Methylation: Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.CpG Islands: Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes.Epigenesis, Genetic: A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.DNA (Cytosine-5-)-Methyltransferase: An enzyme that catalyzes the transfer of a methyl group from S-ADENOSYLMETHIONINE to the 5-position of CYTOSINE residues in DNA.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Sulfites: Inorganic salts of sulfurous acid.Azacitidine: A pyrimidine analogue that inhibits DNA methyltransferase, impairing DNA methylation. It is also an antimetabolite of cytidine, incorporated primarily into RNA. Azacytidine has been used as an antineoplastic agent.Cytosine: A pyrimidine base that is a fundamental unit of nucleic acids.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.Methyltransferases: A subclass of enzymes of the transferase class that catalyze the transfer of a methyl group from one compound to another. (Dorland, 28th ed) EC 2.1.1.DNA Modification Methylases: Enzymes that are part of the restriction-modification systems. They are responsible for producing a species-characteristic methylation pattern, on either adenine or cytosine residues, in a specific short base sequence in the host cell's own DNA. This methylated sequence will occur many times in the host-cell DNA and remain intact for the lifetime of the cell. Any DNA from another species which gains entry into a living cell and lacks the characteristic methylation pattern will be recognized by the restriction endonucleases of similar specificity and destroyed by cleavage. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms.Histones: Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.5-Methylcytosine: A methylated nucleotide base found in eukaryotic DNA. In ANIMALS, the DNA METHYLATION of CYTOSINE to form 5-methylcytosine is found primarily in the palindromic sequence CpG. In PLANTS, the methylated sequence is CpNpGp, where N can be any base.Genomic Imprinting: The variable phenotypic expression of a GENE depending on whether it is of paternal or maternal origin, which is a function of the DNA METHYLATION pattern. Imprinted regions are observed to be more methylated and less transcriptionally active. (Segen, Dictionary of Modern Medicine, 1992)Epigenomics: The systematic study of the global gene expression changes due to EPIGENETIC PROCESSES and not due to DNA base sequence changes.Histone-Lysine N-Methyltransferase: An enzyme that catalyzes the methylation of the epsilon-amino group of lysine residues in proteins to yield epsilon mono-, di-, and trimethyllysine. EC 2.1.1.43.DNA-Cytosine Methylases: Methylases that are specific for CYTOSINE residues found on DNA.Long Interspersed Nucleotide Elements: Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). Copies of the LINE 1 (L1) family form about 15% of the human genome. The jockey elements of Drosophila are LINEs.Protein Methyltransferases: Enzymes that catalyze the methylation of amino acids after their incorporation into a polypeptide chain. S-Adenosyl-L-methionine acts as the methylating agent. EC 2.1.1.S-Adenosylmethionine: Physiologic methyl radical donor involved in enzymatic transmethylation reactions and present in all living organisms. It possesses anti-inflammatory activity and has been used in treatment of chronic liver disease. (From Merck, 11th ed)Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Lysine: An essential amino acid. It is often added to animal feed.Dinucleoside Phosphates: A group of compounds which consist of a nucleotide molecule to which an additional nucleoside is attached through the phosphate molecule(s). The nucleotide can contain any number of phosphates.Protein-Arginine N-Methyltransferases: Enzymes that catalyze the methylation of arginine residues of proteins to yield N-mono- and N,N-dimethylarginine. This enzyme is found in many organs, primarily brain and spleen.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.DNA, Neoplasm: DNA present in neoplastic tissue.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Gene Expression Regulation, Neoplastic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.Genes, p16: Tumor suppressor genes located on human chromosome 9 in the region 9p21. This gene is either deleted or mutated in a wide range of malignancies. (From Segen, Current Med Talk, 1995) Two alternatively spliced gene products are encoded by p16: CYCLIN-DEPENDENT KINASE INHIBITOR P16 and TUMOR SUPPRESSOR PROTEIN P14ARF.RNA, Long Noncoding: A class of untranslated RNA molecules that are typically greater than 200 nucleotides in length and do not code for proteins. Members of this class have been found to play roles in transcriptional regulation, post-transcriptional processing, CHROMATIN REMODELING, and in the epigenetic control of chromatin.Deoxyribonuclease HpaII: One of the Type II site-specific deoxyribonucleases (EC 3.1.21.4). It recognizes and cleaves the sequences C/CGG and GGC/C at the slash. HpaII is from Haemophilus parainfluenzae. Several isoschizomers have been identified. EC 3.1.21.-.S-Adenosylhomocysteine: 5'-S-(3-Amino-3-carboxypropyl)-5'-thioadenosine. Formed from S-adenosylmethionine after transmethylation reactions.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Chromatin: The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.Cell Line, Tumor: A cell line derived from cultured tumor cells.Death-Associated Protein Kinases: A family of calcium/calmodulin-dependent PROETIN-SERINE-THREONINE KINASES. They are ubiquitously expressed in adult and embryonic mammalian tissues, and their functions are tightly related to the early stages of eukaryotic programmed cell death.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Tumor Suppressor Proteins: Proteins that are normally involved in holding cellular growth in check. Deficiencies or abnormalities in these proteins may lead to unregulated cell growth and tumor development.Site-Specific DNA-Methyltransferase (Adenine-Specific): An enzyme responsible for producing a species-characteristic methylation pattern on adenine residues in a specific short base sequence in the host cell DNA. The enzyme catalyzes the methylation of DNA adenine in the presence of S-adenosyl-L-methionine to form DNA containing 6-methylaminopurine and S-adenosyl-L-homocysteine. EC 2.1.1.72.Genes, Tumor Suppressor: Genes that inhibit expression of the tumorigenic phenotype. They are normally involved in holding cellular growth in check. When tumor suppressor genes are inactivated or lost, a barrier to normal proliferation is removed and unregulated growth is possible.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Cyclin-Dependent Kinase Inhibitor p16: A product of the p16 tumor suppressor gene (GENES, P16). It is also called INK4 or INK4A because it is the prototype member of the INK4 CYCLIN-DEPENDENT KINASE INHIBITORS. This protein is produced from the alpha mRNA transcript of the p16 gene. The other gene product, produced from the alternatively spliced beta transcript, is TUMOR SUPPRESSOR PROTEIN P14ARF. Both p16 gene products have tumor suppressor functions.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Acetylation: Formation of an acetyl derivative. (Stedman, 25th ed)Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.RNA, Untranslated: RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.Heterochromatin: The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE.Alu Elements: The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). It is derived from the 7SL RNA component of the SIGNAL RECOGNITION PARTICLE and contains an RNA polymerase III promoter. Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.tRNA Methyltransferases: Enzymes that catalyze the S-adenosyl-L-methionine-dependent methylation of ribonucleotide bases within a transfer RNA molecule. EC 2.1.1.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.Cyclin-Dependent Kinase Inhibitor p15: An INK4 cyclin-dependent kinase inhibitor containing four ANKYRIN-LIKE REPEATS. INK4B is often inactivated by deletions, mutations, or hypermethylation in HEMATOLOGIC NEOPLASMS.Chromatin Immunoprecipitation: A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.Genetic Loci: Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.snRNP Core Proteins: The protein components that constitute the common core of small nuclear ribonucleoprotein particles. These proteins are commonly referred as Sm nuclear antigens due to their antigenic nature.Histone Demethylases: Enzymes that catalyse the removal of methyl groups from LYSINE or ARGININE residues found on HISTONES. Many histone demethylases generally function through an oxidoreductive mechanism.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Insulin-Like Growth Factor II: A well-characterized neutral peptide believed to be secreted by the LIVER and to circulate in the BLOOD. It has growth-regulating, insulin-like and mitogenic activities. The growth factor has a major, but not absolute, dependence on SOMATOTROPIN. It is believed to be a major fetal growth factor in contrast to INSULIN-LIKE GROWTH FACTOR I, which is a major growth factor in adults.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Tumor Markers, Biological: Molecular products metabolized and secreted by neoplastic tissue and characterized biochemically in cells or body fluids. They are indicators of tumor stage and grade as well as useful for monitoring responses to treatment and predicting recurrence. Many chemical groups are represented including hormones, antigens, amino and nucleic acids, enzymes, polyamines, and specific cell membrane proteins and lipids.Glutathione S-Transferase pi: A glutathione transferase that catalyzes the conjugation of electrophilic substrates to GLUTATHIONE. This enzyme has been shown to provide cellular protection against redox-mediated damage by FREE RADICALS.Colorectal Neoplasms: Tumors or cancer of the COLON or the RECTUM or both. Risk factors for colorectal cancer include chronic ULCERATIVE COLITIS; FAMILIAL POLYPOSIS COLI; exposure to ASBESTOS; and irradiation of the CERVIX UTERI.O(6)-Methylguanine-DNA Methyltransferase: An enzyme that transfers methyl groups from O(6)-methylguanine, and other methylated moieties of DNA, to a cysteine residue in itself, thus repairing alkylated DNA in a single-step reaction. EC 2.1.1.63.DNA Repair Enzymes: Enzymes that are involved in the reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule, which contained damaged regions.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.Protein O-Methyltransferase: An enzyme that catalyzes the transfer of methyl groups from S-adenosylmethionine to free carboxyl groups of a protein molecule forming methyl esters. EC 2.1.1.-.Hydroxamic Acids: A class of weak acids with the general formula R-CONHOH.Neoplasm Proteins: Proteins whose abnormal expression (gain or loss) are associated with the development, growth, or progression of NEOPLASMS. Some neoplasm proteins are tumor antigens (ANTIGENS, NEOPLASM), i.e. they induce an immune reaction to their tumor. Many neoplasm proteins have been characterized and are used as tumor markers (BIOMARKERS, TUMOR) when they are detectable in cells and body fluids as monitors for the presence or growth of tumors. Abnormal expression of ONCOGENE PROTEINS is involved in neoplastic transformation, whereas the loss of expression of TUMOR SUPPRESSOR PROTEINS is involved with the loss of growth control and progression of the neoplasm.Euchromatin: Chromosome regions that are loosely packaged and more accessible to RNA polymerases than HETEROCHROMATIN. These regions also stain differentially in CHROMOSOME BANDING preparations.Genes, Neoplasm: Genes whose abnormal expression, or MUTATION are associated with the development, growth, or progression of NEOPLASMS.Jumonji Domain-Containing Histone Demethylases: A family of histone demethylases that share a conserved Jumonji C domain. The enzymes function via an iron-dependent dioxygenase mechanism that couples the conversion of 2-oxoglutarate to succinate to the hydroxylation of N-methyl groups.Methionine: A sulfur-containing essential L-amino acid that is important in many body functions.Tubercidin: An antibiotic purine ribonucleoside that readily substitutes for adenosine in the biological system, but its incorporation into DNA and RNA has an inhibitory effect on the metabolism of these nucleic acids.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Core Binding Factor Alpha 3 Subunit: A transcription factor that dimerizes with the cofactor CORE BINDING FACTOR BETA SUBUNIT to form core binding factor. It contains a highly conserved DNA-binding domain known as the runt domain.Chromatin Assembly and Disassembly: The mechanisms effecting establishment, maintenance, and modification of that specific physical conformation of CHROMATIN determining the transcriptional accessibility or inaccessibility of the DNA.Arginine: An essential amino acid that is physiologically active in the L-form.Cytidine: A pyrimidine nucleoside that is composed of the base CYTOSINE linked to the five-carbon sugar D-RIBOSE.Polycomb-Group Proteins: A family of proteins that play a role in CHROMATIN REMODELING. They are best known for silencing HOX GENES and the regulation of EPIGENETIC PROCESSES.Protein Processing, Post-Translational: Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.Folic Acid: A member of the vitamin B family that stimulates the hematopoietic system. It is present in the liver and kidney and is found in mushrooms, spinach, yeast, green leaves, and grasses (POACEAE). Folic acid is used in the treatment and prevention of folate deficiencies and megaloblastic anemia.Embryonic Stem Cells: Cells derived from the BLASTOCYST INNER CELL MASS which forms before implantation in the uterine wall. They retain the ability to divide, proliferate and provide progenitor cells that can differentiate into specialized cells.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Tumor Cells, Cultured: Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.Arabidopsis Proteins: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Gene Expression Regulation, Developmental: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.Polycomb Repressive Complex 2: A multisubunit polycomb protein complex that catalyzes the METHYLATION of chromosomal HISTONE H3. It works in conjunction with POLYCOMB REPRESSIVE COMPLEX 1 to effect EPIGENETIC REPRESSION.Cadherins: Calcium-dependent cell adhesion proteins. They are important in the formation of ADHERENS JUNCTIONS between cells. Cadherins are classified by their distinct immunological and tissue specificities, either by letters (E- for epithelial, N- for neural, and P- for placental cadherins) or by numbers (cadherin-12 or N-cadherin 2 for brain-cadherin). Cadherins promote cell adhesion via a homophilic mechanism as in the construction of tissues and of the whole animal body.Neoplasms: New abnormal growth of tissue. Malignant neoplasms show a greater degree of anaplasia and have the properties of invasion and metastasis, compared to benign neoplasms.Microsatellite Instability: The occurrence of highly polymorphic mono- and dinucleotide MICROSATELLITE REPEATS in somatic cells. It is a form of genome instability associated with defects in DNA MISMATCH REPAIR.Phosphatidylethanolamine N-Methyltransferase: An enzyme that catalyses three sequential METHYLATION reactions for conversion of phosphatidylethanolamine to PHOSPHATIDYLCHOLINE.Transcription Initiation Site: The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.Methyl-CpG-Binding Protein 2: A DNA-binding protein that interacts with methylated CPG ISLANDS. It plays a role in repressing GENETIC TRANSCRIPTION and is frequently mutated in RETT SYNDROME.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Deoxyribonucleases, Type II Site-Specific: Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 3.1.21.4.Adaptor Proteins, Signal Transducing: A broad category of carrier proteins that play a role in SIGNAL TRANSDUCTION. They generally contain several modular domains, each of which having its own binding activity, and act by forming complexes with other intracellular-signaling molecules. Signal-transducing adaptor proteins lack enzyme activity, however their activity can be modulated by other signal-transducing enzymesAdenosylhomocysteinase: An enzyme which catalyzes the catabolism of S-ADENOSYLHOMOCYSTEINE to ADENOSINE and HOMOCYSTEINE. It may play a role in regulating the concentration of intracellular adenosylhomocysteine.Chromosomal Proteins, Non-Histone: Nucleoproteins, which in contrast to HISTONES, are acid insoluble. They are involved in chromosomal functions; e.g. they bind selectively to DNA, stimulate transcription resulting in tissue-specific RNA synthesis and undergo specific changes in response to various hormones or phytomitogens.Breast Neoplasms: Tumors or cancer of the human BREAST.Chromosomes, Human, X: The human female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in humans.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Dosage Compensation, Genetic: Genetic mechanisms that allow GENES to be expressed at a similar level irrespective of their GENE DOSAGE. This term is usually used in discussing genes that lie on the SEX CHROMOSOMES. Because the sex chromosomes are only partially homologous, there is a different copy number, i.e., dosage, of these genes in males vs. females. In DROSOPHILA, dosage compensation is accomplished by hypertranscription of genes located on the X CHROMOSOME. In mammals, dosage compensation of X chromosome genes is accomplished by random X CHROMOSOME INACTIVATION of one of the two X chromosomes in the female.Arsenic: A shiny gray element with atomic symbol As, atomic number 33, and atomic weight 75. It occurs throughout the universe, mostly in the form of metallic arsenides. Most forms are toxic. According to the Fourth Annual Report on Carcinogens (NTP 85-002, 1985), arsenic and certain arsenic compounds have been listed as known carcinogens. (From Merck Index, 11th ed)Beckwith-Wiedemann Syndrome: A syndrome of multiple defects characterized primarily by umbilical hernia (HERNIA, UMBILICAL); MACROGLOSSIA; and GIGANTISM; and secondarily by visceromegaly; HYPOGLYCEMIA; and ear abnormalities.Tumor Suppressor Protein p14ARF: A gene product of the p16 tumor suppressor gene (GENES, P16). It antagonizes the function of MDM2 PROTEIN (which regulates P53 TUMOR SUPPRESSOR PROTEIN by targeting it for degradation). p14ARF is produced from the beta mRNA transcript of the p16 gene. The other gene product, produced from the alternatively spliced alpha transcript, is CYCLIN-DEPENDENT KINASE INHIBITOR P16. Both p16 gene products have tumor suppressor functions.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.Embryo, Mammalian: The entity of a developing mammal (MAMMALS), generally from the cleavage of a ZYGOTE to the end of embryonic differentiation of basic structures. For the human embryo, this represents the first two months of intrauterine development preceding the stages of the FETUS.Lung Neoplasms: Tumors or cancer of the LUNG.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Histone Deacetylases: Deacetylases that remove N-acetyl groups from amino side chains of the amino acids of HISTONES. The enzyme family can be divided into at least three structurally-defined subclasses. Class I and class II deacetylases utilize a zinc-dependent mechanism. The sirtuin histone deacetylases belong to class III and are NAD-dependent enzymes.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.X Chromosome Inactivation: A dosage compensation process occurring at an early embryonic stage in mammalian development whereby, at random, one X CHROMOSOME of the pair is repressed in the somatic cells of females.Down-Regulation: A negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Stomach Neoplasms: Tumors or cancer of the STOMACH.Loss of Heterozygosity: The loss of one allele at a specific locus, caused by a deletion mutation; or loss of a chromosome from a chromosome pair, resulting in abnormal HEMIZYGOSITY. It is detected when heterozygous markers for a locus appear monomorphic because one of the ALLELES was deleted.Pregnancy: The status during which female mammals carry their developing young (EMBRYOS or FETUSES) in utero before birth, beginning from FERTILIZATION to BIRTH.Homeodomain Proteins: Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).Adenine: A purine base and a fundamental unit of ADENINE NUCLEOTIDES.Germ Cells: The reproductive cells in multicellular organisms at various stages during GAMETOGENESIS.Transgenes: Genes that are introduced into an organism using GENE TRANSFER TECHNIQUES.RNA, Small Interfering: Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.Cell Transformation, Neoplastic: Cell changes manifested by escape from control mechanisms, increased growth potential, alterations in the cell surface, karyotypic abnormalities, morphological and biochemical deviations from the norm, and other attributes conferring the ability to invade, metastasize, and kill.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.Prognosis: A prediction of the probable outcome of a disease based on a individual's condition and the usual course of the disease as seen in similar situations.Case-Control Studies: Studies which start with the identification of persons with a disease of interest and a control (comparison, referent) group without the disease. The relationship of an attribute to the disease is examined by comparing diseased and non-diseased persons with regard to the frequency or levels of the attribute in each group.Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.Homocysteine: A thiol-containing amino acid formed by a demethylation of METHIONINE.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.Antimetabolites, Antineoplastic: Antimetabolites that are useful in cancer chemotherapy.Embryonic Development: Morphological and physiological development of EMBRYOS.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Epigenetic Repression: The turning off of GENETIC TRANSCRIPTION in certain regions of CHROMATIN without changes in the DNA sequence. Typically epigenetic repression is a way that developmental changes are programmed at the cellular level.Carbohydrate Sequence: The sequence of carbohydrates within POLYSACCHARIDES; GLYCOPROTEINS; and GLYCOLIPIDS.Nucleosomes: The repeating structural units of chromatin, each consisting of approximately 200 base pairs of DNA wound around a protein core. This core is composed of the histones H2A, H2B, H3, and H4.Cyclin A1: A cyclin A subtype primarily found in male GERM CELLS. It may play a role in the passage of SPERMATOCYTES into meiosis I.Prader-Willi Syndrome: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229)Mass Spectrometry: An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Mice, Inbred C57BLGenome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Histone Deacetylase Inhibitors: Compounds that inhibit HISTONE DEACETYLASES. This class of drugs may influence gene expression by increasing the level of acetylated HISTONES in specific CHROMATIN domains.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.Receptors, Retinoic Acid: Proteins in the nucleus or cytoplasm that specifically bind RETINOIC ACID or RETINOL and trigger changes in the behavior of cells. Retinoic acid receptors, like steroid receptors, are ligand-activated transcription regulators. Several types have been recognized.Placenta: A highly vascularized mammalian fetal-maternal organ and major site of transport of oxygen, nutrients, and fetal waste products. It includes a fetal portion (CHORIONIC VILLI) derived from TROPHOBLASTS and a maternal portion (DECIDUA) derived from the uterine ENDOMETRIUM. The placenta produces an array of steroid, protein and peptide hormones (PLACENTAL HORMONES).Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Ribose: A pentose active in biological systems usually in its D-form.Retroelements: Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.Genes, Intracisternal A-Particle: Genes of IAP elements (a family of retrovirus-like genetic elements) which code for virus-like particles (IAPs) found regularly in rodent early embryos. ("Intracisternal" refers to the cisternae of the endoplasmic reticulum.) Under certain circumstances, such as DNA hypomethylation they are transcribed. Their transcripts are found in a variety of neoplasms, including plasmacytomas, neuroblastoma, rhabdomyosarcomas, teratocarcinomas, and colon carcinomas.Adenocarcinoma: A malignant epithelial tumor with a glandular organization.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.DNA, Satellite: Highly repetitive DNA sequences found in HETEROCHROMATIN, mainly near centromeres. They are composed of simple sequences (very short) (see MINISATELLITE REPEATS) repeated in tandem many times to form large blocks of sequence. Additionally, following the accumulation of mutations, these blocks of repeats have been repeated in tandem themselves. The degree of repetition is on the order of 1000 to 10 million at each locus. Loci are few, usually one or two per chromosome. They were called satellites since in density gradients, they often sediment as distinct, satellite bands separate from the bulk of genomic DNA owing to a distinct BASE COMPOSITION.Carbohydrate Conformation: The characteristic 3-dimensional shape of a carbohydrate.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Genome-Wide Association Study: An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.Methylenetetrahydrofolate Reductase (NADPH2): A flavoprotein amine oxidoreductase that catalyzes the reversible conversion of 5-methyltetrahydrofolate to 5,10-methylenetetrahydrofolate. This enzyme was formerly classified as EC 1.1.1.171.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Short Interspersed Nucleotide Elements: Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.RNA Interference: A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.Spermatozoa: Mature male germ cells derived from SPERMATIDS. As spermatids move toward the lumen of the SEMINIFEROUS TUBULES, they undergo extensive structural changes including the loss of cytoplasm, condensation of CHROMATIN into the SPERM HEAD, formation of the ACROSOME cap, the SPERM MIDPIECE and the SPERM TAIL that provides motility.MicroRNAs: Small double-stranded, non-protein coding RNAs, 21-25 nucleotides in length generated from single-stranded microRNA gene transcripts by the same RIBONUCLEASE III, Dicer, that produces small interfering RNAs (RNA, SMALL INTERFERING). They become part of the RNA-INDUCED SILENCING COMPLEX and repress the translation (TRANSLATION, GENETIC) of target RNA by binding to homologous 3'UTR region as an imperfect match. The small temporal RNAs (stRNAs), let-7 and lin-4, from C. elegans, are the first 2 miRNAs discovered, and are from a class of miRNAs involved in developmental timing.GuanineOxidoreductases, N-DemethylatingGene Expression Regulation, Enzymologic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.RNA Caps: Nucleic acid structures found on the 5' end of eukaryotic cellular and viral messenger RNA and some heterogeneous nuclear RNAs. These structures, which are positively charged, protect the above specified RNAs at their termini against attack by phosphatases and other nucleases and promote mRNA function at the level of initiation of translation. Analogs of the RNA caps (RNA CAP ANALOGS), which lack the positive charge, inhibit the initiation of protein synthesis.DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.Microsatellite Repeats: A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).Angelman Syndrome: A syndrome characterized by multiple abnormalities, MENTAL RETARDATION, and movement disorders. Present usually are skull and other abnormalities, frequent infantile spasms (SPASMS, INFANTILE); easily provoked and prolonged paroxysms of laughter (hence "happy"); jerky puppetlike movements (hence "puppet"); continuous tongue protrusion; motor retardation; ATAXIA; MUSCLE HYPOTONIA; and a peculiar facies. It is associated with maternal deletions of chromosome 15q11-13 and other genetic abnormalities. (From Am J Med Genet 1998 Dec 4;80(4):385-90; Hum Mol Genet 1999 Jan;8(1):129-35)Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.Immunohistochemistry: Histochemical localization of immunoreactive substances using labeled antibodies as reagents.Colonic Neoplasms: Tumors or cancer of the COLON.Genes, Plant: The functional hereditary units of PLANTS.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Inheritance Patterns: The different ways GENES and their ALLELES interact during the transmission of genetic traits that effect the outcome of GENE EXPRESSION.Folic Acid Deficiency: A nutritional condition produced by a deficiency of FOLIC ACID in the diet. Many plant and animal tissues contain folic acid, abundant in green leafy vegetables, yeast, liver, and mushrooms but destroyed by long-term cooking. Alcohol interferes with its intermediate metabolism and absorption. Folic acid deficiency may develop in long-term anticonvulsant therapy or with use of oral contraceptives. This deficiency causes anemia, macrocytic anemia, and megaloblastic anemia. It is indistinguishable from vitamin B 12 deficiency in peripheral blood and bone marrow findings, but the neurologic lesions seen in B 12 deficiency do not occur. (Merck Manual, 16th ed)Real-Time Polymerase Chain Reaction: Methods used for detecting the amplified DNA products from the polymerase chain reaction as they accumulate instead of at the end of the reaction.

An investigation into the binding of the carcinogen 15,16-dihydro-11-methylcyclopenta[a]phenanthren-17-one to DNA in vitro. (1/8251)

After metabolic activation the carcinogen 15,16-dihydro-11-[3H]methylcyclopenta[a]phenanthren-17-one binds to DNA in vitro, and this binding is prevented by 7,8-benzoflavone. Radioactivity cannot be removed from the DNA with organic solvents or by chromatography on Sephadex G-50, even after heat denaturation of the DNA. Enzymatic hydrolysis yields radioactive fractions, which elute from a column of Sephadex LH-20 immediately after the natural nucleosides. At least two species of reactive metabolites are involved in this bending, those with a half-life of a few hr and others with greater stability. After extraction from the aqueous incubation mixture, they could be detected in discrete polar fractions from separations of the complex metabolite mixture by high-pressure liquid chromatography. Their ability to bind to DNA decreased with time at ambient temperature, and they were rapidly deactivated by acid. 7,8-Benzolflavone acted by suppressing the formation of polar metabolites derived from enzymatic oxidation of the aromatic double bonds. The inhibitor had no effect on the enzymes hydroxylating saturated carbon; hence it is unlikely that metabolism of the methyl group is important in conversion of this carcinogen to its proximate form, although the presence of the 11-methyl group is essential for carcinogenic activity in this series.  (+info)

Arginine methylation and binding of Hrp1p to the efficiency element for mRNA 3'-end formation. (2/8251)

Hrp1p is a heterogeneous ribonucleoprotein (hnRNP) from the yeast Saccharomyces cerevisiae that is involved in the cleavage and polyadenylation of the 3'-end of mRNAs and mRNA export. In addition, Hrplp is one of several RNA-binding proteins that are posttranslationally modified by methylation at arginine residues. By using functional recombinant Hrp1p, we have identified RNA sequences with specific high affinity binding sites. These sites correspond to the efficiency element for mRNA 3'-end formation, UAUAUA. To examine the effect of methylation on specific RNA binding, purified recombinant arginine methyltransferase (Hmt1p) was used to methylate Hrp1p. Methylated Hrp1p binds with the same affinity to UAUAUA-containing RNAs as unmethylated Hrpl p indicating that methylation does not affect specific RNA binding. However, RNA itself inhibits the methylation of Hrp1p and this inhibition is enhanced by RNAs that specifically bind Hrpl p. Taken together, these data support a model in which protein methylation occurs prior to protein-RNA binding in the nucleus.  (+info)

A computational screen for methylation guide snoRNAs in yeast. (3/8251)

Small nucleolar RNAs (snoRNAs) are required for ribose 2'-O-methylation of eukaryotic ribosomal RNA. Many of the genes for this snoRNA family have remained unidentified in Saccharomyces cerevisiae, despite the availability of a complete genome sequence. Probabilistic modeling methods akin to those used in speech recognition and computational linguistics were used to computationally screen the yeast genome and identify 22 methylation guide snoRNAs, snR50 to snR71. Gene disruptions and other experimental characterization confirmed their methylation guide function. In total, 51 of the 55 ribose methylated sites in yeast ribosomal RNA were assigned to 41 different guide snoRNAs.  (+info)

Molecular detection of tumor cells in bronchoalveolar lavage fluid from patients with early stage lung cancer. (4/8251)

BACKGROUND: Conventional cytologic analysis of sputum is an insensitive test for the diagnosis of non-small-cell lung cancer (NSCLC). We have recently demonstrated that polymerase chain reaction (PCR)-based molecular methods are more sensitive than cytologic analysis in diagnosing bladder cancer. In this study, we examined whether molecular assays could identify cancer cells in bronchoalveolar lavage (BAL) fluid. METHODS: Tumor-specific oncogene mutations, CpG-island methylation status, and microsatellite alterations in the DNA of cells in BAL fluid from 50 consecutive patients with resectable (stages I through IIIa) NSCLC were assessed by use of four PCR-based techniques. RESULTS: Of 50 tumors, 28 contained a p53 mutation, and the identical mutation was detected with a plaque hybridization assay in the BAL fluid of 39% (11 of 28) of the corresponding patients. Eight of 19 adenocarcinomas contained a K-ras mutation, and the identical mutation was detected with a mutation ligation assay in the BAL fluid of 50% (four of eight) of the corresponding patients. The p16 gene was methylated in 19 of 50 tumors, and methylated p16 alleles were detected in the BAL fluid of 63% (12 of 19) of the corresponding patients. Microsatellite instability in at least one marker was detected with a panel of 15 markers frequently altered in NSCLC in 23 of 50 tumors; the identical alteration was detected in the BAL fluid of 14% (three of 22) of the corresponding patients. When all four techniques were used, mutations or microsatellite instability was detected in the paired BAL fluid of 23 (53%) of the 43 patients with tumors carrying a genetic alteration. CONCLUSION: Although still limited by sensitivity, molecular diagnostic strategies can detect the presence of neoplastic cells in the proximal airway of patients with surgically resectable NSCLC.  (+info)

Association between nonrandom X-chromosome inactivation and BRCA1 mutation in germline DNA of patients with ovarian cancer. (5/8251)

BACKGROUND: Most human female cells contain two X chromosomes, only one of which is active. The process of X-chromosome inactivation, which occurs early in development, is usually random, producing tissues with equal mixtures of cells having active X chromosomes of either maternal or paternal origin. However, nonrandom inactivation may occur in a subset of females. If a tumor suppressor gene were located on the X chromosome and if females with a germline mutation in one copy of that suppressor gene experienced nonrandom X-chromosome inactivation, then some or all of the tissues of such women might lack the wild-type suppressor gene function. This scenario could represent a previously unrecognized mechanism for development of hereditary cancers. We investigated whether such a mechanism might contribute to the development of hereditary ovarian cancers. METHODS: Patterns of X-chromosome inactivation were determined by means of polymerase chain reaction amplification of the CAG-nucleotide repeat of the androgen receptor (AR) gene after methylation-sensitive restriction endonuclease digestion of blood mononuclear cell DNA from patients with invasive (n = 213) or borderline (n = 44) ovarian cancer and control subjects without a personal or family history of cancer (n = 50). BRCA1 gene status was determined by means of single-strand conformational polymorphism analysis and DNA sequencing. All statistical tests were two-sided. RESULTS AND CONCLUSIONS: Among individuals informative for the AR locus, nonrandom X-chromosome inactivation was found in the DNA of 53% of those with invasive cancer versus 28% of those with borderline cancer (P = .005) and 33% of healthy control subjects (P = .016). Nonrandom X-chromosome inactivation can be a heritable trait. Nine of 11 AR-informative carriers of germline BRCA1 mutations demonstrated nonrandom X-chromosome inactivation (.0002 < P < .008, for simultaneous occurrence of both). IMPLICATIONS: Nonrandom X-chromosome inactivation may be a predisposing factor for the development of invasive, but not borderline, ovarian cancer.  (+info)

Car: a cytoplasmic sensor responsible for arginine chemotaxis in the archaeon Halobacterium salinarum. (6/8251)

A new metabolic signaling pathway for arginine, both a chemoeffector and a fermentative energy source, is described for Halobacterium salinarum. Systematic screening of 80+ potentially chemotactic compounds with two behavioral assays identified leucine, isoleucine, valine, methionine, cysteine, arginine and several peptides as strong chemoattractants. Deletion analysis of a number of potential halobacterial transducer genes led to the identification of Car, a specific cytoplasmic arginine transducer which lacks transmembrane helices and was biochemically shown to be localized in the cytoplasm. Flow assays were used to show specific adaptive responses to arginine and ornithine in wild-type but not Deltacar cells, demonstrating the role of Car in sensing arginine. The signaling pathway from external arginine to the flagellar motor of the cell involves an arginine:ornithine antiporter which was quantitatively characterized for its transport kinetics and inhibitors. By compiling the chemotactic behavior, the adaptive responses and the characteristics of the arginine:ornithine antiporter to arginine and its analogs, we now understand how the combination of arginine uptake and its metabolic conversion is required to build an effective sensing system. In both bacteria and the archaea this is the first chemoeffector molecule of a soluble methylatable transducer to be identified.  (+info)

Sites of reaction of pilocarpine. (7/8251)

Analysis of the sites of reaction of a biologically important compound, pilocarpine, a molecule with imidazole and butyrolactone rings connected by a methylene bridge, has been accomplished in a quadrupole ion trap with the aim of characterizing its structure/reactivity relationships. Ion-molecule reactions of pilocarpine with chemical ionizing agents, dimethyl ether (DME), 2-methoxyethanol, and trimethyl borate (TMB), along with collision-activated dissociation elucidated the reaction sites of pilocarpine and made possible the comparison of structural features that affect sites of reaction. Based on MS/MS experiments, methylation occurs on the imidazole ring upon reactions with CH3OCH2+ or (CH3OCH2CH2OH)H+ ions but methylation occurs on the lactone ring for reactions with (CH3O)2B+ ions. Bracketing experiments with two model compounds, alpha-methyl-gamma-butyrolactone and N-methyl imidazole, show the imidazole ring to have a greater gas-phase basicity and methyl cation affinity than the lactone ring. The contrast of methylation by TMB ions on the lactone ring is explained by initial addition of the dimethoxyborinium ion, (CH3O)2B+, on the imidazole ring with subsequent collisional activation promoting an intramolecular transfer of a methyl group to the lactone ring with concurrent loss of CH3OBO. Semiempirical molecular orbital calculations are undertaken to further address the favored reaction sites.  (+info)

In vivo nuclease hypersensitivity studies reveal multiple sites of parental origin-dependent differential chromatin conformation in the 150 kb SNRPN transcription unit. (8/8251)

Human chromosome region 15q11-q13 contains a cluster of oppositely imprinted genes. Loss of the paternal or the maternal alleles by deletion of the region or by uniparental disomy 15 results in Prader-Willi syndrome (PWS) or Angelman syndrome (AS), respectively. Hence, the two phenotypically distinct neurodevelopmental disorders are caused by the lack of products of imprinted genes. Subsets of PWS and AS patients exhibit 'imprinting mutations', such as small microdeletions within the 5' region of the small nuclear ribonucleoprotein polypeptide N ( SNRPN ) transcription unit which affect the transcriptional activity and methylation status of distant imprinted genes throughout 15q11-q13 in cis. To elucidate the mechanism of these long-range effects, we have analyzed the chromatin structure of the 150 kb SNRPN transcription unit for DNase I- and Msp I-hypersensitive sites. By using an in vivo approach on lymphoblastoid cell lines from PWS and AS individuals, we discovered that the SNRPN exon 1 is flanked by prominent hypersensitive sites on the paternal allele, but is completely inaccessible to nucleases on the maternal allele. In contrast, we identified several regions of increased nuclease hypersensitivity on the maternal allele, one of which coincides with the AS minimal microdeletion region and another lies in intron 1 immediately downstream of the paternal-specific hypersensitive sites. At several sites, parental origin-specific nuclease hypersensitivity was found to be correlated with hypermethylation on the allele contributed by the other parent. The differential parental origin-dependent chromatin conformations might govern access of regulatory protein complexes and/or RNAs which could mediate interaction of the region with other genes.  (+info)

Protein methylation is a common posttranslational modification that mostly occurs on arginine and lysine residues. Arginine methylation has been reported to regulate RNA processing, gene transcription, DNA damage repair, protein translocation, and signal transduction. Lysine methylation is best known to regulate histone function and is involved in epigenetic regulation of gene transcription. To better study protein methylation, we have developed highly specific antibodies against monomethyl arginine, asymmetric dimethyl arginine, and monomethyl, dimethyl, and trimethyl lysine motifs respectively. These antibodies were used to perform immunoaffinity purification (IAP) of methyl peptides followed by LC-MS/MS analysis to identify and quantify arginine and lysine methylation sites in several model studies. Overall, we identified over 1000 arginine methylation sites in human cell lines and mouse tissues, and approximately 160 lysine methylation sites in human cell line HCT116. The methylation sites ...
Define Methylation capacity. Methylation capacity synonyms, Methylation capacity pronunciation, Methylation capacity translation, English dictionary definition of Methylation capacity. n. 1. An alkylation process involving addition of, or substitution by, a methyl group. 2. The process of treating something with methyl alcohol
N6-methyladenosine (m6A) is a common modification of mRNA, with potential roles in fine-tuning the RNA life cycle, but little is known about the pathways regulating this process and its physiological role. Here, we used mass-spectrometry to identify a dense network of proteins physically interacting with METTL3, a core component of the methyltransferase complex, and show that two of them, WTAP and KIAA1429, are required for methylation. Combining high resolution m6A-Seq with knockdown of WTAP allowed us to define accurate maps, at near single-nucleotide resolution, of sites of mRNA methylation across four dynamic programs in human and mouse, including development, differentiation, reprogramming and immune response. Internal WTAP-dependent methylation sites were largely static across the different surveyed conditions and present in the majority of mRNAs. However, methylations were found at much lower levels within highly expressed mRNAs, and methylation is inversely correlated with mRNA stability,
Its not just DNA anymore. RNA is also subject to epigenetic modifications, and lately studies have focused on deciphering the "epitranscriptome", modifications to RNA that can affect RNA metabolism and gene expression, conferring yet another level of epigenetic regulation. RNA modifications are numerous, more so than in DNA. Up to date, there are more than 100 RNA modifications, including RNA methylation, reported in different species. Two major modifications in RNA consist of base methylations, methylation at position 5 in cytosine, 5-methylcytosine (5-mC) and methylation at position 6 in adenosine, 6-methyladenosine (m6A). m6A is the most abundant mRNA modification, and is also present in tRNA, rRNA, snRNAs, and long non-coding RNAs. Although m6A was known to be present in RNA since a few decades ago, it wasnt until recently, with the discovery of its first eraser enzyme, that this modification gained acceptance as a dynamic mark with potential regulatory roles ...
This proposal is targeted at understanding the roles of mRNA methylation and long non-coding RNA, which are two molecular mechanisms of gene regulation, in Cand...
Clades containing significant hits are coloured and labelled with the appropriate taxon name; within these are shown representative annotated species which contain significant hits. An emerging zoonotic clone in the Netherlands provides clues to virulence and zoonotic potential of Streptococcus suis. It is intriguing that all three of these RM systems recognise the same motif, GATC, albeit with different methylation patterns. However, it can also be argued that the majority of cis mQTL are found within a very small distance of the probe location, and it would not be surprising for genetic variation very close to a CpG site to have a genuine effect on methylation levels. Fragile X Syndrome is caused by abnormal methylation of a trinucleotide repeat expansion in the FMR1 gene on the X chromosome and is a common form of mental retardation Verkerk et al; Turner et al We applied linear regression to evaluate variation in methylation M-values as a function of population group AA or EA.. ...
Methylation? What exactly is methylation? It is an overlooked, extremely important biochemical reaction and an essential biochemical reaction that takes place in every single cell of our body. Without methylation, we would cease to exist. It is estimated that a billion methylation reactions occur in our bodies every second! It is probably the second most important biochemical reaction in the human body besides oxidative reactions which are responsible for producing energy in our cells. Furthermore, the methylation process in our bodies is interlinked to several other important biochemical reactions. As a matter of fact, you can think of these biochemical pathways as a machine that contains several gears that intermesh with each other. If one gear is not functioning or out of line it effects all the other gears. So, essentially if the methylation cycle or pathway is not working properly it has widespread effects in the function of the body and can have multiple symptoms that go along with this ...
Causes problems, most related to degenerative disease.. Disease results from high homocysteine, low SAMe, and poor methylation. The homocysteine/SAMe connection is vital to maintaining health, youth, and longevity. Vitamins B6, B12, and folic acid are necessary to reduce homocysteine and keep the methylation process running smoothly.. DNA:. Methylation is also important for DNA expression or suppression. Methyl groups in the cell turn off the DNA we dont need or want. When DNA is properly laced with methyl groups, your cells are protected from abnormal expression of DNA. Poor methylation will cause methyl groups to be taken away from the DNA they are suppressing and use them for other purposes.. In addition to the problems created from poor methylation due to nutrient deficiencies, we can have genetic mutations in the key methylation genes that make it even more difficult for our bodies to carry on these important processes. A Single Nucleotide Polymorphism (SNP) is a single change that can ...
Previously, we found in gastric cancers a significant association between EBV and p16 loss, as determined by IHC.40 This association was confirmed in our current set of tumours (p = 0.0001). Furthermore, the presence of EBV was highly associated with methylation of the CDKN2A promoter (p = 0.0003). In all cases but three, tumours were both negative by immunostaining and methylation positive. In one case, IHC could not be performed, but the tumour showed methylation. In another case, a tumour with methylation was p16 positive by IHC. Such an event could occur if methylation was present in only one allele of the gene. In the third case, no methylation was present, although p16 protein was not detected by IHC. Such results could be explained by gene inactivation by mutation or homozygous deletion.. Suppression of p16 expression associated with EBV infection or EBV proteins has been observed in other systems. In mouse embryo fibroblasts, EBV latent membrane protein 1 (LMP1) acts to prevent ...
Histone Methylation Marks on Circulating Nucleosomes as Novel Blood-Based Biomarker in Colorectal Cancer. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Im wondering if anyone has ever ruled out cytosine methylation at GC dinucleotides (as opposed to CG and CXG) or, for that matter, CXXG. Im familiar with the Gruenbaum et al. Nature paper from 1981 (Vol. 292, 860-862), where nearest neighbor analysis was used to show a high level of methylation at CG and CXG. One nonsymmetrical arrangement, CAT, was tested and was found to be ,4% methylated, but I dont know if that means it was below their limits of detection or they could see almost 4% methylation at those sites. I dont think their approach would have tested for GC symmetry. The reason I am asking is that I occasionally encounter cases of possible incomplete digestion of restriction sites in genomic plant DNA with enzymes like HindIII (recognition sequence AAGCTT). This should not be methylated by the usual rules, but if either GC or CXXG methylation occurs it would block digestion. Appropriate controls indicate that I dont have a problem with dirty DNA or bad enzyme or any of the usual ...
Methods Our replication cohort consisted of 76 AS patients (16 females; 32 smokers; 56 HLA-B27+) that had serial radiographs on average 3 years apart (range 1.2 to 7.5 yrs). Of the 76 patients, 35 patients exhibited radiographic progression (change in mSASSS score ,0). The mean radiographic progression for the entire group was 0.99 mSASSS/yr. The DNA methylation experiments on 17 CpG sites were designed using EpiTyper and performed on a Sequenom MassArray 4 system. The association between methylation score and radiographic progression rate was examined by multiple linear regressions after controlling for age of onset and gender. An interaction between methylation score and smoking status was introduced into the model to examine the association in the smokers and non-smokers, respectively. The Akaike information criterion (AIC) was used to assess the goodness of fit. Methylation sites with more than 15% of data missing were excluded from the analysis. The total methylation score of 7 CpG sites ...
The new data show how the "marking" of DNA sequences by groups of methyl molecules - a process called methylation - can influence the type of cell a stem cell will become. The cellular maturation process, called differentiation, has long been thought to be affected by methylation. Subtle changes in methylation patterns within subsets of a particular cell type have now been observed and closely scrutinized, and they reveal some intriguing mechanisms at work in the process.. A team led by postdoc Dr. Emily Hodges, working in the laboratory of CSHL Professor and HHMI Investigator Gregory Hannon, studied how methylation changes in blood stem cells can affect whether a given stem cell will differentiate into either a myeloid cell or a lymphoid cell. These are the two major lineages of mature blood cells. Sophisticated mathematical analyses of the data were performed under the direction of USC Professor Andrew D. Smith. The study, which will appear in print October 7 in the journal Molecular Cell, ...
Developmental cell fate events in eukaryotes are accompanied by epigenetic changes that remodel the chromatin landscape (Natoli, 2010). Notably, the wide range of post‐translational covalent modifications of nucleosomal histone tails including acetylation, methylation, phosphorylation, ubiquitination and ADP ribosylation, which implies a large diversity of combinatorial patterns at genetic loci, may convey distinctive regulatory information and confer functional properties on specific genomic sites (Jenuwein and Allis, 2001; Li et al, 2007). For example, di‐methylation of H3 lysine 9 (H3K9me2) and tri‐methylation of H3 lysine 27 (H3K27me3) are mainly associated with heterochromatin and gene silencing. On the other hand, the mono‐, di‐ and tri‐methylation of histone H3 lysine 4 (H3K4me1, H3K4me2 and H3K4me3, respectively) are generally associated with euchromatin and ongoing gene expression, while another euchromatic mark, tri‐methylated histone H3 lysine 36 (H3K36me3), is ...
TY - JOUR. T1 - Methylation of CpG sites in exon 2 of the bcl-2 gene occurs in colorectal carcinoma. AU - Babidge, W. J.. AU - Butler, L. M.. AU - Burton, M. A.. AU - Cowled, P. A.. PY - 2001/11/24. Y1 - 2001/11/24. N2 - Background: Aberrant bcl-2 expression frequently occurs in colorectal carcinoma. The current study investigated if CpG sites in bcl-2 were methylated in colorectal carcinoma and if methylation correlated with loss of expression of bcl-2 mRNA. Methods: Methylation was assessed in 23 matched normal mucosae and colonic carcinomas by Southern blotting with methylation-sensitive enzymes. Expression of bcl-2 mRNA was assessed by Northern blotting. Results: A SacII site in exon 2 of the bcl-2 gene was methylated in 5 carcinomas, plus an adjacent HpaII sites in 1 tumour. SacII site in the bcl-2 promoter were not methylated. Elevated levels of bcl-2 mRNA were detected in 3 carcinomas, 5 showed decreased expression and 4 were unchanged. Conclusions: De novo methylation of CpG sites in ...
TY - JOUR. T1 - Methylation of AKAP12α promoter in lung cancer. AU - Jo, Uk Hyun. AU - Whang, Young Mi. AU - Sung, Jae Sook. AU - Kim, Yeul Hong. PY - 2010/11/1. Y1 - 2010/11/1. N2 - AKAP12α plays an important role in tumour growth suppression by inducing apoptosis. This study investigated whether the promoter methylation of AKAP12α is associated with lung cancer. AKAP12α was down-regulated in lung cancer cells and the reduced protein expression was restored by DNA methyl-transferase inhibitor. AKAP12α promoter was more frequently methylated in tumours than in normal tissues. Furthermore, AKAP12α methylation was found more frequently in the cells of non-relapse patients after surgery than in those of early relapse patients. In conclusion, this study demonstrated that AKAP12α expression is regulated by DNA methylation and that AKAP12α promoter methylation is associated with lung cancer prognosis.. AB - AKAP12α plays an important role in tumour growth suppression by inducing apoptosis. ...
We have recently discovered two new methyltransferases - these are the enzymes that add methyl groups on to proteins (e.g. Couttas et al. 2012). We have a number of other proteins that also have sequence homology to methyltransferases; we need to explore these to understand whether these might also be new methyltransferases. If we can confirm these as new methyltransferases, we then have the task of naming the new enzyme something! Also a lot of fun.. Reference: Couttas TA, Raftery MJ, Padula MP, Herbert BR, Wilkins MR. (2012) Methylation of translation-associated proteins in Saccharomyces cerevisiae: Identification of methylated lysines and their methyltransferases. Proteomics. 12(7): 960-72.. ...
Methylation is a form of alkylation, i.e. the transfer of an alkyl group to another molecule. Methylation is specifically the addition or substition of a methyl group to a molecule. Methyl groups are alkyls made from methane and are carbon atoms attached to 3 hydrogen atoms -CH3[1]. It can be involved in the expression of genes, as well as protein function regulation and the metabolism of RNA. An example of this is the tri-methylation of lysine 36 on the H3 protein (of a histone), which is involved in the response of plants to necrotrophic fungal attack[2]. ...
Meythlation is extremely important when it comes to gene expression. not all genes are active at all times which is why DNA methylation is one of the several mechanics that allow cells to control gene expression. Although there are many ways that a gene can be expressed in particularly eukaryotes, the methylation of DNA is a common epigenetic signaling tool that can allow cells to lock genes in the off position. Key experiments were needed in order to provide the early clues for what the role of methylation had on gene expression. One such experiment was conducted by McGhee and Ginder in 1979 where they compared the methylation status of beta-globin loci in cells that did and that did not express the gene. By utilizing restriction enzymes that distinguished between methylated and unmethylatd DNA, the two scientists were capable of dictating that the beta globin locus gene was not being expressed in the cells that were unmethylated. In addition to this experiment, more supporting evidence ...
Methylation is a process that involves moving a methyl group (a carbon plus three hydrogens, CH3) to another molecule. For example, methylation occurs in the cell nucleus where it is involved in turning on or off genes for transcription. It is also involved in converting numerous substances into their active version (e.g. melatonin) or into their inactive version. It is a process that is taking place billions of times per second throughout your body.. These methyl groups are formed, in part, through the conversion of folate to methyl folate using the gene MTHFR along with vitamin B12. The other way you can produce methyl groups is from choline.. ...
From the data reported here, it is shown that viral RNA has the potential to interact with homologous transgenes and that sequence-specific methylation of DNA is associated with this interaction. This type of interaction had been implicated by previous reports. However, it remained possible that there could be either DNA-DNA interactions between homologous transgenes (Mette et al., 1999) or RNA-RNA interactions between viral or viroid RNA and the nascent RNA transcript of a homologous transgene (Wasseneger et al., 1994; Jones et al., 1998b; Guo et al., 1999). In the example described here, with PVX-35S, the only interaction leading to methylation of the 35S transgene promoter would have been between RNA and the promoter DNA. Thus, we have established that a direct RNA-DNA interaction can mediate methylation.. Using VIGS, we found that both transcribed and promoter regions participate in the RNA-DNA interaction and were targeted for methylation. However, the consequences of the interaction ...
Histone methyltransferase (HMT) proteins are involved in the post-translational modification called histone methylation which causes transcription repression or activation, depending on the target sites. Protein arginine...
Methylation Pro Topical will help your bodys methylation process. For more quality methylation supplements, contact Neurobiologix today.
Methylation Pro Topical will help your bodys methylation process. For more quality methylation supplements, contact Neurobiologix today.
When the methyl group is "lost" or removed, or if we are short of methyl groups, the reaction stops. When we are short of methyl groups our body cannot respond to the nutrients, vitamins, minerals or herbs we ingest, affecting many biological reactions in the body.. When a molecule receives a methyl group, this "starts" a reaction (such as turning a gene on or activating an enzyme). For example molecules receiving methyl groups "turn on" detox reactions that detox the body of chemicals, including phenols. So if you are phenol sensitive, and increase your methylation, then theoretically your body can process more phenols and you can eat high phenol containing fruits without enzymes!. Another example is molecules receiving methyl groups "turn on" serotonin, and thus melatonin, production. Therefore, if you are an under-methylator, you can increase your methylation and have higher levels of serotonin and melatonin - both are implicated in mental health and sleep. The methylation cycle requires ...
Methylation is a form of alkylation with a methyl group, rather than a larger carbon chain, replacing a hydrogen atom. This video discusses the benefits of methylation on aging and health. Edited...
This process of moving methyl groups around is necessary for the functioning of several biochemical reactions such as DNA and RNA synthesis, creatinine generation, immune responses involved in silencing viruses etc. Methylation reactions are involved in most body functions, to some degree. This is why compromised methylation can cause or contribute to almost all health conditions. When we look at your Genomix Nutrition profile we can determine whether you have an MTHFR polymorphism, (SNP). About 50% of the population appear to have genetic variants of the MTHFR enzyme, causing them to have some difficulty resynthesizing methionine from homocysteine. This can be a factor in cardiovascular disease, mental illness, and perhaps other health conditions such as fatigue and exhaustion. Methyl groups play a role in ...
This process of moving methyl groups around is necessary for the functioning of several biochemical reactions such as DNA and RNA synthesis, creatinine generation, immune responses involved in silencing viruses etc. Methylation reactions are involved in most body functions, to some degree. This is why compromised methylation can cause or contribute to almost all health conditions. When we look at your Genomix Nutrition profile we can determine whether you have an MTHFR polymorphism, (SNP). About 50% of the population appear to have genetic variants of the MTHFR enzyme, causing them to have some difficulty resynthesizing methionine from homocysteine. This can be a factor in cardiovascular disease, mental illness, and perhaps other health conditions such as fatigue and exhaustion. Methyl groups play a role in ...
This process of moving methyl groups around is necessary for the functioning of several biochemical reactions such as DNA and RNA synthesis, creatinine generation, immune responses involved in silencing viruses etc. Methylation reactions are involved in most body functions, to some degree. This is why compromised methylation can cause or contribute to almost all health conditions. When we look at your Genomix Nutrition profile we can determine whether you have an MTHFR polymorphism, (SNP). About 50% of the population appear to have genetic variants of the MTHFR enzyme, causing them to have some difficulty resynthesizing methionine from homocysteine. This can be a factor in cardiovascular disease, mental illness, and perhaps other health conditions such as fatigue and exhaustion. Methyl groups play a role in ...
What is Methylation? Methylation is a process which occurs in every one of our cells. It involves a chemical methyl group (CH3) being passed around a series of molecules in a cycle. Methylation enables the body to: Detoxify toxins within
Our nervous system is intimately linked with the methylation process so that nerve function is highly dependent on proper methylation. You may have all the messengers your body requires yet if the proteins making each nerves insulation arent methylated, you wont have proper communication between the nerves. This is similar to having frayed electrical cords with highly vulnerable, exposed wires and is the impetus for many of the symptoms of Autism, CFS, and MS. The breakdown leads to faulty or incomplete nerve transmission that leads to physical, emotional, and behavioural changes. Still, methylation goes well beyond nerve transmission and controlling the on/off switch for the genes; it strategically controls the production and break down of neurotransmitters (NT), which are the chemical messengers or neuro talkers in your brain and nervous system. The Vagus Nerve that connects the brain to every body organ and system is a major messaging system. NTs are simply chemicals that allow brain and ...
Testing of methylation goes beyond MTHFR.. Learn about the methylation process, genetic testing for potential defects and clinical protocols for testing the methylation function and effective treatment options which include dietary changes and the proper supplementation.. This webinar will give you clinical and practical guidance in:. ...
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The coordinated activation of early mesodermal and silencing of non-mesodermal genes during mesodermal specification relies on the impact of signalling molecules in the balance of bivalent domain marks. Although the molecular events leading to the establishment of the mesodermal expression pattern have not been studied in detail, it is likely that the following changes take place. As mesodemal genes become active in response to external cues, they lose the repressive H3K27 methylation mark while keeping the H3K4 trimethylation on their regulatory regions. The change in the balance of marks is expected to be correlated with the presence of elongating forms of RNA polymerase II in the coding regions of these genes and activation of transcription. On the contrary, non-mesodermal early genes that are poised in ES cells become irreversibly silenced during mesodermal commitment by losing H3K4 trimethylation, while keeping the H3k27 methylation and accumulating other repressive marks like H3K9 ...
The Nutshell Putative Gay Genes Identified, Questioned A genomic interrogation of homosexuality turns up speculative links between genetic elements and sexual orientation, but researchers say the study is too small to be significant. ...
While there are a number of potential factors that may cause mental illness, one that many people dont consider is that of methylation. It is believed tha
As we age, extraneous methylation forms on the DNA through smoking, too much sun, poor diet, lack of exercise, etc. clouding the original information, like scratches on a CD. Over time the cell may not resemble, say a liver cell anymore and may look more like a mixture of difference cells. Testing the amount of methylation is like seeing how many scratches are on the CD, finding out how well your body can still play the original music as intended ...
Scientists at NEB identified the MspJI family of restriction enzymes, MspJI, LpnPI and FspEI, which are dependent on methylation and hydroxymethylation for cleavage to occur.
L. C. Lindeman, Winata, C. L., Aanes, H., Mathavan, S., Alestrom, P., and Collas, P., "Chromatin states of developmentally-regulated genes revealed by DNA and histone methylation patterns in zebrafish embryos.", Int J Dev Biol, vol. 54, no. 5, pp. 803-13, 2010. ...
This is a thread for people figuring out issues with folates while on methylation protocols. 2 weeks ago, I cut out all supplements with folates...
antibody-antibodies.com is the marketplace for research antibodies. Find the right antibody for your research needs. Methylation Pathways
methylation definition: the inclusion of a methyl group to a molecule; the inclusion of a methyl group to cytosine and adenine residues in DNA that leads on epigenetic adjustment of DNA in addition to…
At Bioarray we have a professional team at your service that will advise you at all times on the steps to take in the methylation analysis study.. Our technology guarantees a thorough quality control, an accurate sequencing with the technology from Life Technologies and simple and specific results.. If you have any questions, do not hesitate to contact us.. ...
Daily News How Gaining and Losing Weight Affects the Body Millions of measurements from 23 people who consumed extra calories every day for a month reveal changes in proteins, metabolites, and gut microbiota that accompany shifts in body mass.. ...
Bartkoski, M.J.J. ; Roizman, B., 1978: Regulation of herpesvirus macro molecular synthesis part 7 inhibition of internal methylation of messenger rna late in infection
Profiles of different levels of methylation for H3K27. The points represent the mean value with the error bars showing the standard error. Each level of methyla
Sawecka, J; Kornacka, L; and Malec, J, "Heterogeneity of fna methylation in murine l5178y lympho- blasts." (1979). Subject Strain Bibliography 1979. 4048 ...
Dr. Anna Cabeca has a very exciting guest on Couch Talk, Dr. Kara Fitzgerald. They will be talking about methylation and why it is so important. It is so important because it turns on the genes we need for greater health and turns off the genes that can disrupt our health (like genes for cancer and dementia).
Improve your health quotient with these health hacks with a focus on microbes, metals (toxic and heavy), and a biochemical process called methylation.
Understanding methylation support is important towards our overall health and wellness, and fortunately, there are several ways your doctor can help.
Arginine methylation[edit]. What was said above of the chemistry of lysine methylation also applies to arginine methylation, ... di-methylation repression[45] repression[45] activation[44] tri-methylation activation[46] repression[43] repression[43] ... mono-methylation activation[42] activation[43] activation[43] activation[43][44] activation[43] activation[43] ... di and tri-methylation appear to have different meanings. Because of this, lysine methylation tends to be a very informative ...
Methylation reagent[edit]. Methyl iodide is an excellent substrate for SN2 substitution reactions. It is sterically open for ... Methylation of these and related enolates can occur on the harder oxygen atom or the (usually desired) carbon atom. With methyl ... This behavior is relevant to the methylation of stabilized enolates such as those derived from 1,3-dicarbonyl compounds. ... For example, it can be used for the methylation of carboxylic acids or phenols:[9] ...
... methylation in cancer[edit]. OSR1 is methylated and downregulated in 51.8% of gastric cancer cells and tissues.[25] When ... Rauch TA, Wang Z, Wu X, Kernstine KH, Riggs AD, Pfeifer GP (2012). "DNA methylation biomarkers for lung cancer". Tumour Biology ...
Histone methylation/Histone methyltransferase *EZH2. *Histone demethylase. *Histone acetylation and deacetylation *Histone ...
... methylation, phosphorylation, ADP-ribosylation, and ubiquitination have also been reported.[3][22] These combinations of ...
... which might be a co-operative event during DNA methylation. DNMT3a prefers CpG methylation to CpA, CpT, and CpC methylation, ... DNA methylation serves a wide variety of biological functions. All the known DNA methyltransferases use S-adenosyl methionine ( ... DNMT3L[16] is a protein closely related to DNMT3A and DNMT3B in structure and critical for DNA methylation, but appears to be ... Jair KW, Bachman KE, Suzuki H, Ting AH, Rhee I, Yen RW, Baylin SB, Schuebel KE (2006). "De novo CpG Island Methylation in Human ...
Histone methylation/Histone methyltransferase *EZH2. *Histone demethylase. *Histone acetylation and deacetylation *Histone ...
Frederick Challenger (1955). "Biological methylation". Q. Rev. Chem. Soc. 9 (3): 255-286. doi:10.1039/QR9550900255.. ... Pentavalent arsenic tends to be reduced to trivalent arsenic and trivalent arsenic tends to proceed via oxidative methylation ... the mold Scopulariopsis brevicaulis produced significant amounts of methyl arsines via methylation[14] of arsenic-containing ... "Microbial Methylation of Metalloids: Arsenic, Antimony, and Bismuth". Microbiology and Molecular Biology Reviews. 66 (2): 250- ...
Bird A (January 2002). "DNA methylation patterns and epigenetic memory". Genes & Development. 16 (1): 6-21. doi:10.1101/gad. ... 8-Hydroxyquinoline is an antifungal transcription inhibitor.[15] The effects of histone methylation may also work to inhibit ... For example, in colorectal cancers about 600 to 800 genes are transcriptionally inhibited by CpG island methylation (see ...
The production of sperm cells involves DNA methylation, an epigenetic process that regulates the expression of genes.[45] ... epigenetic changes, i.e. methylation of the DNA, which can activate or silence certain genes, and is sometimes passed down from ...
DNA methylation: The strong effect of age on DNA methylation levels has been known since the late 1960s.[71] Horvath ... DNA methylation age of blood predicts all-cause mortality in later life.[72][73][74] Furthermore, prematurely aged mice can be ... epigenetic alterations (including DNA methylation patterns, post-translational modification of histones, and chromatin ... methylation of gene promoter regions or alterations of the DNA scaffolding which regulate gene expression), can cause abnormal ...
DNA methylation age. References[edit]. *^ Jabbari K, Bernardi G (May 2004). "Cytosine methylation and CpG, TpG (CpA) and TpA ... 2 Methylation, silencing, cancer, and aging *2.1 CpG islands in promoters. *2.2 Methylation of CpG islands stably silences ... Methylation of CpG islands stably silences genes[edit]. In humans, DNA methylation occurs at the 5 position of the pyrimidine ... Methylation, along with histone modification, is central to imprinting.[11] Most of the methylation differences between tissues ...
Methylation (linkage) analysis To determine linkage between sugars. Amino acid or cDNA sequencing Determination of amino acid ...
Chiang PK, Gordon RK, Tal J, Zeng GC, Doctor BP, Pardhasaradhi K, McCann PP (March 1996). "S-Adenosylmethionine and methylation ... methylation, or glycosylation in that the amino acids typically acquire new functions. This increases the functionality of the ... "Structure and methylation of coenzyme M(HSCH2CH2SO3)". The Journal of Biological Chemistry. 249 (15): 4879-85. PMID 4367810.. ...
Challenger, Frederick; Margaret Isabel Simpson (1948). "Studies on biological methylation. Part XII. A precursor of the ...
One example that seems to refute this biophysical model for methylation is that tri-methylation of histone H3 at lysine 4 is ... The idea that modifications act as docking modules for related factors is borne out by histone methylation as well. Methylation ... Bacteria also use DNA adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA adenine ... Methylation of cytosines can also persist from the germ line of one of the parents into the zygote, marking the chromosome as ...
The average level of methylation varies between organisms-the worm Caenorhabditis elegans lacks cytosine methylation, while ... Walsh CP, Xu GL (2006). "Cytosine methylation and DNA repair". Current Topics in Microbiology and Immunology. 301: 283-315. doi ... Klose RJ, Bird AP (February 2006). "Genomic DNA methylation: the mark and its mediators". Trends in Biochemical Sciences. 31 (2 ... Bird A (January 2002). "DNA methylation patterns and epigenetic memory". Genes & Development. 16 (1): 6-21. doi:10.1101/gad. ...
Normally, oncogenes are silent, for example, because of DNA methylation. Loss of that methylation can induce the aberrant ... Known mechanisms of epigenetic change include DNA methylation, and methylation or acetylation of histone proteins bound to ... See DNA methylation in cancer) A number of authors have questioned the assumption that cancers result from sequential random ... Epimutations include methylations or demethylations of the CpG islands of the promoter regions of genes, which result in ...
See also: Epigenetics of schizophrenia § Methylation of BDNF. A plethora of recent evidence suggests the linkage between ...
Epigenetic promoter methylation in DNA repair genes in NSCLC Gene Frequency of hyper- (or hypo-) methylation DNA repair pathway ... methylation of its promoter region (deficiency of promoter methylation) in NSCLC (see table). ... Safar AM, Spencer H, Su X, Coffey M, Cooney CA, Ratnasinghe LD, Hutchins LF, Fan CY (2005). "Methylation profiling of archived ... "Determination of O⁶-methylguanine DNA methyltransferase promoter methylation in non-small cell lung cancer". Genet Test Mol ...
These methylation patterns are copied to the new chromosomes when cells replicate their genomes and so methylation alterations ... Methylation changes are thought to occur more frequently than mutations in the DNA, and so may account for many of the changes ... Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev. 16 (1): 6-21. doi:10.1101/gad.947102. PMID 11782440 ... Methylation of the cytosine of CpG dinucleotides is a somatically heritable and conserved regulatory mark that is generally ...
These are (1) histone acetylations and histone methylations, (2) DNA methylation at CpG sites, and (3) epigenetic ... Abnormal methylation patterns are thought to be involved in oncogenesis.[2] Histone acetylation is also an important process in ... Often, DNA methylation and histone deacetylation work together in gene silencing. The combination of the two seems to be a ... Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev. 16 (1): 6-21. doi:10.1101/gad.947102. PMID 11782440 ...
Biosynthetically, β-methylations of amino acids are highly unusual in natural products. Polytheonamide B, a peptide natural ... It is interesting to note that the Val3Ala substitution in bottromycin D does not change the β-methylation pattern between ... 2012). "Posttranslational β-methylation and macrolactamidination in the biosynthesis of the bottromycin complex of ribosomal ... Bottromycin A2 is singly methylated on proline, bottromycin B lacks methylation on proline, and bottromycin C contains a doubly ...
"Epigenetics of prostate cancer: beyond DNA methylation". Journal of Cellular and Molecular Medicine. 10 (1): 100-25. doi ...
Examples of such modifications are changes in DNA methylation (hypermethylation and hypomethylation), histone modification[78] ... As an example, one study listed protein coding genes that were frequently altered in their methylation in association with ... "Double strand breaks can initiate gene silencing and SIRT1-dependent onset of DNA methylation in an exogenous promoter CpG ... "DNA damage, homology-directed repair, and DNA methylation". PLoS Genetics. 3 (7): e110. doi:10.1371/journal.pgen.0030110. PMC ...
... in addition to being responsible for GATC methylation, could also function as a methylation-independent transcriptional ... Methylation of the Ade in GATC sequences regulates diverse bacterial cell functions, including gene expression, mismatch repair ... Potential implications for methylation-independent transcriptional repression ... Potential implications for methylation-independent transcriptional repression ...
Methylation study of the 15q11.2-q13 region is considered a first-tier diagnostic test in the work-up of either of these ... If methylation studies are positive, further evaluation, such as FISH analysis to evaluate for chromosome 15 imprinting center ... Methylation studies do not indicate the genetic mechanism responsible for the diagnosis (i.e. deletion, uniparental disomy, etc ... Molecular analysis performed at the Genetics Center analyzes the methylation status of the SNRPN gene within the PWS/AS ...
... maintenance methylation and de novo methylation.[56] Maintenance methylation activity is necessary to preserve DNA methylation ... DNA methylation marks[edit]. DNA methylation marks - genomic regions with specific methylation pattern in a specific biological ... Gene-body methylation appears closely tied to H3K36 methylation. In yeast and mammals, H3K36 methylation is highly enriched in ... Functional DNA methylation has been discovered in Honey Bees.[62][63] DNA methylation marks are mainly on the gene body, and ...
Methylation DNA methylation is a mechanism used to regulate genes and protect DNA from some types of cleavage. It is one of the ... Methylation Genetics Copyright Genetics Society of America. Methylation. DNA methylation is a mechanism used to regulate genes ... Methylation Environmental Encyclopedia COPYRIGHT 2003 The Gale Group Inc.. Methylation. A chemical reaction in which the methyl ... While methylation in eukaryotes does not mark DNA for digestion, methylation can inactivate a promoter and thereby silence gene ...
Methylation: Three types of natural methylation have been reported in DNA. Cytosine can be modified either on the ring to form ... Other methylations of the bases or of the deoxyribose are sometimes induced by carcinogens. These usually lead to mispairing of ... Special enzymes called DNA methyltransferases are responsible for this methylation; they recognize specific sequences within ... Methylation. Three types of natural methylation have been reported in DNA. Cytosine can be modified either on the ring to form ...
Methylation is the addition of a methyl group on to a molecule. This most often takes places at an oxygen atom forming a carbon ... Methylation is also important marine and soil microbiology with respect to bacteria and the methylation of mercury. Inorganic ... Methylation is the addition of a methyl group on to a molecule. This most often takes places at an oxygen atom forming a carbon ... Methylation in DNA occurs on C base pairs (though in simpler (bacteria and yeast) organisms, this occurs on A base pairs - ...
... ... DNA methylation regulates the expression of genes that guide development and define cell types. In mammals, 70 to 80 percent of ... The DNA methylation signatures, called differentially methylated regions, that the researchers identified can be used to guide ... The researchers systematically investigated the DNA methylation of 42 whole-genome bisulphite sequencing data sets across 30 ...
Histone methylation in transcriptional control.. Kouzarides T1.. Author information. 1. Wellcome/CRC Institute and Department ... Over the past year or so, methylation of histones has come to be recognised as a major player in the regulation of gene ... promoter regulation and the propagation of a repressed state via DNA methylation. ...
Identification of the cues that direct de novo methylation may reveal the biological role (or roles) of genomic methylation ... There are two biological properties of genomic methylation patterns that can be regarded as established. First, methylation of ... Second, in most cases methylation patterns are subject to clonal inheritance. These properties suit methylation patterns for a ... Creation of genomic methylation patterns.. Bestor TH1, Tycko B.. Author information. 1. Department of Genetics and Development ...
Epigenetic information encoded by DNA methylation is tightly regulated, but shows a striking drift associated with age that ... Here, the authors provide evidence that age-related methylation drift correlates with lifespan and that caloric restriction in ... The effects of caloric restriction on DNA methylation were detectable across different tissues and correlated with gene ... age showed attenuation of age-related methylation drift compared to ad libitum-fed controls such that their blood methylation ...
The invention discloses a simple method to track cellular aging based on continuous DNA-methylation changes at six specific CpG ...
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... Brian H. Taylor BRIAN at BIO.TAMU.EDU Mon May 10 20:54:06 EST 1993 *Previous message: Poplar Molecular ... Im wondering if anyone has ever ruled out cytosine methylation at GC dinucleotides (as opposed to CG and CXG) or, for that ... 292, 860-862), where nearest neighbor analysis was used to show a high level of methylation at CG and CXG. One nonsymmetrical ... methylation at those sites. I dont think their approach would have tested for GC symmetry. The reason I am asking is that I ...
... one of the most common modifications of secondary metabolites is methylation catalyzed by various methyltransferases. Recently ... Methylation of gibberellins by Arabidopsis GAMT1 and GAMT2. Plant Cell, 2007, 19: 32-45CrossRefGoogle Scholar ... phytohormone SABATH family methyltransferase methylation AtJMT AtBSMT AtIAMT1 AtGAMT1 AtGAMT2 enzyme activity ... In this review, we focus on phytohormone methylation by the SABATH family methyltransferases and the implication of these ...
But DNA methylation of transgene usually leads to target gene silencing in plant genetic engineering. In this research,... ... DNA methylation plays an important role in gene expression in eukaryote. ... DNA methylation plays an important role in gene expression in eukaryote. But DNA methylation of transgene usually leads to ... DNA methylation gene silencing transgene GUS transcriptional product This is a preview of subscription content, log in to check ...
DNA Methylation News and Research. RSS DNA methylation is a type of chemical modification of DNA that can be inherited and ... DNA methylation predicts survival outcome in patients with glioma A new study has shown that survival rates among patients with ... Scientists discover a small family of proteins that control inclusion of DNA methylation marks in genome Not all of your genome ... Researchers have shown that patients with spastic cerebral palsy (CP) can be identified using DNA methylation patterns in ...
DNA Methylation News and Research. RSS DNA methylation is a type of chemical modification of DNA that can be inherited and ... Asthmatics have lower degree of DNA methylation in certain immune cells Children with asthma have epigenetic DNA changes in ... Human airways already demonstrate gender-based differences in DNA methylation signatures at birth, providing an early hint of ... particularly an epigenetic change involving DNA methylation--arise from rogue cells escaping a natural cell deterioration ...
Arginine methylation is a post-translational modification that controls the abundance of γc cytokine receptor on mature T cells ... 1: The butterfly effect of arginine methylation on the expression of and signaling via γc cytokine receptors.. ... Arginine methylation controls the strength of γc-family cytokine signaling in T cell maintenance *Maia Inoue ... Arginine methylation is a post-translational modification that controls the abundance of γc cytokine receptor on mature T cells ...
DNA methylation is probably universal in eukaryotes. In humans, approximately 1% of DNA bases undergo DNA methylation. In adult ... DNA methylation is a type of chemical modification of DNA that can be inherited without changing the DNA sequence. As such, it ... DNA methylation involves the addition of a methyl group to DNA for example, to the number 5 carbon of the cytosine pyrimidine ... Chapter IX - Methylation in Cancer Research; pp. 237-259 (Juan Carlos Roa S., Patricia Garcia M., Dept. of Pathology, Univ. de ...
Now, scientists have developed a method to quickly couple methylation enzymes to their respective methylation pattern. This ... DNA methylation, which regulates vital cell functions, is still a big mystery to the scientific world. ... Scientists uncover mystery of DNA methylation To a large extent, DNA methylation, which regulates vital cell functions, is ... Now, scientists have developed a method to quickly couple methylation enzymes to their respective methylation pattern ...
Phospholipid methylation: a biochemical signal modulating lymphocyte mitogenesis. F Hirata, S Toyoshima, J Axelrod, M J Waxdal ... Phospholipid methylation: a biochemical signal modulating lymphocyte mitogenesis. F Hirata, S Toyoshima, J Axelrod, M J Waxdal ... Phospholipid methylation: a biochemical signal modulating lymphocyte mitogenesis. F Hirata, S Toyoshima, J Axelrod, and M J ... Phospholipid methylation: a biochemical signal modulating lymphocyte mitogenesis Message Subject (Your Name) has sent you a ...
Based on tracking DNA methylation, the new method could help doctors make decisions about preterm newborns care, or study ... Gestational age measured via DNA methylation. Emory Health Sciences. Journal. Genome Biology. Funder. NIH/National Institute on ... By examining methylation at those sites, gestational age could be accurately estimated between 24 and 44 weeks, the authors ... The researchers also found that the difference between a newborns age predicted by DNA methylation and by an obstetrician may ...
PCR to investigate aberrant gene methylation in their studies of the molecular ... ... Principles of Genome-wide DNA methylation analysis and RRBS: Dr Aniruddha Chatterjee - Duration: 17:58. aniruddha chatterjee ... See how researchers in John Wienckes laboratory at UCSF use Droplet Digital™ PCR to investigate aberrant gene methylation in ...
... and our cells use a chemical tag known as DNA methylation to mark out certain parts of the genome, helping cells to remember ... 01:07 - Peter Jones - DNA methylation. To get the low-down on the mysteries of methylation I spoke to one of the leading ... Peter Jones - DNA methylation with Peter Jones, Van Andel Institute, Michigan. Kat - This month Im reporting back from a ... Kat - With DNA methylation, its a mark thats put onto DNA. It could be copied as cells divide. What do we know about the ...
... Nucleic Acids Res. 2010 Sep;38(16):5327-35. doi: 10.1093/nar/gkq266. Epub 2010 Apr 26. ... As methylation is distributed across all mRNA size ranges, it is likely that m(6)A is not limited to a small population of ... Methylation of these and other targets suggests mechanisms by which IME4 could control developmental choices leading to meiosis ... We demonstrate that in S. cerevisiae, substantial levels of internal adenosine methylation are present in the GpA context in ...
  • Methylation of the Ade in GATC sequences regulates diverse bacterial cell functions, including gene expression, mismatch repair and chromosome replication. (osti.gov)
  • I'm wondering if anyone has ever ruled out cytosine methylation at GC dinucleotides (as opposed to CG and CXG) or, for that matter, CXXG. (bio.net)
  • Post-transcriptional silencing of a neomycin phosphotransferase II transgene correlates with the accumulation of unproductive RNAs and with increase cytosine methylation of 3′-flanking regions, Plant J., 1997, 12(2): 379. (springer.com)
  • To further investigate these modifications, Matthias Schaefer and colleagues from the German Cancer Research Center have developed a protocol for "Detection of Cytosine Methylation in RNA Using Bisulfite Sequencing. (redorbit.com)
  • Electrophysiological analysis revealed that the increased excitability could be explained by reduced activity of a specific potassium channel, and inhibiting this channel pharmacologically produced the same enhancement of intrinsic membrane excitability as produced by inhibiting DNA cytosine methylation. (sciencemag.org)
  • Epigenetic modifications, such as DNA cytosine methylation, contribute to the mechanisms underlying learning and memory by coordinating adaptive gene expression and neuronal plasticity. (sciencemag.org)
  • Rather, our results suggest that for organisms with cytosine methylation nucleosome occupancy might be primarily linked to gene expression, with no strong impact on methylation. (frontiersin.org)
  • In plants and other organisms, DNA methylation is found in three different sequence contexts: CG (or CpG ), CHG or CHH (where H correspond to A, T or C). In mammals however, DNA methylation is almost exclusively found in CpG dinucleotides, with the cytosines on both strands being usually methylated. (wikipedia.org)
  • First, methylation of 5'-CpG-3' dinucleotides within promoters represses transcription, often to undetectable levels. (nih.gov)
  • Methylation at CpG dinucleotides is a chemical modification of DNA hypothesized to play important roles in regulating gene expression. (jove.com)
  • Since this cycle is so fundamental to other biochemical cycles, including trans-sulphuration and folate metabolism, it can't change the vitamin B6, folic acid and cobalamin into the active forms necessary for the methylation cycles to work. (ei-resource.org)
  • Standard methylation analysis methods provide only qualitative or semi-quantitative data, which can lead to inaccurate conclusions regarding the effects of epigenetic DNA methylation on cell cycle and metabolism. (qiagen.com)
  • Circulating levels of homocysteine are usually low due to its rapid metabolism via one of two pathways: a cobalamin (vitamin B12) and folate dependent re-methylation pathway that regenerates methionine, or a pyridoxal 5' phosphate (PLP, vitamin B6) dependent trans-sulphuration pathway that converts homocysteine into cysteine. (foodforthebrain.org)
  • Here, we will discuss the DNA methylation events that impact metabolism and the functional roles of DNMTs and TET proteins in adipose biology, with an emphasis on those that may be associated with obesity and T2D. (diabetesjournals.org)
  • This research evidences that methylation levels in the gene involved in lipid metabolism -Lipoprotein lipase (LPL)- are higher in obese people with a metabolic disease in contrast to healthy people. (ehealthweek2010.org)
  • The project is expected to contribute to understanding of the possible role of DNA methylation as marker of exposure to carcinogenic exposure among WTC responders. (cdc.gov)
  • Our results suggest that DNA methylation in Apis is used for storing epigenetic information, that the use of that information can be differentially altered by nutritional input, and that the flexibility of epigenetic modifications underpins, profound shifts in developmental fates, with massive implications for reproductive and behavioral status. (sciencemag.org)
  • The findings from our study suggest that DNA methylation contribute to age-related changes in circadian rhythms in certain slave oscillators. (sigmaaldrich.com)
  • Methylation at lysine 4 and lysine 9 are mutually exclusive and the consequences of site-specific methylation are diametrically opposed. (wikipedia.org)
  • It also requires site-specific methylation of a small number of nucleotides within the rRNA, a process that utilizes Adomet. (nih.gov)
  • This technology has been used to correlate DNA methylation to tumor type and gene expression, to measure cellular response to treatment with demethylating agents, and to assess changes in methylation state in relation to tumorigenesis, genetic imprinting, and exposure to environmental toxins (1). (qiagen.com)
  • An experimental blood test may read a chemical modification called methylation in the dying cells that indicate the development of a tumor or autoimmune disease. (medindia.net)
  • The researchers also found that the difference between a newborn's age predicted by DNA methylation and by an obstetrician may be another indicator of developmental maturity, and is correlated with birthweight, commonly used as an indicator of perinatal health. (eurekalert.org)
  • In a group of newborns from Tennessee, the researchers observed that developmental maturity based on DNA methylation tended to be lower for the children of women in the Medicaid program compared to those with private health insurance. (eurekalert.org)
  • See how researchers in John Wiencke's laboratory at UCSF use Droplet Digital™ PCR to investigate aberrant gene methylation in their studies of the molecular subgroups of glioma, cancer arising from glial cells -- the most common source of brain tumors. (youtube.com)
  • COLD SPRING HARBOR, NY (GenomeWeb) - Researchers from the UK and Germany have identified gene expression and DNA methylation profiles that appear to distinguish between intestinal epithelial samples from children with or without inflammatory bowel disease (IBD), attendees heard at the Biology of Genomes meeting last night. (genomeweb.com)
  • The EZ DNA Methylation Kits innovative in-column desulphonation reaction eliminates several precipitation steps and provides researchers with consistent reaction conditions. (bio-medicine.org)
  • NEW YORK (GenomeWeb) - Researchers in Germany have found that a PCR-based method to detect methylation of a biomarker gene found in biopsy samples could anticipate prostate cancer recurrence and be used to prevent unneeded radical treatments. (genomeweb.com)
  • Now, a team of researchers has developed a machine learning algorithm, based on differential DNA methylation, to distinguish primary lung squamous cell carcinomas (LUSCs) from head and neck metastases. (genengnews.com)
  • While a number of other pipelines and packages for 450k or EPIC array analysis are available (including IMA 17 , minfi 5 , methylumi 18 , RnBeads 19 and wateRmelon 20 ), ChAMP provides a more comprehensive and complete analysis pipeline from reading original data files to final tertiary analysis results, such as GSEA, which streamlines methylation array analysis for researchers. (bioconductor.org)
  • In a new study, published online in the July 26 issue of PNAS , researchers at University of California San Diego School of Medicine, with colleagues in Xijing Hospital and Sun Yat-sen Cancer Center in China, report that DNA methylation can provide effective markers for at least four major cancers, not only correctly differentiating malignant tissues from normal, but also providing information on prognosis and survival. (ucsd.edu)
  • An investigational test for DNA methylation may help improve diagnosis of methylation-associated cancers, researchers reported. (nanotech-now.com)
  • The researchers' description of methylation in the fly will facilitate the use of this powerful experimental system to study methylation. (innovations-report.com)
  • The researchers plan to explore whether and how a mechanism involving polymorphisms and methylation might be at work in autism. (sfari.org)
  • To analyze methylation across the genome, the researchers digest the entire genome using special enzymes that break the DNA strand at all potential methylation sites, except those that are actually methylated. (sfari.org)
  • Researchers have already linked polymorphisms to methylation in DNA from unaffected individuals, with the interesting qualification that the variations specify only a greater propensity toward methylation and not necessarily constant methylation. (sfari.org)
  • The group employed AI-based methods to analyze DNA methylation data from several hundred head and neck and lung cancers in order to train a deep neural network to distinguish between the two types of cancer. (genengnews.com)
  • The biological function of prenylcysteine methylation is to facilitate the targeting of CAAX proteins to membrane surfaces within cells. (wikipedia.org)
  • Many of these proteins participate in cell signaling, and they utilize prenylcysteine methylation to concentrate them on the cytosolic surface of the plasma membrane where they are functional. (wikipedia.org)
  • Epigenetic silencing of the MGMT gene by promoter methylation has been associated with decreased production of the enzyme which may compromise this DNA repair mechanism and may predict response to alkylating agent therapy (such as temozolomide). (mdanderson.org)
  • He also suggested that DNA methylation at this location could be a mechanism of synaptic plasticity. (alzforum.org)
  • The project aims at correlating a detailed assessment of exposure of World Trade Center (WTC) responders enrolled at program at Stony Brook with alterations the mechanism of regulation of DNA called methylation, which may be relevant to cancer risk. (cdc.gov)
  • Publication date: Available online 17 February 2020Source: Neuroscience &Biobehavioral ReviewsAuthor(s): Charlotte A.M. Cecil, Yuning Zhang, Tobias NolteAbstractDNA methylation (DNAm) - an epigenetic process that regulates gene expression - may represent a mechanism for the biological embedding of early traumatic experiences, including childhood maltreatment. (medworm.com)
  • In mammals, methylation has also been proposed to be a genome defense system against foreign DNA such as viruses. (encyclopedia.com)
  • In mammals, methylation takes place selectively within the dinucleotide sequence CG-a rare sequence, presumably because it has been lost by mutation. (britannica.com)
  • This is often done in female mammals with the deactivation of one of the X chromosomes through methylation - the cell randomly picks one of the X chromosomes to turn off. (everything2.com)
  • In mammals, 5mC is mostly found in the context of paired symmetrical methylation of a CpG site, a site in which a cytosine is located next to a guanidine ( 7 ). (diabetesjournals.org)
  • DNA methylation (DNAm), a reversible chemical modification of DNA, is a way for cells to regulate their gene expression program without changing their DNA sequence. (autismspeaks.org)
  • The use of DNA methylation (DNAm) to obtain additional information in forensic investigations showed to be a promising and increasing field of interest. (uva.nl)
  • By modifying its DNA with a pattern of methylation specific to its strain, a bacterium can use this system of modification and restriction to distinguish its own DNA from invading foreign DNA. (encyclopedia.com)
  • Methylation serves to protect the bacterial DNA from digestion by its own restriction enzymes. (encyclopedia.com)
  • In bacteria and archaea, methylation forms an essential part of the immune system by protecting DNA molecules from fragmentation by restriction endonucleases . (britannica.com)
  • Twenty-two to 30-year-old rhesus monkeys exposed to 30% caloric restriction since 7-14 years of age showed attenuation of age-related methylation drift compared to ad libitum-fed controls such that their blood methylation age appeared 7 years younger than their chronologic age. (nature.com)
  • The effects of caloric restriction on DNA methylation were detectable across different tissues and correlated with gene expression. (nature.com)
  • Scientists at NEB recently identified the MspJI family of restriction enzymes (MspJI ( NEB #R0661 ), LpnPI ( NEB #R0663 ), FspEI ( NEB #R0662 )), which are dependent on methylation and hydroxymethylation for cleavage to occur (1). (neb.com)
  • These EpiMark ® validated, methylation-dependent restriction enzymes expand the potential for mapping epigenetic modifications and simplify the study of DNA methylation. (neb.com)
  • The recovered, treated DNA template is ideal for Methylation Specific PCR (MSP) followed by methylation analysis using restriction endonucleases, sequencing, microarrays, etc. (bio-medicine.org)
  • Physiological and genetic analyses show that methylation of phytohormones plays important roles in regulating various biological processes in plants, including stress responses, leaf development, and seed maturation/germination. (springer.com)
  • Human airways already demonstrate gender-based differences in DNA methylation signatures at birth, providing an early hint of which infants may be predisposed to develop respiratory disorders like asthma later in life, a research team reports in a paper published online April 3, 2018, in Scientific Reports. (news-medical.net)
  • nshejazi ### 2018-07-27 10:55:00 --- # Preview: Summary * __Slides:__ https://bit.ly/bioc_methyvim_2018 * DNA methylation data is high-dimensional -- we can collect data on 850K genomic sites with modern arrays! (berkeley.edu)
  • For example, the paradigm that more gene methylation is associated with less expression has many exceptions, most notably that more methylation in the body of a gene has been observed to be globally correlated with more gene expression [ 3 , 9 , 11 ]. (mdpi.com)
  • The process of methylation was first described in bacteria in 1948. (encyclopedia.com)
  • Methylation is also important marine and soil microbiology with respect to bacteria and the methylation of mercury . (everything2.com)
  • Scientists often run into problems with methylation, when they try to introduce foreign DNA to a host organism, for instance bacteria or yeast. (eurekalert.org)
  • We aim to better understand the relation between folate-producing bacteria, folate levels and DNA methylation in the large intestine. (wur.nl)
  • Nature paper from 1981 (Vol. 292, 860-862), where nearest neighbor analysis was used to show a high level of methylation at CG and CXG. (bio.net)
  • No mRNA of uidA was detected in these plants by Northern blotting analysis, and DNA methylation of promoter region was found. (springer.com)
  • Pyrosequencing solves this limitation by generating highly reproducible quantification of methylation frequencies at individual consecutive CpG sites (see figures Pyrosequencing analysis of CpG methylation pattern in the RASSF1A gene and Linearity of methylation quantification by Pyrosequencing ). (qiagen.com)
  • These features have established Pyrosequencing as the gold standard for DNA methylation analysis. (qiagen.com)
  • The analysis of methylation status exploits the quantitative nature of Pyrosequencing data. (qiagen.com)
  • This example shows the analysis of a sequence with a CpN site (CpA in this case) in the first position, followed by 2 classical CpG sites (see figure New mode for analyzing CpN methylation ). (qiagen.com)
  • This slide deck is for a brief (10-15 minute) talk on a recently developed statistical methodology for using data-adaptive estimates of nonparametric variable importance measures for differential methylation analysis. (berkeley.edu)
  • The ChAMP package is designed for the analysis of Illumina Methylation beadarray data (EPIC and 450k) and provides a pipeline that integrates currently available 450k and EPIC analysis methods. (bioconductor.org)
  • They found that DNA methylation analysis could predict cancer versus normal tissue with more than 95 percent accuracy in the three cohorts, comparable to typical diagnostic methods, according to Zhang. (ucsd.edu)
  • Although we focused on just four common cancers here, we expect that DNA methylation analysis could be easily expanded to aid diagnoses of a much larger number of cancers," said Zhang. (ucsd.edu)
  • Further methylome analysis through methylation sensitive high-resolution melting (MS-HRM) and pyrosequencing demonstrated that CD4+ T cells share more demethylated regions with Th17 cells when compared to Th1 cells, and that overall Th17 cells display the highest number of demethylated regions. (zymoresearch.com)
  • To a large extent, DNA methylation, which regulates vital cell functions, is still a mystery to the scientific world. (eurekalert.org)
  • Methylation is a ubiquitous process that turns on, or turns off DNA expression, regulates the synthesis of many essential substances within the body, and breaks down hormones, medications, and toxins. (drhoffman.com)
  • Dr. Hoffman continues his conversation with Dr. Kara Fitzgerald about Methylation, a process that turns on, or turns off, DNA expression, regulates the synthesis of many essential substances within the body, and breaks down hormones, medications, and toxins. (drhoffman.com)