Methylation. Medical search

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)

Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.

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.

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.

An enzyme that catalyzes the transfer of a methyl group from S-ADENOSYLMETHIONINE to the 5-position of CYTOSINE residues in DNA.

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.

Inorganic salts of sulfurous acid.

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.

A pyrimidine base that is a fundamental unit of nucleic acids.

Interruption or suppression of the expression of a gene at transcriptional or translational levels.

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.

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.

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.

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.

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)

The systematic study of the global gene expression changes due to EPIGENETIC PROCESSES and not due to DNA base sequence changes.

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.

Methylases that are specific for CYTOSINE residues found on DNA.

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.

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.

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)

The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.

An essential amino acid. It is often added to animal feed.

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.

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.

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 present in neoplastic tissue.

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).

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.

Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.

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.

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.

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.-.

5'-S-(3-Amino-3-carboxypropyl)-5'-thioadenosine. Formed from S-adenosylmethionine after transmethylation reactions.

A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.

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.

A cell line derived from cultured tumor cells.

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.

The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.

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.

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 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.

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.

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.

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.

Formation of an acetyl derivative. (Stedman, 25th ed)

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 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.

The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE.

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.

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.

Enzymes that catalyze the S-adenosyl-L-methionine-dependent methylation of ribonucleotide bases within a transfer RNA molecule. EC 2.1.1.

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.

Established cell cultures that have the potential to propagate indefinitely.

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.

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.

The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.

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.

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.

An INK4 cyclin-dependent kinase inhibitor containing four ANKYRIN-LIKE REPEATS. INK4B is often inactivated by deletions, mutations, or hypermethylation in HEMATOLOGIC NEOPLASMS.

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.

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.

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.

Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.

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.

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.

Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.

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.

Deoxyribonucleic acid that makes up the genetic material of plants.

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.

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.

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.

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.

Enzymes that are involved in the reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule, which contained damaged regions.

The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.

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.

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.-.

A class of weak acids with the general formula R-CONHOH.

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.

Chromosome regions that are loosely packaged and more accessible to RNA polymerases than HETEROCHROMATIN. These regions also stain differentially in CHROMOSOME BANDING preparations.

Genes whose abnormal expression, or MUTATION are associated with the development, growth, or progression of NEOPLASMS.

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.

A sulfur-containing essential L-amino acid that is important in many body functions.

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.

The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.

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.

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.

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.

The mechanisms effecting establishment, maintenance, and modification of that specific physical conformation of CHROMATIN determining the transcriptional accessibility or inaccessibility of the DNA.

An essential amino acid that is physiologically active in the L-form.

A pyrimidine nucleoside that is composed of the base CYTOSINE linked to the five-carbon sugar D-RIBOSE.

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.

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.

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.

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.

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.

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).

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.

The parts of a macromolecule that directly participate in its specific combination with another molecule.

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.

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.

The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.

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.

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.

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.

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.

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.

An enzyme that catalyses three sequential METHYLATION reactions for conversion of phosphatidylethanolamine to PHOSPHATIDYLCHOLINE.

The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.

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.

Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.

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.

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 enzymes

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.

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.

Tumors or cancer of the human BREAST.

The human female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in humans.

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.

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.

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)

A syndrome of multiple defects characterized primarily by umbilical hernia (HERNIA, UMBILICAL); MACROGLOSSIA; and GIGANTISM; and secondarily by visceromegaly; HYPOGLYCEMIA; and ear abnormalities.

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.

Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.

Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.

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.

Tumors or cancer of the LUNG.

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.

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.

A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.

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.

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.

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 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.

Tumors or cancer of the STOMACH.

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.

The status during which female mammals carry their developing young (EMBRYOS or FETUSES) in utero before birth, beginning from FERTILIZATION to BIRTH.

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).

A purine base and a fundamental unit of ADENINE NUCLEOTIDES.

The reproductive cells in multicellular organisms at various stages during GAMETOGENESIS.

Genes that are introduced into an organism using GENE TRANSFER TECHNIQUES.

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 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.

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.

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.

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.

Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.

A thiol-containing amino acid formed by a demethylation of METHIONINE.

Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.

Antimetabolites that are useful in cancer chemotherapy.

Morphological and physiological development of EMBRYOS.

The systematic study of the complete DNA sequences (GENOME) of organisms.

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.

The sequence of carbohydrates within POLYSACCHARIDES; GLYCOPROTEINS; and GLYCOLIPIDS.

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.

A cyclin A subtype primarily found in male GERM CELLS. It may play a role in the passage of SPERMATOCYTES into meiosis I.

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)

An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.

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.

The genetic complement of a plant (PLANTS) as represented in its DNA.

Compounds that inhibit HISTONE DEACETYLASES. This class of drugs may influence gene expression by increasing the level of acetylated HISTONES in specific CHROMATIN domains.

A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

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.

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).

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.

A pentose active in biological systems usually in its D-form.

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 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.

A malignant epithelial tumor with a glandular organization.

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.

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.

The characteristic 3-dimensional shape of a carbohydrate.

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.

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)

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.

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.

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.

Transport proteins that carry specific substances in the blood or across cell membranes.

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).

Any method used for determining the location of and relative distances between genes on a chromosome.

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.

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.

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.

Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.

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.

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.

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).

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)

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.

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.

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.

The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.

Histochemical localization of immunoreactive substances using labeled antibodies as reagents.

Tumors or cancer of the COLON.

The functional hereditary units of PLANTS.

The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.

The different ways GENES and their ALLELES interact during the transmission of genetic traits that effect the outcome of GENE EXPRESSION.

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)

Methods used for detecting the amplified DNA products from the polymerase chain reaction as they accumulate instead of at the end of the reaction.

The rate dynamics in chemical or physical systems.

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)

These modifications include: methylation, acetylation and serine phosphorylation. Methylation. STAT3 can be dimethylated (have ... Johan, M. F.; Bowen, D. T.; Frew, M. E.; Goodeve, A. C.; Reilly, J. T. (2005). "Aberrant methylation of the negative regulators ... "Reversible methylation of promoter-bound STAT3 by histone-modifying enzymes". Proceedings of the National Academy of Sciences. ... and what the function of this methylation could be. Acetylation. STAT1, STAT2, STAT3, STAT5 and STAT6 have been shown to be ...

https://en.wikipedia.org/wiki/JAK-STAT_signaling_pathway

Epigenetic regulations such as DNA methylation and histone methylation can repress gene expression by inhibiting initiation of ... The biological consequences of histone methylation are context dependent. In general, histone methylation leads to gene ... DNA methylation can result in long term downregulation of specific genes. Repression of functional proteins via asRNA induced ... Evidence has shown histone methylation can be induced by asRNAs. For instance, ANRIL, in addition to the ability to induce DNA ...

https://en.wikipedia.org/wiki/Antisense_RNA

Under wet conditions, the mold Microascus brevicaulis produces significant amounts of methyl arsines via methylation of arsenic ... Index by Molecular Formula Information on Hazardous Chemicals by Class Microbial Methylation of Metalloids: Arsenic, Antimony, ... Frederick Challenger (1955). "Biological methylation". Q. Rev. Chem. Soc. 9 (3): 255-286. doi:10.1039/QR9550900255. Ronald ... Bentley & Thomas G. Chasteen (2002). "Microbial Methylation of Metalloids: Arsenic, Antimony, and Bismuth". Microbiology and ...

https://en.wikipedia.org/wiki/Trimethylarsine

Pentavalent arsenic tends to be reduced to trivalent arsenic and trivalent arsenic tends to proceed via oxidative methylation ... "Mold Types and Mold Species". Frederick Challenger (1955). "Biological methylation". Q. Rev. Chem. Soc. 9 (3): 255-286. doi: ... Under wet conditions, the mold Scopulariopsis brevicaulis produced significant amounts of methyl arsines via methylation of ... Ronald Bentley & Thomas G. Chasteen (2002). "Microbial Methylation of Metalloids: Arsenic, Antimony, and Bismuth". Microbiology ...

https://en.wikipedia.org/wiki/Scheele's_Green

Histone methylation Histone methyltransferase Blanc, Roméo S.; Richard, Stéphane (2017). "Arginine Methylation: The Coming of ... Arginine methylation plays a major role in gene regulation because of the ability of the PRMTs to deposit key activating ( ... In epigenetics, arginine methylation of histones H3 and H4 is associated with a more accessible chromatin structure and thus ... Arginine methylation affects the interactions between proteins and has been implicated in a variety of cellular processes, ...

https://en.wikipedia.org/wiki/H3R8me2

... consequences of aberrant DNA methylation in complex chronic diseases, existing modulators of DNA methylation used in the clinic ... ISBN 978-1-84973-882-8. Heightman, Tom D.; McCullar, Michael (20 November 2015). "CHAPTER 4. Targeting DNA Methylation". In ... "on the biochemical mechanisms controlling DNA methylation, ...

https://en.wikipedia.org/wiki/Nessa_Carey

Dynamic DNA methylation. (2009) Science. 323(5921):1568-9. DOI: 10.1126/science.1172782 Johnson, L.M., Law, J.A., Khattar, A., ... DOI: 10.1073/pnas.1810582115 Zhou, M., Palanca, A.M.S., Law, J.A. Locus-specific control of the de novo DNA methylation pathway ... Law's pioneering work on DNA methylation patterns led to the discovery of the role of the CLASSY protein family in DNA ... Law's postdoctoral work, studying DNA methylation at UC Los Angeles, was followed by her recruitment for a faculty position at ...

https://en.wikipedia.org/wiki/Julie_Law

https://en.wikipedia.org/wiki/H3R2me2

https://en.wikipedia.org/wiki/H4R3me2

O-methylation occurs. O-methylation Cyclic-ether formation Monocerin produced by Exserohilum turcicum causes Northern Corn Leaf ...

https://en.wikipedia.org/wiki/Monocerin

Common modifications include acetylation, methylation, or ubiquitination of lysine; methylation of arginine; and ... Allfrey VG, Faulkner R, Mirsky AE (May 1964). "Acetylation and Methylation of Histones and Their Possible Role in the ...

https://en.wikipedia.org/wiki/Nucleosome

Histone methylation Histone methyltransferase Blanc, Roméo S.; Richard, Stéphane (2017). "Arginine Methylation: The Coming of ... Arginine methylation plays a major role in gene regulation because of the ability of the PRMTs to deposit key activating ( ... In epigenetics, arginine methylation of histones H3 and H4 is associated with a more accessible chromatin structure and thus ... Methylation of H3R26me2 is mediated by CARM1 and is recruited to promoter upon gene activation along with acetyltransferases ...

https://en.wikipedia.org/wiki/H3R26me2

Enzymatic DNA Methylation. Springer Science & Business Media. 7 March 2013. pp. 3-. ISBN 978-3-642-74734-2. (Articles with ...

https://en.wikipedia.org/wiki/Iain_Macintyre

The first methylation, that of PE to PMME, has been shown to be the rate-limiting step in conversion of PE to PC. It is ... The exact mechanism by which PEMT catalyzes the sequential methylation of PE by three molecules of SAM to form PC remains ... PC molecules produced by PEMT-catalyzed methylation of PE are more diverse, and tend to contain longer chain, polyunsaturated ... The enzyme is further regulated by S-adenosylhomocysteine produced after each methylation. PEMT gene expression is regulated by ...

https://en.wikipedia.org/wiki/Phosphatidylethanolamine_N-methyltransferase

Chaperone proteins are also regulated by methylation. This can occur through a conformational change (or a change in the ... methylation, etc.-that are added to molecular chaperones to modulate their activity. Molecular chaperones are proteins ... methylation, ubiquitination, control protein folding/unfolding and protein complex assembly/disassembly by modulating: 1) ... "Smyd2 controls cytoplasmic lysine methylation of Hsp90 and myofilament organization". Genes & Development. 26 (2): 114-119. doi ...

https://en.wikipedia.org/wiki/Chaperone_code

Methylation also influences oxygenation. The peoples of the Ethiopian highlands also live at extremely high altitudes, around ...

https://en.wikipedia.org/wiki/High-altitude_adaptation_in_humans

"Memo:Protein Methylation Prediction". www.bioinfo.tsinghua.edu.cn. Archived from the original on 2016-03-14. Retrieved 2016-05- ... CCDC142 is predicted to have 6 phosphorylation sites, 4 methylation sites, 1 palmitoylation site, 1 sumoylation site, and 1 ...

https://en.wikipedia.org/wiki/CCDC142

Methylation begins to increase at 3.5 days after fertilization in the blastocyst, and a large wave of methylation then occurs ... In the case of methylation, this is a short step that results in the methylation of cytosine to 5-methylcytosine. Stage 3: Base ... Thus, while there were many methylations in the hippocampus shortly after memory was formed, all these hippocampus methylations ... DNA methylation levels were associated both with recent and chronic exposure to Black Carbon as well as benzene. After injury, ...

https://en.wikipedia.org/wiki/DNA_demethylation

Histone methylation is responsible for either activation or repression of genes, depending on the target site, and plays an ... Histone methylation involves adding methyl groups to histones, primarily on lysine (K) or arginine (R) residues. The addition ... Near H3P38 lies near the lysine (K) residue H3K36, and changes in P38 can affect the methylation status of K36. The two ... Both DNA methylation and histone modifications show patterns of distribution in cancer cells. These epigenetic alterations may ...

https://en.wikipedia.org/wiki/Histone-modifying_enzymes

Challenger, F. Biological methylation. Chem. Rev., 1945, vol. 36, pp. 315-361. Challenger, F., C. Higginbottom, L. Ellis. The ... Bentley R., Chasteen T.G. Microbial Methylation of Metalloids: Arsenic, Antimony, and Bismuth. Microbiology and Molecular ...

https://en.wikipedia.org/wiki/Pietro_Biginelli

DNA methylation is a key regulator in epigenetic modification during mammalian cell development and differentiation. In mouse ... SAM serves as the methyl donor in cytosine methylation, which is a key epigenetic regulatory process. Because of this impact on ... In eukaryotic cells, SAM serves as a regulator of a variety of processes including DNA, tRNA, and rRNA methylation; immune ... Chiang P, Gordon R, Tal J, Zeng G, Doctor B, Pardhasaradhi K, McCann P (1996). "S-Adenosylmethionine and methylation". FASEB J ...

https://en.wikipedia.org/wiki/S-Adenosyl_methionine

Taylor CD, Wolfe RS (August 1974). "Structure and methylation of coenzyme M(HSCH2CH2SO3)". The Journal of Biological Chemistry ... These alterations are distinct from other post-translation protein modifications, such as phosphorylation, methylation, or ... "S-Adenosylmethionine and methylation". FASEB Journal. 10 (4): 471-80. doi:10.1096/fasebj.10.4.8647346. PMID 8647346. S2CID ...

https://en.wikipedia.org/wiki/Cofactor_(biochemistry)

Challenger, Frederick; Margaret Isabel Simpson (1948). "Studies on biological methylation. Part XII. A precursor of the ...

https://en.wikipedia.org/wiki/Dimethylsulfoniopropionate

... see DNA methylation in cancer). A number of recently devised methods can assess the DNA methylation status in cancers versus ... Some methods assess methylation of CpGs located in different classes of loci, including CpG islands, shores, and shelves as ... Access to methylation profiling is important to cancer research because: Epi-drivers, along with Mut-drivers, can act as ... Li D, Zhang B, Xing X, Wang T (2015). "Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation". Methods. 72 ...

https://en.wikipedia.org/wiki/Oncogenomics

High methylation rates of mercury bound to cysteine by Geobacter sulfurreducens. Nature Geoscience. (2009) Shi, D., Y. Xu, B.M ... This work encompassed the cycling and methylation of mercury, the contributions of metals to the nitrogen cycle, the use of ... "Mercury Cycling and Methylation". Environmental Science & Technology. 58 (15). Retrieved 2022-01-09.{{cite journal}}: CS1 maint ...

https://en.wikipedia.org/wiki/François_M._M._Morel

Methylation polymorphism and amplification". The Biochemical Journal. 242 (1): 205-10. doi:10.1042/bj2420205. PMC 1147684. PMID ...

https://en.wikipedia.org/wiki/ODC1

... the role of DNA methylation in normal plant development. DNA methylation is a biochemical process that modifies DNA, with ... Finnegan, E. J.; Genger, R. K.; Peacock, W. J.; Dennis, E. S. (1998). "DNA Methylation in Plants". Annual Review of Plant ... Finnegan, E J; Peacock, W J; Dennis, E S (2000). "DNA methylation, a key regulator of plant development and other processes". ... The focus of her current research is investigating the role of DNA methylation in regulating traits of agronomic importance in ...

https://en.wikipedia.org/wiki/Jean_Finnegan

... where they seem to inhibit these methylation patterns with some success at reducing symptoms. The DNA methylation inhibitor ... DNA methylation is a process by which methyl groups attach to DNA structure causing the gene to not be expressed. This is ... In general, DNA methylation attracts proteins which fold that section of the chromatin and repress the related genes. The ... DNA methylation occurs throughout the human genome and is believed to be a natural method of suppressing genes during ...

https://en.wikipedia.org/wiki/Epigenetic_therapy

Enzymatic methylation of O-demethylpuromycin". J. Biol. Chem. 244 (1): 112-8. PMID 5773275. Portal: Biology v t e (EC 2.1.1, ...

https://en.wikipedia.org/wiki/O-demethylpuromycin_O-methyltransferase

Cowling, Victoria H. (15 January 2010). "Regulation of mRNA cap methylation". Biochemical Journal. 425 (2): 295-302. doi: ... "mRNA Cap Methylation in Pluripotency and Differentiation". Cell Reports. 16 (5): 1352-1365. doi:10.1016/j.celrep.2016.06.089. ... Victoria Cowling developed her interest in transcriptional control with her report that Myc can induce mRNA cap methylation. ... Adenosyl Homocysteine Hydrolase Is Required for Myc-Induced mRNA Cap Methylation, Protein Synthesis, and Cell Proliferation". ...

https://en.wikipedia.org/wiki/Victoria_Cowling

... but it is unclear how predicted methylation relates to measured methylation, given that methylation varies with age and ... Table 2. Description of methylation-based measures Methylation-based measures. MCCS. EPIC-IARC. EPIC-Italy. PLCO. ... BMI methylation score. 1.17 [1.01-1.36]. 1.06 [0.92-1.23]. 1.25 [1.03-1.52]. 1.02 [0.91-1.15]. 26. 1.10 [1.02-1.18] 0.01. ... Smoking methylation score. 0.98 [0.84-1.14]. 0.95 [0.82-1.11]. 1.11 [0.90-1.35]. 1.13 [1.00-1.27]. 24. 1.04 [0.97-1.12] 0.25. ...

http://www.medscape.com/viewarticle/984569

Epigenetic mechanisms include DNA methylation, histone modifications, and miRNAs. This review systematical … ... DNA Methylation of ADME Genes Clin Pharmacol Ther. 2016 May;99(5):512-27. doi: 10.1002/cpt.343. Epub 2016 Feb 19. ... This review systematically outlines the influence of DNA methylation on ADME gene expression and highlights the consequences ... Epigenetic mechanisms include DNA methylation, histone modifications, and miRNAs. ...

https://pubmed.ncbi.nlm.nih.gov/27061006/

The main objective of the project is to assess and validate the role of DNA methylation as objective marker of WTC exposure- ...

https://wwwn.cdc.gov/ResearchGateway/ResearchProjects/Details/174

... - Genomics and Precision Health Blog ... From Polygenic Risk Scores to Methylation Risk Scores: What are ... A recent study used methylation risk scores to improve predictive value of baseline models for a range of clinical diagnoses ...

https://blogs.cdc.gov/genomics/tag/methylation-risk-scores/

Investigation of NR3C1 promoter methylation In a rodent model, research has emerged linking early environmental influence, i.e ... Furthermore, analysis of methylation pattern was undertaken using bisulfite modification in order to answer the question ... Remarkably, expression of exon 17 containing mRNA seems to be unique to hippocampus, so that methylation of exon 17 ... Low maternal care results in increased methylation of the nerve growth factor-inducible protein A (Ngfi-A) binding site located ...

https://www.uni-trier.de/universitaet/fachbereiche-faecher/fachbereich-i/faecher-und-institute/psychobiologie/professuren/verhaltensgenetik/forschung/hpa-axis/gr-methylation

Silencing of demethylated genes is characterized by the polycomb mark H3K27me3 or by DNA methylation. De novo methylation by ... Failing cardiomyocytes partially resemble neonatal methylation patterns. This study establishes DNA methylation as a highly ... DNA methylation is essential for proper gene expression, development and genome stability. Here the authors present whole- ... The significance of DNA methylation in shaping the phenotype of the heart remains only partially known. Here we generate and ...

https://www.nature.com/articles/ncomms6288?error=cookies_not_supported&code=033158a2-5974-408f-84df-e3f69e8bd0dc

Home FAQs Is HpaII affected by methylation? FAQ: Is HpaII affected by methylation?. HpaII will not cut sites if 2nd Cytosine of ...

https://www.neb.com/faqs/2012/01/12/is-hpaii-affected-by-methylation

The NIH team analyzed the global levels of DNA methylation as well as the methylation status of 105 putative tumor suppressor ... Home Topics Cancer Gene Methylation Holds Prognostic Value for Liver Cancer Patients ... The extent to which the genome of a persons liver cancer cells is modified by methylation correlates with clinical outcome, ... The team suggests that in individuals with liver cancer, analyzing the methylation status of the genome of their tumor cells ...

https://www.genengnews.com/topics/omics/gene-methylation-holds-prognostic-value-for-liver-cancer-patients/

Trail: Methylation. This page is read-only View other revisions Administration. Search:. ...

https://www.dadamo.com/dadamowiki/wiki.pl/Methylation

3 Abstracts with Methylation Downregulation Research. Filter by Study Type. Animal Study. ... Additional Keywords : Methylation Downregulation, Transgenerational Epigenetic Modification. Problem Substances : Sodium ... Sodium fluoride may adversely affect early embryonic development by disrupting the methylation of H19 and Peg3 through ...

https://greenmedinfo.com/keyword/methylation-downregulation

... researchers show that the main driver of DNA demethylation in mouse development is the selective impairment of DNA methylation ... DNA methylation patterns change differently in maternal and paternal pronuclei, with both exhibiting passive demethylation. * ... Interestingly, there was no overall change in the methylation levels of maternal DNA, but there was an increased level of ... This technique, previously developed by the same researchers, lets you examine whether DNA methylation is symmetric across ...

https://epigenie.com/passive-demethylation-drives-development/?pg=119

Were building a better ClinicalTrials.gov. Check it out and tell us what you think ...

https://www.clinicaltrials.gov/ct2/keydates/NCT01038492

... shows that BRCA1 methylation in early embryotic life leads to increased cancer risk in the adult. ... BRCA1 methylation predicts cancer risk. A new study published in JAMA Oncology (September 2022) shows that BRCA1 methylation in ... In the study, we found that women with low-level mosaic methylation of BRCA1, had a 2.5-fold increased risk of TNBC and 1.8 ... BRCA1 methylation in early embryonic life leads to increased cancer risk in the adult. ...

https://www.uib.no/en/rg/g18/157021/brca1-methylation-predicts-cancer-risk

This page displays all documents tagged with DNA methylation on Sciweavers ... Background: DNA methylation, a molecular feature used to investigate tumor heterogeneity, can be measured on many genomic ... Background: DNA methylation patterns have been shown to significantly correlate with different tissue types and disease states ... Methylation patterns of CpG islands are involved in tissue-specific gene expression and regulatio... ...

http://www.sciweavers.org/subject/dna-methylation

Exposure was associated with a 2% increase in mean CpG methylation in FRMD4A (p = 0.01) and Cllorf52 (p = 0.001) compared to no ... Using beta-regression, we screened loci for differential methylation related to prenatal smoke exposure, adjusting for gender, ... Methods Using Illumina HumanMethylation27 microarrays, we estimated the degree of methylation at 27,578 distinct DNA sequences ... DNA methylation Is the Subject Area "DNA methylation" applicable to this article? Yes. No. ...

https://journals.plos.org/plosone/article/comment?id=info:doi/10.1371/annotation/dafc6432-8714-48a7-b91d-b8920bd51dd9

... was used to generate epigenome-wide array DNA methylation (DNAm) data at 485,512 CpG sites for 453 cases and 515 controls, ... DNA methylation data quality control (QC) and processing. For the SEED samples, genomic DNA was isolated from 980 whole blood ... Andrews, S.V., Sheppard, B., Windham, G.C. et al. Case-control meta-analysis of blood DNA methylation and autism spectrum ... The DNA methylation assays were supported by Autism Speaks Award #7659 and the genotype assays were supported by NIEHS ( ...

https://link.springer.com/article/10.1186/s13229-018-0224-6

DNA methylation mediates imprinted gene expression by passing an epigenomic state across generations and differentially marking ... DNA methylation mediates imprinted gene expression by passing an epigenomic state across generations and differentially marking ... We present a statistical model to describe allele-specific methylation (ASM) in data from high-throughput short-read bisulfite ... Although recent advances in genome sequencing have revolutionized the study of DNA methylation, existing methylome data remain ...

https://www.rti.org/publication/genomic-landscape-human-allele-specific-dna-methylation

DNA Methylation: Timekeeper of Biological Age. Join us to learn more about the role of epigenetic modifications in biological ... DNA Methylation: Timekeeper of Biological Age from thescientistllc on Vimeo.. Cellular senescence, telomere shortening, and ... For a detailed look at the biology of human aging and the dynamics of DNA methylation, The Scientist is bringing together a ... have clarified the relationship between DNA methylation and aging, to the point that such phenomena may even be used to predict ...

https://www.the-scientist.com/sponsored-multimedia/dna-methylation-timekeeper-of-biological-age-30056

Methylation-Based Cancer Early Detection Method Shows Promise in Preliminary Studies Nov 14, 2018 , staff reporter ... The group is not the only academic team to investigate methylation or other epigenetic changes for early cancer detection. ... Numerous commercial companies in the space have also named methylation as part of their strategies, including Grail, Freenome, ... This has restricted many previous blood-based methylation efforts to locus-specific PCR-based assays. And although whole-genome ...

https://www.genomeweb.com/liquid-biopsy/methylation-based-cancer-early-detection-method-shows-promise-preliminary-studies

Antineoplastic Agent, Methylation Inhibitors. Class Summary. Demethylation agents are a ntineoplastics that exert anticancer ...

https://emedicine.medscape.com/article/207347-medication

Global methylation levels showed that CG sites exhibited the highest methylation level in all stages with an average of 49.5%, ... Global methylation levels showed that CG sites exhibited the highest methylation level in all stages with an average of 49.5%, ... The overall methylation levels alternately decreased and increased during the entire tissue culture process and the ... The overall methylation levels alternately decreased and increased during the entire tissue culture process and the ...

https://www.frontiersin.org/articles/10.3389/fpls.2021.765383/full

Its a biochemical process involved in almost all of your bodys functions.What is methylation? Without getting too technical, ... methylation is the addition of a single carbon and three hydrogen atoms (called a methyl group) to another molecule. The ... Methylation is the latest buzzword in the health industry, and for good reason. ... How To Improve Methylation. Below are a few all-natural ways that may improve your methylation pathways, that I recommend as a ...

https://scifidimensions.com/methylation-why-it-matters-for-your-immunity-inflammation-more/

Inhibits DNA methylation by inhibition of MAPK (EC50 = 2.96 μM). Multiple, direct effects on vascular smooth muscle; ... Inhibits DNA methylation by inhibition of MAPK (EC50 = 2.96 μM). Multiple, direct effects on vascular smooth muscle; ...

https://www.abcam.com/hydralazine-hydrochloride-dna-methylation-inhibitor-ab120863.html

RNA Methylation kits from Zymo Research offer fast, easy bisulfite conversion in RNA for methylation analysis. ... RNA Methylation. Methylation analysis made easy. RNA Methylation kits from Zymo Research offer fast, easy bisulfite conversion ...

https://www.zymoresearch.com/pages/rna-methylation

DNA methylation Latest DNA methylation posts. Towards early diagnosis of Parkinsons disease: the role of DNA methylation. Yu- ... More DNA methylation posts. Large hypomethylated blocks could be a universal cancer signature. 26/08/2014. ... Abnormalities in DNA methylation have been linked to a number of health conditions and theres now growing interest in the role ... Comprehensive DNA methylation study identifies novel progression-related and prognostic markers for cutaneous melanoma. Dr. ...

https://blogs.biomedcentral.com/on-medicine/tag/dna-methylation/

DNA methylation at promoters leads to gene repression, but intragenic methylation can enhance transcription, iii) Wnt ... The potential role of DNA methylation is supported by: i) AD patients and mouse models exhibit global DNA hypomethylation and ... some Wnt components are regulated by DNA methylation in cancer. My work will define the role of epigenetic regulation of Wnt ... I will examine the role of DNA methylation at Wnt component genes in AD and how this affects synapse integrity. ...

https://www.alzheimer-europe.org/research/projects/unbalanced-wnt-signalling-ad-dna-methylation-effect

Microarray Analysis in Methylation Detection. A number of hypomethylation intervals (hypomethylated blocks) are prevalent in ... Ninety-five percent of the DNA methylation changes in cancer occur in those regions. Epigenetics microarrays are products ... Epigenetic factors such as DNA methylation, histone modifications, and non-coding RNAs are associated with a variety of ... CpG microarrays specialize in differentially methylated regions and can be used to detect methylation changes between samples ...

https://www.pharmiweb.com/article/array-based-methylation-detection-explores-the-mysteries-of-cancer

Deliverables, publications, datasets, software, exploitable results

https://cordis.europa.eu/project/id/897843/results

Remote conformational control of a molecular switch via methylation and deprotonation P. C. Knipe, I. M. Jones, S. Thompson and ...

https://pubs.rsc.org/en/content/articlelanding/2014/ob/c4ob01991a

Methylation Details Created: April 01 2012 Last Updated: December 16 2016 I recently posted a radio show on methylation and ... Methylation involves B6, B12, and folic acid. Folic acid is the key nutrient in the methylation pathway. Many people cannot ... The body uses methylation to create T-cells to kill viruses, bacteria, and cancers. It is a series of over 100 reactions in the ... Methylation is involved in the production of T-cells which address viruses, bacteria, and cancers. Low T-cells can lead to the ...

https://www.betterhealthguy.com/methylation

Furthermore, analysis of methylation pattern was undertaken using bisulfite modification in order to answer the question whether differential methylation as shown in rats can also be observed in humans. (uni-trier.de)
This model provides a novel approach for differential methylation analysis that generates distinct and testable hypotheses regarding gene expression. (ku.edu)
discuss the effect of model directionality, i.e. whether the condition of interest (phenotype) may be affected by methylation or whether it may affect methylation, in differential methylation analyses at the cell-type level. (unibo.it)
They show that correctly accounting for model directionality has a significant impact on the ability to identify cell type specific differential methylation. (unibo.it)
Finally, we showed that differential methylation during progression preferentially occurs at somatic mutational hotspots and putative regulatory regions. (duke.edu)

Numerous studies have investigated the association of blood DNA methylation and breast cancer risk, for example, at breast cancer-specific genes, [ 1-3 ] and overall found mixed results. (medscape.com)
Silencing of demethylated genes is characterized by the polycomb mark H3K27me3 or by DNA methylation. (nature.com)
De novo methylation by DNA methyltransferases 3A/B causes repression of fetal cardiac genes, including essential components of the cardiac sarcomere. (nature.com)
Repression of demethylated genes is achieved by polycomb-mediated histone H3K27 trimethylation or by de novo methylation by DNA methyltransferases DNMT3A/B. Dynamic DNA methylation is important for the perinatal switch in sarcomere protein isoforms and postnatal cardiomyocyte maturation and adaptation. (nature.com)
The NIH team analyzed the global levels of DNA methylation as well as the methylation status of 105 putative tumor suppressor genes of human liver cells. (genengnews.com)
The scientists also found that these changes in methylation were associated with selective inactivation of a number of genes including inhibitors of Ras and some inhibitors of angiogenesis. (genengnews.com)
The functional enrichment of the DMR-related genes indicated that genes involved in hormone metabolic processes, plant development and the stress response changed methylation throughout the tissue culture process. (frontiersin.org)
Finally, the quantitative real-time PCR (qRT-PCR) was conducted to examine the association of methylation and gene expression of a set of different methylated genes. (frontiersin.org)
Given that Wnt signalling is crucial for synapse maintenance, and that my preliminary results suggest a coordinated downregulation of the Wnt pathway in AD, I will examine the role of DNA methylation at Wnt component genes in AD and how this affects synapse integrity. (alzheimer-europe.org)
DNA methylation varies across chromosomes, genomic regions, and genes. (ku.edu)
D NA methylation is an epigenetic mechanism that occurs by the addition of a methyl (CH3) group to DNA, thereby often modifying the function of the genes and affecting gene expression. (penelopethemovie.com)
Typically, methylation turns genes "off" and demethylation turns genes "on. (penelopethemovie.com)
One example of an epigenetic change is DNA methylation - the addition of a methyl group, or a "chemical cap," to part of the DNA molecule, which prevents certain genes from being expressed. (penelopethemovie.com)
Quantitative multiplex methylation-specific PCR will be used for analyses of several tumor suppressor genes including APC1, Cyclin D2, RARB, RASSF1A, Twist, Hin1 and GSTP1. (knowcancer.com)
A second group is measuring 'methylation capacity,' an indirect measure of how well a cell can methylate genes, in pregnant women to determine whether abnormal levels can predict a later autism diagnosis for the child. (spectrumnews.org)
Methylation is the process of taking a methyl group, one carbon and three hydrogens, into your body to support some major body functions, such as DNA methylation, thinking, fighting off toxins, and turning genes on and off. (agapenutrition.com)
We also identified intergenic regions where methylation is associated with RNA expression of the oncogenic driver genes AR, MYC and ERG. (duke.edu)
While 989 genes were differentially expressed, 333 promoters had altered methylation (247 hypermethylated, 86 hypomethylated) in response to maternal folate depletion. (northumbria.ac.uk)
Only 16 genes had both expression and methylation changes. (northumbria.ac.uk)
Thirty-three bone marrow samples from 28 non-M3 AML patients were subjected to DNA methylation sequencing to identify the differentially methylated regions and genes of interest. (bvsalud.org)
And the methylation -silencing genes , LIN7A, CEBPA, BASP1, and EMB were identified as critical decitabine -sensitive genes in t(8;21) AML. (bvsalud.org)
Pathway analysis of genes proximal to variable enhancer elements showed enrichment in epithelial-to-mesenchymal transition (EMT), and response to inflammation pathways, and expression of mesenchymal-associated genes was significantly correlated with enhancer methylation level. (who.int)
An important area is methylation, the process by which genes are switched on and off. (futurity.org)
Parallel DNA and RNA sequencing, which reduces costs and speeds results by sequencing both at the same time, and DNA methylation analyses, which identifies a common signaling tool that cells use to turn off genes that suppress cancer cells, are also underway. (mdanderson.org)
Yin X , Huang H , Huang S , Xu A , Fan F , Luo S , Yan H , Chen L , Sun C , Hu Y . A Novel Scoring System for Risk Assessment of Elderly Patients With Cytogenetically Normal Acute Myeloid Leukemia Based on Expression of Three AQP1 DNA Methylation-Associated Genes. (wjgnet.com)

This review systematically outlines the influence of DNA methylation on ADME gene expression and highlights the consequences for interindividual variability in drug response or drug-induced toxicity and the implications for personalized medicine. (nih.gov)
Methylation patterns of CpG islands are involved in tissue-specific gene expression and regulatio. (sciweavers.org)
DNA methylation mediates imprinted gene expression by passing an epigenomic state across generations and differentially marking specific regulatory regions on maternal and paternal alleles. (rti.org)
Here we conduct the first analysis of the Mimulus guttatus methylome, with a focus on the relationship between DNA methylation and gene expression. (ku.edu)
We develop a model that predicts gene expression based on DNA methylation (R2 = 0.2). (ku.edu)
Post hoc analysis of this model confirms prior relationships, and identifies novel relationships between methylation and gene expression. (ku.edu)
Using a model-based approach, we demonstrate that methylation patterns are an important predictor of variation in gene expression. (ku.edu)
DNA methylation is an epigenetic mechanism used by cells to control gene expression. (penelopethemovie.com)
One group is using a method called CHARM, or comprehensive high-throughput arrays for relative methylation, to assess methylation, the addition of a methyl group to DNA that typically turns off gene expression. (spectrumnews.org)
Although DNA methylation is a key regulator of gene expression, the comprehensive methylation landscape of metastatic cancer has never been defined. (duke.edu)
Epigenetic marks, including DNA methylation, regulate gene expression and are modifiable by folate supply. (northumbria.ac.uk)
At 17.5-day gestation, genome-wide gene expression and promoter methylation were measured by microarray analysis in male fetal livers. (northumbria.ac.uk)
Integrating gene expression, DNA methylation, copy number, and somatic variant datasets with MOFA resulted in a molecular map of MPM that displayed a continuous profile across the three histological types, rather than distinct clusters. (who.int)
Epigenetic marks like methylation of cytosines at CpG dinucleotides are essential for mammalian development and play a major role in the regulation of gene expression and chromatin architecture. (mdc-berlin.de)

The primary aims of this study were (1) to compare blood DNA methylation profiles of WTC-exposed community members with breast cancer and WTC-unexposed pre-diagnostic breast cancer blood samples, and (2) to compare the DNA methylation differences among the WTC EHC breast cancer cases and WTC-exposed cancer-free controls. (cdc.gov)

A new study published in JAMA Oncology (September 2022) shows that BRCA1 methylation in early embryotic life leads to increased cancer risk in the adult. (uib.no)

If we dig a little deeper and peruse the pathways of metabolism, we stumble upon a potent homocysteine-raiser: poor methylation status. (planetthrive.com)
What are symptoms of poor methylation? (camillestyles.com)
Disrupted or poor methylation in the body can have far-reaching effects since it affects so many processes in your body. (camillestyles.com)
Most importantly, you know what to do and expect in case you or a loved one has poor methylation. (agapenutrition.com)

Eating dark leafy green veggies daily provides you with natural folate (a methyl donor), necessary for proper methylation. (scifidimensions.com)
Vitamin B12 and Folic Acid - Proper Methylation (NERD ALERT! (pureprescriptions.com)

Methylation involves B6, B12, and folic acid. (betterhealthguy.com)
Folic acid is the key nutrient in the methylation pathway. (betterhealthguy.com)
We observed transcriptional changes in fetal liver in response to maternal folate depletion and hypothesized that these changes are concomitant with altered gene promoter methylation.METHODS AND RESULTS: Female C57BL/6J mice were fed diets containing 2 or 0.4 mg folic acid/kg for 4 wk before mating and throughout pregnancy. (northumbria.ac.uk)

DNA methylation patterns change differently in maternal and paternal pronuclei, with both exhibiting passive demethylation. (epigenie.com)
Interestingly, there was no overall change in the methylation levels of maternal DNA, but there was an increased level of dispersion of the hemi-methylated dyads throughout development, indicating some passive demethylation. (epigenie.com)
While providing some detailed dynamics on passive demethylation, the group also reminds us not to forget about the role of active demethylation, which teams up with the passive demethylation to counteract de novo methylation and achieve the patterns required to drive development. (epigenie.com)
That's methylation and demethylation. (scifidimensions.com)
DALY J, AXELROD J, WITKOP B. "Methylation and demethylation in relation to the in vitro metabolism of mescaline" Ann N Y Acad Sci . (erowid.org)

In a study published in a letter in Nature today , the team described an immunoprecipitation-based protocol to analyze the methylome of small quantities of circulating cell-free DNA, which could detect large-scale DNA methylation changes specific to different types of cancer, including early pancreatic tumors. (genomeweb.com)
As it typically happens with omic data, processing, analyzing and interpreting large-scale DNA methylation datasets requires computational methods and software tools that address multiple challenges. (unibo.it)

To provide insight into the dynamics of DNA methylation in development and disease of cardiomyocytes as a prototypical terminally differentiated cell type, we generated DNA methylomes of newborn, adult healthy and adult failing cardiomyocytes. (nature.com)
For a detailed look at the biology of human aging and the dynamics of DNA methylation, The Scientist is bringing together a panel of experts to share their research, to discuss how the epigenome influences aging, and to highlight the approaches scientists are taking to study the possibility of targeting epigenetic modifications for therapeutic intervention. (the-scientist.com)

Technological advances, including microarray analysis and next-generation sequencing, have clarified the relationship between DNA methylation and aging, to the point that such phenomena may even be used to predict one's chronological age. (the-scientist.com)

[ 11 ] Another study with a large sample size found that genetically predicted methylation levels were associated with breast cancer risk, [ 12 ] but it is unclear how predicted methylation relates to measured methylation, given that methylation varies with age and exposures accumulated over the life course. (medscape.com)

Methylation patterns are "written" by enzymes in response to signals and then "read" by effector proteins recognizing methyl residues on highly specific lysine residues, leading to either large- or small-scale alterations in the transcriptional state of chromatin. (yeastgenome.org)
Given orthology within each class of writers and erasers (as defined by the particular lysines methylated or demethylated), this makes yeast a perfect model system for digging into the links that connect cellular signals to specific methylation patterns on chromatin. (yeastgenome.org)
DNA methylation, chromatin inheritance, and cancer. (bvsalud.org)
This comprises 426 ERGs classified into the main categories: histone modifiers, chromatin remodellers, and DNA methylation regulators. (who.int)

Background: DNA methylation, a molecular feature used to investigate tumor heterogeneity, can be measured on many genomic regions using the MethyLight technology. (sciweavers.org)
Differentially methylated regions (DMRs), that is genomic regions that show significant differences in methylation levels across distinct biological and/or medical conditions (e.g., normal vs. disease), have been reported to be implicated in a variety of disorders (Rakyan et al. (unibo.it)
However, most methylation changes occurred in genomic regions neighboring expression changes. (northumbria.ac.uk)
DNA methylation data were further analysed by examining the global methylation level, and that of three distinct genomic regions: promoter, enhancer, and gene body. (who.int)

One of the reasons is the role of methylation in the production and recycling of glutathione, the body's master antioxidant and master "splinter" remover. (scifidimensions.com)
This study is a large integrated study of whole-genome, whole-methylome and whole-transcriptome sequencing in metastatic cancer that provides a comprehensive overview of the important regulatory role of methylation in metastatic castration-resistant prostate cancer. (duke.edu)

Various experiments provided proof of principle that the approach can detect patterns of methylation that distinguish individuals with cancer from those without. (genomeweb.com)
This study reveals the chronology of three epigenetic marks (H3K4me2, H3K4me3 and 5mC) and the patterns of methylation of H19 and Snrpn differentially methylated regions in rat gonocytes during perinatal development. (nih.gov)

Given that epigenetics plays a relevant role during distance signalling in plants, we studied the genome-wide DNA methylation changes induced in eggplant (Solanum melongena) scion using two interspecific rootstocks to increase vigour. (cam.ac.uk)

Epigenetic mechanisms include DNA methylation, histone modifications, and miRNAs. (nih.gov)
Thereby, those changes include DNA methylation, histone modifications and non-coding RNAs. (pharmiweb.com)

High-throughput methylation arrays enable large-sca. (sciweavers.org)
We present a statistical model to describe allele-specific methylation (ASM) in data from high-throughput short-read bisulfite sequencing. (rti.org)

Gover J, Kendall T, Baten A, Burgess D, Freeling M, King GJ Mosher R (2018) Maternal components of RNA-directed DNA methylation are required for seed development in Brassica rapa. (edu.au)

DNA methylation patterns are maintained during cell division by DNA methyltransferase 1 (DNMT1). (nature.com)
One school of thought is that DNA must be unwrapped from nucleosomes to allow methyltransferase access before methylation can occur, but a new study in Nature suggests that this theory isn't all that it's cracked up to be. (epigenie.com)
Answer and Explanation: DNA methylation is accomplished by an enzyme called DNA methyltransferase. (tumericalive.com)

Support methylation with supplements. (scifidimensions.com)
Make sure you get adequate amounts of magnesium and zinc, which can support methylation. (scifidimensions.com)
How do nutrition and lifestyle support methylation ? (planetthrive.com)

Then, in 388 samples from seven different tumor types (acute myeloid leukemia, and pancreatic, colorectal, breast, lung, renal, and bladder cancer), they demonstrated that the test could identify specific methylation profiles that don't just pick out cancer cases from healthy controls but also differentiate the cancers. (genomeweb.com)

Background: There is great interest in probing the temporal and spatial patterns of cytosine methylation states in genomes of a variety of organisms. (sciweavers.org)
Although CHH accounted for the lowest proportion of total cytosine methylation, it showed the most obvious methylation change and the most of these changes occurred in the transposable element regions. (frontiersin.org)

Epigenetic factors such as DNA methylation, histone modifications, and non-coding RNAs are associated with a variety of diseases such as tumorigenesis, immunodeficiency diseases, neurological disorders, cardiovascular diseases, and psychiatric disorders. (pharmiweb.com)
It can detect changes in DNA methylation, histone modifications and transcription factor binding sites. (pharmiweb.com)
Histone modifications, such as methylation and acetylation, or incorporation of histone variants can alter nucleosomal dynamics. (harvard.edu)

The team suggests that in individuals with liver cancer, analyzing the methylation status of the genome of their tumor cells might have prognostic value. (genengnews.com)
Our approach awaits further validation in completely independent datasets, but our findings underscore the potential utility of cfDNA methylation profiles as a basis for noninvasive, cost-effective, sensitive and accurate early tumor detection for cancer interception, and for multi-cancer classification," the team concluded. (genomeweb.com)
CpG microarrays specialize in differentially methylated regions and can be used to detect methylation changes between samples to study tumor epigenomics from a new perspective. (pharmiweb.com)
Our goal is to examine using locally advanced and metastatic breast cancer tumor tissue and plasma, the methylation profile patterns pre- and post chemotherapy of a panel of biomarkers most commonly expressed in breast cancer and correlate them with tumor response and patient outcome. (knowcancer.com)
This preliminary study can be used to determine the clinical utility of DNA methylation in breast tumor tissue and plasma as a predictive marker for response to chemotherapy and a prognostic marker for patient outcome. (knowcancer.com)
In conclusion, methylation-mediated silencing of tumor suppressive miRNAs contributes to acquisition of an anchorage independent phenotype. (oncotarget.com)
Finally, since short-term VPA treatment induced a reversal of the MGMT methylation status, we aimed to sensitize GSCs to temozolomide, the drug commonly used for this tumor, using this regimen. (unimib.it)
The childhood brain tumor medulloblastoma is classified into multiple DNA methylation-based subtypes. (cell.com)

Either modifying genome methylation or targeting the Ras pathway might have therapeutic value, they add. (genengnews.com)
A lot of inflammation control comes from the methylation pathway. (betterhealthguy.com)
The most commonly known methylation issue is methylenetetrahydrofolate reductase (MTHFR) , a family of enzymes in the methylation pathway. (agapenutrition.com)

In embryonic stem cells and somatic cells, DNA methylation at these ICRs was associated with histone H4-lysine 20 and H3-lysine 9 trimethylation. (penelopethemovie.com)
Although DNA methylation patterns remain stable during normal somatic cell growth, alterations in genomic methylation may be caused by genetic alterations, or vice versa. (unibo.it)

If you have a shortage of methyl groups, or your methylation cycle is interrupted, any or all of these processes can become compromised, and you could get sick. (scifidimensions.com)
The presence of methyl groups on cytosine nucleotides across an organism's genome (methylation) is a major regulator of genome stability, crossing over, and gene regulation. (ku.edu)
This reaction also plays an important role in regulating the addition of methyl groups, consisting of one carbon atom and three hydrogen atoms, to other compounds (methylation). (medlineplus.gov)

In a perfect world, your body makes its own glutathione from the amino acids cysteine, glycine and glutamine, then recycles it via methylation using methyl donors like vitamin B12, folate, betaine and other nutrients. (scifidimensions.com)
You need several B vitamins for smooth methylation- folate and B12 are critical, but others like B6 and B2 and compounds such as choline, betaine,and glycine play major roles. (planetthrive.com)
We observed transcriptional changes in fetal liver in response to maternal folate depletion and hypothesized that these changes are concomitant with altered gene promoter methylation. (northumbria.ac.uk)
CONCLUSION: In response to maternal folate depletion, altered expression at the mRNA level was not associated with altered promoter methylation of the same gene in fetal liver. (northumbria.ac.uk)

The results for the alcohol and smoking methylation-based predictors were consistent with a null association. (medscape.com)
Age predictors based on DNA methylation levels at a small set of CpG sites, DNAm clocks, have been developed for humans and extended to several other species. (elifesciences.org)
Methylation-based Predictors of Lifestyle. (medscape.com)

Herein, the DNA methylation landscape of de novo patients with the t(8;21) translocation was compared with that of patients without the translocation. (bvsalud.org)
Moreover, the methylation changes induced by decitabine -based combination regimens in de novo/complete remission paired samples were investigated to elucidate the mechanisms underlying the better responses observed in t(8;21) AML patients treated with decitabine . (bvsalud.org)

After learning about methylation in her Functional Nutrition Training course, Sara thought about her uncle, had a hunch, and decided to test her genetics. (planetthrive.com)
She says she feels certain that learning about her genetics- and a bit about methylation- saved her life. (planetthrive.com)
These measures are calculated using methylation data at 353, 71, 513 and 1,030 CpGs, respectively, and were obtained using Horvath's online calculator https://dnamage.genetics.ucla.edu/new . (medscape.com)
As a step toward this, the current study investigated how DNA methylation at CoRSIVs is affected by genetics. (eurekalert.org)

The group is not the only academic team to investigate methylation or other epigenetic changes for early cancer detection. (genomeweb.com)
These manuscripts address novel computational solutions for copy number variation detection, cell-type deconvolution and methylation pattern imputation, while others discuss interpretations of well-established computational techniques. (unibo.it)
Methylation measures with a detection P -value higher than 0.01 were considered missing. (medscape.com)
Population variance is essential not only for mQTL detection, but also for detecting associations between DNA methylation and risk of disease," said co-corresponding author Dr. Cristian Coarfa , associate professor of molecular and cellular biology and in the Dan L Duncan Comprehensive Cancer Center and the Center for Precision Environmental Health at Baylor. (eurekalert.org)

The potential role of DNA methylation is supported by: i) AD patients and mouse models exhibit global DNA hypomethylation and gene-specific DNA hypermethylation, ii) DNA methylation at promoters leads to gene repression, but intragenic methylation can enhance transcription, iii) Wnt components contain CpG islands at their promoters and/or intragenic regions, and iv) some Wnt components are regulated by DNA methylation in cancer. (alzheimer-europe.org)

DNA from 968 blood samples from children in the Study to Explore Early Development (SEED 1) was used to generate epigenome-wide array DNA methylation (DNAm) data at 485,512 CpG sites for 453 cases and 515 controls, using the Illumina 450K Beadchip. (springer.com)

Sodium fluoride may adversely affect early embryonic development by disrupting the methylation of H19 and Peg3 through downregulation of DNMT1. (greenmedinfo.com)
BRCA1 methylation in early embryonic life leads to increased cancer risk in the adult. (uib.no)

RNA Methylation kits from Zymo Research offer fast, easy bisulfite conversion in RNA for methylation analysis. (zymoresearch.com)

Environmental factors, including rapid urbanisation and lifestyle habits, have also contributed to this disease through their ability to modulate the establishment and maintenance of epigenetic modifications such as DNA methylation. (endocrinology.org)
DNA methylation is among the most studied epigenetic modifications in eukaryotes. (unibo.it)

compares the first and second generation of epigenetic clocks that predict cancer risk and discusses pathways known to exhibit altered methylation in aging tissues and cancer. (unibo.it)
Results: We have found that LINE-1 methylation patterns among normal tissues are distinct. (who.int)
For the last 15 years, the Waterland lab and colleagues have focused on a different set of CpG sites: those at which DNA methylation differs substantially among people but is consistent across the different tissues of each person. (eurekalert.org)
The team developed an approach to target CoRSIVs and studied their methylation in DNA samples from multiple tissues of nearly 200 individuals. (eurekalert.org)

Is H3K9me3 methylation in embryonic stem cells associated with histone h4-lysine 20? (penelopethemovie.com)

Subsequently, the mechanism was elucidated, showing that variations in maternal care lead to stable alterations of DNA methylation patterns. (uni-trier.de)
Low maternal care results in increased methylation of the nerve growth factor-inducible protein A (Ngfi-A) binding site located in the Nr3c1 gene exon 1 7 promoter, leading to decreased GR expression. (uni-trier.de)

Remarkably, expression of exon 1 7 containing mRNA seems to be unique to hippocampus, so that methylation of exon 1 7 specifically reduces Nr3c1 expression in hippocampal sites (Weaver et al 2004). (uni-trier.de)

Methylation is a process happening at the cellular level in your body that could be the key to unlocking your healthiest self. (camillestyles.com)
Reference-based approaches use DMRs specific to cell types (reference library) to determine the underlying cellular composition within a DNA methylation sample. (unibo.it)
Within a cellular population, the methylation patterns of different cell types and at specific genomic locations are indicative of cellular heterogeneity. (unibo.it)
Methylation is important in many cellular processes. (medlineplus.gov)
In response to the cellular environment, signals are sent for the opposing processes of "writing" and "erasing" methylation. (yeastgenome.org)
Upon analysis of differential expression for the sets of phosphonull and phosphomimetic mutants, they showed the proteins most affected by histone methylation clustered into GO categories consistent with cellular response to stress, e.g. ion membrane transport, lipid biosynthesis, ergosterol biosynthesis, and protein mannosylation. (yeastgenome.org)
In the fourth episode of the Longevity & Aging Series, Dr. Carly Bobak from Dartmouth College, Dr. Cristian Coarfa from Baylor College of Medicine, and Dr. Andrew DiNardo from Baylor College of Medicine, discuss a research paper they co-authored that was published in Volume 14, Issue 5 of Aging (Aging-US), entitled, "Increased DNA methylation, cellular senescence and premature epigenetic aging in guinea pigs and humans with tuberculosis. (labtube.tv)
The transcriptome in TB in multiple cohorts was enriched for DNA methylation and cellular senescence. (labtube.tv)

Methylation analysis made easy. (zymoresearch.com)
Owing to its potential as a prognostic marker for preventive medicine, in recent years, the analysis of DNA methylation data has garnered interest in many different contexts of computational biology (Bock, 2012). (unibo.it)
In the present Research Topic, we collected papers that tackle different aspects of computational approaches for the analysis of DNA methylation data. (unibo.it)
However, standard DMR analysis often ignores whether methylation alterations should be viewed as a cause or an effect. (unibo.it)
Methods relating to DNA extraction and bisulphite conversion, and DNA methylation data processing have been described previously and are detailed in Additional file 1 and are the same as in our previous pooled analysis. (medscape.com)
IMSEAR at SEARO: Quantitative PCR analysis for methylation level of genome: clinical implications in cancer. (who.int)
Lastly, motif enrichment analysis identified differential enhancer methylation in the binding sites of key transcription factors in EMT and inflammatory response pathways. (who.int)
Ph.D. in "Analysis of DNA methylation in male infertility and germ cells development. (ucsb.edu)
Methods: Guinea pigs were infected with Mycobacterium tuberculosis (Mtb) for 45 days, followed by RRBS DNA methylation analysis. (labtube.tv)

This has restricted many previous blood-based methylation efforts to locus-specific PCR-based assays. (genomeweb.com)
The standard tool for population studies of DNA methylation is a commercial array that assays hundreds of thousands of CpG sites distributed throughout the genome. (eurekalert.org)
DMS can be used for methylation protection or methylation interference assays. (tumericalive.com)

The microarray can not only focus on cancer-specific regions of large-scale epigenetic changes, but also specifically detect small-scale methylation changes. (pharmiweb.com)

Over the last 10 years, DNA methylation profiles have been successfully exploited to develop biomarkers of age, also referred to as epigenetic clocks (Bell et al. (unibo.it)
The hypothesis is that epigenome changes associated with risk of childhood cancer and exposure to environmental, dietary, and lifestyle factors during pregnancy can be identified in blood cells at birth, and that these methylation changes can serve as sensitive biomarkers in primary and secondary prevention as well as targeted therapy of childhood cancer. (who.int)

Correlations between a genetic variant and methylation at a specific CpG site are called methylation quantitative trait loci (mQTL). (eurekalert.org)

Using data from four prospective case-control studies nested in three cohorts of European ancestry participants, including a total of 1,655 breast cancer cases, we calculated three methylation-based measures of lifestyle factors (body mass index [BMI], tobacco smoking and alcohol consumption) and seven measures of epigenetic aging (Horvath-based, Hannum-based, PhenoAge and GrimAge ). (medscape.com)
We used the normalised DNA methylation data to calculate the epigenetic measures of aging developed by Horvath [ 7 ] and Hannum et al. (medscape.com)
It is computed as the residuals of the methylation age (Horvath or Hannum) on chronological age and methylation-based blood cell count estimates. (medscape.com)
Extrinsic' epigenetic age acceleration (EEAA) is computed as the residual of the Horvath methylation age on chronological age and a weighted average of age-related changes in blood cell composition. (medscape.com)
Horvath (DNA methylation) and RNA-seq biological clocks were used to investigate shifts in chronological age among humans with TB. (labtube.tv)

When methylation is impaired, B-cells will be high and you will have ongoing inflammation. (betterhealthguy.com)

DNA methylation in blood may reflect adverse exposures accumulated over the lifetime and could therefore provide potential improvements in the prediction of cancer risk. (medscape.com)
We found no evidence that methylation-based measures of aging, smoking or alcohol consumption were associated with risk of breast cancer. (medscape.com)
A methylation-based marker of BMI was associated with risk and may provide insights into the underlying associations between BMI and breast cancer. (medscape.com)
The main objective of the project is to assess and validate the role of DNA methylation as objective marker of WTC exposure-related breast cancer among general population of survivors, specifically women. (cdc.gov)
The extent to which the genome of a person's liver cancer cells is modified by methylation correlates with clinical outcome, say researchers at the NIH. (genengnews.com)
In our present study, performed in collaboration with the American Women's Health Initiative, we found BRCA1 methylation in blood samples collected many years prior to the cancer diagnosis to be associated with an elevated risk for TNBC as well as HGSOC. (uib.no)
For the first time, this confirms such methylation to be a cancer risk factor. (uib.no)
Among the six possible mechanisms leading to oncogenes with an altered expression that cause cancer, three of them are directly related to DNA methylation and histone acetylation. (pharmiweb.com)
Ninety-five percent of the DNA methylation changes in cancer occur in those regions. (pharmiweb.com)
More than 10,000 cancer-specific DMR regions have been identified, among which the regions of hypermethylated CpG islands are sensitive regions for cancer-related methylation changes. (pharmiweb.com)
From this data, we will identify a preliminary gene panel associated with breast cancer which undergoes the most changes in methylation following systemic therapy. (knowcancer.com)
Bisulfite sequencing and methylation-specific PCR showed increased methylation of hsa-mir-129-2/-137/-935/-3663/-3665 and -4281 in anchorage independent HPV-transformed keratinocytes and cervical cancer cell lines. (oncotarget.com)
Particularly, there is strong evidence that methylation pattern alterations in mammals are linked to developmental disorders and cancer (Kulis and Esteller, 2010). (unibo.it)
The DNA methylation landscape of advanced prostate cancer. (duke.edu)
Global DNA methylation profiles in peripheral blood of WTC-exposed community members with breast cancer. (cdc.gov)
There were significant differences in DNA methylation between WTC-exposed breast cancer cases and unexposed prediagnostic breast cancer cases. (cdc.gov)
Septin-9 methylation has been found to be common in patients with colorectal cancer, whereas this gene is not methylated in most healthy individuals. (medpagetoday.com)

The researchers had previously found that women who have children with autism have an abnormal methylation capacity , defined as the ratio of S-adenosyl methionine (SAM) to S-adenosylhomocysteine (SAH) SAM is a critical ingredient of methylation. (spectrumnews.org)
Methylation issues are present in virtually all children along the autism spectrum. (agapenutrition.com)

Without getting too technical, methylation is the addition of a single carbon and three hydrogen atoms (called a methyl group) to another molecule. (scifidimensions.com)
Methylation is the process of adding a carbon and three hydrogen atoms to a molecule. (betterhealthguy.com)

A recent study used methylation risk scores to improve predictive value of baseline models for a range of clinical diagnoses and laboratory tests. (cdc.gov)
This study establishes DNA methylation as a highly dynamic process during postnatal growth of cardiomyocytes and their adaptation to pathological stress in a process tightly linked to gene regulation and activity. (nature.com)
In the study, we found that women with low-level mosaic methylation of BRCA1, had a 2.5-fold increased risk of TNBC and 1.8 fold increased risk of HGSOC. (uib.no)
Although recent advances in genome sequencing have revolutionized the study of DNA methylation, existing methylome data remain largely untapped in the study of imprinting. (rti.org)
In this study, we used whole-genome bisulfite sequencing (WGBS) to study genomic DNA methylation changes of a wild strawberry Fragaria nilgerrensis at six stages: from explants of shoot tips to outplanting and acclimation. (frontiersin.org)
If a relationship is found, we can then further study if the change in methylation pattern has clinical utility in influencing therapeutic decision-making which may be further expanded to the adjuvant setting. (knowcancer.com)
Now a new study from Uppsala and Umeå University demonstrates that the molecular composition of the sediment organic matter plays a central role for mercury methylation. (scienzaonline.com)
This article reviewed what have been learned by applying this technique to study methylation level of repetitive sequences from several sources of genomic DNA. (who.int)
To look for such differences, epigeneticists study DNA methylation, which occurs at specific locations called CpG sites. (eurekalert.org)
The "language" of histone methylation has been a subject of intensive study due to numerous diseases and disorders linked to faulty methylation patterns. (yeastgenome.org)

Here, using a variety of diverse approaches, we functionally characterise the critically important molecular process DNA methylation in B. glabrata, which is mediated by a suite of biological participants and is involved in a wide range of metazoan functions. (archives-ouvertes.fr)
Data from the methylation of an asphalt and its fractions with diazomethane suggest the occurrence of molecular aggregation via hydrogen bonding. (cdc.gov)

Background: Patterns of genome-wide methylation vary between tissue types. (sciweavers.org)
Background: DNA methylation patterns have been shown to significantly correlate with different tissue types and disease states. (sciweavers.org)
In plant tissue culture, variation of DNA methylation is a potential source of phenotypic variation in regenerated plants. (frontiersin.org)
However, the genome wide dynamic methylation patterns of strawberry tissue culture remain unclear. (frontiersin.org)
The overall methylation levels alternately decreased and increased during the entire tissue culture process and the distribution of DNA methylation was non-uniform among different genetic regions. (frontiersin.org)
While the latter are more broadly applicable, as they do not rely on the availability of methylation profiles from each of the purified cell types that compose a tissue of interest, they are also less precise. (unibo.it)
COBRALINE-1 is a highly effective technique for evaluating the genome-wide level of methylation, in particular from tissue samples with minute amounts of low quality DNA. (who.int)

Anatomy21

Organisms5

Diseases25

Chemicals and Drugs103

Analytical, Diagnostic and Therapeutic Techniques and Equipment28

Phenomena and Processes83

Disciplines and Occupations3

Information Science4

Health Care4

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

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

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

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

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

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

Sites of reaction of pilocarpine. (7/8251)

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

Methylation

DNA Methylation

CpG Islands

Epigenesis, Genetic

DNA (Cytosine-5-)-Methyltransferase

Promoter Regions, Genetic

Sulfites

Azacitidine

Cytosine

Gene Silencing

Methyltransferases

DNA Modification Methylases

Histones

5-Methylcytosine

Genomic Imprinting

Epigenomics

Histone-Lysine N-Methyltransferase

DNA-Cytosine Methylases

Long Interspersed Nucleotide Elements

Protein Methyltransferases

S-Adenosylmethionine

Base Sequence

Lysine

Dinucleoside Phosphates

Protein-Arginine N-Methyltransferases

Molecular Sequence Data

DNA, Neoplasm

DNA

Polymerase Chain Reaction

Gene Expression Regulation, Neoplastic

Genes, p16

RNA, Long Noncoding

Deoxyribonuclease HpaII

S-Adenosylhomocysteine

Sequence Analysis, DNA

Chromatin

Cell Line, Tumor

Death-Associated Protein Kinases

Transcription, Genetic

Tumor Suppressor Proteins

Site-Specific DNA-Methyltransferase (Adenine-Specific)

Genes, Tumor Suppressor

Genome, Human

Cyclin-Dependent Kinase Inhibitor p16

Gene Expression Regulation

Acetylation

Mutation

RNA, Untranslated

Heterochromatin

Alu Elements

Nuclear Proteins

tRNA Methyltransferases

Reverse Transcriptase Polymerase Chain Reaction

Cell Line

Oligonucleotide Array Sequence Analysis

DNA-Binding Proteins

Gene Expression Profiling

RNA, Messenger

Repressor Proteins

Cyclin-Dependent Kinase Inhibitor p15

Chromatin Immunoprecipitation

Genetic Loci

DNA Primers

Transcription Factors

snRNP Core Proteins

Histone Demethylases

Alleles

Insulin-Like Growth Factor II

DNA, Plant

Tumor Markers, Biological

Glutathione S-Transferase pi

Colorectal Neoplasms

O(6)-Methylguanine-DNA Methyltransferase

DNA Repair Enzymes

Genome

Arabidopsis

Protein O-Methyltransferase

Hydroxamic Acids

Neoplasm Proteins

Euchromatin