DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Methylation: Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)CpG Islands: Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes.Epigenesis, Genetic: A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Sulfites: Inorganic salts of sulfurous acid.Genes, p16: Tumor suppressor genes located on human chromosome 9 in the region 9p21. This gene is either deleted or mutated in a wide range of malignancies. (From Segen, Current Med Talk, 1995) Two alternatively spliced gene products are encoded by p16: CYCLIN-DEPENDENT KINASE INHIBITOR P16 and TUMOR SUPPRESSOR PROTEIN P14ARF.Azacitidine: A pyrimidine analogue that inhibits DNA methyltransferase, impairing DNA methylation. It is also an antimetabolite of cytidine, incorporated primarily into RNA. Azacytidine has been used as an antineoplastic agent.Death-Associated Protein Kinases: A family of calcium/calmodulin-dependent PROETIN-SERINE-THREONINE KINASES. They are ubiquitously expressed in adult and embryonic mammalian tissues, and their functions are tightly related to the early stages of eukaryotic programmed cell death.DNA (Cytosine-5-)-Methyltransferase: An enzyme that catalyzes the transfer of a methyl group from S-ADENOSYLMETHIONINE to the 5-position of CYTOSINE residues in DNA.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.DNA, Neoplasm: DNA present in neoplastic tissue.Cyclin-Dependent Kinase Inhibitor p15: An INK4 cyclin-dependent kinase inhibitor containing four ANKYRIN-LIKE REPEATS. INK4B is often inactivated by deletions, mutations, or hypermethylation in HEMATOLOGIC NEOPLASMS.Tumor Suppressor Proteins: Proteins that are normally involved in holding cellular growth in check. Deficiencies or abnormalities in these proteins may lead to unregulated cell growth and tumor development.Gene Expression Regulation, Neoplastic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.Cyclin-Dependent Kinase Inhibitor p16: A product of the p16 tumor suppressor gene (GENES, P16). It is also called INK4 or INK4A because it is the prototype member of the INK4 CYCLIN-DEPENDENT KINASE INHIBITORS. This protein is produced from the alpha mRNA transcript of the p16 gene. The other gene product, produced from the alternatively spliced beta transcript, is TUMOR SUPPRESSOR PROTEIN P14ARF. Both p16 gene products have tumor suppressor functions.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Genes, Tumor Suppressor: Genes that inhibit expression of the tumorigenic phenotype. They are normally involved in holding cellular growth in check. When tumor suppressor genes are inactivated or lost, a barrier to normal proliferation is removed and unregulated growth is possible.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Cell Line, Tumor: A cell line derived from cultured tumor cells.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Tumor Markers, Biological: Molecular products metabolized and secreted by neoplastic tissue and characterized biochemically in cells or body fluids. They are indicators of tumor stage and grade as well as useful for monitoring responses to treatment and predicting recurrence. Many chemical groups are represented including hormones, antigens, amino and nucleic acids, enzymes, polyamines, and specific cell membrane proteins and lipids.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Cytosine: A pyrimidine base that is a fundamental unit of nucleic acids.Methyltransferases: A subclass of enzymes of the transferase class that catalyze the transfer of a methyl group from one compound to another. (Dorland, 28th ed) EC 2.1.1.DNA Modification Methylases: Enzymes that are part of the restriction-modification systems. They are responsible for producing a species-characteristic methylation pattern, on either adenine or cytosine residues, in a specific short base sequence in the host cell's own DNA. This methylated sequence will occur many times in the host-cell DNA and remain intact for the lifetime of the cell. Any DNA from another species which gains entry into a living cell and lacks the characteristic methylation pattern will be recognized by the restriction endonucleases of similar specificity and destroyed by cleavage. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms.Neoplasm Proteins: Proteins whose abnormal expression (gain or loss) are associated with the development, growth, or progression of NEOPLASMS. Some neoplasm proteins are tumor antigens (ANTIGENS, NEOPLASM), i.e. they induce an immune reaction to their tumor. Many neoplasm proteins have been characterized and are used as tumor markers (BIOMARKERS, TUMOR) when they are detectable in cells and body fluids as monitors for the presence or growth of tumors. Abnormal expression of ONCOGENE PROTEINS is involved in neoplastic transformation, whereas the loss of expression of TUMOR SUPPRESSOR PROTEINS is involved with the loss of growth control and progression of the neoplasm.Histones: Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.5-Methylcytosine: A methylated nucleotide base found in eukaryotic DNA. In ANIMALS, the DNA METHYLATION of CYTOSINE to form 5-methylcytosine is found primarily in the palindromic sequence CpG. In PLANTS, the methylated sequence is CpNpGp, where N can be any base.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Genomic Imprinting: The variable phenotypic expression of a GENE depending on whether it is of paternal or maternal origin, which is a function of the DNA METHYLATION pattern. Imprinted regions are observed to be more methylated and less transcriptionally active. (Segen, Dictionary of Modern Medicine, 1992)Lung Neoplasms: Tumors or cancer of the LUNG.Epigenomics: The systematic study of the global gene expression changes due to EPIGENETIC PROCESSES and not due to DNA base sequence changes.Histone-Lysine N-Methyltransferase: An enzyme that catalyzes the methylation of the epsilon-amino group of lysine residues in proteins to yield epsilon mono-, di-, and trimethyllysine. EC 22.214.171.124.DNA-Cytosine Methylases: Methylases that are specific for CYTOSINE residues found on DNA.Long Interspersed Nucleotide Elements: Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). Copies of the LINE 1 (L1) family form about 15% of the human genome. The jockey elements of Drosophila are LINEs.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Prognosis: A prediction of the probable outcome of a disease based on a individual's condition and the usual course of the disease as seen in similar situations.Protein Methyltransferases: Enzymes that catalyze the methylation of amino acids after their incorporation into a polypeptide chain. S-Adenosyl-L-methionine acts as the methylating agent. EC 2.1.1.S-Adenosylmethionine: Physiologic methyl radical donor involved in enzymatic transmethylation reactions and present in all living organisms. It possesses anti-inflammatory activity and has been used in treatment of chronic liver disease. (From Merck, 11th ed)Lysine: An essential amino acid. It is often added to animal feed.Dinucleoside Phosphates: A group of compounds which consist of a nucleotide molecule to which an additional nucleoside is attached through the phosphate molecule(s). The nucleotide can contain any number of phosphates.Protein-Arginine N-Methyltransferases: Enzymes that catalyze the methylation of arginine residues of proteins to yield N-mono- and N,N-dimethylarginine. This enzyme is found in many organs, primarily brain and spleen.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.RNA, Long Noncoding: A class of untranslated RNA molecules that are typically greater than 200 nucleotides in length and do not code for proteins. Members of this class have been found to play roles in transcriptional regulation, post-transcriptional processing, CHROMATIN REMODELING, and in the epigenetic control of chromatin.Deoxyribonuclease HpaII: One of the Type II site-specific deoxyribonucleases (EC 126.96.36.199). It recognizes and cleaves the sequences C/CGG and GGC/C at the slash. HpaII is from Haemophilus parainfluenzae. Several isoschizomers have been identified. EC 3.1.21.-.S-Adenosylhomocysteine: 5'-S-(3-Amino-3-carboxypropyl)-5'-thioadenosine. Formed from S-adenosylmethionine after transmethylation reactions.Chromatin: The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Site-Specific DNA-Methyltransferase (Adenine-Specific): An enzyme responsible for producing a species-characteristic methylation pattern on adenine residues in a specific short base sequence in the host cell DNA. The enzyme catalyzes the methylation of DNA adenine in the presence of S-adenosyl-L-methionine to form DNA containing 6-methylaminopurine and S-adenosyl-L-homocysteine. EC 188.8.131.52.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Acetylation: Formation of an acetyl derivative. (Stedman, 25th ed)Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.RNA, Untranslated: RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.Heterochromatin: The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE.Alu Elements: The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). It is derived from the 7SL RNA component of the SIGNAL RECOGNITION PARTICLE and contains an RNA polymerase III promoter. Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.tRNA Methyltransferases: Enzymes that catalyze the S-adenosyl-L-methionine-dependent methylation of ribonucleotide bases within a transfer RNA molecule. EC 2.1.1.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.Chromatin Immunoprecipitation: A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.Genetic Loci: Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.snRNP Core Proteins: The protein components that constitute the common core of small nuclear ribonucleoprotein particles. These proteins are commonly referred as Sm nuclear antigens due to their antigenic nature.Histone Demethylases: Enzymes that catalyse the removal of methyl groups from LYSINE or ARGININE residues found on HISTONES. Many histone demethylases generally function through an oxidoreductive mechanism.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Insulin-Like Growth Factor II: A well-characterized neutral peptide believed to be secreted by the LIVER and to circulate in the BLOOD. It has growth-regulating, insulin-like and mitogenic activities. The growth factor has a major, but not absolute, dependence on SOMATOTROPIN. It is believed to be a major fetal growth factor in contrast to INSULIN-LIKE GROWTH FACTOR I, which is a major growth factor in adults.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Glutathione S-Transferase pi: A glutathione transferase that catalyzes the conjugation of electrophilic substrates to GLUTATHIONE. This enzyme has been shown to provide cellular protection against redox-mediated damage by FREE RADICALS.Colorectal Neoplasms: Tumors or cancer of the COLON or the RECTUM or both. Risk factors for colorectal cancer include chronic ULCERATIVE COLITIS; FAMILIAL POLYPOSIS COLI; exposure to ASBESTOS; and irradiation of the CERVIX UTERI.O(6)-Methylguanine-DNA Methyltransferase: An enzyme that transfers methyl groups from O(6)-methylguanine, and other methylated moieties of DNA, to a cysteine residue in itself, thus repairing alkylated DNA in a single-step reaction. EC 184.108.40.206.DNA Repair Enzymes: Enzymes that are involved in the reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule, which contained damaged regions.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.Protein O-Methyltransferase: An enzyme that catalyzes the transfer of methyl groups from S-adenosylmethionine to free carboxyl groups of a protein molecule forming methyl esters. EC 2.1.1.-.Hydroxamic Acids: A class of weak acids with the general formula R-CONHOH.Euchromatin: Chromosome regions that are loosely packaged and more accessible to RNA polymerases than HETEROCHROMATIN. These regions also stain differentially in CHROMOSOME BANDING preparations.Genes, Neoplasm: Genes whose abnormal expression, or MUTATION are associated with the development, growth, or progression of NEOPLASMS.Jumonji Domain-Containing Histone Demethylases: A family of histone demethylases that share a conserved Jumonji C domain. The enzymes function via an iron-dependent dioxygenase mechanism that couples the conversion of 2-oxoglutarate to succinate to the hydroxylation of N-methyl groups.Methionine: A sulfur-containing essential L-amino acid that is important in many body functions.Tubercidin: An antibiotic purine ribonucleoside that readily substitutes for adenosine in the biological system, but its incorporation into DNA and RNA has an inhibitory effect on the metabolism of these nucleic acids.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Core Binding Factor Alpha 3 Subunit: A transcription factor that dimerizes with the cofactor CORE BINDING FACTOR BETA SUBUNIT to form core binding factor. It contains a highly conserved DNA-binding domain known as the runt domain.Chromatin Assembly and Disassembly: The mechanisms effecting establishment, maintenance, and modification of that specific physical conformation of CHROMATIN determining the transcriptional accessibility or inaccessibility of the DNA.Arginine: An essential amino acid that is physiologically active in the L-form.Cytidine: A pyrimidine nucleoside that is composed of the base CYTOSINE linked to the five-carbon sugar D-RIBOSE.Polycomb-Group Proteins: A family of proteins that play a role in CHROMATIN REMODELING. They are best known for silencing HOX GENES and the regulation of EPIGENETIC PROCESSES.Protein Processing, Post-Translational: Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.Folic Acid: A member of the vitamin B family that stimulates the hematopoietic system. It is present in the liver and kidney and is found in mushrooms, spinach, yeast, green leaves, and grasses (POACEAE). Folic acid is used in the treatment and prevention of folate deficiencies and megaloblastic anemia.Embryonic Stem Cells: Cells derived from the BLASTOCYST INNER CELL MASS which forms before implantation in the uterine wall. They retain the ability to divide, proliferate and provide progenitor cells that can differentiate into specialized cells.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Tumor Cells, Cultured: Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.Arabidopsis Proteins: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Gene Expression Regulation, Developmental: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.Polycomb Repressive Complex 2: A multisubunit polycomb protein complex that catalyzes the METHYLATION of chromosomal HISTONE H3. It works in conjunction with POLYCOMB REPRESSIVE COMPLEX 1 to effect EPIGENETIC REPRESSION.Cadherins: Calcium-dependent cell adhesion proteins. They are important in the formation of ADHERENS JUNCTIONS between cells. Cadherins are classified by their distinct immunological and tissue specificities, either by letters (E- for epithelial, N- for neural, and P- for placental cadherins) or by numbers (cadherin-12 or N-cadherin 2 for brain-cadherin). Cadherins promote cell adhesion via a homophilic mechanism as in the construction of tissues and of the whole animal body.Neoplasms: New abnormal growth of tissue. Malignant neoplasms show a greater degree of anaplasia and have the properties of invasion and metastasis, compared to benign neoplasms.Microsatellite Instability: The occurrence of highly polymorphic mono- and dinucleotide MICROSATELLITE REPEATS in somatic cells. It is a form of genome instability associated with defects in DNA MISMATCH REPAIR.Phosphatidylethanolamine N-Methyltransferase: An enzyme that catalyses three sequential METHYLATION reactions for conversion of phosphatidylethanolamine to PHOSPHATIDYLCHOLINE.Transcription Initiation Site: The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.Methyl-CpG-Binding Protein 2: A DNA-binding protein that interacts with methylated CPG ISLANDS. It plays a role in repressing GENETIC TRANSCRIPTION and is frequently mutated in RETT SYNDROME.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Deoxyribonucleases, Type II Site-Specific: Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 220.127.116.11.Adaptor Proteins, Signal Transducing: A broad category of carrier proteins that play a role in SIGNAL TRANSDUCTION. They generally contain several modular domains, each of which having its own binding activity, and act by forming complexes with other intracellular-signaling molecules. Signal-transducing adaptor proteins lack enzyme activity, however their activity can be modulated by other signal-transducing enzymesAdenosylhomocysteinase: An enzyme which catalyzes the catabolism of S-ADENOSYLHOMOCYSTEINE to ADENOSINE and HOMOCYSTEINE. It may play a role in regulating the concentration of intracellular adenosylhomocysteine.Chromosomal Proteins, Non-Histone: Nucleoproteins, which in contrast to HISTONES, are acid insoluble. They are involved in chromosomal functions; e.g. they bind selectively to DNA, stimulate transcription resulting in tissue-specific RNA synthesis and undergo specific changes in response to various hormones or phytomitogens.Breast Neoplasms: Tumors or cancer of the human BREAST.Chromosomes, Human, X: The human female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in humans.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Dosage Compensation, Genetic: Genetic mechanisms that allow GENES to be expressed at a similar level irrespective of their GENE DOSAGE. This term is usually used in discussing genes that lie on the SEX CHROMOSOMES. Because the sex chromosomes are only partially homologous, there is a different copy number, i.e., dosage, of these genes in males vs. females. In DROSOPHILA, dosage compensation is accomplished by hypertranscription of genes located on the X CHROMOSOME. In mammals, dosage compensation of X chromosome genes is accomplished by random X CHROMOSOME INACTIVATION of one of the two X chromosomes in the female.Arsenic: A shiny gray element with atomic symbol As, atomic number 33, and atomic weight 75. It occurs throughout the universe, mostly in the form of metallic arsenides. Most forms are toxic. According to the Fourth Annual Report on Carcinogens (NTP 85-002, 1985), arsenic and certain arsenic compounds have been listed as known carcinogens. (From Merck Index, 11th ed)Beckwith-Wiedemann Syndrome: A syndrome of multiple defects characterized primarily by umbilical hernia (HERNIA, UMBILICAL); MACROGLOSSIA; and GIGANTISM; and secondarily by visceromegaly; HYPOGLYCEMIA; and ear abnormalities.Tumor Suppressor Protein p14ARF: A gene product of the p16 tumor suppressor gene (GENES, P16). It antagonizes the function of MDM2 PROTEIN (which regulates P53 TUMOR SUPPRESSOR PROTEIN by targeting it for degradation). p14ARF is produced from the beta mRNA transcript of the p16 gene. The other gene product, produced from the alternatively spliced alpha transcript, is CYCLIN-DEPENDENT KINASE INHIBITOR P16. Both p16 gene products have tumor suppressor functions.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.Embryo, Mammalian: The entity of a developing mammal (MAMMALS), generally from the cleavage of a ZYGOTE to the end of embryonic differentiation of basic structures. For the human embryo, this represents the first two months of intrauterine development preceding the stages of the FETUS.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Histone Deacetylases: Deacetylases that remove N-acetyl groups from amino side chains of the amino acids of HISTONES. The enzyme family can be divided into at least three structurally-defined subclasses. Class I and class II deacetylases utilize a zinc-dependent mechanism. The sirtuin histone deacetylases belong to class III and are NAD-dependent enzymes.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.X Chromosome Inactivation: A dosage compensation process occurring at an early embryonic stage in mammalian development whereby, at random, one X CHROMOSOME of the pair is repressed in the somatic cells of females.Down-Regulation: A negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Stomach Neoplasms: Tumors or cancer of the STOMACH.Loss of Heterozygosity: The loss of one allele at a specific locus, caused by a deletion mutation; or loss of a chromosome from a chromosome pair, resulting in abnormal HEMIZYGOSITY. It is detected when heterozygous markers for a locus appear monomorphic because one of the ALLELES was deleted.Pregnancy: The status during which female mammals carry their developing young (EMBRYOS or FETUSES) in utero before birth, beginning from FERTILIZATION to BIRTH.Homeodomain Proteins: Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).Adenine: A purine base and a fundamental unit of ADENINE NUCLEOTIDES.Germ Cells: The reproductive cells in multicellular organisms at various stages during GAMETOGENESIS.Transgenes: Genes that are introduced into an organism using GENE TRANSFER TECHNIQUES.RNA, Small Interfering: Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.Cell Transformation, Neoplastic: Cell changes manifested by escape from control mechanisms, increased growth potential, alterations in the cell surface, karyotypic abnormalities, morphological and biochemical deviations from the norm, and other attributes conferring the ability to invade, metastasize, and kill.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.Case-Control Studies: Studies which start with the identification of persons with a disease of interest and a control (comparison, referent) group without the disease. The relationship of an attribute to the disease is examined by comparing diseased and non-diseased persons with regard to the frequency or levels of the attribute in each group.Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.Homocysteine: A thiol-containing amino acid formed by a demethylation of METHIONINE.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.Antimetabolites, Antineoplastic: Antimetabolites that are useful in cancer chemotherapy.Embryonic Development: Morphological and physiological development of EMBRYOS.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Epigenetic Repression: The turning off of GENETIC TRANSCRIPTION in certain regions of CHROMATIN without changes in the DNA sequence. Typically epigenetic repression is a way that developmental changes are programmed at the cellular level.Carbohydrate Sequence: The sequence of carbohydrates within POLYSACCHARIDES; GLYCOPROTEINS; and GLYCOLIPIDS.Nucleosomes: The repeating structural units of chromatin, each consisting of approximately 200 base pairs of DNA wound around a protein core. This core is composed of the histones H2A, H2B, H3, and H4.Cyclin A1: A cyclin A subtype primarily found in male GERM CELLS. It may play a role in the passage of SPERMATOCYTES into meiosis I.Prader-Willi Syndrome: An autosomal dominant disorder caused by deletion of the proximal long arm of the paternal chromosome 15 (15q11-q13) or by inheritance of both of the pair of chromosomes 15 from the mother (UNIPARENTAL DISOMY) which are imprinted (GENETIC IMPRINTING) and hence silenced. Clinical manifestations include MENTAL RETARDATION; MUSCULAR HYPOTONIA; HYPERPHAGIA; OBESITY; short stature; HYPOGONADISM; STRABISMUS; and HYPERSOMNOLENCE. (Menkes, Textbook of Child Neurology, 5th ed, p229)Mass Spectrometry: An analytical method used in determining the identity of a chemical based on its mass using mass analyzers/mass spectrometers.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Mice, Inbred C57BLGenome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Histone Deacetylase Inhibitors: Compounds that inhibit HISTONE DEACETYLASES. This class of drugs may influence gene expression by increasing the level of acetylated HISTONES in specific CHROMATIN domains.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.Receptors, Retinoic Acid: Proteins in the nucleus or cytoplasm that specifically bind RETINOIC ACID or RETINOL and trigger changes in the behavior of cells. Retinoic acid receptors, like steroid receptors, are ligand-activated transcription regulators. Several types have been recognized.Placenta: A highly vascularized mammalian fetal-maternal organ and major site of transport of oxygen, nutrients, and fetal waste products. It includes a fetal portion (CHORIONIC VILLI) derived from TROPHOBLASTS and a maternal portion (DECIDUA) derived from the uterine ENDOMETRIUM. The placenta produces an array of steroid, protein and peptide hormones (PLACENTAL HORMONES).Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Ribose: A pentose active in biological systems usually in its D-form.Retroelements: Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.Genes, Intracisternal A-Particle: Genes of IAP elements (a family of retrovirus-like genetic elements) which code for virus-like particles (IAPs) found regularly in rodent early embryos. ("Intracisternal" refers to the cisternae of the endoplasmic reticulum.) Under certain circumstances, such as DNA hypomethylation they are transcribed. Their transcripts are found in a variety of neoplasms, including plasmacytomas, neuroblastoma, rhabdomyosarcomas, teratocarcinomas, and colon carcinomas.Adenocarcinoma: A malignant epithelial tumor with a glandular organization.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.DNA, Satellite: Highly repetitive DNA sequences found in HETEROCHROMATIN, mainly near centromeres. They are composed of simple sequences (very short) (see MINISATELLITE REPEATS) repeated in tandem many times to form large blocks of sequence. Additionally, following the accumulation of mutations, these blocks of repeats have been repeated in tandem themselves. The degree of repetition is on the order of 1000 to 10 million at each locus. Loci are few, usually one or two per chromosome. They were called satellites since in density gradients, they often sediment as distinct, satellite bands separate from the bulk of genomic DNA owing to a distinct BASE COMPOSITION.Carbohydrate Conformation: The characteristic 3-dimensional shape of a carbohydrate.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Genome-Wide Association Study: An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.Methylenetetrahydrofolate Reductase (NADPH2): A flavoprotein amine oxidoreductase that catalyzes the reversible conversion of 5-methyltetrahydrofolate to 5,10-methylenetetrahydrofolate. This enzyme was formerly classified as EC 18.104.22.168.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Short Interspersed Nucleotide Elements: Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.RNA Interference: A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.Spermatozoa: Mature male germ cells derived from SPERMATIDS. As spermatids move toward the lumen of the SEMINIFEROUS TUBULES, they undergo extensive structural changes including the loss of cytoplasm, condensation of CHROMATIN into the SPERM HEAD, formation of the ACROSOME cap, the SPERM MIDPIECE and the SPERM TAIL that provides motility.MicroRNAs: Small double-stranded, non-protein coding RNAs, 21-25 nucleotides in length generated from single-stranded microRNA gene transcripts by the same RIBONUCLEASE III, Dicer, that produces small interfering RNAs (RNA, SMALL INTERFERING). They become part of the RNA-INDUCED SILENCING COMPLEX and repress the translation (TRANSLATION, GENETIC) of target RNA by binding to homologous 3'UTR region as an imperfect match. The small temporal RNAs (stRNAs), let-7 and lin-4, from C. elegans, are the first 2 miRNAs discovered, and are from a class of miRNAs involved in developmental timing.Guanine
Neonatal diabetes mellitus
... the mother's genes are affected by DNA methylation (DNA methylation is the process in which methyl groups or CH3- are added to ... every cells have two copies of each gene-one gene is inherited from the mother and one gene is inherited from the father. ... KCNJ11 and ABCC8 Genes In addition, TNDM initiated by the genes, KCNJ11 or ABCC8 mutations are similar to mutations in ... INS Gene Recessive mutations in the INS gene encoding insulin were discovered to trigger both PNDM and TNDM. Diabetes occurs ...
DNA base flipping
Nakao, M (2001). "Epigenetics: Interaction of DNA Methylation and Chromatin". Gene. 278 (1-2): 25-31. doi:10.1016/s0378-1119(01 ... This process causes the activation or inactivation of gene expression, thereby resulting in gene regulation in eukaryotic cells ... DNA methylation process is also known to be involved in certain types of cancer formation. In order for this chemical ... DNA methylation is the process in which a methyl group is added to either a cytosine or adenine. ...
Bird A (January 2002). "DNA methylation patterns and epigenetic memory". Genes & Development. 16 (1): 6-21. doi:10.1101/gad. ... A gene is a unit of heredity and is a region of DNA that influences a particular characteristic in an organism. Genes contain ... A gene is a sequence of DNA that contains genetic information and can influence the phenotype of an organism. Within a gene, ... In bacteria, this overlap may be involved in the regulation of gene transcription, while in viruses, overlapping genes increase ...
... a large proportion of carcinogenic gene silencing is a result of altered DNA methylation (see DNA methylation in cancer). DNA ... Silencing of a gene may be initiated by other mechanisms, but this is often followed by methylation of CpG sites in the ... Silencing of DNA repair genes through methylation of CpG islands in their promoters appears to be especially important in ... Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev. 16 (1): 6-21. doi:10.1101/gad.947102. PMID 11782440 ...
Genetic memory (biology)
Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes & Development. 16 (1): 6-21. doi:10.1101/gad.947102. ... Antibody genes in B and T lymphocytes are assembled from separate gene segments, giving each lymphocyte a unique antibody ... Examples are methylation patterns of the DNA molecule itself and proteins involved in packaging DNA, such as histones (also ... Selection of organisms carrying genes coding for the best adapted proteins results in the evolution of species. An example for ...
For example, in colorectal cancers about 600 to 800 genes are transcriptionally silenced by CpG island methylation (see ... Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev. 16 (1): 6-21. doi:10.1101/gad.947102. PMID 11782440 ... In vertebrates, the majority of gene promoters contain a CpG island with numerous CpG sites. When many of a gene's promoter CpG ... The latter (heterochromatin) includes gene-poor regions such as telomeres and centromeres but also regions with normal gene ...
For example, in colorectal cancers about 600 to 800 genes are transcriptionally silenced by CpG island methylation (see ... Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev. 16 (1): 6-21. doi:10.1101/gad.947102. PMID 11782440 ... In vertebrates, the majority of gene promoters contain a CpG island with numerous CpG sites. When many of a gene's promoter CpG ... Similarly, enhancers can regulate more than one gene without linkage restriction and are said to "skip" neighboring genes to ...
Somatic evolution in cancer
The best-understood epigenetic alterations in tumors are the silencing or expression of genes by changes in the methylation of ... Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev. 16 (1): 6-21. doi:10.1101/gad.947102. PMID 11782440 ... The retinoblastoma gene was the first tumor suppressor gene to be cloned in 1986. Cairns hypothesized a different, but ... These methylation patterns are copied to the new chromosomes when cells replicate their genomes and so methylation alterations ...
Bird, A (2002). "DNA methylation patterns and epigenetic memory". Genes & Development. 16 (1): 6-21. doi:10.1101/gad.947102. ... Bird, A. P.; Southern, E. M. (1978). "Use of restriction enzymes to study eukaryotic DNA methylation: I. The methylation ... "for his pioneering discoveries on DNA methylation and its role in gene expression." The following year Bird won the 2012 ... "fundamental discoveries concerning DNA methylation and gene expression" though the prize later went to James Rothman, Randy ...
CpG island methylation is important in regulation of gene expression, yet cytosine methylation can lead directly to ... Real-time methylation-specific polymerase chain reaction (PCR) suggests that many other genes are also hypermethylated. Gene ... These histone modifications can silence tumor suppressor genes despite the drop in methylation of the gene's CpG island (an ... a DNA repair gene; APC, a cell cycle regulator; MLH1, a DNA-repair gene; and BRCA1, another DNA-repair gene. Indeed, cancer ...
The effects of histone methylation may also work to inhibit the action of transcription. In vertebrates, the majority of gene ... For example, in colorectal cancers about 600 to 800 genes are transcriptionally inhibited by CpG island methylation (see ... Bird A (January 2002). "DNA methylation patterns and epigenetic memory". Genes & Development. 16 (1): 6-21. doi:10.1101/gad. ... The stretch of DNA transcribed into an RNA molecule is called a transcription unit and encodes at least one gene. If the gene ...
... one with a mutated gene and one with a functional copy of the same gene. When the mutated chromosome is randomly inactivated in ... Riggs, A.D. (1975). "X inactivation, differentiation, and DNA methylation". Cytogenet Cell Genet. 14: 9-25. doi:10.1159/ ... Males only have one copy of any gene on the X-chromosome, and because they do not undergo X-inactivation, they only have the ... An obligate carrier is an individual who may be clinically unaffected but who must carry a gene mutation based on analysis of ...
1987). "Mouse and human ornithine decarboxylase genes. Methylation polymorphism and amplification". Biochem. J. 242 (1): 205-10 ... Ornithine decarboxylase is an enzyme that in humans is encoded by the ODC1 gene. This gene encodes the rate-limiting enzyme of ... Originally localized to both chromosomes 2 and 7, the gene encoding this enzyme has been determined to be located on 2p25, with ... Yoshida M, Hayashi H, Taira M, Isono K (1992). "Elevated expression of the ornithine decarboxylase gene in human esophageal ...
Shilatifard A (2006). "Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene ... "Proline isomerization of histone H3 regulates lysine methylation and gene expression". Cell. 126 (5): 905-16. doi:10.1016/j. ... The packaging of the eukaryotic genome into highly condensed chromatin makes it inaccessible to the factors required for gene ... Klose RJ, Zhang Y (2007). "Regulation of histone methylation by demethylimination and demethylation". Nat. Rev. Mol. Cell Biol ...
DNA Methylation and Gene Regulation. Holliday, R., M. Monk and J.E. Pugh (eds). The Royal Society, London (1990). Proceedings ... The main focus of his experimental work was the epigenetic control of gene expression by DNA methylation in CHO cells. These ... In 1975 he suggested that DNA methylation could be an important mechanism for the control of gene expression in higher ... experiments provide direct evidence that DNA methylation is a primary cause of gene silencing in mammalian cells. Holliday was ...
"Entrez Gene: HOXA3 homeobox A3". Han L, Witmer PD, Casey E, Valle D, Sukumar S (August 2007). "DNA methylation regulates ... This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene ... In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C ... Three transcript variants encoding two different isoforms have been found for this gene. The HOXA3 gene is repressed by the ...
Survival of motor neuron
Gene. 491 (2): 135-41. doi:10.1016/j.gene.2011.10.006. PMID 22020225. SMN protein (spinal muscular atrophy) at the US National ... Hebert MD, Shpargel KB, Ospina JK, Tucker KE, Matera AG (September 2002). "Coilin methylation regulates nuclear body formation ... Survival of motor neuron or survival motor neuron (SMN) is a protein that in humans is encoded by the SMN1 and SMN2 genes. SMN ... "Entrez Gene: SMN1 survival of motor neuron 1, telomeric". Gubitz AK, Feng W, Dreyfuss G (May 2004). "The SMN complex". ...
As an example, one study listed protein coding genes that were frequently altered in their methylation in association with ... Oncogenes are genes that promote cell growth and reproduction. Tumor suppressor genes are genes that inhibit cell division and ... "Double strand breaks can initiate gene silencing and SIRT1-dependent onset of DNA methylation in an exogenous promoter CpG ... These included 147 hypermethylated and 27 hypomethylated genes. Of the hypermethylated genes, 10 were hypermethylated in 100% ...
October 2011). "Promoter methylation status of hMLH1, hMSH2, and MGMT genes in colorectal cancer associated with adenoma- ... December 2012). "Epigenetic screen of human DNA repair genes identifies aberrant promoter methylation of NEIL1 in head and neck ... The gene designations shown in red, gray or cyan indicate genes frequently epigenetically altered in various types of cancers. ... In particular, the gene-rich, early-replicating regions of the human genome exhibit lower mutation frequencies than the gene- ...
In human cancer cells DNMT1 is responsible for both de novo and maintenance methylation of tumor suppressor genes. The enzyme ... "DNMT1". Gene Symbol Report. HUGO Gene Nomenclature Committee. Retrieved 2012-09-27. "DNMT3A". Gene Symbol Report. HUGO Gene ... "DNMT3B". Gene Symbol Report. HUGO Gene Nomenclature Committee. Retrieved 2012-09-27. "DNMT3L". Gene Symbol Report. HUGO Gene ... which might be a co-operative event during DNA methylation. DNMT3a prefers CpG methylation to CpA, CpT, and CpC methylation, ...
"Arginine methylation facilitates the nuclear export of hnRNP proteins". Genes & Development. 12 (5): 679-691. doi:10.1101/gad. ... PA Silver; LP Keegan; M Ptashine (October 1, 1984). "Amino terminus of the yeast GAL4 gene product is sufficient for nuclear ... Yu MC, Lamming DW, Eskin JA, Sinclair DA & Silver PA (December 1, 2006). "The role of arginine methylation in formation of ... doi:10.1016/S1535-6108(03)00303-9. Silver, P.; Keegan, L. & Ptashne, M. (1984). "The amino terminus of the yeast GAL4 gene ...
Chromosome 1 open reading frame 162
"Gene methylation as a novel marker in gastric cancer". Cancer Research. 8 (73): 643. "NCBI Gene Orthologs". ... "Entrez Gene: Chromosome 1 open reading frame 162". Retrieved 2016-05-09. "NCBI GenBank". "GeneCards". "NCBI Gene". "M-fold ... The gene is located at p13.2 on chromosome 1 in humans and contains 8 exons. It is 11,026 bases long and is oriented on the ... The gene has no known paralogs. Orthologs have been noted in many mammal species in addition to a few birds and reptiles. The ...
"Entrez Gene: GNMT glycine N-methyltransferase". Blumenstein J, Williams GR (September 1960). "The enzymic N-methylation of ... regulatory region of the human Glycine N-methyltransferase gene". Gene. 443 (1-2): 151-7. doi:10.1016/j.gene.2009.05.001. PMID ... The human GMNT gene was cloned in 2000 by Chen and coworkers. GNMT is an abundant enzyme in liver cytosol and consists of 0.9% ... Chen SY, Lin JR, Darbha R, Lin P, Liu TY, Chen YM (May 2004). "Glycine N-methyltransferase tumor susceptibility gene in the ...
For example, in PBR322 methylation at the tetracyclin resistant gene makes the plasmid liable to tetracyclin; after methylation ... Methylation makes the resistant gene inactive; this is called Insertional Inactivation or Insertional mutagenesis. ... Diversity of T cell receptor (TCR) genes is generated by nucleotide insertions upon rearrangement from their germ line-encoded ... Palindromic sequences may also have methylation sites. These are the sites where a methyl group can be ...
Protein arginine N-methyltransferase 1 is an enzyme that in humans is encoded by the PRMT1 gene. The HRMT1L2 gene encodes a ... Kim S, Park GH, Paik WK (1999). "Recent advances in protein methylation: enzymatic methylation of nucleic acid binding proteins ... Kwak YT, Guo J, Prajapati S, Park KJ, Surabhi RM, Miller B, Gehrig P, Gaynor RB (April 2003). "Methylation of SPT5 regulates ... Nikawa J, Nakano H, Ohi N (1996). "Structural and functional conservation of human and yeast HCP1 genes which can suppress the ...
Methylation is a chemical alteration made to a cytosine (C) when it occurs in a particular DNA sequence, "CpG". Many genes have ... The expression of a few genes may be regulated through methylation of their CpG island, and MECP2 may play a role in a subset ... As a result, the protein is unable to bind to DNA or turn other genes on or off. Genes that are normally repressed by MeCP2 ... Other genes that are normally activated by MeCP2 remain inactive leading to a lack of gene product. This defect probably ...
Transvection can lead to either gene activation or repression. It can also occur between nonallelic regions of the genome as ... Rassoulzadegan M, Magliano M, Cuzin F (Feb 1, 2002). "Transvection effects involving DNA methylation during meiosis in the ... In light of these findings, transvection may represent a potent and widespread form of gene regulation. Transvection appears to ... Lee AM, Wu CT (Dec 2006). "Enhancer-promoter communication at the yellow gene of Drosophila melanogaster: diverse promoters ...
Phosphoglycerate kinase 1 is an enzyme that in humans is encoded by the PGK1 gene. Click on genes, proteins and metabolites ... 1989). "Genomic sequencing and methylation analysis by ligation mediated PCR". Science. 246 (4931): 810-3. doi:10.1126/science. ... McCarrey JR, Thomas K (1987). "Human testis-specific PGK gene lacks introns and possesses characteristics of a processed gene ... Johnson P, Friedmann T (1990). "Limited bidirectional activity of two housekeeping gene promoters: human HPRT and PGK". Gene. ...
The gene is highly expressed in the brain and a number of behavioral phenotypes have been described for the mice. Lack of ... "Antenatal prediction of postpartum depression with blood DNA methylation biomarkers". Molecular Psychiatry. 19 (5): 560-7. doi: ... Ouyang J, Shi Y, Valin A, Xuan Y, Gill G (April 2009). "Direct binding of CoREST1 to SUMO-2/3 contributes to gene-specific ... Heterochromatin protein 1, binding protein 3 is a protein that in humans is encoded by the HP1BP3 gene. It has been identified ...
... -mediated MDH1 methylation reduces cellular NADPH level and sensitizes cells to oxidative stress, thereby suppressing cell ... encoded by the CARM1 gene found in human beings, as well as many other mammals. It has a polypeptide (L) chain type that is 348 ... "Arginine Methylation of MDH1 by CARM1 Inhibits Glutamine Metabolism and Suppresses Pancreatic Cancer". Molecular Cell. 64 (4): ... "Histone arginine methylation regulates pluripotency in the early mouse embryo". Nature. 445 (7124): 214-8. doi:10.1038/ ...
Type 2 diabetes
There are a number of rare cases of diabetes that arise due to an abnormality in a single gene (known as monogenic forms of ... with one proposed mechanism being that of DNA methylation. The intestinal bacteria Prevotella copri and Bacteroides ... Most cases of diabetes involve many genes, with each being a small contributor to an increased probability of becoming a type 2 ... All of these genes together still only account for 10% of the total heritable component of the disease. The TCF7L2 allele, ...
Category:DNA - Simple English Wikipedia, the free encyclopedia
... to video stimuli of mother-infant separation as being associated with decreased glucocorticoid receptor gene methylation in the ... de Kloet ER, Sibug RM, Helmerhorst FM, Schmidt MV, Schmidt M (April 2005). "Stress, genes and the mechanism of programming the ... For example, increased maternal licking and grooming has been shown to alter expression of the glutocorticoid receptor gene ... Methylation of NR3C1 is related to maternal PTSD, parenting stress and maternal medial prefrontal cortical activity in response ...
... is a eukaryotic gene. The enzyme encoded by this gene is a member of the RAD51 protein family which assists in repair of ... Methylation of the promoter of miR-34a, resulting in under-expression of miR-34a, is observed in 79% of prostate cancers and 63 ... Many cancers have epigenetic deficiencies in various DNA repair genes (see Frequencies of epimutations in DNA repair genes in ... Gene ontology. Molecular function. • nucleotide binding. • DNA binding. • DNA-dependent ATPase activity. • recombinase activity ...
"Gene. 389 (1): 52-65. doi:10.1016/j.gene.2006.09.029. PMC 1955227. PMID 17123746.. ... Histone methylation/Histone methyltransferase *EZH2. *Histone demethylase. *Histone acetylation and deacetylation *Histone ... and viral genes. The TATA box was found in protein coding genes transcribed by RNA polymerase II. ... of genes have promoter regions containing the TATA box. Genes containing the TATA-box tend to be involved in stress- ...
Sun ZW, Allis CD (Jul 2002). "Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast". Nature. 418 ... Arginine methylation. What was said above of the chemistry of lysine methylation also applies to arginine methylation, ... di-methylation repression repression activation tri-methylation activation repression repression ... This affects their function of gene regulation. In general, genes that are active have less bound histone, while inactive genes ...
Pyruvate dehydrogenase (lipoamide) alpha 2
As this gene is mostly inactive, save for in testis tissue, a methylation mechanism is in place that inactivates this gene in ... 2010). "Human testis-specific PDHA2 gene: methylation status of a CpG island in the open reading frame correlates with ... "Entrez Gene: pyruvate dehydrogenase (lipoamide) alpha 2".. *^ Dahl HH, Brown RM, Hutchison WM, Maragos C, Brown GK (October ... Click on genes, proteins and metabolites below to link to respective articles. [§ 1] ...
Brain-derived neurotrophic factor
Kaplan AS, Levitan RD, Yilmaz Z, Davis C, Tharmalingam S, Kennedy JL (January 2008). "A DRD4/BDNF gene-gene interaction ... See also: Epigenetics of schizophrenia § Methylation of BDNF. A plethora of recent evidence suggests the linkage between ... Brain-derived neurotrophic factor (BDNF), or abrineurin, is a protein that, in humans, is encoded by the BDNF gene. ... Gene ontology. Molecular function. • receptor binding. • neurotrophin TRKB receptor binding. • growth factor activity. • GO: ...
Although single genes are neither necessary nor sufficient for anxiety by themselves, several gene polymorphisms have been ... "BDNF Methylation and Maternal Brain Activity in a Violence-Related Sample". PLoS ONE. 10 (12): e0143427. Bibcode:2015PLoSO.. ... The epigenetic signature of at least one of these genes BDNF has also been associated with anxiety and specific patterns of ... Sep 2011). "Evidence of association between Val66Met polymorphism at BDNF gene and anxiety disorders in a community sample of ...
Amyotrophic lateral sclerosis
Other protein degradation genes that can cause ALS when mutated include VCP, OPTN, TBK1, and SQSTM1. Three genes implicated in ... As of 2013[update] it appeared that differences in the methylation of arginine residues in FUS protein may be relevant, and ... the most common ALS gene in Europe is C9orf72, followed by SOD1, TARDBP, and FUS, while the most common ALS gene in Asia is ... The first gene to be associated with ALS was SOD1, which was identified in 1993. This led to the development of the first ...
Innate immune system
a b c d e f g h i j k l m n o p q IMMUNOLOGY - CHAPTER ONE - INNATE (NON-SPECIFIC) IMMUNITY Gene Mayer, Ph.D. Immunology ... Methylation of the host's own DNA marks it as "self" and prevents it from being attacked by endonucleases. Restriction ... On one hand, γδ T cells may be considered a component of adaptive immunity in that they rearrange TCR genes to produce ... "Resistance" (R) proteins, encoded by R genes, are widely present in plants and detect pathogens. These proteins contain domains ...
Brome mosaic virus
Epigenetics of neurodegenerative diseases
... gene-specific hypermethylation, however, would indicate that these hypermethylated genes are repressed by the methylation marks ... Hallmarks include mutations to the alpha-synuclein gene, SNCA, as well as PARK2, PINK1, UCHL1, DJ1, and LRRK2 genes, and ... There may be some effect of age in levels of DNA methylation at specific gene promoters, as one study found greater levels of ... DNA methylation. In Alzheimer's disease cases, global DNA hypomethylation and gene-specific hypermethylation has been observed ...
Insulin-like growth factor 2
Gene structure. In humans, the IGF2 gene is located on chromosome 11p15.5, a region which contains numerous imprinted ... Neidhart, M (2016). DNA Methylation and Complex Human Disease (1st ed.). San Diego: Academic Press. p. 22.. ISBN 978-0124201941 ... Gene ontology. Molecular function. • insulin receptor binding. • hormone activity. • GO:0001948 protein binding. • growth ... regulation of gene expression by genetic imprinting. • skeletal system development. • cellular protein metabolic process. • ...
Brain-derived neurotrophic factor
Kaplan AS, Levitan RD, Yilmaz Z, Davis C, Tharmalingam S, Kennedy JL (January 2008). "A DRD4/BDNF gene-gene interaction ... See also: Epigenetics of schizophrenia § Methylation of BDNF. A plethora of recent evidence suggests the linkage between ... Brain-derived neurotrophic factor, also known as BDNF, is a protein that, in humans, is encoded by the BDNF gene. BDNF ... The BDNF protein is encoded by a gene that is also called BDNF, found in humans on chromosome 11. Structurally, BDNF ...
In Alphaproteobacteria, methylation of adenine regulates the cell cycle and couples gene transcription to DNA replication. In ... About 50% of miRNA genes are associated with CpG islands, that may be repressed by epigenetic methylation. Transcription ... Morris KL (2008). "Epigenetic Regulation of Gene Expression". RNA and the Regulation of Gene Expression: A Hidden Layer of ... Examples of mechanisms that produce such changes are DNA methylation and histone modification, each of which alters how genes ...
Small nuclear ribonucleoprotein polypeptide N
"Gene structure, DNA methylation, and imprinted expression of the human SNRPN gene". Am. J. Hum. Genet. 58 (2): 335-46. PMC ... White HE, Durston VJ, Harvey JF, Cross NC (2006). "Quantitative analysis of SNRPN(correction of SRNPN) gene methylation by ... 2017). "Polymorphisms in the SRNPN gene are associated with obesity susceptibility among Spanish population". J. Gene Med. doi: ... a neighboring gene that is also imprinted), the methylation test (of SNRPN) can reveal whether the patient has uniparental ...
CRH - Wicipedia
"Promoter Methylation Pattern Controls Corticotropin Releasing Hormone Gene Activity in Human Trophoblasts. ". PLoS One. 2017. ... positive regulation of gene expression. • positive regulation of digestive system process. • Genedigaeth. • response to pain. • ... negative regulation of gene expression. • cellular response to dexamethasone stimulus. • positive regulation of corticosterone ... "https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid=1392. ...
Role in gene regulationEdit. Histone methylation plays an important role in epigenetic gene regulation. Methylated histones can ... Histone methylation is a principal epigenetic modification of chromatin that determines gene expression, genomic stability, ... For example, it is likely that the methylation of lysine 9 on histone H3 (H3K9me3) in the promoter region of genes prevents ... The methylation of histone lysine has an important role in choosing the pathway for repairing DNA double-strand breaks. As ...
Eboluzio, entziklopedia askea.
Milioi urtero hamarnakatik ehunaka gene bikoizten dira. Gene gehienek aurreko gene bateko eraldaketaz sortu direnez gene ... Experimental alteration of DNA methylation affects the phenotypic plasticity of ecologically relevant traits in Arabidopsis ... DNA molekulan unitate funtzional bakar bat eratzen duten zatiei gene izena ematen zaie; gene ezberdinek base sekuentzia ... Gene-fluxua[aldatu , aldatu iturburu kodea]. Ondorioak[aldatu , aldatu iturburu kodea]. Adaptazioa[aldatu , aldatu iturburu ...
2004). "A high-density admixture map for disease gene discovery in African Americans". Am J Hum Genet. 74: 1001-1013.. ... DNA methylation analysis is used to diagnose certain genetic disorders that are caused by disruptions of epigenetic mechanisms ... Weiss KM, Terwilliger JD (2000). "How many diseases does it take to map a gene with SNPs?". Nat Genet. 26: 151-157. doi:10.1038 ... Kittles RA, Weiss KM (2003). "Race, ancestry, and genes: implications for defining disease risk". Annu Rev Genomics Hum Genet. ...
Single cell sequencing
When RRBS is applied to bulk samples, majority of the CpG sites in gene promoters are detected, but site in gene promoters only ... Single-cell DNA methylome sequencing quantifies DNA methylation. There are several known types of methylation that occur in ... Pennisi E (April 2018). "Chronicling embryos, cell by cell, gene by gene". Science. 360 (6387): 367. Bibcode:2018Sci...360.. ... Other methods to detect DNA methylation include methylation-sensitive restriction enzymes. Restriction enzymes also enable the ...
Glossary of gene expression terms. References. *^ a b c d e f Slonczewski, Joan, and John Watkins. Foster. Microbiology: ... Histone methylation/Histone methyltransferase *EZH2. *Histone demethylase. *Histone acetylation and deacetylation *Histone ... lacZYA transcribes the proteins needed for lactose breakdown. lacI synthesizes the repressor of the lacZYA gene. The gene ... Top: The gene is essentially turned off. There is no lactose to inhibit the repressor, so the repressor binds to the operator, ...
Mir-9/mir-79 microRNA precursor family
The miR-9 microRNA (homologous to miR-79), is a short non-coding RNA gene involved in gene regulation. The mature ~21nt miRNAs ... Hildebrandt MA, Gu J, Lin J, Ye Y, Tan W, Tamboli P, Wood CG, Wu X (2010). "Hsa-miR-9 methylation status is associated with ... show that two genes encoding for has-miR-9 are significantly hypermethylated in clear cell renal carcinoma tumours. Ambros V ( ... Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001). "Identification of novel genes coding for small expressed RNAs". ...
... is necessary for the production and maintenance of new cells, for DNA synthesis and RNA synthesis through methylation, ... 2010). "Variations in folate pathway genes are associated with unexplained female infertility". Fertil. Steril. 94 (1): 130-137 ... 5-MTHF also plays both direct & indirect roles in DNA methylation, NO2 synthesis, and one-carbon metabolism. ... polymorphisms in genes of enzymes involved in folate metabolism could be one reason for fertility complications in some women ...
Nakayama K, Hara T, Hibi M, Hirano T, Miyajima A (August 1999). "A novel oncostatin M-inducible gene OIG37 forms a gene family ... "Effects of histone acetylation and DNA methylation on p21( WAF1) regulation". World J. Gastroenterol. 8 (3): 400-5. doi ... "Entrez Gene: CDKN1A cyclin-dependent kinase inhibitor 1A (p21, Cip1)".. *^ Gartel AL, Radhakrishnan SK (May 2005). "Lost in ... Gene ontology. Molecular function. • metal ion binding. • protein binding. • cyclin-dependent protein serine/threonine kinase ...
"DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells". Mol. Cell. ... di-methylation repression repression repression activation tri-methylation activation repression repression ... mono-methylation activation activation activation activation activation activation ... Together with similar modifications such as DNA methylation it is part of the epigenetic code. Histones associate with DNA ...
Smoking During Pregnancy Significantly Affects DNA Methylation, Gene Expression - Redorbit
Kjersti Aagaard and her colleagues found changes in methylation and gene expression of only 25 genes in non-smokers but 438 ... "Just as we expected from our previous studies in one gene, this dysregulation between DNA methylation and gene expression when ... This kind of altered methylation or chemical add-on in as few as six sites in the landscape of methylated genes and DNA can be ... Methylation is a chemical change to DNA that can affect the ways genes are expressed and regulated.) ...
Fine tuning of globin gene expression by DNA methylation. - PubMed - NCBI
Fine tuning of globin gene expression by DNA methylation.. Goren A1, Simchen G, Fibach E, Szabo PE, Tanimoto K, Chakalova L, ... These studies demonstrate that DNA methylation serves as an elegant in vivo fine-tuning device for selecting appropriate genes ... For each ChIP preparation, the Acta1 gene (green) was assayed as a negative control and the Actb gene (yellow) as a positive ... methylation during development. DNA methylation causes a 20-fold repression of gamma(A) both in non-erythroid and adult ...
JCI - Methylation of immune synapse genes modulates tumor immunogenicity
When the methylation status of key immune synapse genes was interrogated, we observed disproportionately hypermethylated ... Therefore, the methylation status of immune synapse genes reflects tumor immunogenicity and correlates with survival. ... costimulatory genes and hypomethylation of immune checkpoint genes, which were negatively associated with functional T cell ...
JCI - Methylation of immune synapse genes modulates tumor immunogenicity
For each gene, a set of probes was selected using the following criteria to minimize noise: r , -0.2 (methylation vs. gene ... E) The methylation status of the CD40 gene in mock- or 5-azacytidine-treated CAMA1 cell line. *P , 0.05, **P , 0.01, ***P , ... Methylation of immune synapse genes modulates tumor immunogenicity. Anders Berglund,1 Matthew Mills,2 Ryan M. Putney,1 Imène ... Methylation and demethylation in the regulation of genes, cells, and responses in the immune system. Clin Immunol. 2003;109(1): ...
Establishment of Methylation-Specific PCR for the Mouse p53 Gene
Y. Gondo, K. Nakamura, K. Nakao et al., "Gene replacement of the p53 gene with the lacZ gene in mouse embryonic stem cells and ... Establishment of Methylation-Specific PCR for the Mouse p53 Gene. Ryuji Okazaki,1 Akira Ootsuyama,1 Yasuhiro Yoshida,2 and ... M. C. Fruhwald, M. S. ODorisio, Z. Dai et al., "Aberrant promoter methylation of previously unidentified target genes is a ... CpG island methylation," Cancer Research, vol. 59, no. 14, pp. 3352-3356, 1999. View at Google Scholar · View at Scopus ...
Functions of DNA methylation: islands, start sites, gene bodies and beyond. - PubMed - NCBI
Functions of DNA methylation: islands, start sites, gene bodies and beyond.. Jones PA1. ... Now, thanks to improved genome-scale mapping of methylation, we can evaluate DNA methylation in different genomic contexts: ... DNA methylation is frequently described as a silencing epigenetic mark, and indeed this function of 5-methylcytosine was ... The emerging picture is that the function of DNA methylation seems to vary with context, and the relationship between DNA ...
Obesity-Related Gene Methylation Changes Connected to BMI in Healthy Adolescents | GenomeWeb
Researchers saw an over-representation of CpG methylation shifts in 11 obesity-related genes in more than 260 adolescents from ... Obesity-Related Gene Methylation Changes Connected to BMI in Healthy Adolescents. Feb 15, 2019 ... China Considers Gene-Editing Protections. China may include regulations protecting genes and embryos in its update of its civil ... NEW YORK (GenomeWeb) - Adolescent body weight appears to coincide with DNA methylation patterns at genes previously implicated ...
Reactivating the expression of methylation silenced genes in human cancer
A significant number of tumor suppressor genes are transcriptionally silenced by promoter hypermethylation, and recent research ... DNA methylation alterations are now widely recognized as a contributing factor in human tumorigenesis. ... Reactivating the expression of methylation silenced genes in human cancer Oncogene. 2002 Aug 12;21(35):5496-503. doi: 10.1038/ ... In this review, we will discuss in detail the mechanisms of gene silencing by DNA methylation, the techniques used to decipher ...
Parent-of-origin differences in DNA methylation of X chromosome genes in T lymphocytes | PNAS
Since DNA methylation typically silences gene expression, parental imprinting of X genes can induce gene expression differences ... All 5 X genes showed higher DNA methylation on Xp, consistent with the role of DNA methylation in X gene expression (Table 1). ... Since DNA methylation usually suppresses gene expression, this result was consistent with higher expression of X genes in XY ... Indeed, DNA methylation analysis for differentially expressed genes in CD4+ T lymphocyte transcriptome data showed that X genes ...
PLOS ONE: Fine Tuning of Globin Gene Expression by DNA Methylation
These studies demonstrate that DNA methylation serves as an elegant in vivo fine-tuning device for selecting appropriate genes ... we generated a YAC transgenic mouse system that allowed us to control γA methylation during development. DNA methylation causes ... While the γA and γG genes are expressed in fetal liver, both are silenced in adult erythrocytes. In order to decipher the role ... In erythroid cells this modification works as a dominant mechanism to repress γ gene expression, probably through changes in ...
Modulation of histone methylation and MLH1 gene silencing by hexavalent chromium
... Toxicol Appl Pharmacol. 2009 Jun 15;237(3):258 ... which in turn affect both global and gene promoter specific histone methylation, leading to the silencing of specific tumor ... H3K9 dimethylation was enriched in the human MLH1 gene promoter following chromate exposure and this was correlated with ...
BioC] Analyzing 'differential variability' of methylation (and gene expression)
Any suggestions about the best way to analyze changes in variability of , methylation (and gene expression) values? , Which ... I would like to do this gene-wise, to see if and , which genes show increased/decreased variability. , , Several studies ... I am currently trying to analyze differential variability of gene , expression and, above all, methylation data (Illumina ... BioC] Analyzing differential variability of methylation (and gene expression). Pekka Kohonen pkpekka at gmail.com Wed Mar 27 ...
DNA methylation of developmental genes in pediatric medulloblastomas identified by denaturation analysis of methylation...
DNA methylation of developmental genes in pediatric medulloblastomas identified by denaturation analysis of methylation ... DNA methylation of developmental genes in pediatric medulloblastomas identified by denaturation analysis of methylation ... DNA methylation of developmental genes in pediatric medulloblastomas identified by denaturation analysis of methylation ... DNA methylation of developmental genes in pediatric medulloblastomas identified by denaturation analysis of methylation ...
Research of the Methylation Status of miR-124a Gene Promoter among Rheumatoid Arthritis Patients
... Qiao Zhou,1 Li Long,1 Guixiu ... J. G. Herman, J. R. Graff, S. Myöhänen, B. D. Nelkin, and S. B. Baylin, "Methylation-specific PCR: a novel PCR assay for ... with a focus on the crosstalk between DNA methylation and the microRNA machinery," Cellular Signalling, vol. 25, no. 5, pp. ... methylation status of CpG islands," Proceedings of the National Academy of Sciences of the United States of America, vol. 93, ...
Combinatorial Roles of DNA Methylation and Histone Modifications on Gene Expression | SpringerLink
The mechanisms that control gene expression is one of the open problems. Epigenetic... ... Gene regulation, despite being investigated in a large number of works, is still yet to be well understood. ... DNA methylation Histone modification Gene regulation Gene expression This is a preview of subscription content, log in to check ... Also, some interesting patterns of DNA methylation and PTMs that can explain the low expression of genes in CD4\(+\) T cell. ...
Quantitative DNA Methylation Analysis of Candidate Genes in Cervical Cancer
... that several genes are common targets for aberrant methylation in cervical cancer and DNA methylation level of four genes ... A Methylation Index was calculated as the mean percent methylation across all CpG sites analyzed per gene (~4-9 CpG site) per ... whereas there was no difference in median methylation for 2 genes. Compared to HPV and age, the combination of DNA methylation ... of methylation in individual genes or a panel was examined. The median methylation index was significantly higher in cases ...
GlioMethyl - Promotor methylation of the DUSP-4 gene as predictive parameter for gliomas
... 30.07.2009 ... methylation and treatment of Glioblastoma patients with alkylating agents. The present invention therefore provides a ... It further describes an improved method for the determination of the promoter methylation, which is applicable for the clinical ... with hypermethylation of the promoter region of the DUSP4 gene. Further studies have shown a significant correlation between ...
Epigenetic Gene Promoter Methylation at Birth Is Associated With Child's Later Adiposity | Diabetes
... between overall gene methylation status and DEXA measurements of adiposity at age 9 years and from these genes chose five genes ... DNA methylation was measured with the Sequenom MassARRAY Compact System (www.sequenom.com/). Briefly, gene-specific ... Selection of candidate genes.. DNA from 15 randomly selected PAH study umbilical cords underwent methylation-specific chromatin ... Here we first measured the methylation status of CpGs in the promoters of candidate genes in DNA extracted from umbilical cord ...
DNA Methylation-Related Chromatin Remodeling in Activity-Dependent Bdnf Gene Regulation | Science Signaling
DNA methylation plays critical roles in gene silencing through chromatin remodeling. Changes in DNA methylation perturb ... DNA Methylation-Related Chromatin Remodeling in Activity-Dependent Bdnf Gene Regulation. By Keri Martinowich, Daisuke Hattori, ... DNA Methylation-Related Chromatin Remodeling in Activity-Dependent Bdnf Gene Regulation. By Keri Martinowich, Daisuke Hattori, ... DNA Methylation-Related Chromatin Remodeling in Activity-Dependent Bdnf Gene Regulation Message Subject. (Your Name) has ...
Abnormal PITX1 gene methylation in adolescent idiopathic scoliosis: a pilot study
The gene of pituitary homeobox 1 (PITX1) has been reported to be down-regulated in adolescent idiopathic scoliosis (AIS), of ... Source: Genes and Diseases - January 25, 2020. Category: Genetics & Stem Cells Source Type: research ... The gene of pituitary homeobox 1 (PITX1) has been reported to be down-regulated in adolescent idiopathic scoliosis (AIS), of ... Publication date: Available online 25 January 2020Source: Genes &DiseasesAuthor(s): Haoyue Xu, Hang Liu, Tao Chen, Bo song, Jin ...
International Conference on Gene Expression, Regulation and DNA Methylation in March 2020 in Rome
Regulation and DNA Methylation scheduled on March 05-06, 2020 in March 2020 in Rome is for the researchers, scientists, ... Gene Expression, Regulation and DNA Methylation. ICGERDNAM 2020: 14. International Conference on Gene Expression, Regulation ... DNA methylation. Histone methylation. DNA looping. Expression profiling. Mirna and post-translational gene silencing. ... International Conference on Gene Expression, Regulation and DNA Methylation aims to bring together leading academic scientists ...
Exposure to diethylhexyl phthalate (DEHP) results in a heritable modification of imprint genes DNA methylation in mouse oocytes...
DEHP Primordial germ cells Oocytes Imprint genes DNA methylation This is a preview of subscription content, log in to check ... This study was designed to assess the effects of DEHP on DNA methylation of imprinting genes in germ cells from fetal and adult ... In conclusion, DEHP exposure can affect the DNA methylation of imprinting genes not only in fetal mouse germ cells and growing ... More surprisingly, the modification of the DNA methylation of imprinted genes in F1 mouse oocytes was heritable to F2 offspring ...
Methylation Studies | DNA Sequencing Software - Sequencher from Gene Codes Corporation
For decades DNA Methylation had been thought to play an important role in gene expression. When DNA is treated with bisulfite, ... Methylation Studies. You are here. Home » Products » Sequencher » Sequencher Features » Next-Generation Sequencing » ... Gene Codes will send an email update when the new, fully compatible version is released. We understand that these unforeseen ... 2017 Gene Codes Corporation , 525 Avis Drive , Suite 4 , Ann Arbor, MI , 48108-8948 , (734) 769-7249 ...
Methylation of housekeeping genes? - DNA Methylation, Histone and Chromatin Study
Top : Forum Archives: : DNA Methylation, Histone and Chromatin Study. Methylation of housekeeping genes? - (Jun/09/2005 ). Hi, ... I think you mean that you have not heard of housekeeping gene methylation in either normall tissues or cancer cells.. I guess ... I have not heard of any housekeeping gene methylation, although they have CpG island. So the question is why CpG islands are ... I also presume that people cannot find methylation of housekeeping genes because if that happens the cells cannot survive, but ...
Relationship between promoter methylation of RASSF1A gene and gastric cardia adenocarcinoma | Cancer Research
Methylation of RASSF1A gene promoter was detected using methylation-specific PCR (MSP). Promoter methylation of RASSF1A could ... Relationship between promoter methylation of RASSF1A gene and gastric cardia adenocarcinoma. Li Dong Wang, Huixing Yi, Xin He, ... Relationship between promoter methylation of RASSF1A gene and gastric cardia adenocarcinoma. Li Dong Wang, Huixing Yi, Xin He, ... Relationship between promoter methylation of RASSF1A gene and gastric cardia adenocarcinoma. Li Dong Wang, Huixing Yi, Xin He, ...
DNA methylation and mRNA expression of SYN III, a candidate gene for schizophrenia.
... gene on chromosome 22q is a candidate gene for schizophrenia susceptibility due to its chromosome location, neurological ... DNA Methylation*. Gene Expression. Genetic Predisposition to Disease. Humans. Organ Specificity. RNA, Messenger / genetics. ... 19102774 - Dna methylation and mrna expression of syn iii, a candidate gene for schizophrenia.. 17344034 - Additional support ... DNA methylation and mRNA expression of SYN III, a candidate gene for schizophrenia ...
IJMS | Free Full-Text | A Genome-Wide Methylation Approach Identifies a New Hypermethylated Gene Panel in Ulcerative Colitis
We finally found that three genes (FAM217B, KIAA1614 and RIBC2) that were significantly elevating the promoter methylation ... Technical validations for methylation analyses in a larger series of UC patients (n = 79) were performed by methylation- ... Using these methylation profiles, 48 probes associated with CpG promoter methylation showed differential hypermethylation ... The aim of this study was to identify newly hypermethylated genes in ulcerative colitis (UC) using a genome-wide DNA ...
Identifying Stages of Kidney Renal Cell Carcinoma by Combining Gene Expression and DNA Methylation Data - IEEE Journals &...
Determination of DNA Methylation of Imprinted Genes in Arabidopsis Endosperm | Protocol
DNA methylation plays an important role in mechanisms of imprinting.... ... Determination of DNA Methylation of Imprinted Genes in Arabidopsis Endosperm. doi: 10.3791/2327 Published: January 28, 2011 ... DNA methylation is critical for determining whether the maternal or paternal alleles of an imprinted gene is expressed or ... In order to determine imprinting status of a gene and methylation pattern in endosperm, we need to be able to isolate endosperm ...
CG island methylation changes near the GSTP1 gene in prostatic intraepithelial neoplasia. | Cancer Epidemiology, Biomarkers &...
CG island methylation changes near the GSTP1 gene in prostatic intraepithelial neoplasia.. J D Brooks, M Weinstein, X Lin, Y ... CG island methylation changes near the GSTP1 gene in prostatic intraepithelial neoplasia. ... CG island methylation changes near the GSTP1 gene in prostatic intraepithelial neoplasia. ... CG island methylation changes near the GSTP1 gene in prostatic intraepithelial neoplasia. ...
RegulationMechanismsSpecific methylationProteinEpigeneticTranscriptionalGenomicChromatinMeasured the methylation statusAnalysis of DNA MethylationAssociated with gene expressionAltered DNA methylation and gene expressionTumor suppColorectalTissuesHistone modificationsGenome wide DNAGenomesExpression of geTumorsNegatively correlated with gene expressionMicroarrayCONCLUSIONSGeneticCorrelationSilenced gene expressionRelated methylation statusDifferentially methylatedAnalysesRegulation of gene exSignificantlyLevels and DNA methylationQuantitativeInversely correlatedTarget genesRole of DNA methylationMeasurement of DNA methylationLocus-specific methylationMRNA expressionDifferences in methylationPutative imprinted genes in maizeDifferentiationChanges in methylationBiomarkerSurrounding CpG sitesBody methylationIsland DNA methylationRelationships between methylationAbnormal DNA methylationRelationship between methylation
- These are a specific CpG methylation at a single CpG, and adequate levels of the methyl CpG binding protein 2 (MeCP2). (unthsc.edu)
- Bhave, SA & Uht, RM 2017, ' CpG methylation and the methyl CpG binding protein 2 (MeCP2) are required for restraining corticotropin releasing hormone (CRH) gene expression ', Molecular and Cellular Endocrinology , vol. 454, pp. 158-164. (unthsc.edu)
- DNA methylation is frequently described as a 'silencing' epigenetic mark, and indeed this function of 5-methylcytosine was originally proposed in the 1970s. (nih.gov)
- An important distinction between DNA methylation (epigenetic) and mutation or deletion (genetic) tumor suppressor gene inactivation is that epigenetic inactivation can be abrogated by small molecules, including DNA methyltransferase and histone deacetylase inhibitors. (nih.gov)
- Whereas genetic mutations in PTCH1 have previously been shown to lead to medulloblastoma, our study indicates that epigenetic silencing of PTCH1 , and other critical developmental loci, by DNA methylation is a fundamental process of pediatric medulloblastoma formation. (pnas.org)
- In animal models, maternal diet alters offspring body composition, accompanied by epigenetic changes in metabolic control genes. (diabetesjournals.org)
- Focusing on one epigenetic marker, DNA methylation, this work has employed a hypothesis driven targeted approach with candidate genes selected after a review of relevant literature. (bl.uk)
- Arsenic exposure was correlated with increased methylation , in blood, of genes encoding enzymes that suppress carcinogenesis, and the arsenic metabolism efficiency modified the degree of epigenetic alterations. (rsc.org)
- Recently, great attentions has been paid to the epigenetic studies due to the great achievement on the novel knowledge in the regulation of gene expression. (frontiersin.org)
- DNA methylation is one of the most extensively investigated epigenetic mechanisms. (frontiersin.org)
- In mammals, formation of DNA methylation pattern is one of the important epigenetic events that affect development of various tissues, including testis. (frontiersin.org)
- DNA methylation levels at distinct regions in the genome were substantially increased at relapse compared to matched cells from diagnosis.Collectively, the results presented in this thesis provide new insights into the patterns of gene expression and epigenetic changes in ALL and further increase our understanding of the development and progression of the disease, which will hopefully lead to better treatment options in the future. (avhandlingar.se)
- DNA methylation is a key epigenetic mechanism for driving and stabilizing cell-fate decisions. (sigmaaldrich.com)
- It will also develop methods to regulate DNA methylation through genetic and/or chemical manipulations and explore the possibility of an epigenetic memory in reprogrammed cells that are derived in vitro. (his.se)
- One potential mechanism explaining how early life exposures are memorized and persist throughout the life course is epigenetic modifications, whereby mitotically heritable changes in gene expression and chromatin organization occur independently of changes to the DNA sequence itself. (diabetesjournals.org)
- The most widely examined epigenetic modification is DNA methylation where cytosine bases, primarily located next to guanine residues, are covalently bound at the carbon 5 position to a methyl group. (diabetesjournals.org)
- We further evaluated the potential epigenetic influence on MGAT3 expression by treating the cell lines with 5-azacytidine, a DNA methylation inhibitor. (mcponline.org)
- This study aims to uncover insight into the epigenetic modifications for Kashin-Beck disease (KBD) by integrating genome-wide association studies (GWAS), methylation quantitative trait loci (meQTLs), and DNA methylation profiles data. (unboundmedicine.com)
- The results suggest that GC genes of DNA methylation may lead to the erosion of cartilage in KBD, which may help us in understanding the epigenetic alteration of KBD. (unboundmedicine.com)
- DNA methylation, the best known epigenetic marker, can be used as a prognostic biomarker in many cancers. (aacrjournals.org)
- Here, we defined profiles of DNA methylation in primary renal cell carcinomas (RCC) and assessed the association of these profiles with the expression of genes required for the establishment and maintenance of epigenetic marks. (pubmedcentralcanada.ca)
- Combined, these data support an epigenetic model of PTGS in which transgene methylation is associated with an RNA-DNA interaction that ensures that PTGS is maintained. (plantcell.org)
- Together, these results validate the WNK2 gene as a recurrent target for epigenetic silencing in glia-derived brain tumours and provide first mechanistic evidence for a tumour suppressing role of WNK2 that is related to Rac1 signalling and tumour cell invasion and proliferation. (biomedsearch.com)
- Although programmed dynamics of cytosine methylation was known to occur during mammalian development, the developmental role of this epigenetic tool in plants had remained controversial until recently ( Schöb and Grossniklaus, 2006 ). (plantphysiol.org)
- Epigenetic modifications (especially altered DNA methylation) resulting in altered gene expression may be one reason for development failure or abnormalities in cloned animals, but the underlying mechanism of the abnormal phenotype in cloned piglets remains unknown. (biomedcentral.com)
- Abnormal epigenetic marking is well documented in gene promoters of cancer cells, but the study of distal regulatory siteshas lagged behind.We performed a systematic analysis of DNA methylation sites connected with gene expression profilesacross normal and cancerous human genomes. (biomedcentral.com)
- DNA methylation provides a mechanism by which additional information is imparted to DNA, and such epigenetic information can alter the timing and targeting of cellular events ( 47 ). (asm.org)
- DNA methylation is an epigenetic mechanism which plays a crucial role in development and gene expression regulation. (biomedcentral.com)
- Epigenetic modifications, like DNA methylation, are important regulators of tissue differentiation during development. (arvojournals.org)
- BACKGROUND: Precursor B-cell acute lymphoblastic leukemia (B-cell ALL) is the most common neoplasm in children and is characterized by genetic and epigenetic aberrations in hematopoietic transcription factor (TF) genes. (koreamed.org)
- Epigenetic changes in CRC such as aberrant DNA methylation alterations are common changes in human cancer. (helsinki.fi)
- To establish a link between DNA methylation, a model epigenetic gene silencing modification, and autoantigen gene expression and disease status in ANCA-associated vasculitis, we measured gene-specific DNA methylation of the autoantigen genes myeloperoxidase ( MPO ) and proteinase 3 ( PRTN3 ) in leukocytes of patients with ANCA-associated vasculitis observed longitudinally ( n =82) and of healthy controls ( n =32). (asnjournals.org)
- DNA methylation, an epigenetic event, plays an important role in cancer susceptibility. (altmetric.com)
- Cytosine methylation of promoters provides an epigenetic mark for transmitting patterns of gene transcription across cell division and for protecting the genome against transposons. (embopress.org)
- Because epigenetic changes may cause or contribute to gene silencing, our data may have relevance for the therapeutic approach to FRDA. (bmj.com)
- In summary, our studies provide evidence that epigenetic processes regulate gene expression, physiological processes, and the development of crown gall tumors. (prolekare.cz)
- Epigenetic regulation of multidrug resistance 1 gene expression: profiling CpG methylation status using bisulphite sequencing. (monash.edu)
- Methylation of CpG dinucleotides is one of the major epigenetic processes involved in the regulation of gene expression. (monash.edu)
- The capacity for DNA methylation to be altered by environmental conditions, and potentially passed between generations, makes it a prime candidate for transgenerational epigenetic inheritance. (nih.gov)
- Animal models have shown methylation and other epigenetic regulation mechanisms to be associated with conditions of aging, neurodegenerative diseases, and intellectual disability (Rubinstein-Taybi Syndrome, X-linked mental retardation). (wikipedia.org)
- Now, thanks to improved genome-scale mapping of methylation, we can evaluate DNA methylation in different genomic contexts: transcriptional start sites with or without CpG islands, in gene bodies, at regulatory elements and at repeat sequences. (nih.gov)
- Hypermethylation of CpG island promoters is associated with transcriptional inactivation of tumor suppressor genes in neoplasia. (diva-portal.org)
- NEP is encoded by a gene that contains a 5′ CpG island spanning a transcriptional regulatory region. (aacrjournals.org)
- Post-transcriptional gene silencing (PTGS) is a homology-dependent process that reduces cytoplasmic RNA levels. (plantcell.org)
- These sites bind transcription factors in a methylation-dependent manner, and carry the chromatin marks of a particular class of transcriptional enhancers. (biomedcentral.com)
- Transcriptional enhancers support tissue-specific expression profiles through physical interactions with gene promoters. (biomedcentral.com)
- DNA methylation and demethylation processes together with histone modification affect chromatin condensation and accessibility of transcription factor binding sites, thus either blocking or enabling transcriptional activation. (biomedcentral.com)
- Gene ontology analysis revealed that transcriptional repressors were more likely to be regulated by positive T-DMRs. (arvojournals.org)
- Differentially regulated genes were involved in developmental processes, stem cell markers, proliferation and transcriptional regulation. (spandidos-publications.com)
- First, the observation that intragenic methylation levels are often correlated with transcriptional strength indicates that DNA methylation is coupled to transcriptional elongation. (embopress.org)
- pRb binds to and inhibits a subset of transcriptional regulatory proteins termed the E2Fs, which then act as repressors of E2F target genes. (asm.org)
- We conclude that in Neurospora , siRNAs produced from the transgenic locus are used in the RNA-induced silencing complex-mediated PTGS pathway and do not communicate with an RNAi-induced initiation of transcriptional gene silencing complex to effect chromatin-based silencing. (asm.org)
- Inactivation of the invading nucleic acid often leads to silencing of all homologous sequences, including endogenous genes, and this inactivation can take place at the transcriptional or posttranscriptional level ( 7 ). (asm.org)
- Several studies have revealed transcriptional regulation of the hTERT gene by direct DNA-protein binding of the trans -regulatory factors and involvement of DNA methylation of the 5′-CpG island of the hTERT promoter ( 8 , 9 ). (pubmedcentralcanada.ca)
- The differential methylation pattern of crown galls and the stem tissue from which they originate correlated with transcriptional changes. (prolekare.cz)
- Three CpG islands within a 1.15- kb region characterize the chromatin landscape surrounding the transcriptional start site of the multidrug resistance 1 (MDR1) gene. (monash.edu)
- Additionally, we find that DNA methylation is significantly depleted near gene transcriptional start sites, which may explain the recently discovered elevated rate of recombination in these same regions.Using a model-based approach, we demonstrate that methylation patterns are an important predictor of variation in gene expression.This model provides a novel approach for differential methylation analysis that generates distinct and testable hypotheses regarding gene expression. (nih.gov)
- Additionally, we find that DNA methylation is significantly depleted near gene transcriptional start sites, which may explain the recently discovered elevated rate of recombination in these same regions. (nih.gov)
- Histone methylation can be associated with either transcriptional repression or activation. (wikipedia.org)
- Methylation of some lysine (K) and arginine (R) residues of histones results in transcriptional activation. (wikipedia.org)
- Such processes are involved not only in cell differentiation and parental genomic imprinting but also in developmental plasticity through which the environment in early life can affect the developmental trajectory, with long-term effects on gene expression and phenotypic outcome ( 12 - 14 ). (diabetesjournals.org)
- RESULTS: The results show that the cytosine methylation in this genomic region is 1) restricted to cytosines in CpG dinucleotides 2) similar in brain regions and blood and 3) appears conserved in primate evolution. (biomedsearch.com)
- We found that the methylome transition from day 1 to day 7 is characterized by the excess of genomic regions which gain over those that lose DNA methylation. (biomedcentral.com)
- The promoter genomic regions exhibiting increased DNA methylation at day 7 as compared to day 1 are significantly enriched in the genes critical for heart maturation and muscle development. (biomedcentral.com)
- In species with low genomic methylation-such as the honeybee or the sea squirt-gene bodies are the exclusive targets of DNA methylation. (embopress.org)
- DNA methylation plays an important role in normal differentiation, development, and maintenance of genomic stability, with aberrant CpG methylation being linked with a number of disease states. (monash.edu)
- DNA methylation varies across chromosomes, genomic regions, and genes. (nih.gov)
- DNA methylation is essential for normal development and is associated with a number of key processes including genomic imprinting, X-chromosome inactivation, repression of transposable elements, aging and carcinogenesis. (wikipedia.org)
- A significant number of tumor suppressor genes are transcriptionally silenced by promoter hypermethylation, and recent research implicates alterations in chromatin structure as the mechanistic basis for this repression. (nih.gov)
- In conjunction with histone modifications, DNA methylation plays critical roles in gene silencing through chromatin remodeling. (sciencemag.org)
- Our findings suggest that DNA methylation-related chromatin remodeling is important for activity-dependent gene regulation that may be critical for neural plasticity. (sciencemag.org)
- DNA methylation is a key determinant of regulatory chromatin complexes transmitted through cell divisions. (biomedcentral.com)
- Then, we applied the derived model to methylation sites away from gene promoters and characterized the chromatin structure and binding profile of the discovered sites. (biomedcentral.com)
- Recently, a link among aberrant CpG methylation, chromatin organisation and GAA repeat was proposed. (bmj.com)
- Here we tested the hypothesis that transgenically derived siRNAs may contemporaneously both activate the PTGS mechanism and induce chromatin modifications at the transgene and the homologous endogenous gene. (asm.org)
- The majority of CpG islands are constitutively unmethylated and enriched for permissive chromatin modification such as H3K4 methylation. (wikipedia.org)
- Histone methylation, as a mechanism for modifying chromatin structure is associated with stimulation of neural pathways known to be important for formation of long-term memories and learning. (wikipedia.org)
- Studies of these sites have found that that methylation of histone tails at different residues serve as markers for the recruitment of various proteins or protein complexes that serve to regulate chromatin activation or inactivation. (wikipedia.org)
Measured the methylation status1
Analysis of DNA Methylation3
- Moreover, we generated a workflow for integrated analysis of DNA methylation and mRNA expression, which is expandable to other study types. (frontiersin.org)
- Analysis of DNA methylation in promoter regions of the genes displaying ASE using DNA-microarrays revealed frequent regulation of gene expression by DNA methylation. (avhandlingar.se)
- A genome-wide analysis of DNA methylation identified regions with reduced endosperm DNA methylation in, or near, 19 of the 100 imprinted genes. (plantcell.org)
Associated with gene expression2
- We conducted a methodical analysis of distal DNA methylation sites associated with gene expression in normal and cancerous human cells. (biomedcentral.com)
- Whether and how the divergence of DNA methylation between duplicate pairs is associated with gene expression and evolutionary time are poorly understood. (g3journal.org)
Altered DNA methylation and gene expression1
- (13) recently reported methylation of p14 A R F in 28% of primary colorectal carcinomas and suggested that methylation-associated inactivation of p14 A R F is independent of p16 I N K 4 a methylation and p53 mutational status. (aacrjournals.org)
- Recently, considerable attention has been paid to gene expression-based classifications of colorectal cancers (CRC) and their association with patient prognosis. (mdpi.com)
- We studied genome-wide DNA methylation differences between colorectal tumors carrying a BRAF mutation and BRAF wildtype tumors. (altmetric.com)
- We investigated the aberrant methylation profile of potential tumor suppressor genes of p15, p16, SOCS-1, and Wnt signaling pathway in colorectal cancers and correlated the data with clinical findings. (spandidos-publications.com)
- Mokarram P, Naghibalhossaini F, Firoozi MS, Hosseini SV, Izadpanah A, Salahi H, Malek-Hosseini SA, Talei A, Mojallal M. Methylenetetrahydrofolate reductase C677T genotype affects promoter methylation of tumor-specific genes in sporadic colorectal cancer through an interaction with folate/vitamin B 12 status. (wjgnet.com)
- To evaluate joint effects of Methylentetrahydrofolate reductase ( MTHFR ) C677T genotypes, and serum folate/vitamin B 12 concentrations on promoter methylation of tumor-associated genes among Iranian colorectal cancer patients. (wjgnet.com)
- We examined the associations between MTHFR C677T genotype, and promoter methylation of P16, hMLH1, and hMSH2 tumor-related genes among 151 sporadic colorectal cancer patients. (wjgnet.com)
- Method for detecting the methylation of colorectal-cancer-specific methylation marker genes for colorectal. (patents.com)
- The present invention relates to a method for detecting the methylation of colorectal cancer-specific marker genes for colorectal cancer diagnosis, and more. (patents.com)
- I think you mean that you have not heard of housekeeping gene methylation in either normall tissues or cancer cells. (protocol-online.org)
- The present study was undertaken to determine RASSF1A methylation in the gastric cardia adenocarcinoma (GCA) tissue and adjacent non-cancer tissues to further understand the moleculer mechanism of GCA and to screen the possible biomarkers to identify the high-risk subjects and early GCA patients. (aacrjournals.org)
- Promoter methylation of RASSF1A could be detected in GCA (27/42, 64%), while only one was found in adjacent non-cancer tissues. (aacrjournals.org)
- We conclude that these findings confirm in a large sample that methylation is a frequent event in NSCLC, can also occur in smoking-damaged nonmalignant lung tissues, and may be the most common mechanism to inactivate cancer-related genes in NSCLC. (aacrjournals.org)
- Therefore, we decided to investigate methylation of multiple genes in a large sample collection of primary resected NSCLCs and their associated nonmalignant lung tissues, for which we also had clinical data and results about certain other molecular abnormalities. (aacrjournals.org)
- In this study, we examined DNA methylation and mRNA expression status in a set of testicular tissues of SO patients ( n = 3), and compared methylated data with those derived from obstructive azoospermia (OA) patients ( n = 3) with normal spermatogenesis phenotype. (frontiersin.org)
- DNA isolated from PC cell lines and from normal and neoplastic human prostate tissues was restriction-digested with a methylation-sensitive restriction endonuclease and analyzed by Southern blot using a 5′ sequence-specific NEP probe. (aacrjournals.org)
- However, there might be interactions between GDF-15 levels and methylation in other tissues not addressed in this study. (ovid.com)
- Here we conducted DNA methylation (DNAm) immunoprecipitation and high throughput sequencing (MeDIP-seq) and RNA sequencing (RNA-seq) of muscle tissues of cloned piglets to investigate the relationship of abnormal DNAm with gene dysregulation and the unusual phenotypes in cloned piglets. (biomedcentral.com)
- DNA methylation profiling of two adult mouse tissues, retina and brain, was conducted using c omprehensive h igh-throughput a rray for r elative m ethylation (CHARM) tiling array identifying 2,498 T-DMRs. (arvojournals.org)
- In this work, we focus on DNA methylation and post-translational histone modifications (PTMs). (springer.com)
- For example, in the rat unbalanced maternal diet during pregnancy induces changes in DNA methylation and covalent histone modifications in the 5′ regulatory regions of specific nonimprinted genes ( 15 - 17 ) and affects the offspring's later body composition and metabolic phenotype. (diabetesjournals.org)
- Altered histone modifications implicated in gene silencing associate with aberrant autoantigen expression. (asnjournals.org)
Genome wide DNA7
- The aim of this study was to identify newly hypermethylated genes in ulcerative colitis (UC) using a genome-wide DNA methylation approach. (mdpi.com)
- Genome wide DNA methylation was assessed using the HumanMethylation450 BeadChip platform and Genome Studio (Illumina). (bmj.com)
- To investigate a possible association between GDF-15 levels and DNA methylation, we performed a genome-wide DNA methylation study of white blood cells in a population-based study (N = 717). (ovid.com)
- In the present study, genome-wide DNA methylation (n = 486,428 CpG sites) of 84 placentas was analyzed in relation to 16 species of placental microorganisms using samples collected from the Extremely Low Gestation Age Newborns (ELGAN) cohort. (harvard.edu)
- Experimental Design: We determined genome-wide DNA methylation profiles of 72 hrHPV-positive self-samples, using the Infinium Methylation 450K Array. (eur.nl)
- Results: Genome-wide DNA methylation profiling revealed 12 DNA methylation markers for CIN3 detection. (eur.nl)
- Conclusions: By genome-wide DNA methylation profiling on self-samples, we identified a highly effective 3-gene methylation classifier for direct triage on hrHPV-positive self-samples, which is superior to currently available methods. (eur.nl)
Expression of ge2
- 10 Altered expression of genes contributing to the regulation of 5-HT have been observed in populations showing high impulsive aggression. (rcpsych.org)
- This suggests that the high ABA levels in crown galls may mediate DNA methylation and regulate expression of genes involved in drought stress protection. (prolekare.cz)
- Body mass index is associated with gene methylation in estrogen receptor-positive breast tumors. (sigmaaldrich.com)
- In the current study, we examined the methylation status of the NEP promoter in human PC cell lines and in primary prostate tumors. (aacrjournals.org)
- A bead-based methylation array platform was used to measure methylation of 1,413 CpG loci in ~800 cancer-associated genes and three methylation classes were derived by unsupervised clustering of tumors using recursively partitioned mixture modeling (RPMM). (pubmedcentralcanada.ca)
Negatively correlated with gene expression1
- Data deposition: The microarray data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. (pnas.org)
- Large-scale technologies, such as methylation microarray assays and specific sequencing of methylated DNA, have been used to determine whole genome profiles of CpG island methylation in tissue samples. (mdpi.com)
- In this article, publicly available microarray-based gene expression and methylation data sets are used to characterize expression subtypes with respect to locus-specific methylation. (mdpi.com)
- Microarray based analysis of methylation refers to CpG site selected by a biostatistic algorithm without proof for actual involvement. (bmj.com)
- The MeDIP-chip (methylated DNA immunoprecipitation microarray) approach was used in order to compare global DNA methylation profiles in whole murine hearts at day 1, 7, 14 and 56 complemented with microarray transcriptome profiling. (biomedcentral.com)
- KBD GWAS single nucleotide polymorphisms (SNPs) and normal meQTLs SNPs were integrated with DNA methylation profiles of KBD articular cartilage to identify genetic control (GC) genes of DNA methylation for KBD. (unboundmedicine.com)
- Finally, as Vogel Ciernia summarizes, "The genes we identified that had differences in methylation and changes in expression showed an enrichment for genes that had been identified as genetic risk factors for autism, as well as genes that were differentially expressed in autism human brain samples. (epigenie.com)
- Effects of genetic variation in H3K79 methylation regulatory genes on clinical blood pressure and blood pressure respons. (ufl.edu)
- By integrating above DNA methylation data and mRNA expression results, we totally identified 72 methylated CpG sites located in 65 genes with anti-correlation between DNA methylation and mRNA expression. (frontiersin.org)
- T-DMRs were divided into 2 groups: negative and positive, based on the correlation of DNA methylation with gene expression. (arvojournals.org)
- Through linear modeling and analysis of variance, we obtain genes that show a significant correlation between methylation and gene expression. (altmetric.com)
- A significant positive correlation was observed between hgcA gene abundance and methylmercury (MeHg) concentrations, suggesting that microbes containing the genes contribute to Hg methylation in the sampled soils. (asm.org)
- We showed a direct correlation between CpG methylation and triplet expansion size. (bmj.com)
- Le Stunff C, Castell A, Todd N, Mille C, Belot M, Frament N, Brailly-Tabard S, Benachi A, Fradin D. Fetal growth is associated with CpG methylation in the correlation coefficient is indicated in bold, and P P2 promoter of the IGF1 gene. (deepdyve.com)
- Our analyses showed that the cis- regulation of DNA methylation and gene expression was dominated by the negative correlation, while the trans- regulation was more complex. (deepdyve.com)
Silenced gene expression1
Related methylation status1
- This study shows that GDF-15 levels are associated with differences in DNA methylation in blood cells, and a subset of the loci are also differentially methylated in participants with MI. (ovid.com)
- To better understand the function of tissue-specific differentially methylated regions (T-DMRs), we characterized tissue-specific DNA methylation between mouse retina and brain and compared the T-DMRs with tissue-specific gene expression. (arvojournals.org)
- Whole genome methylation and expression profiling identified differentially methylated sites and expressed genes between placebo and genistein groups. (spandidos-publications.com)
- Methods: Using the TCGA HCC dataset, we classified HCC patients into different methylation subtypes, identified differentially methylated and expressed genes, and analyzed cis- and trans-regulation of DNA methylation and gene expression. (deepdyve.com)
- Pathway analyses were performed using GO and KEGG databases with differentially hypermethylated genes in UC. (mdpi.com)
- Exploratory analyses were performed using microarrays to identify differentially expressed genes in whole blood from children defined as "slow" ( n = 10) compared with "rapid" ( n = 10) postnatal (term to 12 weeks corrected age) growers. (diabetesjournals.org)
- An oral glucose tolerance test was used, and blood samples were collected for biochemical and DNA methylation analyses. (termedia.pl)
- Methylation and expression analyses of Pallister-Killian syndrome reveal partial dosage compensation of tetrasomy 12p and hypomethylation of gene-poor regions on 12p. (lu.se)
Regulation of gene ex3
- The extent to which glycosylation changes are influenced by aberrant regulation of gene expression is nearly unknown for ovarian cancer and remains crucial in understanding the development and progression of this disease. (mcponline.org)
- Background and Objective Site specific methylation of DNA may contribute to the regulation of gene expression. (bmj.com)
- This process is critical for the regulation of gene expression that allows different cells to express different genes. (wikipedia.org)
- We finally found that three genes ( FAM217B , KIAA1614 and RIBC2 ) that were significantly elevating the promoter methylation levels in UC compared to normal controls. (mdpi.com)
- 0.008) were significantly associated with methylation class membership. (pubmedcentralcanada.ca)
- NTSR1 gene showed significantly increased methylation of normal colonic mucosae from UC-CRC vs. LS patients (p value=0.01). (helsinki.fi)
- The majority (89%) of the significantly deregulated genes were not. (lu.se)
- The majority (89%) of the significantly deregulated genes were not situated on 12p, indicating that global perturbation of gene expression is a key pathogenetic event in PKS. (lu.se)
Levels and DNA methylation1
- In the second study we used technology developed for large-scale single nucleotide polymorphism (SNP) genotyping for quantitative analysis of allele-specific gene expression (ASE), revealing widespread ASE in ALL cells. (avhandlingar.se)
- Quantitative polymerase chain reaction (qPCR) was performed to validate the mRNA expression of several identified candidate genes. (unboundmedicine.com)
- Gene expression changes were validated by quantitative PCR (qPCR). (spandidos-publications.com)
- In this study, using pyrosequencing technology, we have performed a quantitative analysis of the methylation status of five CpG sites located within the region upstream of GAA repeat, in 67 FRDA patients. (bmj.com)
- The selected DNA methylation markers were evaluated by multiplex quantitative methylation-specific PCR (qMSP) in both hrHPV-positive lavage (n ¼ 245) and brush (n ¼ 246) self-samples from screening cohorts. (eur.nl)
- Although it is well-established that promoter methylation is inversely correlated with gene expression, the role of intragenic methylation is still unclear. (arvojournals.org)
- Aberrant promoter methylation of previously unidentified target genes is a common abnormality in medulloblastomas-implications for tumor biology and potential clinical utility," Oncogene , vol. 20, no. 36, pp. 5033-5042, 2001. (hindawi.com)
- Phosphorylation of pRb in these complexes allows the E2F proteins to transactivate their target genes, and their products then promote cell cycle progression (reviewed in reference 64 ). (asm.org)
Role of DNA methylation2
- In order to decipher the role of DNA methylation in this process, we generated a YAC transgenic mouse system that allowed us to control gamma(A) methylation during development. (nih.gov)
- We further found that the expression pattern of at least some genic TDMRs was correlated with its tissue-specific methylation state, implicating a developmental role of DNA methylation in regulating tissue-specific or -preferential gene expression in sorghum. (plantphysiol.org)
Measurement of DNA methylation1
- Most interestingly, H3K9 dimethylation was enriched in the human MLH1 gene promoter following chromate exposure and this was correlated with decreased MLH1 mRNA expression. (nih.gov)
- DNA methylation and mRNA expression of SYN III, a candidate gene for schizophrenia. (biomedsearch.com)
- METHODS: This research has established the mRNA expression of SYN III in 22 adult human brain regions as well as the methylation specificity in the closest CpG island of this gene. (biomedsearch.com)
Differences in methylation1
Putative imprinted genes in maize1
- DNA methylation might have a significant role in preventing normal differentiation in pediatric cancers. (pnas.org)
- Consistent with this, siRNA-mediated PU.1 knockdown in primary monocytes impaired the acquisition of DNA methylation and expression changes, and reduced the association of TET2 and DNMT3b at PU.1 targets during osteoclast differentiation. (sigmaaldrich.com)
- The work described here identifies key changes in DNA methylation during monocyte-to-osteoclast differentiation and reveals novel roles for PU.1 in this process. (sigmaaldrich.com)
- Variations in DNA methylation has been demonstrated upon differentiation of hPSC and these differences may underlie the functionality impairment of in vitro differentiated cells. (his.se)
- For this purpose DNA methylation arrays and mRNA arrays will be run on samples from defined stages during the differentiation process and will be compared to data from primary cells. (his.se)
- The project will identify key genes involved in changes in DNA methylation during differentiation towards the hepatic lineages. (his.se)
Changes in methylation3
- In a study that correlated changes in DNA methylation (a chemical change that affects the level of gene expression) to changes in gene expression across the genome of the placenta (the small ovoid organ that nourishes the embryo in the uterus), Dr. Kjersti Aagaard and her colleagues found changes in methylation and gene expression of only 25 genes in non-smokers but 438 genes among smokers. (redorbit.com)
- Despite seeing an increase in -3 PUFAs EPA and DHA in PBMCs, there were no changes in methylation of the candidate genes over the intervention period and therefore postulated that this might be because an inflammatory stimulus was absent in this cohort of healthy males. (bl.uk)
- Changes in methylation levels of stress reactivity genes such as the glucocorticoid receptor gene (NR3C1) can be induced by adversity. (eur.nl)
- CG island methylation changes near the GSTP1 gene in prostatic carcinoma cells detected using the polymerase chain reaction: a new prostate cancer biomarker. (aacrjournals.org)
- Here we describe a new biomarker for human prostate cancer: extensive methylation of deoxycytidine nucleotides distributed throughout a 5' "CG island" region of the pi-class glutathione S-transferase gene (GSTP1). (aacrjournals.org)
- Methylation of the NTSR1 in the normal colonic mucosa suggests a possible field defect in UC-CRC, and could thus be used as an early biomarker to detect increased UC-CRC risk in non-neoplastic epithelium. (helsinki.fi)
- Since the analysis can be performed in peripheral blood leucocytes (PBL), evaluation of the methylation status of specific CpG sites in FRDA patients could be a convenient biomarker. (bmj.com)
Surrounding CpG sites1
- Studies of phylogenetically basal invertebrates such as corals will further elucidate the fundamental functional aspects of gene body methylation in Metazoa. (utexas.edu)
- Points represent actual genes CG gene body methylation, gene expression, and their color represents their interaction sum on the same scale as the model colors. (nih.gov)
Island DNA methylation1
Relationships between methylation1
Abnormal DNA methylation2
Relationship between methylation2
- We performed a cross sectional study to investigate the relationship between methylation levels of the gene which encodes tumor necrosis factor alpha (TNFα), and levels of fatty acids within the blood. (bl.uk)
- In this paper, we use DNA methylation and gene expression data integration and pathway analysis to further explore and understand the complex relationship between methylation and gene expression. (altmetric.com)