DNA damage signaling and epigenetic gene expression. Protein arginine methylation is a covalent modification that results in the addition of methyl groups to the nitrogen atoms of the arginine side chains and is catalyzed by a family of protein arginine methyltransferases (PRMTs). In the past, arginine methylation was mainly observed on abundant proteins such as RNA-binding proteins and histones, but recent advances have revealed a plethora of arginine-methylated proteins implicated in a variety of cellular processes including signal transduction, epigenetic regulation and DNA repair pathways. Herein, we discuss these recent advances, focusing on the role of PRMT1, the major asymmetric arginine methyltransferase, in cellular processes and its link to human diseases.
Topics: Animals; DNA Methylation; Heart Diseases; Humans; Kidney Diseases; Methylation; Neoplasms; Protein-Arginine N-Methyltransferases; Repressor Proteins
PubMed: 19643181
DOI: 10.1016/j.phrs.2009.07.006 -
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 -
Brain Research Mar 2019Lysine methylation is well-documented and relatively well-understood with respect to histone modification and the epigenetic regulation of gene expression. Enzymes... (Review)
Review
Lysine methylation is well-documented and relatively well-understood with respect to histone modification and the epigenetic regulation of gene expression. Enzymes called lysine methyltransferases (KMTs) are capable of methylating lysine residues on histone tails, while the opposing lysine demethylases (KDMs) are capable of removing the methyl groups. This balance of dynamic methylation of histone proteins effectively alters gene expression, and has been widely studied with many applications in neurological disease. While histone methylation is an extensive field of research, lysine methylation has received considerable attention in recent years, following the discovery of a handful of non-histone substrates for KMTs. With the expanding repertoire of non-histone substrates, exploration into the cellular functions regulated by this dynamic post-translational modification has become an intriguing research question. Recent studies have implicated non-histone methylation in many crucial cell processes, such as signal transduction, apoptosis, and proliferation. Although most of the current research in this emerging field is streamlined for applications in cancer, it seems that lysine methylation of non-histone proteins could also be relevant in neurodegenerative disease. This review will summarize what is known about the role of histone lysine methylation in neurodegenerative diseases, and explore the links between recently identified non-histone methylated proteins, and the brain. Our goal is to connect the emerging field of non-histone protein methylation with neurodegenerative research.
Topics: Animals; Epigenesis, Genetic; Histone-Lysine N-Methyltransferase; Histones; Humans; Lysine; Methylation; Neurodegenerative Diseases; Protein Processing, Post-Translational; Signal Transduction
PubMed: 30465751
DOI: 10.1016/j.brainres.2018.11.024 -
IEEE/ACM Transactions on Computational... 2019DNA methylation is a critical epigenetic modification that plays an important role in cancers. The available algorithms fail to fully characterize epigenetic modules. To...
DNA methylation is a critical epigenetic modification that plays an important role in cancers. The available algorithms fail to fully characterize epigenetic modules. To address this issue, we first characterize the epigenetic module as a group of well-connected genes in the protein interaction network and are also co-methylated based on gene methylation profiles. Then, the epigenetic module discovery problem is transformed into an optimization problem. Then, a regularized nonnegative matrix factorization algorithm for methylation modules (RNMF-MM) is presented, where the co-methylation constraint is treated as a regularizer. Using the artificial networks with known module structure, we demonstrate that the proposed algorithm outperforms state-of-the-art approaches in terms of accuracy. On the basis of breast cancer methylation data and protein interaction network, the RNMF-MM algorithm discovers methylation modules that are significantly more enriched by the known pathways than those obtained by other algorithms. These modules serve as biomarkers for predicting cancer stages and estimating survival time of patients. The proposed model and algorithm provide an effective way for the integrative analysis of protein interaction network and methylation data.
Topics: Algorithms; Biomarkers; Breast Neoplasms; Computational Biology; DNA Methylation; Epigenesis, Genetic; Female; Gene Expression Regulation, Neoplastic; Humans; Kaplan-Meier Estimate; Methylation; Models, Statistical; Neural Networks, Computer; Protein Interaction Mapping; Proteins
PubMed: 29994031
DOI: 10.1109/TCBB.2018.2831666 -
Amino Acids 1998Heterogeneous nuclear RNP protein A1, one of the major proteins in hnRNP particle (precursor for mRNA), is known to be posttranslationally arginine-methylated in vivo on... (Comparative Study)
Comparative Study Review
Heterogeneous nuclear RNP protein A1, one of the major proteins in hnRNP particle (precursor for mRNA), is known to be posttranslationally arginine-methylated in vivo on residues 193, 205, 217 and 224 within the RGG box, the motif postulated to be an RNA binding domain. Possible effect of NG-arginine methyl-modification in the interaction of protein A1 to nucleic acid was investigated. The recombinant hnRNP protein A1 was in vitro methylated by the purified nuclear protein/histone-specific protein methylase I (S-adenosylmethionine:protein-arginine N-methyltransferase) stoichiometrically and the relative binding affinity of the methylated and the unmethylated protein A1 to nucleic acid was compared: Differences in their binding properties to ssDNA-cellulose, pI values and trypsin sensitivities in the presence and absence of MS2-RNA all indicate that the binding property of hnRNP protein A1 to single-stranded nucleic acid has been significantly reduced subsequent to the methylation. These results suggest that posttranslational methyl group insertion to the arginine residue reduces protein-RNA interaction, perhaps due to interference of H-bonding between guanidino nitrogen arginine and phosphate RNA.
Topics: Amino Acid Sequence; Animals; Brain; Cattle; Heterogeneous Nuclear Ribonucleoprotein A1; Heterogeneous-Nuclear Ribonucleoprotein Group A-B; Heterogeneous-Nuclear Ribonucleoproteins; Liver; Methylation; Models, Chemical; Molecular Sequence Data; Nuclear Proteins; Protein Processing, Post-Translational; Protein-Arginine N-Methyltransferases; Rats; Ribonucleoproteins; Time Factors
PubMed: 9891755
DOI: 10.1007/BF01320895