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Cold Spring Harbor Symposia on... 1993DNA methylation is ancestrally a mechanism for neutralizing potentially damaging DNA elements in the genome. The genomes of most multicellular organisms contain a small... (Review)
Review
DNA methylation is ancestrally a mechanism for neutralizing potentially damaging DNA elements in the genome. The genomes of most multicellular organisms contain a small fraction of methylated DNA that contains the methylated elements, whereas the organism's own genes remain free of methylation. Vertebrates are exceptional among animals in that their genomes, including genes, are predominantly methylated. They retain the ability to inactivate viral DNA but have recruited the DNA methylation system for new functions. Widespread low-density methylation can contribute to lowering of the level of transcriptional "noise" from cryptic or inappropriate promoters. This may be the major advantage of DNA methylation in these organisms and may be sufficiently beneficial to offset the disadvantage of m5C mutability. The other novel feature of DNA methylation in vertebrates is the capacity to de novo methylate certain CpG islands, causing long-term strong repression. These evolutionary innovations may explain the high complexity of vertebrate organs and cell types.
Topics: 5-Methylcytosine; Animals; Binding Sites; Biological Evolution; Cytosine; DNA; Genes, Regulator; Genome; Methylation; Transcription, Genetic; Vertebrates
PubMed: 7956040
DOI: 10.1101/sqb.1993.058.01.033 -
The Journal of Experimental Biology Jul 2020The epigenome determines heritable patterns of gene expression in the absence of changes in DNA sequence. The result is programming of different cellular-, tissue- and... (Review)
Review
The epigenome determines heritable patterns of gene expression in the absence of changes in DNA sequence. The result is programming of different cellular-, tissue- and organ-specific phenotypes from a single organismic genome. Epigenetic marks that comprise the epigenome (e.g. methylation) are placed upon or removed from chromatin (histones and DNA) to direct the activity of effectors that regulate gene expression and chromatin structure. Recently, the cytoskeleton has been identified as a second target for the cell's epigenetic machinery. Several epigenetic 'readers, writers and erasers' that remodel chromatin have been discovered to also remodel the cytoskeleton, regulating structure and function of microtubules and actin filaments. This points to an emerging paradigm for dual-function remodelers with 'chromatocytoskeletal' activity that can integrate cytoplasmic and nuclear functions. For example, the SET domain-containing 2 methyltransferase (SETD2) has chromatocytoskeletal activity, methylating both histones and microtubules. The SETD2 methyl mark on chromatin is required for efficient DNA repair, and its microtubule methyl mark is required for proper chromosome segregation during mitosis. This unexpected convergence of SETD2 activity on histones and microtubules to maintain genomic stability suggests the intriguing possibility of an expanded role in the cell for chromatocytoskeletal proteins that read, write and erase methyl marks on the cytoskeleton as well as chromatin. Coordinated use of methyl marks to remodel both the epigenome and the (epi)cytoskeleton opens the possibility for integrated regulation (which we refer to as 'epiregulation') of other higher-level functions, such as muscle contraction or learning and memory, and could even have evolutionary implications.
Topics: Chromatin; Cytoskeleton; DNA Methylation; Epigenesis, Genetic; Epigenome; Histones; Methylation; Microtubules
PubMed: 32620673
DOI: 10.1242/jeb.220632 -
Journal of the American Chemical Society Feb 2023Methyl groups are well understood to play a critical role in pharmaceutical molecules, especially those bearing saturated heterocyclic cores. Accordingly, methods that...
Methyl groups are well understood to play a critical role in pharmaceutical molecules, especially those bearing saturated heterocyclic cores. Accordingly, methods that install methyl groups onto complex molecules are highly coveted. Late-stage C-H functionalization is a particularly attractive approach, allowing chemists to bypass lengthy syntheses and facilitating the expedited synthesis of drug analogues. Herein, we disclose the direct introduction of methyl groups via C()-H functionalization of a broad array of saturated heterocycles, enabled by the merger of decatungstate photocatalysis and a unique nickel-mediated S2 bond formation. To further demonstrate its synthetic utility as a tool for late-stage functionalization, this method was applied to a range of drug molecules en route to an array of methylated drug analogues.
Topics: Methylation; Nickel
PubMed: 36696091
DOI: 10.1021/jacs.2c13396 -
Physical Chemistry Chemical Physics :... Nov 2022UV and VUV-induced processes in DNA/RNA nucleobases are central to understand photo-damaging and photo-protecting mechanisms in our genetic material. Here we model the...
UV and VUV-induced processes in DNA/RNA nucleobases are central to understand photo-damaging and photo-protecting mechanisms in our genetic material. Here we model the events following photoionisation and electronic excitation in uracil, methylated in the 1' and 3' positions, using the correlated XMS-CASPT2 method. We compare our results against those for uracil and 5-methyl-uracil (thymine) previously published. We find 3-methylation, an epigenetic modification in non-negligible amounts, shows the largest differences in photoionised decay of all three derivatives studied compared to uracil itself. At the S minimum, 3-methyl-uracil (3mUra) shows almost degenerate excited cation states. Upon populating the cation manifold, a crossing is predicted featuring different topography compared to other methylated uracil species in this study. We find an effective 3-state conical intersection accessible for 3mUra, which points towards an additional pathway for radiationless decay. 3-Methylation reduces the potential energy barrier mediating decay to the cation ground state, making it vanish and leading to a pathway that we expect will contribute to the fastest radiationless decay amongst all methylated uracil species studied to date. 1- and 5-methylation, on the other hand, give differences from uracil in detail only: ionisation potentials are slightly red-shifted and the potential energy barrier mediating decay to the cation ground state is small but almost unchanged. By comparing against CASSCF calculations, we establish XMS-CASPT2 is essential to correctly describe conical intersections for 3mUra. Our calculations show how a chemical modification that seems relatively small electronically can nevertheless have a significant impact on the behaviour of electronic excited states: a single methylation in the 3' position alters the behaviour of the RNA base uracil and appears to open an additional pathway for radiationless decay following ionisation and electronic excitation.
Topics: Uracil; Methylation; Thymine; RNA
PubMed: 36321485
DOI: 10.1039/d2cp03460c -
Biochemistry. Biokhimiia May 2005In eukaryotic cells nuclear DNA is subjected to enzymatic methylation resulting in formation of 5-methylcytosine residues mainly in CG and CNG sequences. In plants and... (Review)
Review
In eukaryotic cells nuclear DNA is subjected to enzymatic methylation resulting in formation of 5-methylcytosine residues mainly in CG and CNG sequences. In plants and animals, this DNA methylation is species-, tissue-, and organelle-specific. It changes (diminishes) with age and is regulated by hormones. On the other hand, genome methylation can control hormonal signal. There are replicative and post-replicative DNA methylations. They are served by multiple DNA-methyltransferases with different site specificity. Replication is accompanied by appearance of hemi-methylated sites in DNA; pronounced asymmetry of DNA chain methylation disappears at the end of the cell cycle; a model of regulation of replication by DNA methylation is suggested. DNA methylation controls all genetic processes in the cell (replication, transcription, DNA repair, recombination, gene transposition) and it is a mechanism of cell differentiation, gene discrimination, and silencing. Prohibition of DNA methylation stops development (embryogenesis), switches on apoptosis, and is usually lethal. Distortions in DNA methylations result in cancerous cell transformation, and the DNA methylation pattern is one of the safe cancer diagnostics at early stages of carcinogenesis. The malignant cell has a different DNA methylation pattern and a set of DNA-methyltransferase activities expressed as compared with normal cells. Inhibition of DNA methylation in plants is accompanied by induction of genes of seed storage proteins and flowering. In eukaryotes one and the same gene can be methylated both on cytosine and adenine residues; thus, there are, at least, two different and probably interdependent systems of DNA methylation in the cell. First higher eukaryotic adenine DNA-methyltransferase was isolated from plants; this enzyme methylates DNA with formation of N6-methyladenine residues in the sequence TGATCA --> TGm6ATCA. Plants have AdoMet-dependent endonucleases sensitive to DNA methylation status; therefore, like microorganisms, plants seem to have a restriction-modification (R-S) system. Revelation of an essential role of DNA methylation in the regulation of genetic processes has laid a foundation for and materialized epigenetics and epigenomics.
Topics: Animals; Cell Cycle; Chromatin; DNA Methylation; DNA Modification Methylases; DNA, Plant; Epigenesis, Genetic; Gene Silencing
PubMed: 15948703
DOI: 10.1007/s10541-005-0143-y -
Cellular and Molecular Neurobiology 2006: 1. DNA methylation is a critical epigenetic modification that silences gene transcription, participates in X-chromosome inactivation in females, and regulates genomic... (Review)
Review
: 1. DNA methylation is a critical epigenetic modification that silences gene transcription, participates in X-chromosome inactivation in females, and regulates genomic imprinting. 2. We have devised a method to inhibit transcriptional initiation by constructing short methylated oligonucleotides which induce DNA methylation at specific loci. 3. The methodology by which we devise these oligonucleotides is described, using oligonucleotides directed against the oncogene, Bcl-2.4. The human Bcl-2 gene contains two promoters, each of which contains a CpG island in its core region. Oligonucleotides are designed which can inhibit Bcl-2 transcription and lead to decreased mRNA and protein in vitro. When compared to standard anti-sense oligonucleotide action, these methylated oligonucleotides are far more sensitive and potentially, longer acting. 5. In principle, using this methodology, it should be possible to design methylated oligonucleotides that can methylate CpG islands and thereby downregulate any gene.
Topics: Animals; Base Sequence; DNA Methylation; Gene Expression Regulation; Gene Silencing; Genes, bcl-2; Genetic Therapy; Humans; Insulin-Like Growth Factor II; Models, Biological; Molecular Sequence Data; Neoplasms; Proteins
PubMed: 16710755
DOI: 10.1007/s10571-006-9057-5 -
Genetika Sep 2006In eukaryotic cells, nuclear DNA is subject to enzymatic methylation with the formation of 5-methylcytosine residues, mostly within the CG and CNG sequences. In plants... (Review)
Review
In eukaryotic cells, nuclear DNA is subject to enzymatic methylation with the formation of 5-methylcytosine residues, mostly within the CG and CNG sequences. In plants and animals this DNA methylation is species-, tissue-, and organelle-specific. It changes (decreases) with age and is regulated by hormones. On the other hand, genome methylation can control hormonal signal. Replicative and post-replicative DNA methylation types are distinguished. They are mediated by multiple DNA methyltransferases with different site-specificity. Replication is accompanied by the appearance of hemimethylated DNA sites. Pronounced asymmetry of the DNA strand methylation disappears to the end of the cell cycle. A model of methylation-regulated DNA replication is proposed. DNA methylation controls all genetic processes in the cell (replication, transcription, DNA repair, recombination, and gene transposition). It is the mechanism of cell differentiation, gene discrimination and silencing. In animals, suppression of DNA methylation stops development (embryogenesis), switches on apoptosis, and is usually lethal. Disruption of DNA methylation pattern results in the malignant cell transformation and serves as one of the early diagnostic features of carcinogenesis. In malignant cell the pattern of DNA methylation, as well as the set of DNA methyltransferase activities, differs from that in normal cell. In plants inhibition of DNA methylation is accompanied by the induction of seed storage and florescence genes. In eukaryotes one and the same gene can be simultaneously methylated both at cytosine and adenine residues. It can be thus suggested, that the plant cell contains at least two different, and probably, interdependent systems of DNA methylation. The first eukaryotic adenine DNA methyltransferase was isolated from plants. This enzyme methylates DNA with the formation of N6-methyladenine residues in the sequence TGATCA (TGATCA-->TGm6ATCA). Plants possess AdoMet-dependent endonucleases sensitive to DNA methylation. It seems likely that plants, similarly to microorganisms and some lower eukaryotes, have restriction--modification (R--M) system. Discovery of the essential role of DNA methylation in regulation of genetic processes served as a principle basis and materialization of epigenetics and epigenomics.
Topics: 5-Methylcytosine; Animals; Cell Cycle; DNA Methylation; DNA Replication; Epigenesis, Genetic; Humans; Phylogeny; Plants
PubMed: 17100087
DOI: No ID Found -
International Journal of Molecular... Mar 2024Epitranscriptomic mechanisms, which constitute an important layer in post-transcriptional gene regulation, are involved in numerous cellular processes under health and... (Review)
Review
Epitranscriptomic mechanisms, which constitute an important layer in post-transcriptional gene regulation, are involved in numerous cellular processes under health and disease such as stem cell development or cancer. Among various such mechanisms, RNA methylation is considered to have vital roles in eukaryotes primarily due to its dynamic and reversible nature. There are numerous RNA methylations that include, but are not limited to, 2'-O-dimethyladenosine (mAm), -methylguanosine (mG), -methyladenosine (mA) and -methyladenosine (mA). These biochemical modifications modulate the fate of RNA by affecting the processes such as translation, target site determination, RNA processing, polyadenylation, splicing, structure, editing and stability. Thus, it is highly important to quantitatively measure the changes in RNA methylation marks to gain insight into cellular processes under health and disease. Although there are complicating challenges in identifying certain methylation marks genome wide, various methods have been developed recently to facilitate the quantitative measurement of methylated RNAs. To this end, the detection methods for RNA methylation can be classified in five categories such as antibody-based, digestion-based, ligation-based, hybridization-based or direct RNA-based methods. In this review, we have aimed to summarize our current understanding of the detection methods for RNA methylation, highlighting their advantages and disadvantages, along with the current challenges in the field.
Topics: RNA Methylation; Methylation; RNA; Gene Expression Regulation; Eukaryota; RNA Processing, Post-Transcriptional
PubMed: 38542072
DOI: 10.3390/ijms25063098 -
Cellular and Molecular Neurobiology Mar 19881. The protein-carboxyl methylating system has been studied in adrenal medullary cells either using disrupted cell components or with intact cells. Whereas the enzyme... (Review)
Review
1. The protein-carboxyl methylating system has been studied in adrenal medullary cells either using disrupted cell components or with intact cells. Whereas the enzyme protein-carboxyl methylase (PCM) is cytosolic, the majority of its substrates is on or within chromaffin granules. With intact granules, methylation of surface proteins results in solubilization of membrane proteins. 2. Membrane PCM substrates have been identified as two proteins with apparent molecular weights of 55,000 and 32,000. Among the substrates located inside the granules, the chromogranins are excellent substrates, while dopamine beta-hydroxylase is poorly methylated. 3. Under physiological conditions, stimulation of the splanchnic nerve results in an increase in adrenal medullary protein-methyl ester formation as well as in an augmented methanol production. With adrenal medullary cells in culture, carboxyl-methylated chromogranin A is detected in mature chromaffin granules between 3 and 6 hr after labeling. Methylated chromogranins are secreted concomitantly with catecholamines following cholinergic stimulation. 4. These data coupled with those of Chelsky et al. (J. Biol. Chem. 262:4303-4309, 1987) on lamin B suggest that PCM methylates residues other than D-aspartyl and L-isoaspartyl in proteins. They further suggest that methylation may occur on nascent peptide chains before they are injected into the rough endoplasmic reticulum.
Topics: Adrenal Medulla; Animals; Chromogranins; Cytosol; Humans; Methylation; Molecular Weight; Protein Methyltransferases; Protein O-Methyltransferase
PubMed: 3042145
DOI: 10.1007/BF00712915 -
RNA (New York, N.Y.) Nov 2023U7 snRNP is a multisubunit endonuclease required for 3' end processing of metazoan replication-dependent histone pre-mRNAs. In contrast to the spliceosomal snRNPs, U7...
U7 snRNP is a multisubunit endonuclease required for 3' end processing of metazoan replication-dependent histone pre-mRNAs. In contrast to the spliceosomal snRNPs, U7 snRNP lacks the Sm subunits D1 and D2 and instead contains two related proteins, Lsm10 and Lsm11. The remaining five subunits of the U7 heptameric Sm ring, SmE, F, G, B, and D3, are shared with the spliceosomal snRNPs. The pathway that assembles the unique ring of U7 snRNP is unknown. Here, we show that a heterodimer of Lsm10 and Lsm11 tightly interacts with the methylosome, a complex of the arginine methyltransferase PRMT5, MEP50, and pICln known to methylate arginines in the carboxy-terminal regions of the Sm proteins B, D1, and D3 during the spliceosomal Sm ring assembly. Both biochemical and cryo-EM structural studies demonstrate that the interaction is mediated by PRMT5, which binds and methylates two arginine residues in the amino-terminal region of Lsm11. Surprisingly, PRMT5 also methylates an amino-terminal arginine in SmE, a subunit that does not undergo this type of modification during the biogenesis of the spliceosomal snRNPs. An intriguing possibility is that the unique methylation pattern of Lsm11 and SmE plays a vital role in the assembly of the U7 snRNP.
Topics: Animals; Ribonucleoprotein, U7 Small Nuclear; Methylation; Ribonucleoproteins, Small Nuclear; Histones; Arginine
PubMed: 37562960
DOI: 10.1261/rna.079709.123