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.
Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.
Tracts of land completely surrounded by water.
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.
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.
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.
Interruption or suppression of the expression of a gene at transcriptional or translational levels.
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.
Inorganic salts of sulfurous acid.
Numerous islands in the Indian Ocean situated east of Madagascar, north to the Arabian Sea and east to Sri Lanka. Included are COMOROS (republic), MADAGASCAR (republic), Maldives (republic), MAURITIUS (parliamentary democracy), Pemba (administered by Tanzania), REUNION (a department of France), and SEYCHELLES (republic).
The islands of the Pacific Ocean divided into MICRONESIA; MELANESIA; and POLYNESIA (including NEW ZEALAND). The collective name Oceania includes the aforenamed islands, adding AUSTRALIA; NEW ZEALAND; and the Malay Archipelago (INDONESIA). (Webster's New Geographical Dictionary, 1988, p910, 880)
An enzyme that catalyzes the transfer of a methyl group from S-ADENOSYLMETHIONINE to the 5-position of CYTOSINE residues in DNA.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
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.
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
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.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.
Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)
DNA present in neoplastic tissue.
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.
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.
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.
An island in the Gulf of St. Lawrence constituting a province of Canada in the eastern part of the country. It is very irregular in shape with many deep inlets. Its capital is Charlottetown. Discovered by the French in 1534 and originally named Ile Saint-Jean, it was renamed in 1799 in honor of Prince Edward, fourth son of George III and future father of Queen Victoria. (From Webster's New Geographical Dictionary, 1988, p981 & Room, Brewer's Dictionary of Names, 1992, p433)
Scattered islands in the Mediterranean Sea. The chief islands are the Balearic Islands (belong to Spain; Majorca and Minorca are among these), Corsica (belongs to France), Crete (belongs to Greece), CYPRUS (a republic), the Cyclades, Dodecanese and Ionian Islands (belong to Greece), MALTA (a republic), Sardinia and SICILY (belong to Italy). (From Webster's New Geographical Dictionary, 1988, p747)
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.
A pyrimidine base that is a fundamental unit of nucleic acids.
The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.
One of the Type II site-specific deoxyribonucleases (EC 3.1.21.4). It recognizes and cleaves the sequences C/CGG and GGC/C at the slash. HpaII is from Haemophilus parainfluenzae. Several isoschizomers have been identified. EC 3.1.21.-.
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.
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).
A cell line derived from cultured tumor cells.
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)
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.
The systematic study of the global gene expression changes due to EPIGENETIC PROCESSES and not due to DNA base sequence changes.
A group of islands in the Lesser Antilles in the West Indies, the three main islands being St. Croix, St. Thomas, and St. John. The capital is Charlotte Amalie. Before 1917 the U.S. Virgin Islands were held by the Danish and called the Danish West Indies but the name was changed when the United States acquired them by purchase.
A methylated nucleotide base found in eukaryotic DNA. In ANIMALS, the DNA METHYLATION of CYTOSINE to form 5-methylcytosine is found primarily in the palindromic sequence CpG. In PLANTS, the methylated sequence is CpNpGp, where N can be any base.
The collective name for the islands of the Pacific Ocean northeast of Australia, including NEW CALEDONIA; VANUATU; New Hebrides, Solomon Islands, Admiralty Islands, Bismarck Archipelago, FIJI, etc. Melanesia (from the Greek melas, black + nesos, island) is so called from the black color of the natives who are generally considered to be descended originally from the Negroid Papuans and the Polynesians or Malays. (From Webster's New Geographical Dictionary, 1988, p748 & Room, Brewer's Dictionary of Names, 1992, p344)
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.
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.
An INK4 cyclin-dependent kinase inhibitor containing four ANKYRIN-LIKE REPEATS. INK4B is often inactivated by deletions, mutations, or hypermethylation in HEMATOLOGIC NEOPLASMS.
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.
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.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
The collective name for islands of the Pacific Ocean east of the Philippines, including the Mariana, PALAU, Caroline, Marshall, and Kiribati Islands. (From Webster's New Geographical Dictionary, 1988, p761 & Room, Brewer's Dictionary of Names, 1992, p350)
A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
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.
Genes whose abnormal expression, or MUTATION are associated with the development, growth, or progression of NEOPLASMS.
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.
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.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
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.
The science dealing with the earth and its life, especially the description of land, sea, and air and the distribution of plant and animal life, including humanity and human industries with reference to the mutual relations of these elements. (From Webster, 3d ed)
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.
A raf kinase subclass found at high levels in neuronal tissue. The B-raf Kinases are MAP kinase kinase kinases that have specificity for MAP KINASE KINASE 1 and MAP KINASE KINASE 2.
A group of four British islands and several islets in the English Channel off the coast of France. They are known to have been occupied prehistorically. They were a part of Normandy in 933 but were united to the British crown at the time of the Norman Conquest in 1066. Guernsey and Jersey originated noted breeds of cattle. (From Webster's New Geographical Dictionary, 1988, p242)
Any method used for determining the location of and relative distances between genes on a chromosome.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
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.
One of the Indian Ocean Islands, east of Madagascar. Its capital is Saint-Denis. It was discovered in 1507 by the Portuguese and claimed by France in 1638. It was first colonized in 1662 as Isle de Bourbon but renamed Reunion in 1793. In 1946 it was made an overseas department of France. The name commemorates the reunion of the revolutionaries from Marseilles with the National Guard in Paris in 1792. (From Webster's New Geographical Dictionary, 1988, p1011; Room, Brewer's Dictionary of Names, 1992, p454; French Embassy)
A British colony in the Atlantic Islands, comprising two principal islands, East Falkland and West Falkland. Its capital is Stanley. Discovered in 1592, it was not occupied until the French settled there briefly in 1764. Later the English settled there but were expelled by the Spanish in 1770. The Falklands were claimed by Argentina but were occupied in 1833 by the British who, after an April 1982 invasion by Argentina, regained them in June. The islands were named by British Captain John Strong in 1690 for the fifth Viscount Falkland who financed Strong's expedition. The Spanish name for the islands, Malvinas, is from the French Malouins, inhabitants of St. Malo who attempted to colonize the islands in 1764. (From Webster's New Geographical Dictionary, 1988, p389 & Room, Brewer's Dictionary of Names, 1992, p182)
The collective name for the islands of the central Pacific Ocean, including the Austral Islands, Cook Islands, Easter Island, HAWAII; NEW ZEALAND; Phoenix Islands, PITCAIRN ISLAND; SAMOA; TONGA; Tuamotu Archipelago, Wake Island, and Wallis and Futuna Islands. Polynesians are of the Caucasoid race, but many are of mixed origin. Polynesia is from the Greek poly, many + nesos, island, with reference to the many islands in the group. (From Webster's New Geographical Dictionary, 1988, p966 & Room, Brewer's Dictionary of Names, 1992, p426)
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.
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.
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.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
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.
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.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
A 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.
A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).
The relationships of groups of organisms as reflected by their genetic makeup.
A specific pair of GROUP G CHROMOSOMES of the human chromosome classification.
Established cell cultures that have the potential to propagate indefinitely.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
The female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in human and other male-heterogametic species.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
A pattern recognition receptor that binds unmethylated CPG CLUSTERS. It mediates cellular responses to bacterial pathogens by distinguishing between self and bacterial DNA.
Methylases that are specific for CYTOSINE residues found on DNA.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
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.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
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.
Tumors or cancer of the STOMACH.
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.
Formation of an acetyl derivative. (Stedman, 25th ed)
Tumors or cancer of the COLON.
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.
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.
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.
The region of DNA which borders the 5' end of a transcription unit and where a variety of regulatory sequences are located.
Genotypic differences observed among individuals in a population.
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.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
An enzyme catalyzing the formation of AMP from adenine and phosphoribosylpyrophosphate. It can act as a salvage enzyme for recycling of adenine into nucleic acids. EC 2.4.2.7.
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.
The systematic study of the complete DNA sequences (GENOME) of organisms.
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.
A broad category of carrier proteins that play a role in SIGNAL TRANSDUCTION. They generally contain several modular domains, each of which having its own binding activity, and act by forming complexes with other intracellular-signaling molecules. Signal-transducing adaptor proteins lack enzyme activity, however their activity can be modulated by other signal-transducing enzymes

Detailed methylation analysis of the glutathione S-transferase pi (GSTP1) gene in prostate cancer. (1/4270)

Glutathione-S-Transferases (GSTs) comprise a family of isoenzymes that provide protection to mammalian cells against electrophilic metabolites of carcinogens and reactive oxygen species. Previous studies have shown that the CpG-rich promoter region of the pi-class gene GSTP1 is methylated at single restriction sites in the majority of prostate cancers. In order to understand the nature of abnormal methylation of the GSTP1 gene in prostate cancer we undertook a detailed analysis of methylation at 131 CpG sites spanning the promoter and body of the gene. Our results show that DNA methylation is not confined to specific CpG sites in the promoter region of the GSTP1 gene but is extensive throughout the CpG island in prostate cancer cells. Furthermore we found that both alleles are abnormally methylated in this region. In normal prostate tissue, the entire CpG island was unmethylated, but extensive methylation was found outside the island in the body of the gene. Loss of GSTP1 expression correlated with DNA methylation of the CpG island in both prostate cancer cell lines and cancer tissues whereas methylation outside the CpG island in normal prostate tissue appeared to have no effect on gene expression.  (+info)

Comparative sequence analysis of human minisatellites showing meiotic repeat instability. (2/4270)

The highly variable human minisatellites MS32 (D1S8), MS31A (D7S21), and CEB1 (D2S90) all show recombination-based repeat instability restricted to the germline. Mutation usually results in polar interallelic conversion or occasionally in crossovers, which, at MS32 at least, extend into DNA flanking the repeat array, defining a localized recombination hotspot and suggesting that cis-acting elements in flanking DNA can influence repeat instability. Therefore, comparative sequence analysis was performed to search for common flanking elements associated with these unstable loci. All three minisatellites are located in GC-rich DNA abundant in dispersed and tandem repetitive elements. There were no significant sequence similarities between different loci upstream of the unstable end of the repeat array. Only one of the three loci showed clear evidence for putative coding sequences near the minisatellite. No consistent patterns of thermal stability or DNA secondary structure were shared by DNA flanking these loci. This work extends previous data on the genomic environment of minisatellites. In addition, this work suggests that recombinational activity is not controlled by primary or secondary characteristics of the DNA sequence flanking the repeat array and is not obviously associated with gene promoters as seen in yeast.  (+info)

Inactivation of the DNA repair gene O6-methylguanine-DNA methyltransferase by promoter hypermethylation is a common event in primary human neoplasia. (3/4270)

The DNA repair protein O6-methylguanine DNA methyltransferase (MGMT) removes alkyl adducts from the O6 position of guanine. MGMT expression is decreased in some tumor tissues, and lack of activity has been observed in some cell lines. Loss of expression is rarely due to deletion, mutation, or rearrangement of the MGMT gene, but methylation of discrete regions of the CpG island of MGMT has been associated with the silencing of the gene in cell lines. We used methylation-specific PCR to study the promoter methylation of the MGMT gene. All normal tissues and expressing cancer cell lines were unmethylated, whereas nonexpressing cancer cell lines were methylated. Among the more than 500 primary human tumors examined, MGMT hypermethylation was present in a subset of specific types of cancer. In gliomas and colorectal carcinomas, aberrant methylation was detected in 40% of the tumors, whereas in non-small cell lung carcinomas, lymphomas, and head and neck carcinomas, this alteration was found in 25% of the tumors. MGMT methylation was found rarely or not at all in other tumor types. We also analyzed MGMT expression by immunohistochemistry in relation to the methylation status in 31 primary tumors. The presence of aberrant hypermethylation was associated with loss of MGMT protein, in contrast to retention of protein in the majority of tumors without aberrant hypermethylation. Our results suggest that epigenetic inactivation of MGMT plays an important role in primary human neoplasia.  (+info)

Methylation-associated silencing of the tissue inhibitor of metalloproteinase-3 gene suggest a suppressor role in kidney, brain, and other human cancers. (4/4270)

Tissue inhibitor of metalloproteinase-3 (TIMP-3) antagonizes matrix metalloproteinase activity and can suppress tumor growth, angiogenesis, invasion, and metastasis. Loss of TIMP-3 has been related to the acquisition of tumorigenesis. Herein, we show that TIMP-3 is silenced in association with aberrant promoter-region methylation in cell lines derived from human cancers. TIMP-3 expression was restored after 5-aza-2'deoxycytidine-mediated demethylation of the TIMP-3 proximal promoter region. Genomic bisulfite sequencing revealed that TIMP-3 silencing was related to the overall density of methylation and that discrete regions within the TIMP-3 CpG island may be important for the silencing of this gene. Aberrant methylation of TIMP-3 occurred in primary cancers of the kidney, brain, colon, breast, and lung, but not in any of 41 normal tissue samples. The most frequent TIMP-3 methylation was found in renal cancers, which originate in the tissue that normally expresses the highest TIMP-3 levels. This methylation correlated with a lack of detectable TIMP-3 protein in these tumors. Together, these data show that methylation-associated inactivation of TIMP-3 is frequent in many human tumors.  (+info)

Chlamydia infections and heart disease linked through antigenic mimicry. (5/4270)

Chlamydia infections are epidemiologically linked to human heart disease. A peptide from the murine heart muscle-specific alpha myosin heavy chain that has sequence homology to the 60-kilodalton cysteine-rich outer membrane proteins of Chlamydia pneumoniae, C. psittaci, and C. trachomatis was shown to induce autoimmune inflammatory heart disease in mice. Injection of the homologous Chlamydia peptides into mice also induced perivascular inflammation, fibrotic changes, and blood vessel occlusion in the heart, as well as triggering T and B cell reactivity to the homologous endogenous heart muscle-specific peptide. Chlamydia DNA functioned as an adjuvant in the triggering of peptide-induced inflammatory heart disease. Infection with C. trachomatis led to the production of autoantibodies to heart muscle-specific epitopes. Thus, Chlamydia-mediated heart disease is induced by antigenic mimicry of a heart muscle-specific protein.  (+info)

Molecular detection of tumor cells in bronchoalveolar lavage fluid from patients with early stage lung cancer. (6/4270)

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

Genomic structure and expression of the mouse growth factor receptor related to tyrosine kinases (Ryk). (7/4270)

We report the genomic organization of the mouse orphan receptor related to tyrosine kinases (Ryk), a structurally unclassified member of the growth factor receptor family. The mouse RYK protein is encoded by 15 exons distributed over a minimum of 81 kilobases. Genomic DNA sequences encoding a variant protein tyrosine kinase ATP-binding motif characteristic of RYK are unexpectedly found in two separate exons. A feature of the gene is an unmethylated CpG island spanning exon 1 and flanking sequences, including a TATA box-containing putative promoter and single transcription start site. Immunohistochemical examination of RYK protein distribution revealed widespread but developmentally regulated expression, which was spatially restricted within particular adult organs. Quantitative reduction of Southern blotting stringency for the detection of Ryk-related sequences provided evidence for a retroprocessed mouse pseudogene and a more distantly related gene paralogue. Extensive cross-species reactivity of a mouse Ryk kinase subdomain probe and the cloning of a Ryk orthologue from Caenorhabditis elegans demonstrate that Ryk and its relatives encode widely conserved members of a novel receptor tyrosine kinase subfamily.  (+info)

Isolation of DNA fragments associated with methylated CpG islands in human adenocarcinomas of the lung using a methylated DNA binding column and denaturing gradient gel electrophoresis. (8/4270)

We have constructed a library of DNA fragments heavily methylated in human adenocarcinomas of the lung to permit the comprehensive isolation of methylated CpG islands in cancer. Heavily methylated genomic DNA fragments from tumors of nine male patients were enriched using a methylated DNA binding column and used for construction of the library. From this library, DNA fragments having properties of CpG islands were isolated on the basis of their reduced rate of strand dissociation during denaturing gradient gel electrophoresis. Approximately 1,000 clones, corresponding to 0.3% of the library were analyzed, and nine DNA fragments were identified as being associated with CpG islands that were methylated in tumor DNA. One CpG island was methylated specifically in tumor DNA, whereas the remaining eight CpG islands were methylated both in normal and tumor DNA derived from the same patients. Our results suggest that the number of CpG islands methylated specifically in tumors is not large. The library, which contains DNA fragments from methylated CpG islands comprehensively, is expected to be valuable when elucidating epigenetic processes involved in carcinogenesis.  (+info)

MSI is a common feature of many types of cancer, including colorectal cancer, gastrointestinal cancers, and endometrial cancer. It is estimated that up to 15% of all cancers exhibit MSI, with the highest prevalence found in colon cancer (40-50%).

MSI can be caused by a variety of genetic mutations, including defects in DNA repair genes such as MLH1 and MSH2, which are involved in the repair of microsatellites. Other causes of MSI include defects in the proofreading mechanism of DNA replication and the absence of the protein that corrects errors during DNA replication.

The significance of MSI in cancer is that it can be used as a biomarker for predicting the response of cancer cells to immunotherapy, such as checkpoint inhibitors. Cancer cells that exhibit MSI are more likely to respond to these therapies and have a better prognosis compared to those that do not exhibit MSI. Additionally, MSI can be used as a predictive biomarker for the presence of Lynch syndrome, an inherited condition that increases the risk of developing colorectal cancer and other cancers.

Overall, the study of microsatellite instability is an important area of cancer research, as it can provide valuable insights into the mechanisms of cancer development and progression, and may lead to the development of new diagnostic and therapeutic strategies for cancer treatment.

The causes of colorectal neoplasms are not fully understood, but factors such as age, genetics, diet, and lifestyle have been implicated. Symptoms of colorectal cancer can include changes in bowel habits, blood in the stool, abdominal pain, and weight loss. Screening for colorectal cancer is recommended for adults over the age of 50, as it can help detect early-stage tumors and improve survival rates.

There are several subtypes of colorectal neoplasms, including adenomas (which are precancerous polyps), carcinomas (which are malignant tumors), and lymphomas (which are cancers of the immune system). Treatment options for colorectal cancer depend on the stage and location of the tumor, but may include surgery, chemotherapy, radiation therapy, or a combination of these.

Research into the causes and treatment of colorectal neoplasms is ongoing, and there has been significant progress in recent years. Advances in screening and treatment have improved survival rates for patients with colorectal cancer, and there is hope that continued research will lead to even more effective treatments in the future.

There are several types of stomach neoplasms, including:

1. Adenocarcinoma: This is the most common type of stomach cancer, accounting for approximately 90% of all cases. It begins in the glandular cells that line the stomach and can spread to other parts of the body.
2. Squamous cell carcinoma: This type of cancer begins in the squamous cells that cover the outer layer of the stomach. It is less common than adenocarcinoma but more likely to be found in the upper part of the stomach.
3. Gastric mixed adenocarcinomasquamous cell carcinoma: This type of cancer is a combination of adenocarcinoma and squamous cell carcinoma.
4. Lymphoma: This is a cancer of the immune system that can occur in the stomach. It is less common than other types of stomach cancer but can be more aggressive.
5. Carcinomas of the stomach: These are malignant tumors that arise from the epithelial cells lining the stomach. They can be subdivided into adenocarcinoma, squamous cell carcinoma, and others.
6. Gastric brunner's gland adenoma: This is a rare type of benign tumor that arises from the Brunner's glands in the stomach.
7. Gastric polyps: These are growths that occur on the lining of the stomach and can be either benign or malignant.

The symptoms of stomach neoplasms vary depending on the location, size, and type of tumor. Common symptoms include abdominal pain, nausea, vomiting, weight loss, and difficulty swallowing. Diagnosis is usually made through a combination of endoscopy, imaging studies (such as CT or PET scans), and biopsy. Treatment depends on the type and stage of the tumor and may include surgery, chemotherapy, radiation therapy, or a combination of these. The prognosis for stomach neoplasms varies depending on the type and stage of the tumor, but early detection and treatment can improve outcomes.

There are several types of colonic neoplasms, including:

1. Adenomas: These are benign growths that are usually precursors to colorectal cancer.
2. Carcinomas: These are malignant tumors that arise from the epithelial lining of the colon.
3. Sarcomas: These are rare malignant tumors that arise from the connective tissue of the colon.
4. Lymphomas: These are cancers of the immune system that can affect the colon.

Colonic neoplasms can cause a variety of symptoms, including bleeding, abdominal pain, and changes in bowel habits. They are often diagnosed through a combination of medical imaging tests (such as colonoscopy or CT scan) and biopsy. Treatment for colonic neoplasms depends on the type and stage of the tumor, and may include surgery, chemotherapy, and/or radiation therapy.

Overall, colonic neoplasms are a common condition that can have serious consequences if left untreated. It is important for individuals to be aware of their risk factors and to undergo regular screening for colon cancer to help detect and treat any abnormal growths or tumors in the colon.

It is useful to consider a particular tumor type, called CpG island methylator prototype, or CIMP: higher levels of CpG island ... the CpG island is hypomethylated, and the rest of the genome is methylated. It is evident that the hypomethylation of the CpG ... A CpG island is a cytosine and guanine linked by a phosphate in a repeated sequence. These are genetic hotspots as they are ... CpG island hypermethylation is a phenomenon that is important for the regulation of gene expression in cancer cells, as an ...
CpG dinucleotides frequently occur in CpG islands (see definition of CpG islands, below). There are 28,890 CpG islands in the ... occur a short distance from the CpG islands (at "CpG island shores") rather than in the islands themselves. CpG islands ... CpG islands (or CG islands) are regions with a high frequency of CpG sites. Though objective definitions for CpG islands are ... CpG sites occur with high frequency in genomic regions called CpG islands (or CG islands). Cytosines in CpG dinucleotides can ...
"CpG Island Info". genome.ucsc.edu. Retrieved 2020-05-03. Gardiner-Garden M, Frommer M (July 1987). "CpG islands in vertebrate ... The CpG island associated with this promoter has 75 CpGs (22% of island), and is 676bp long. The C count plus G count is 471, ... the percentage C or G is 70% within this island, and the ratio of observed to expected CpG is 0.91. As determined by ...
"Predicting aberrant CpG island methylation". Proceedings of the National Academy of Sciences. 100 (21): 12253-12258. doi: ...
... contain a CpG island. CpG islands are generally 200 to 2000 base pairs long, have a C:G base pair content >50%, and have ... and these frequently contain CpG islands as well. An example is the promoter of the DNA repair gene ERCC1, where the CpG island ... there are about 600 to 800 heavily methylated CpG islands in promoters of genes in the tumors while these CpG islands are not ... The presence of multiple methylated CpG sites in CpG islands of promoters causes stable inhibition (silencing) of genes. ...
"CpG islands. They showed that CpG islands are a distinct feature of vertebrate genomes and that CpG islands are associated with ... that the majority of neural and neuroendocrine genes were associated with CpG islands and therefore proposed that CpG islands ... CpG-rich DNA. Cell 40: 91-99. Gardiner-Garden, M. and Frommer, M. (1987). CpG islands in vertebrate genomes. J. Mol. Biol. 196 ... Gardiner-Garden, M. and Frommer, M. (1994). Transcripts and CpG islands associated with the pro-opiomelanocortin gene and other ...
... which in turn tend to cluster in regions called CpG islands. There is a small fraction of CpG islands that can overlap or be in ... February 2000). "Aberrant CpG-island methylation has non-random and tumour-type-specific patterns". Nat. Genet. 24 (2): 132-8. ... Gardiner-Garden M, Frommer M (July 1987). "CpG islands in vertebrate genomes". J. Mol. Biol. 196 (2): 261-82. doi:10.1016/0022- ... October 2002). "An AscI Boundary Library for the Studies of Genetic and Epigenetic Alterations in CpG Islands". Genome Res. 12 ...
Distal promoters also frequently contain CpG islands, such as the promoter of the DNA repair gene ERCC1, where the CpG island- ... The presence of multiple methylated CpG sites in CpG islands of promoters causes stable silencing of genes. Silencing of a gene ... MicroRNA promoters often contain CpG islands. DNA methylation forms 5-methylcytosines at the 5' pyrimidine ring of CpG cytosine ... but this is often followed by methylation of CpG sites in the promoter CpG island to cause the stable silencing of the gene. ...
... contain a CpG island (see CpG islands in promoters). If the initially nonmethylated CpG sites in a CpG island become largely ... the CpG islands that control promoters tend to gain methylation with age. The gain of methylation at CpG islands in promoter ... of CpG cytosines are methylated. However, in vertebrates there are CpG islands, about 300 to 3,000 base pairs long, with ... These CpG islands are predominantly nonmethylated. In humans, about 70% of promoters located near the transcription start site ...
Toyota M, Ahuja N, Ohe-Toyota M, Herman JG, Baylin SB, Issa JP (July 1999). "CpG island methylator phenotype in colorectal ... Thus, mutations in IDH1 and IDH2 generate a "DNA CpG island methylator phenotype or CIMP" that causes promoter hypermethylation ... Nazemalhosseini Mojarad E, Kuppen PJ, Aghdaei HA, Zali MR (2013). "The CpG island methylator phenotype (CIMP) in colorectal ... strand breaks can initiate gene silencing and SIRT1-dependent onset of DNA methylation in an exogenous promoter CpG island". ...
CpG island Law J, Jacobsen SE (2010). "Establishing, maintaining and modifying DNA methylation patterns in plants and animals ... In adult somatic tissues, cytosine residues may be methylated, and this occurs almost exclusively within a symmetric CpG ... Methylated C residues spontaneously deaminate to form T residues; hence CpG dinucleotides steadily mutate to TpG dinucleotides ... which gives rise to the under-representation of CpG dinucleotides in the human genome (they occur at only 21% of the expected ...
Toyota, M.; Ahuja, N.; Ohe-Toyota, M.; Herman, J.G.; Baylin, S.B.; Issa, J.P. (July 1999). "CpG island methylator phenotype in ... Her work initially as a postdoctoral research fellow twenty years ago identified the concept of CpG island methylator phenotype ... or CpG island hypermethylation in colorectal cancer. This concept of CIMP now is known to have implications for prognosis as ...
... has one CpG island within the promoter. SMIM15 has lower levels of H3K4Me1 but higher levels of H3K4Me3 and H3K27Ac ...
In mammalian cells, clusters of CpG at the 5' ends of genes are termed CpG islands. 1% of all mammalian DNA is 5mC. While ... CpG islands overlapping gene promoters are de novo methylated resulting in aberrant inactivation of genes normally associated ... Bird, Adrian P. (May 1986). "CpG-rich islands and the function of DNA methylation". Nature. 321 (6067): 209-213. Bibcode: ... There are reports of age estimators with the methylation state of only one CpG in the gene ELOVL2. Estimation of age allows for ...
October 2013). "The CpG island methylator phenotype: what's in a name?". review. Cancer Research. 73 (19): 5858-68. doi:10.1158 ... Curtin K, Slattery ML, Samowitz WS (April 2011). "CpG island methylation in colorectal cancer: past, present and future". ...
Blackledge NP, Zhou JC, Tolstorukov MY, Farcas AM, Park PJ, Klose RJ (Apr 2010). "CpG islands recruit a histone H3 lysine 36 ... This mechanism acts to create a chromatin environment at CpG islands that highlights these regulatory elements and ... within FBXL11/KDM2A has the capacity to interact with non-methylated DNA and this domain targets FBXL11/KDM2A to CpG island ...
January 2006). "De novo CpG island methylation in human cancer cells". Cancer Research. 66 (2): 682-92. doi:10.1158/0008-5472. ... Work with DNMT3a1 showed it preferentially localized to CpG islands bivalently marked by H3K4me3 (a transcription promoting ... "Isoform-specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands". EMBO J. 36 (23): 3421-3434 ... DNMT3a methylates CpG sites at a rate much slower than DNMT1, but greater than DNMT3b. The expression of DNMT3a2 differs from ...
Regions in which cytosines prior to guanines are clustered and highly unmethylated are called CpG islands, and often serve as ... PRC2 is recruited by many elements, including CpG islands. PRC1, meanwhile, ubiquitinates H2AK119 using Ring1A/B's E3 ligase ... DNA methylation in humans and most other mammals refers to the methylation of a CpG. Methylation of these cytosines are common ...
Klose, Rob (2010). "CpG islands recruit a histone H3 lysine 36 demethylase". Mol. Cell. 38 (2): 179-90. doi:10.1016/j.molcel. ... In particular, he has focused on understanding how DNA encoded regulatory elements in vertebrates, called CpG islands, help to ... Klose, Rob (2013). "ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection". Biochem Soc Trans. 41 (3): ... Klose, Rob (2005). "DNA binding selectivity of MeCP2 due to a requirement for A/T sequences adjacent to methyl-CpG". Mol. Cell ...
Blackledge NP, Zhou JC, Tolstorukov MY, Farcas AM, Park PJ, Klose RJ (Apr 2010). "CpG islands recruit a histone H3 lysine 36 ... KDM2A and KDM2B possess CXXC zinc finger domains responsible for binding to unmethylated CpG islands, and it is believed that ...
His research focuses on understanding DNA methylation and CpG islands, and their role in diseases such as Rett syndrome. Bird ... Bird's research has focused on CpG islands and their associated binding-factor MeCP2. He led the team which first identified ... Bird, A. P. (1986). "CpG-rich islands and the function of DNA methylation". Nature. 321 (6067): 209-13. Bibcode:1986Natur.321.. ... CpG islands-originally named "HpaII tiny fragments"-in vertebrate genomes. These are short genomic regions with a high density ...
Curtin, Karen; Slattery, Martha L; Samowitz, Wade S (2011). "CpG Island Methylation in Colorectal Cancer: Past, Present and ... CpG island methylator phenotype (CIMP) and BRAF mutation frequency from the database analyses of over 1,400 colorectal cancer ... "The CpG Island Methylator Phenotype: What's in a Name?". Cancer Research. 73 (19): 5858-68. doi:10.1158/0008-5472.CAN-12-4306. ...
This gene maps to a GC-rich region of the X chromosome and was identified by its proximity to a CpG island. It is thought to be ... Alcalay M, Toniolo D (1988). "CpG islands of the X chromosome are gene associated". Nucleic Acids Res. 16 (20): 9527-43. doi: ...
Jair KW, Bachman KE, Suzuki H, Ting AH, Rhee I, Yen RW, Baylin SB, Schuebel KE (January 2006). "De novo CpG island methylation ... DNA (cytosine-5)-methyltransferase 1 is an enzyme that catalyzes the transfer of methyl groups to specific CpG structures in ...
Cross SH, Charlton JA, Nan X, Bird AP (1994). "Purification of CpG islands using a methylated DNA binding column". Nat. Genet. ...
"Isolation of estrogen-responsive genes with a CpG island library". Mol Cell Biol. 18 (1): 442-9. doi:10.1128/mcb.18.1.442. PMC ...
Cross SH, Charlton JA, Nan X, Bird AP (1994). "Purification of CpG islands using a methylated DNA binding column". Nat. Genet. ...
"Isolation of estrogen-responsive genes with a CpG island library". Mol. Cell. Biol. 18 (1): 442-9. doi:10.1128/mcb.18.1.442. ...
Aïssani B, Bernardi G (October 1991). "CpG islands, genes and isochores in the genomes of vertebrates". Gene. 106 (2): 185-95. ...
Cross SH, Charlton JA, Nan X, Bird AP (1994). "Purification of CpG islands using a methylated DNA binding column". Nat. Genet. ...
"A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes". Genome Research. 12 (4 ...
... downregulated by CpG island hypermethylation in human esophageal squamous cell carcinoma". World J. Gastroenterol. 9 (6): 1174- ...
... is embedded within a CpG island, a genomic region containing high frequency of CpG dinucleotides, and is reported to be ...
These pseudogenes, though non-functional may in some cases still possess promoters, CpG islands, and other features which ... in mouse and human chromosomes and determined that this distribution was very similar to genomic distributions of genes and CpG ...
... strand breaks can initiate gene silencing and SIRT1-dependent onset of DNA methylation in an exogenous promoter CpG island". ...
Thus it is likely that these CpG islands are locations where genes on the male Z chromosome are methylated and silenced, but ... One study found that CpG islands were found primarily in compensated areas of the Z chromosome-areas that are differentially ... Similar to mammals, chickens seem to use CpG islands (segments of Cytosine-phosphate-Guanine that are more readily methylated ... "The role of LINEs and CpG islands in dosage compensation on the chicken Z chromosome". Chromosome Research. 17 (6): 727-736. ...
Cancer cells show a significant increase in the accumulation of methylation in CpG islands in the promoter region of p16. This ...
Treasure Island (FL): StatPearls Publishing. PMID 31082031. Retrieved 2022-04-28. Schenkman NS, Manger JP (2020-06-11). Gest TR ... In the United Kingdom the Cambridge Prognostic Group (CPG) is used for categorising prostate cancer into 5 risk groups (CPG1 to ... Treasure Island (FL): StatPearls Publishing. PMID 32966007. Retrieved 2022-04-28. Walsh PC, Lepor H, Eggleston JC (1983). " ... The UK National Institute for Health and Care Excellence guidelines recommends use of the Cambridge Prognostic Groups (CPG) 5- ...
CpG island - cristae - cryptobiology - crystal structure - crystallography - cuticula - CXCR4 receptor - cyclic AMP receptor - ...
Contained within the promoter region of the gene are three CpG islands. These imprint regions function in the regulation of ...
Leitir Móir CPG = Cumann Peil Gaelach, Irish for "Gaelic Football Club" GAA = Gaelic Athletic Association GAC = Gaelic Athletic ... a final played between two teams from the island of Ireland. The winning team then plays the overseas team in the final proper ...
Lantau Island, and over 200 other islands. Of the total area, 1,073 km2 (414 sq mi) is land and 35 km2 (14 sq mi) is water. The ... mainland criminal procedure law applies to cases investigated by the Office for Safeguarding National Security of the CPG in ... originally referred to a small inlet located between Aberdeen Island and the southern coast of Hong Kong Island. Aberdeen was ... Hong Kong was established as a colony of the British Empire after the Qing Empire ceded Hong Kong Island from Xin'an County at ...
2007). "Peptidyl argininedeiminase 2 CpG island in multiple sclerosis white matter is hypomethylated". J. Neurosci. Res. 85 (9 ...
On April 19, 2021, the Office announced that it was taking over the Island Pacific Hotel in Sai Ying Pun as an additional work ... However, the structuring of the approval process effectively means that the CPG can, since it also administers the CPGNSO, ... CPG). Statutorily, the office is only to be granted jurisdiction in cases of complexity due to the presence of foreign or ... United Front Work Department Chinese oversight of Hong Kong Hong Kong Liaison Office of the CPG Hong Kong Garrison of the PLA ...
... deputations were replaced by island councils in each of the islands or group of islands. For Majorca, Menorca and Ibiza- ... Aggregated data for CDS and CPG in Orense in the 1987 elections. "Municipal elections in Spain 1979-2011". interior.gob.es (in ... Deputations and island councils Provincial deputations were the governing bodies of provinces in Spain, having an ... Seats were allocated to provincial deputations based on the following scale: Island councils and foral deputations were elected ...
Fox has already handled Care Bears in Wonderland and A Man in Love for Virgin, and will release Pascali's Island for the ... CPG Products Corp. {{cite AV media}}: ,access-date= requires ,url= (help) DeWolf, Rose (October 12, 1982). "Out to launch: Is ... According to the Long Island newspaper Newsday, Cineplex Odeon chairman Garth Drabinsky "shrugged off [this film] as 'a favour ...
Human DNA has about 80-90% of CpG sites methylated, but there are certain areas, known as CpG islands, that are CG-rich (high ... One to two percent of the human genome are CpG clusters, and there is an inverse relationship between CpG methylation and ... The formation of Me-CpG is catalyzed by the enzyme DNA methyltransferase. In mammals, DNA methylation is common in body cells, ... DNA methylation in vertebrates typically occurs at CpG sites (cytosine-phosphate-guanine sites-that is, where a cytosine is ...
"Amplified region of chromosome band 11q13 in breast and squamous cell carcinomas encompasses three CpG islands telomeric of ... "Amplified region of chromosome band 11q13 in breast and squamous cell carcinomas encompasses three CpG islands telomeric of ...
In another study, methylation of the EFS CpG island was observed in 69% of cases of uveal melanoma (UM) and only UM with EFS ... At the level of EFS mRNA expression, the local and systemic recurrence of prostate cancer is associated with CpG site ...
... strand breaks can initiate gene silencing and SIRT1-dependent onset of DNA methylation in an exogenous promoter CpG island". ...
An epigenetic mechanism (hypermethylation of CpG islands in the NET gene promoter region) that results in reduced expression of ...
Designed by CPG Corporation, with Skidmore, Owings and Merrill designing the roof feature and interior design by Woodhead, ... Provisions will also be made on the Cross Island MRT line for a possible extension towards the airport. More details will be ... "First phase of Cross Island Line to open by 2029 with 12 stations". 25 January 2019. Retrieved 26 May 2019. "Changi ... Singapore Changi Airport was developed on reclaimed land on the eastern tip of the island. As the country's primary ...
"What the Fastest-Growing CPG Companies Do Differently". bcg.com. Retrieved 2019-03-01. "Inspired by Musical Films, the Fall ... Some foreign conservationists criticize the Resnicks for "hogging the archipelago's precious water supply... while island ...
"A novel homeodomain-encoding gene is associated with a large CpG island interrupted by the myotonic dystrophy unstable (CTG)n ...
... promoter and its 5′-upstream CpG island are methylated in a number of cancers. An inverse correlation between TMEFF2 ...
August 2003). "Association of the CpG island methylator phenotype with family history of cancer in patients with colorectal ...
Braastad CD, Leguia M, Hendrickson EA (2002). "Ku86 autoantigen related protein-1 transcription initiates from a CpG island and ...
Confounding by repetitive elements and CpG islands does not explain the association between hypomethylation and genomic ... Confounding by repetitive elements and CpG islands does not explain the association between hypomethylation and genomic ...
MORF and MOZ acetyltransferases target unmethylated CpG islands through the winged helix domain Dustin C Becht # 1 , Brianna J ... The CpG sequence in the SAMD1-DNA structure is colored green, and the CpG sequence (C22, G23 in a, b) in NCP is colored red. d ... MORF and MOZ acetyltransferases target unmethylated CpG islands through the winged helix domain Dustin C Becht et al. Nat ... The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain. Weber LM, ...
We observed a significant difference in the incidence of CpG island methylator phenotype between UC-Cs and S-CRCs (8 of 48 [17 ... Rare CpG island methylator phenotype in ulcerative colitis-associated neoplasias.. Rare CpG island methylator phenotype in ...
CpG Islands. CpG Islands (Islands < 300 Bases are Light Green). Unmasked CpG CpG Islands on All Sequence (Islands < 300 Bases ... CpG Islands (Islands < 300 Bases are Light Green) Track collection: CpG Islands (Islands < 300 Bases are Light Green) ... The CpG count is the number of CG dinucleotides in the island. The Percentage CpG is the ratio of CpG nucleotide bases (twice ... CpG islands are associated with genes, particularly housekeeping genes, in vertebrates. CpG islands are typically common near ...
CpG islands (CGIs) are associated with most mammalian gene promoters. A subset of CGIs act as polycomb response elements (PREs ... CpG islands (CGIs) are associated with most mammalian gene promoters. A subset of CGIs act as polycomb response elements (PREs ... KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. ... Chicken, Chromatin, CpG island, Demethylase, Epigenetics, Human, Methylation, Mouse, Transcription, Xenopus, Zebrafish, Animals ...
Investigating CpG Islands in Mammalian Genomes 7R03LM009598-02 Vanderbilt University. Top. National Centers for Biomedical ...
Here, we demonstrate that DNA methylation of promoter-associated CpG islands (CGIs) can be transmitted from parents to their ... Transgenerational inheritance of acquired epigenetic signatures at CpG islands in mice.. Takahashi, Yuta; Morales Valencia, ... Metilação de DNA Epigênese Genética Camundongos Humanos Animais Ilhas de CpG Padrões de Herança Mamíferos/genética ...
CpG Islands. hide. show. ENC+EPD Enhc-Gene. hide. dense. squish. pack. full. ENCODE Regulation. hide. show. EPDnew Promoters. ...
CpG Islands. hide. show. ENC Chromatin. hide. show. ENC DNA Methyl. hide. show. ENC DNase/FAIRE. hide. show. ...
Some studies implicate Fusobacterium in certain epigenetic changes of CRC, such as CpG island methylation phenotype (CIMP), MSI ... Fusobacterium detected in colorectal cancer tissues was related to CpG island methylator phenotype (CIMP) status, high MSI and ... The high level of methylation of CpG island indicates chronic inflammation and an aggravated immune response (99). ... CIMP is characterized by simultaneous hypermethylation of numerous CpG islands surrounding the promoter regions of several ...
involved_in negative regulation of gene expression via CpG island methylation IMP Inferred from Mutant Phenotype. more info ...
CpG islands,. *. genes. : genes,. *. meth. : methylation for CpG sites from WGBS,. *. rpkm. : gene expression from RNASeq. ... Also we downsampled 100000 CpG sites for methylation data.. We first visualize how H3K4me3 histone modification is enriched ...
MeSH Terms: Adult; Aged; Carcinoma, Squamous Cell/epidemiology; Carcinoma, Squamous Cell/genetics*; CpG Islands; DNA ... First, a methylation score, the sum of individual hypermethylated tumor suppressor associated CpG sites, was calculated and ... using linear modeling with empirical Bayesian variance estimation were conducted to identify if methylation at individual CpG ...
CpG Islands* Actions. * Search in PubMed * Search in MeSH * Add to Search ...
CpG islands--a rough guide.. Illingworth RS; Bird AP. FEBS Lett; 2009 Jun; 583(11):1713-20. PubMed ID: 19376112. [TBL] ... Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes.. Jiang C; Han L; Su B; Li WH; ... Isolation and enrichment of human genomic CpG islands by methylation-sensitive mirror orientation selection.. Huang Q; Baum L; ... 1. Silencing of Peroxiredoxin 2 and aberrant methylation of 33 CpG islands in putative promoter regions in human malignant ...
Another major force forming CpG islands is biased gene conversion that stabilizes constitutively methylated CpG islands by ... Currently, CpG islands are defined based on their genomic sequences alone. Here, we develop evolutionary models to show that ... Mammalian CpG islands are key epigenomic elements that were first characterized experimentally as genomic fractions with low ... Primate CpG Islands Are Maintained by Heterogeneous Evolutionary Regimes Involving Minimal Selection ...
Number of protein-coding genes, lncRNA, and CpG islands in each interval shown in bottom. b Average mRNA expression (log2(TPM ... Then the fold enrichment of each chromatin state for each external gene element (e.g., exon, CpG islands) was calculated by (C/ ... e Average enrichment of chromatin states for genomic annotations, including CpG islands, genes, TSS/TES_1K (±1 kb around TSS ... and CpG islands for each 2 Mb fragment by BEDTools70 (v.2.29.2). We also calculated the average TPM and average methylation ...
Trinucleotide repeat amplification and hypermethylation of a CpG island in FRAXE mental retardation. Cell. 1993 Jul 16;74(1): ...
... a CpG site located within a promoter-associated CpG island upstream of ATG7. Although methylation at this site was negatively ... B Location of the CpG site cg03800765 in a CpG island adjacent to the ATG7 gene, demonstrating overlap with the CREB1 motif ( ... D proportional distribution of CpG Island-associated DMPs. E Heatmap and hierarchical clustering of DMPs according to each ... D proportional distribution of CpG Island-associated DMPs. E Heatmap and hierarchical clustering of DMPs according to each ...
CpG islands recruit a histone H3 lysine 36 demethylase. Mol Cell 2010; 38:179-90. PubMed ...
Genome-scale anaylsis of DNA methylation in CpG Islands with bisulfite sequencing. ...
CpG Islands on All Sequence (Islands < 300 Bases are Light Green). CpG Islands. hide. dense. squish. pack. full. CpG Islands ( ... CpG Islands. hide. show. CpG Islands (Islands < 300 Bases are Light Green). ... Islands < 300 Bases are Light Green). GeneHancer. hide. dense. squish. pack. full. GeneHancer Regulatory Elements and Gene ...
CpG island 363. MGI feature type. CpG island. MGI marker type. Other Genome Feature. ...
Maybe by methylation of the CpG islands in their promoter regions. Or by some histone code. The simple truth is that, at the ...
CpG islands) that impact chromatin structure and modify the ability of a gene to be regulated epigenetically. Investigations ...
  • Here, we demonstrate that DNA methylation of promoter-associated CpG islands (CGIs) can be transmitted from parents to their offspring in mice . (bvsalud.org)
  • Also we downsampled 100000 CpG sites for methylation data. (bioconductor.org)
  • First, a methylation score, the sum of individual hypermethylated tumor suppressor associated CpG sites, was calculated and associated with dietary intake of micronutrients involved in one-carbon metabolism and antioxidant activity, and food groups abundant in these nutrients. (nih.gov)
  • Second, gene specific analyses using linear modeling with empirical Bayesian variance estimation were conducted to identify if methylation at individual CpG sites was associated with diet. (nih.gov)
  • 1. Silencing of Peroxiredoxin 2 and aberrant methylation of 33 CpG islands in putative promoter regions in human malignant melanomas. (nih.gov)
  • 8. Genome-wide profiling of CpG methylation identifies novel targets of aberrant hypermethylation in myeloid leukemia. (nih.gov)
  • 9. Larger numbers of silenced genes in cancer cell lines with increased de novo methylation of scattered CpG sites. (nih.gov)
  • 15. Regulation of human endogenous retrovirus-K expression in melanomas by CpG methylation. (nih.gov)
  • 18. Isolation and enrichment of human genomic CpG islands by methylation-sensitive mirror orientation selection. (nih.gov)
  • To complicate matters, scientists have long believed that methylation could only silence genes at sites in the genome where CG sequences are highly concentrated, regions known as "CpG islands. (goodnewsnetwork.org)
  • Since nearly a third of human genes lack CpG islands, the researchers assumed methylation wouldn't switch these genes off. (goodnewsnetwork.org)
  • Actually DNA methylation is the covalent addition of a methyl group to the 5 position of cytosine within CpG dinucleotides and is a fundamental process that not only modulates gene expression, but is also key to regulating chromosomal stability. (nih.gov)
  • Local CpG density may determine their complementary binding patterns and therefore that the methylation landscape is encoded in the DNA sequence. (biomedcentral.com)
  • We found that the expression of Ard1b in mouse spermatogenic cells and tissues correlated with the CpG island methylation pattern of the gene. (nih.gov)
  • Our data suggest that the regulatory mechanism of the transcription of Ard1b/ARD1B is evolutionarily conserved and involves CpG island methylation. (nih.gov)
  • Therefore, we determined the percent methylation for CpG islands from DNA extracted from mononuclear blood cells of 24 male spray-painters exposed to 1,6-hexamethylene diisocyanate (HDI) monomer and HDI isocyanurate. (cdc.gov)
  • CpG islands are associated with genes, particularly housekeeping genes, in vertebrates. (ucsc.edu)
  • Rare CpG island methylator phenotype in ulcerative colitis-associated neoplasias. (nih.gov)
  • 6. Identification of genes targeted by CpG island methylator phenotype in neuroblastomas, and their possible integrative involvement in poor prognosis. (nih.gov)
  • 16. The CpG island methylator phenotype: what's in a name? (nih.gov)
  • Trinucleotide repeat amplification and hypermethylation of a CpG island in FRAXE mental retardation. (medlineplus.gov)
  • CpG islands hypermethylation in the promoter regions of genes- as pejorative prognostic markers in adrenocortical cancer (ACC). (endocrine-abstracts.org)
  • Abstract: DESCRIPTION (provided by applicant): Hypermethylation of promoter CpG islands is an important mechanism to silence the expression of many tumor suppressors, DNA repair, and other genes in cancer. (nih.gov)
  • To quantify the demethylation and reactivation of hypermethylation-silenced genes (MSGs) such as RARbeta, p16, MGMT, and hMLH1 by EGCG, characterize the pattern of CpG demethylation, and determine the sustainability of the reactivated gene expression. (nih.gov)
  • CpG islands (CGIs) are associated with most mammalian gene promoters. (ox.ac.uk)
  • The CpG count is the number of CG dinucleotides in the island. (ucsc.edu)
  • A variety of regulatory proteins including DNA methyltransferases, methyl-CpG binding proteins, histone- modifying enzymes, chromatin remodeling factors, and their multimolecular complexes are involved in the overall epigenetic process. (nih.gov)
  • Normally a C (cytosine) base followed immediately by a G (guanine) base (a CpG) is rare in vertebrate DNA because the Cs in such an arrangement tend to be methylated. (ucsc.edu)
  • Transgenerational inheritance of acquired epigenetic signatures at CpG islands in mice. (bvsalud.org)
  • CpG islands are typically common near transcription start sites and may be associated with promoter regions. (ucsc.edu)
  • CpG islands are regions where CpGs are present at significantly higher levels than is typical for the genome as a whole. (ucsc.edu)
  • The entire genome sequence, masking areas included, was used for the construction of the track Unmasked CpG . (ucsc.edu)
  • In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. (nih.gov)
  • 3. Identification of 27 5' CpG islands aberrantly methylated and 13 genes silenced in human pancreatic cancers. (nih.gov)
  • 12. Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes. (nih.gov)
  • The unmasked version of the track displays potential CpG islands that exist in repeat regions and would otherwise not be visible in the repeat masked version. (ucsc.edu)
  • CpG islands and its associated tables can be explored interactively using the REST API , the Table Browser or the Data Integrator . (ucsc.edu)
  • The source for the cpg_lh program can be obtained from src/utils/cpgIslandExt/ . (ucsc.edu)
  • CpG islands were predicted by searching the sequence one base at a time, scoring each dinucleotide (+17 for CG and -1 for others) and identifying maximally scoring segments. (ucsc.edu)
  • Rare CpG island methylator phenotype in ulcerative colitis-associated neoplasias. (nih.gov)
  • CpG island methylator phenotype in plasma is associated with hepatocellular carcinoma prognosis. (cdc.gov)
  • CpG island methylator phenotype identifies high risk patients among microsatellite stable BRAF mutated colorectal cancers. (cdc.gov)
  • Predictive value of CpG island methylator phenotype for tumor recurrence in hepatitis B virus-associated hepatocellular carcinoma following liver transplantation. (cdc.gov)
  • CpG island methylator phenotype predicts progression of malignant melanoma. (cdc.gov)
  • To determine the methylation profile of multiple tumor-related genes during multistep hepatocarcinogenesis, we investigated the methylation status of CpG islands of 9 genes, using methylation-specific polymerase chain reaction for 60 paired hepatocellular carcinoma (HCC) and non-HCC liver tissue samples, 22 dysplastic nodule (DN), 30 liver cirrhosis (LC), 34 chronic hepatitis (CH) and 20 normal liver samples. (nih.gov)
  • First, a methylation score, the sum of individual hypermethylated tumor suppressor associated CpG sites, was calculated and associated with dietary intake of micronutrients involved in one-carbon metabolism and antioxidant activity, and food groups abundant in these nutrients. (nih.gov)
  • Second, gene specific analyses using linear modeling with empirical Bayesian variance estimation were conducted to identify if methylation at individual CpG sites was associated with diet. (nih.gov)
  • Methylation changes were prominent in a 500 bp non-CpG island-like region of the Ha- ras promoter and less prominent in a 525 bp CpG island-like region. (cdc.gov)
  • Methylation of the CpG sites only on the sense strand of the APC gene is specific for hepatocellular carcinoma. (cdc.gov)
  • Aberrant CpG island hypermethylation in dysplastic nodules and early HCC of hepatitis B virus-related human multistep hepatocarcinogenesis. (cdc.gov)