Cpg islands. Medical search

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)

CpG islands[edit]. In mammals, the only exception for this global CpG depletion resides in a specific category of GC- and CpG- ... Reciprocally, around 60-70% of human genes have a CpG island in their promoter region.[21][22] The majority of CpG islands are ... In mouse and human, around 60-70% of genes have a CpG island in their promoter region and most of these CpG islands remain ... rich sequences termed CpG islands that are generally unmethylated and therefore retained the expected CpG content.[19] CpG ...

https://en.wikipedia.org/wiki/DNA_methylation?wprov=sfti1

"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 ...

https://en.wikipedia.org/wiki/C7orf50

"Predicting aberrant CpG island methylation". Proceedings of the National Academy of Sciences. 100 (21): 12253-12258. doi: ...

https://en.wikipedia.org/wiki/Eva_K._Lee

... 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. ...

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

"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 ...

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

... 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 ...

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

... 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 ...

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

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". ...

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

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 ...

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

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 ... "CpG island methylator phenotype in colorectal cancer". Proc. Natl. Acad. Sci. U.S.A. 96: 8681-6. doi:10.1073/pnas.96.15.8681. ...

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

... has one CpG island within the promoter. SMIM15 has lower levels of H3K4Me1 but higher levels of H3K4Me3 and H3K27Ac ...

https://en.wikipedia.org/wiki/SMIM15

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 ...

https://en.wikipedia.org/wiki/5-Methylcytosine

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". ...

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

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 ...

https://en.wikipedia.org/wiki/KDM2A

January 2006). "De novo CpG island methylation in human cancer cells". Cancer Research. 66 (2): 682-92. doi:10.1158/0008-5472. ... DNMT3a prefers CpG methylation to CpA, CpT, and CpC methylation, though there appears to be some sequence preference of ... DNMT3a methylates CpG sites at a rate much slower than DNMT1, but greater than DNMT3b. DNMT3L contains DNA methyltransferase ... The recognition motif for the human enzyme involves only three of the bases in the CpG dinucleotide pair: a C on one strand and ...

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

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 ...

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

In particular, he has focused on understanding how DNA encoded regulatory elements in vertebrates, called CpG islands, help to ... CS1 maint: discouraged parameter (link) Klose, Rob (2010). "CpG islands recruit a histone H3 lysine 36 demethylase". Mol. Cell ... Klose, Rob (2013). "ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection". Biochem Soc Trans. 41 (3): ... Sir Adrian Bird at the Wellcome Centre for Cell Biology at the University of Edinburgh, Scotland, he studied the methyl CpG ...

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

Blackledge NP, Zhou JC, Tolstorukov MY, Farcas AM, Park PJ, Klose RJ (Apr 2010). "CpG islands recruit a histone H3 lysine 36 ... In many eukaryotes, the KDM2A protein contains a CXXC zinc finger domain capable of binding unmethylated CpG islands. It is ...

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

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 ...

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

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. ...

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

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: ...

https://en.wikipedia.org/wiki/P3_protein

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 ...

https://en.wikipedia.org/wiki/DNMT1

Cross SH, Charlton JA, Nan X, Bird AP (1994). "Purification of CpG islands using a methylated DNA binding column". Nat. Genet. ...

https://en.wikipedia.org/wiki/60S_ribosomal_protein_L24

"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 ...

https://en.wikipedia.org/wiki/COX7A2L

Cross SH, Charlton JA, Nan X, Bird AP (1994). "Purification of CpG islands using a methylated DNA binding column". Nat. Genet. ...

https://en.wikipedia.org/wiki/FKBP3

Aïssani B, Bernardi G (October 1991). "CpG islands, genes and isochores in the genomes of vertebrates". Gene. 106 (2): 185-95. ...

https://en.wikipedia.org/wiki/GC-content

Cross SH, Charlton JA, Nan X, Bird AP (March 1994). "Purification of CpG islands using a methylated DNA binding column". Nature ...

https://en.wikipedia.org/wiki/PAX7

"Purification of CpG islands using a methylated DNA binding column". Nat. Genet. 6 (3): 236-44. doi:10.1038/ng0394-236. PMID ...

https://en.wikipedia.org/wiki/PCDH10

Cross SH, Charlton JA, Nan X, Bird AP (Mar 1994). "Purification of CpG islands using a methylated DNA binding column". Nature ...

https://en.wikipedia.org/wiki/Vasopressin_receptor_1A

The Kuomintang had no choice but to leave mainland China and relocate to the island of Taiwan in 1945 from Japan, then fled ... Office for Safeguarding National Security of the CPG in the HKSAR. *Urban Management (chengguan) ...

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

2010). "Human testis-specific PDHA2 gene: methylation status of a CpG island in the open reading frame correlates with ...

https://en.m.wikipedia.org/wiki/Pyruvate_dehydrogenase_

A cluster of CpG dinucleotides clustered together is called a CpG island, and in mammals, these CpG islands are one of the ... Methylation of CpG dinucleotides and/or islands within gene promoters is associated with transcriptional repression via ... Hypothetically, global hypomethylation should be associated with global increases in transcription, since CpG islands are most ... a CpG transformation technique which is sensitive to CpG methylation status, in which global hypomethylation has been observed. ...

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

CpG sites are frequently mutated and become rare in the genome, except at CpG islands where they remain unmethylated. ... Transcription from methylated CpG islands is strongly and heritably repressed.[69] Other miRNAs are epigenetically regulated by ... About 50% of miRNA genes are associated with CpG islands,[64] that may be repressed by epigenetic methylation. ... "Role of nucleosomal occupancy in the epigenetic silencing of the MLH1 CpG island". Cancer Cell. 12 (5): 432-44. PMC 4657456 . ...

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

This method leverages the tendency of methylated cytosines to cluster at CpG islands (CGIs) to enrich for areas of the genome ... of CpG sites in the entire genome.[34] In single cells, 40% of the CpG sites from the bulk sample are detected. To increase ... When RRBS is applied to bulk samples, majority of the CpG sites in gene promoters are detected, but site in gene promoters only ... In a sample of 20 pooled single cells, 63% of the CpG sites from the bulk sample were detected. Pooling single cells is one ...

https://en.wikipedia.org/wiki/Single_cell_sequencing?source=post_page---------------------------

Strand Breaks Can Initiate Gene Silencing and SIRT1-Dependent Onset of DNA Methylation in an Exogenous Promoter CpG Island". ...

https://en.wikipedia.org/wiki/Non-small-cell_lung_carcinoma

CpG islands (or CG islands) are regions with a high frequency of CpG sites. Though objective definitions for CpG islands are ... "CpG island shores") rather than in the islands themselves.[12]. CpG islands typically occur at or near the transcription start ... CpG islands[edit]. How methylation of CpG sites followed by spontaneous deamination leads to a lack of CpG sites in methylated ... Unlike CpG sites in the coding region of a gene, in most instances the CpG sites in the CpG islands of promoters are ...

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

hypomethylation of CpG island. • positive regulation of peptidyl-serine phosphorylation. • platelet activation. • Fc-epsilon ...

https://en.wikipedia.org/wiki/PIK3CA

... strand breaks can initiate gene silencing and SIRT1-dependent onset of DNA methylation in an exogenous promoter CpG island". ...

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

Graff JR, Gabrielson E, Fujii H, Baylin SB, Herman JG (January 2000). "Methylation patterns of the E-cadherin 5' CpG island are ... The methylation patterns of the E-cadherin 5' CpG island are not stable. During metastatic progression of many cases of ...

https://en.wikipedia.org/wiki/CDH1_

... strand breaks can initiate gene silencing and SIRT1-dependent onset of DNA methylation in an exogenous promoter CpG island»։ ...

https://hy.wikipedia.org/wiki/Քաղցկեղ

... alterations in cancers that change gene expression levels include direct hypermethylation or hypomethylation of CpG islands of ...

https://en.m.wikipedia.org/wiki/Colon_cancer

Aïssani B, Bernardi G (1991). "CpG islands, genes and isochores in the genomes of vertebrates". Gene 106 (2): 185-95. PMID ...

https://gl.m.wikipedia.org/wiki/Contido_GC

Jan 2000). "Methylation patterns of the E-cadherin 5' CpG island are unstable and reflect the dynamic, heterogeneous loss of E- ... Os patróns de metilación da illa 5' CpG da E-cadherina non son estables. Durante a progresión da metástase de moitos casos de ...

https://gl.wikipedia.org/wiki/E-cadherina

"R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters". Molecular Cell. 45 (6): 814-25. ...

https://en.wikipedia.org/wiki/R-loop

Alabat Island Agta'}, ['dum'] = {'Middle Dutch (ca. 1050-1350)'}, ['dun'] = {'Dusun Deyah'}, ['duo'] = {'Dupaninan Agta'}, [' ... cpg'] = {'Cappadocian Greek'}, ['cpi'] = {'Chinese Pidgin English'}, ['cpn'] = {'Cherepon'}, ['cpo'] = {'Kpeego'}, ['cps'] = {' ... Solomon Islands)'}, ['mtf'] = {'Murik (Papua New Guinea)'}, ['mtg'] = {'Una'}, ['mth'] = {'Munggui'}, ['mti'] = {'Maiwa (Papua ... Solomon Islands Sign Language'}, ['szv'] = {'Isu (Fako Division)'}, ['szw'] = {'Sawai'}, ['taa'] = {'Lower Tanana'}, ['tab ...

https://arz.wikipedia.org/wiki/وحدة:Language/data/ISO_639-3

Distal promoters also frequently contain CpG islands, such as the promoter of the DNA repair gene ERCC1, where the CpG island- ... contain a CpG island.[27][28] CpG islands are generally 200 to 2000 base pairs long, have a C:G base pair content ,50%, and ... The presence of multiple methylated CpG sites in CpG islands of promoters causes stable silencing of genes.[30] Silencing of a ... but this is often followed by methylation of CpG sites in the promoter CpG island to cause the stable silencing of the gene.[30 ...

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

Two PCRs are then carried out on the modified DNA, using primer sets identical except at any CpG islands within the primer ... a novel PCR assay for methylation status of CpG islands". Proc Natl Acad Sci USA. 93 (13): 9821-9826. Bibcode:1996PNAS... ... and is used to detect methylation of CpG islands in genomic DNA. DNA is first treated with sodium bisulfite, which converts ...

https://en.m.wikipedia.org/wiki/Polymerase_chain_reaction

600 to 800 somatically heritable heavily methylated CpG islands in promoters of genes in the tumors while these CpG islands are ... CpG islands keep their overall un-methylated state (or methylated state) extremely stably through multiple cell generations.[62 ... "Orphan CpG islands identify numerous conserved promoters in the mammalian genome". PLoS Genet. 6 (9): e1001134. doi:10.1371/ ... caused by somatically heritable promoter hypermethylation of CpG islands) than by mutations. As Vogelstein et al. point out, in ...

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

Epimutations include methylations or demethylations of the CpG islands of the promoter regions of genes, which result in ... strand breaks can initiate gene silencing and SIRT1-dependent onset of DNA methylation in an exogenous promoter CpG island". ...

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

... the majority of gene promoters contain a CpG island with numerous CpG sites.[4] When many of a gene's promoter CpG sites are ... For example, in colorectal cancers about 600 to 800 genes are transcriptionally silenced by CpG island methylation (see ... "CpG islands" when densely clustered). Analysis of the pattern of methylation in a given region of DNA (which can be a promoter ... more than 18,000 CpG sites (of the roughly 450,000 analyzed CpG sites in the genome) had frequently altered methylation among ...

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

Ionian Islands (Corfu, Ithaca, Kefalonia, Kythira, Lefkada, Paxi, Zakynthos). *Macedonia (Chalkidiki, Drama, Florina, Grevena, ... cpg. - Cappadocian Greek. gmy. - Mycenaean Greek. pnt. - Pontic. tsd. - Tsakonian. yej. - Yevanic. ... North Aegean islands (Chios, Ikaria, Lemnos, Lesbos, Samos). *Peloponnese (Arcadia, Argolis, Corinthia, Laconia, Messenia, ... Central Greece (Aetolia-Acarnania (Aetolia, Acarnania), Attica, Boeotia, Euboea, Evrytania, Phocis, Phthiotis, Saronic Islands) ...

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

1949 (of CPG). 1954 (of PRC) Wang Yi. 王毅. State Councilor and Minister of Foreign Affairs CPC General Secretary Xi Jinping ( ... 1949 (of CPG) Fu Zhenghua. 傅政华. Minister of Justice CPC Guo Shengkun (Secretary of the CPC Central Political and Legal Affairs ... 1949 (of CPG). 1954 (of PRC) Police Commissioner-General [zh]. Zhao Kezhi. 赵克志. State Councilor and Minister of Public Security ... 1949 (of CPG). 1954 (of PRC) E Jingping. 鄂竟平. Minister of Water Resources CPC Vice-Premier Hu Chunhua ...

https://en.wikipedia.org/wiki/State_Council_of_the_People's_Republic_of_China

... the majority of gene promoters contain a CpG island with numerous CpG sites.[16] When many of a gene's promoter CpG sites are ... For example, in colorectal cancers about 600 to 800 genes are transcriptionally inhibited by CpG island methylation (see ... "A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters". Proceedings ...

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

"Promoter CpG island hypermethylation of the DNA repair enzyme MGMT predicts clinical response to dacarbazine in a phase II ... strand breaks can initiate gene silencing and SIRT1-dependent onset of DNA methylation in an exogenous promoter CpG island". ...

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

Cross SH, Charlton JA, Nan X, Bird AP (1994). "Purification of CpG islands using a methylated DNA binding column.". Nat. Genet. ...

https://sh.wikipedia.org/wiki/Arginin_vazopresinski_receptor_1A

"The nucleotide sequence of a CpG island demonstrates the presence of the first exon of the gene encoding the human lysosomal ...

https://en.wikipedia.org/wiki/LAMP2

"Hypomethylation of CD30 CpG islands with aberrant JunB expression drives CD30 induction in Hodgkin lymphoma and anaplastic ...

https://en.wikipedia.org/wiki/Anaplastic_large-cell_lymphoma

... volume examines bioinformatic and molecular biological methods useful to identify and to explore the functions of CpG islands, ... Prediction of CpG Islands as an Intrinsic Clustering Property Found in Many Eukaryotic DNA Sequences and Its Relation to DNA ... Authoritative and practical, CpG Islands: Methods and Protocols aims to provide readers with the information and methodologies ... Methods for the Measurement of DNA Methylation at CpG Islands. * Front Matter Pages 81-81 ...

https://link.springer.com/book/10.1007/978-1-4939-7768-0

G/C boxes were found to be rare in CpG-depleted DNA and plentiful in CpG islands, where they occurred in 3 CpG islands, as ... Two theories for the maintenance of a high frequency of CpG dinucleotides in CpG islands were tested: that CpG islands in ... CpG islands, separated by several thousand base-pairs of CpG-depleted DNA. The 5 CpG islands extended through 5-flanking DNA ... In this study, a large number of sequences of vertebrate genes were screened for the presence of CpG islands. Each CpG island ...

https://www.ncbi.nlm.nih.gov/pubmed/3656447?dopt=Abstract

... for CpG islands with a GC content greater than 50% and a CpGobserved/CpGexpected ratio greater than 60%. ... CpG islands greater than the minimum island size, and all potential CpG islands for the specified criteria. Choices are true. ... CpG islands greater than the minimum island size, and all potential CpG islands for the specified criteria. Choices are true. ... a MATLAB structure containing the starting and ending bases of the CpG islands greater than the minimum island size of 200. ...

https://www.mathworks.com/help/bioinfo/ref/cpgisland.html

... called CpG island methylator prototype, or CIMP. Higher levels of CpG island hypermethylation are found in CIMP. The frequent ... 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 ... Hypermethylated CpG islands also act as biomarkers, as they can help distinguish cancer from normal cells in the same sample. ...

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

CpG Islands (Islands < 300 Bases are Light Green) (. CpG Islands). This track is part of a parent called CpG Islands. To show ... 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 are regions where CpGs are present at significantly higher levels than is typical for the genome as a whole. ...

http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=816211363_A13xicmdxxUhehANrB9yesdQGBwl&c=chr4&g=cpgIslandExt

CpG islands are short, dispersed regions of unmethylated DNA with a high frequency of CpG dinucleotides relative to the bulk ... CpG islands as gene markers in the human genome.. Larsen F1, Gundersen G, Lopez R, Prydz H. ... We have analyzed 375 genes and 58 pseudogenes from the human entries in the EMBL Database for the presence of CpG islands. All ... More than half of the genes analyzed were associated with islands. All housekeeping and widely expressed genes have a CpG ...

https://www.ncbi.nlm.nih.gov/pubmed/1505946?dopt=Abstract

Combining the number of CpG islands with the proportion of island-associated genes, we estimate that the total number of genes ... Number of CpG islands and genes in human and mouse. F Antequera and A Bird ... Analysis of a selection of genes suggests that both human and mouse are losing CpG islands over evolutionary time due to de ... Our results suggest that there are approximately 45,000 CpG islands per haploid genome in humans and 37,000 in the mouse. ...

https://www.pnas.org/content/90/24/11995?ijkey=d22df8a6bda9e658b9878f7399dc33bd4dca2cf6&keytype2=tf_ipsecsha

CpG islands are usually unmethylated in a genome, especially in the promoter regions [2], in contrast, ~80% of CpG ... There has been much interest in CpG islands (CGIs), clusters of CpG dinucleotides in GC-rich regions, because they are ... F. Antequera and A. P. Bird, "Number of CpG islands and genes in human and mouse," Proceedings of the National Academy of ... CpG islands in this table were identified by Takai and Jones algorithm [7]. The number of genes in each fish genome was based ...

https://www.hindawi.com/journals/ijg/2008/565631/

CpG Islands CpG Islands (Islands < 300 Bases are Light Green) hide. dense. squish. pack. full. Unmasked CpG CpG Islands on All ... 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 (Islands < 300 Bases are Light Green) Tracks (. All Regulation tracks). Display mode: hide. show. All. ...

https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=793711277_fZfHhTdXuIBazZK9cCRWxHjLUcoR&c=chr5&g=cpgIslandSuper

Methylated CpG dinucleotides at position 5 of cytosine are associated with transcriptional repression and an inactive chromatin ... Figure 3. Chromatin structure of CpG islands. The distribution of methylated and nonmethylated CpG dinucleotides is shown at ... 2010) CpG islands influence chromatin structure via the CpG‐binding protein Cfp1. Nature 464: 1082-1086. ... genes are associated with CpG islands, as is clearly shown by the high density of CpG dinucleotides around their 5′ ends. In ...

http://www.els.net/WileyCDA/ElsArticle/refId-a0005027.html

CpG island, DNA hypermethylation and restored GSTP1 expression. Using a PCR assay, somatic GSTP1 ,CpG island, DNA ... GSTP1 CpG island DNA hypermethylation in hepatocellular carcinomas Int J Oncol. 2000 Apr;16(4):663-76. doi: 10.3892/ijo.16.4. ... GSTP1 ,CpG island, DNA hypermethylation in HCC DNA was assessed by Southern blot analysis, via a polymerase chain reaction (PCR ... The data indicate that GSTP1 ,CpG island, DNA hypermethylation changes appear frequently in human HCC. In addition, the data ...

https://pubmed.ncbi.nlm.nih.gov/10717233/?dopt=Abstract

... mechanism for carcinogenesis in colorectal carcinomas and adenomas characterized by methylation of multiple CpG islands. The ... The CpG island methylator phenotype (CIMP) is a newly described ... Concordant CpG island methylation in hyperplastic polyposis Am ... The CpG island methylator phenotype (CIMP) is a newly described mechanism for carcinogenesis in colorectal carcinomas and ... Our findings of concordant CpG island methylation of HPs in multiple/large HPs or hyperplastic polyposis supports the concept ...

https://pubmed.ncbi.nlm.nih.gov/11839573/?dopt=Abstract

... which can rapidly assess the methylation status of virtually any group of CpG sites within a CpG island, independent of the use ... Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. J G Herman, J R Graff, S Myöhänen, B D ... MSP requires only small quantities of DNA, is sensitive to 0.1% methylated alleles of a given CpG island locus, and can be ... Precise mapping of DNA methylation patterns in CpG islands has become essential for understanding diverse biological processes ...

https://www.pnas.org/content/93/18/9821?ijkey=84270cf4cdb27845520a84defc8a7c109e60e523&keytype2=tf_ipsecsha

Functional Relevance of CpG Island Length for Regulation of Gene Expression Message Subject (Your Name) has forwarded a page to ... Functional Relevance of CpG Island Length for Regulation of Gene Expression. Navin Elango and Soojin V. Yi ... Functional Relevance of CpG Island Length for Regulation of Gene Expression. Navin Elango and Soojin V. Yi ... Functional Relevance of CpG Island Length for Regulation of Gene Expression. Navin Elango and Soojin V. Yi ...

http://www.genetics.org/content/187/4/1077.supplemental

To investigate the association between CpG island methylator phenotype (CIMP) and the overall survival of sporadic colorectal ... The CpG island methylation phenotype (CIMP), characterized by the extensive hypermethylation of multiple gene CpG islands, was ... "CpG island methylator phenotype-low (CIMP-low) colorectal cancer shows not only few methylated CIMP-high-specific CpG islands, ... "CpG island methylator phenotype in colorectal cancers: comparison of the new and classic CPG island methylator phenotype marker ...

https://www.hindawi.com/journals/bmri/2014/236361/

this methylation at CpG islands thats found in cancer.. So this is, tends to be called CpG island hypermethylation, or CGI ... CPG island, so you dont see methylation in general at CPG islands. ... 7.2 Hypermethylation of CpG islands in cancer. To view this video please enable JavaScript, and consider upgrading to a web ... CpG island spread throughout the genome in general are hypomethylated.. And so whats unusual to find is one thats ...

https://www.coursera.org/learn/epigenetics/lecture/AnWDn/7-2-hypermethylation-of-cpg-islands-in-cancer

2) ⇓ . The CpG island at MGMT was methylated in a single case of the primary prostate cancers (1%; Fig. 2C ⇓ ). CpG islands at ... In this study, by using a Kaplan-Meier analysis, we found that of all of the CpG islands tested, only PTGS2 CpG island ... A, NIM at 16 CpG islands for normal prostate tissues taken from 13 transplant tissue donors. B, NIM at 16 CpG islands for tumor ... For instance, hypermethylation at the GSTP1 CpG island in combination with hypermethylation at the MDR1 CpG island yields a ...

http://cancerres.aacrjournals.org/content/64/6/1975

The effect of CpG islands on transgene expression was first tested in cultured cells. In transient transfection it was ... Transgenic mice were used to study the effect of CpG islands on the level and pattern of transgene expression in vivo. ... Even when integrated into the genome of cultured cells, CpG islands are not able to confer position-independent, copy number- ... However, the results from bulk analysis of primary clones suggest that CpG islands improve the level of expression in cultured ...

http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.654021

Abstract 5004: CpG island methylator phenotype in bladder cancer. Woonbok Chung, Jolanta Bondaruk, Nianxiang Zhang, Jaroslav ... Abstract 5004: CpG island methylator phenotype in bladder cancer. Woonbok Chung, Jolanta Bondaruk, Nianxiang Zhang, Jaroslav ... Abstract 5004: CpG island methylator phenotype in bladder cancer. Woonbok Chung, Jolanta Bondaruk, Nianxiang Zhang, Jaroslav ... Abstract 5004: CpG island methylator phenotype in bladder cancer Message Subject (Your Name) has forwarded a page to you from ...

http://cancerres.aacrjournals.org/content/72/8_Supplement/5004

C in CpG islands that were methylated remains unaffected. Asterisks show two CpG islands not methylated. ... CpG Island Methylation in Sporadic and Neurofibromatis Type 2-Associated Schwannomas. Pilar Gonzalez-Gomez, M. Josefa Bello, M ... CpG Island Methylation in Sporadic and Neurofibromatis Type 2-Associated Schwannomas. Pilar Gonzalez-Gomez, M. Josefa Bello, M ... CpG Island Methylation in Sporadic and Neurofibromatis Type 2-Associated Schwannomas. Pilar Gonzalez-Gomez, M. Josefa Bello, M ...

http://clincancerres.aacrjournals.org/content/9/15/5601

I use CpG Island Explorer to predicate CpG islands,but in one gene I did not get CpG island in the promoter region adjacent to ... I only get one CpG island about 4kb upstream the ATG codon, does the CpG region could be representative for study? If it is not ... Can these CpG islands be representative? - (Jul/11/2005 ). I get the DNA sequence 5kb upstream from exon1 and exon1 to ... If the CpG island is far away from the promoter or transcriptional start site, it is hard to say whether its methylation has ...

http://www.protocol-online.org/biology-forums/posts/7851.html

Virus-like attachment sites and plastic CpG islands:landmarks of diversity in plant Del retrotransposons.. [Guilherme M Q Cruz ... While some features are common to all Del elements, CpG island patterns within the LTRs were particular to lineage specific ...

https://www.sigmaaldrich.com/catalog/papers/24849372

CpG island coordinates CGIs genomic coordinates were obtained from the UCSC GB CpgIslandExt track. In this track CpG islands ... To estimate the methylation of each CpG island we calculated the mean of all CpGs methylation values into a CpG island. We were ... Additionally, by analyzing SNP frequency in CpG islands, we demonstrated that CpG islands in regions under selective pressure ... Additionally, by analyzing SNP frequency in CpG islands, we demonstrated that CpG islands in regions under selective pressure ...

http://pubmedcentralcanada.ca/pmcc/articles/PMC3149076/?lang=en-ca

... John P. Thomson,1,* Peter J. Skene,1,* Jim ... CpG islands (CGIs) are prominent in the mammalian genome owing to their GC-rich base composition and high density of CpG ... A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol. 2008;6:e22. [PMC free ... Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island. Genes Dev. 1994;8:2282-2292. [ ...

http://pubmedcentralcanada.ca/pmcc/articles/PMC3730110/?lang=en-ca

CpG island 8641. Synonyms: CGI8641. Gene nomenclature, locus information, and GO, OMIM, and PMID associations are updated daily ...

https://www.komp.org/geneinfo.php?geneid=165244

CpG island 899. Synonyms: CGI899. Gene nomenclature, locus information, and GO, OMIM, and PMID associations are updated daily ...

https://www.komp.org/geneinfo.php?geneid=165630

CpG island 8613. Synonyms: CGI8613. Gene nomenclature, locus information, and GO, OMIM, and PMID associations are updated daily ...

https://www.komp.org/geneinfo.php?geneid=165215

Detection of Breast Cancer in Nipple Aspirate Fluid by CpG Island Hypermethylation. Rachel Krassenstein, Edward Sauter, Essel ... Katzenellenbogen R. A., Baylin S. B., Herman J. G. Hypermethylation of the DAP-kinase CpG island is a common alteration in B- ... Dammann R., Yang G., Pfeifer G. P. Hypermethylation of the CpG island of Ras association domain family 1A (RASSF1A), a putative ... Detection of Breast Cancer in Nipple Aspirate Fluid by CpG Island Hypermethylation ...

https://clincancerres.aacrjournals.org/content/10/1/28

... and widespread hypermethylation of CpG islands, especially in the promoters of genes, referred to as the CpG island methylator ... Association of smoking, CpG island methylator phenotype, and V600E BRAF mutations in colon cancer. J Natl Cancer Inst 2006;98: ... CpG island methylator phenotype in colorectal cancer. Proc Natl Acad Sci U S A 1999;96:8681-6. ... Ethnicity and Risk for Colorectal Cancers Showing Somatic BRAF V600E Mutation or CpG Island Methylator Phenotype. Dallas R. ...

http://cebp.aacrjournals.org/content/17/7/1774

... in a setting of widespread promoter CpG island methylation called the CpG island methylator phenotype (CIMP; refs. 26-28). A ... CpG island methylator phenotype, microsatellite instability, BRAF mutation and clinical outcome in colon cancer. Gut 2009;58:90 ... CpG island methylator phenotype-low (CIMP-low) in colorectal cancer: possible associations with male sex and KRAS mutations. J ... The CpG island methylator phenotype in colorectal cancer. J Mol Diagn 2007;9:281-3. ...

http://cebp.aacrjournals.org/content/19/3/822.long

There has been much interest in CpG islands (CGIs), clusters of CpG dinucleotides in GC-rich regions, because they are considered gene markers and involved in gene regulation. (hindawi.com)
CGIs are clusters of CpG dinucleotides in GC-rich regions, usually ~1 kb long [ 1 ]. (hindawi.com)
The mutation rate of the methylated CpG (5mCpG) to TpG was estimated to be ~10-50-folds higher than that of the unmethylated CpG site due to a high rate of deamination at the 5mCpG, which subsequently leads to an overall loss of CpG dinucleotides and a potential loss of CGIs [ 4 , 5 ]. (hindawi.com)
6 ] found an association of DNA methylation in CpG-poor promoters in the germline with an increased loss of CpG dinucleotides, implying that characteristics of the CGIs have been weakened or even vanished in the course of evolution. (hindawi.com)
Those studies revealed that the mouse has undergone a faster CpG loss than the human, thus, has fewer CGIs and weaker CGI characteristics. (hindawi.com)
CGIs represent approximately 1% of the genome, and the large majority of them remain nonmethylated despite their high density of CpG dinucleotides. (els.net)
DNA methylation at CpG islands (CGIs) is one of the most intensively studied epigenetic mechanisms. (pubmedcentralcanada.ca)
These CGIs are enriched at genes, about 60% of all genes in the human genome containing a CpG island upstream [2] . (pubmedcentralcanada.ca)
CpG islands (CGIs) are prominent in the mammalian genome owing to their GC-rich base composition and high density of CpG dinucleotides 1 , 2 . (pubmedcentralcanada.ca)
The data indicate that a primary function of non-methylated CGIs is to genetically influence the local chromatin modification state by interaction with Cfp1 and perhaps other CpG-binding proteins. (pubmedcentralcanada.ca)
To characterize the chromatin modifications typical of CGIs, we used the methyl-CpG-sensitive restriction endonuclease HinPI (cleavage site GCGC) to release small chromatin fragments from purified brain nuclei, as described previously 9 . (pubmedcentralcanada.ca)
CGIs have known functions in the transcription initiation and outstanding compositional features like high G+C content and CpG ratios when compared to the bulk DNA. (springer.com)
In addition, we illustrate how to easily cross the output of a CpG island prediction algorithm with our methylation database to detect differentially methylated CGIs. (springer.com)
CpG islands (CGIs) are associated with most mammalian gene promoters. (elifesciences.org)
CpG islands (CGIs) function as promoters for approximately 60% of human genes. (fpwr.org)
Hypomethylated, CpG-rich DNA segments (CpG islands, CGIs) are epigenome markers involved in key biological processes. (ugr.es)
In particular, histone modifications in CpG islands (CGIs) are associated with different chromatin states and with transcription activity. (biomedcentral.com)
We have characterized the regions of H3K9me2 nucleation, with our analysis revealing that H3K9me2 is nucleated in HSPCs at CpG islands (CGIs) and CGI-like sequences across the genome. (biomedcentral.com)
Aberrant DNA methylation is induced at specific promoter CpG islands (CGIs) in contrast with mutations. (diagenode.com)
The human genome contains ∼30,000 CpG islands (CGIs). (ox.ac.uk)
CpG islands (CGIs) are interspersed DNA sequences that have unusually high CpG ratios and GC contents. (biomedcentral.com)
Despite their involvement in the regulation of gene expression and their importance as genomic markers for promoter prediction, no objective standard exists for defining CpG islands (CGIs), since all current approaches rely on a large parameter space formed by the thresholds of length, CpG fraction and G+C content. (ugr.es)
Given the higher frequency of CpG dinucleotides at CGIs, as compared to bulk DNA, the distance distributions between neighboring CpGs should differ for bulk and island CpGs. (ugr.es)
CpGcluster's CGIs overlapping with the Transcription Start Site (TSS) show the highest statistical significance, as compared to the islands in other genome locations, thus qualifying CpGcluster as a valuable tool in discriminating functional CGIs from the remaining islands in the bulk genome. (ugr.es)
Another outstanding feature is that all predicted CGIs start and end with a CpG dinucleotide, which should be appropriate for a genomic feature whose functionality is based precisely on CpG dinucleotides. (ugr.es)
Regions known as CpG islands (CGIs), which are refractory to DNA methylation, are often associated with gene promoters and play central roles in gene regulation. (cam.ac.uk)
In this study, we generated whole genome bisulfite sequencing (WGBS) data with high sequencing depth in induced pluripotent stem cell (iPSC) and neuronal progentior cell (NPC), and investigated the relationship between DNA methylation changes in CpG islands (CGIs) and corresponding gene expression during NPC differentiation. (yonsei.ac.kr)

CpG islands (CGI) are regions of approximately 1 kb, which colocalise with the origins of DNA replication and with the promoters of about 70% of all genes. (els.net)
Antequera F (2003) Structure, function and evolution of CpG islands promoters. (els.net)
islands are found, they're in the promoters of tumour suppressor genes. (coursera.org)
The results suggest that full size CpG islands used as promoters do not necessarily overcome the negative effects of neighbouring chromatin to give ubiquitous transgene expression independent of the integration site. (bl.uk)
In prior work, we analyzed CpG island methylation levels within gene promoters (nﾠ=ﾠ16,421) in leukocytes collected from mothers and their infants from a pregnancy cohort in Durham County, North Carolina. (rice.edu)
ZBTB 2 preferentially binds to CpG island promoters, where it acts as a transcriptional activator. (embopress.org)
ZBTB 2 is a novel reader of unmethylated DNA in mouse embryonic stem cells, and regulates cellular differentiation as an activator at CpG island promoters. (embopress.org)
ZBTB 2 preferentially binds to unmethylated CpG island promoters. (embopress.org)
Although hypermethylation of the INK4a and INK4b promoters is frequently involved in murine lymphomas, the p19 ARF CpG island is infrequently methylated in the murine primary lymphomas studied in this work. (oup.com)
In mammalian genomes, CpG islands are typically 300-3,000 base pairs in length, and have been found in or near approximately 40% of promoters of mammalian genes. (wikipedia.org)
[9] About 70% of human promoters have a high CpG content. (wikipedia.org)
Unlike CpG sites in the coding region of a gene, in most instances the CpG sites in the CpG islands of promoters are unmethylated if the genes are expressed. (wikipedia.org)
In humans, about 70% of promoters located near the transcription start site of a gene (proximal promoters) contain a CpG island. (wikipedia.org)
Over 60% of human genes and almost all house-keeping genes have their promoters embedded in CpG islands. (wikipedia.org)
CpG islands are gene regulatory elements associated with the majority of mammalian promoters, yet how they regulate gene expression remains poorly understood. (ox.ac.uk)
We discover that FBXL19 recruits CDK-Mediator to CpG island-associated promoters of non-transcribed developmental genes to prime these genes for activation during cell lineage commitment. (ox.ac.uk)
Together this reveals a new CpG island-centric mechanism for CDK-Mediator recruitment to developmental gene promoters in ES cells and a requirement for CDK-Mediator in priming these developmental genes for activation during cell lineage commitment. (ox.ac.uk)
A direct comparison of eluted DNA using PCR primers for both unmethylated and methylated promoters reveals the ability of MethylCollector™ Ultra to specifically isolate CpG-methylated DNA. (activemotif.com)

The CpG island methylator phenotype (CIMP) is a newly described mechanism for carcinogenesis in colorectal carcinomas and adenomas characterized by methylation of multiple CpG islands. (nih.gov)
Our findings of concordant CpG island methylation of HPs in multiple/large HPs or hyperplastic polyposis supports the concept that some patients have a hypermethylator phenotype characterized by methylation of multiple HPs and other colorectal lesions. (nih.gov)
To investigate the association between CpG island methylator phenotype (CIMP) and the overall survival of sporadic colorectal cancer (CRC) in Northeast China. (hindawi.com)
CpG island methylation phenotype (CIMP), characterized by the extensive hypermethylation of multiple CpG islands, is currently recognized as one of the major mechanisms in the colorectal carcinogenesis [ 7 , 8 ]. (hindawi.com)
DNA hypermethylation is a common epigenetic abnormality in cancer, and some cancers are characterized by the presence of intense hypermethylation at multiple loci, termed CpG island methylation phenotype (CIMP). (aacrjournals.org)
Colorectal cancers arising from serrated polyps are characterized by the CpG island methylator phenotype (CIMP) and somatic mutation (V600E) in the BRAF proto-oncogene. (aacrjournals.org)
PTGS2 (COX-2) expression in colon cancer has been inversely associated with survival as well as tumoral microsatellite instability (MSI) and the CpG island methylator phenotype (CIMP). (aacrjournals.org)
The CpG island methylator phenotype (CIMP), characterised by widespread promoter methylation, is associated with microsatellite instability (MSI) and BRAF mutation in colorectal cancer. (bmj.com)
Aims CpG island methylator phenotype (CIMP) involves the targeting of multiple genes by promoter hypermethylation, and the cell-cycle regulatory proteins often change in human neoplasms. (bmj.com)
Background: In colorectal cancer a distinct subgroup of tumours demonstrate the CpG island methylator phenotype (CIMP). (uib.no)
CpG island methylator phenotype (CIMP) is a unique epigenetic phenomenon observed in cancer. (grantome.com)
We hypothesized that cellular DNMT3B level might influence the occurrence of widespread CpG island methylation (i.e., the CpG island methylator phenotype, CIMP) in colon cancer. (umn.edu)
Background CpG island methylator phenotype (CIMP) has been identified as a distinct molecular subtype of gastric cancer, yet associations with survival are conflicting. (cf.ac.uk)

In order to understand the role of CpG island hypermethylation in cancer, it is useful to consider a particular tumor type, called CpG island methylator prototype, or CIMP. (wikipedia.org)

The reason for methylation to be almost exclusive to CpG dinucleotides is the symmetry of the dinucleotide. (wikipedia.org)
Although vertebrate DNA is generally depleted in the dinucleotide CpG, it has recently been shown that some vertebrate genes contain CpG islands, regions of DNA with a high G+C content and a high frequency of CpG dinucleotides relative to the bulk genome. (nih.gov)
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)
DNA methylation occurs naturally throughout the genome, mostly at positions where cytosine is bonded to guanine to form a CpG dinucleotide. (elifesciences.org)
Unmethylated CpG dinucleotide sites can be detected by Toll-like receptor 9 [2] ( TLR 9 ) on plasmacytoid dendritic cells , monocytes, natural killer (NK) cells, and B cells in humans. (wikipedia.org)
CpG islands are characterized by CpG dinucleotide content of at least 60% of that which would be statistically expected (~4-6%), whereas the rest of the genome has much lower CpG frequency (~1%), a phenomenon called CG suppression . (wikipedia.org)
The cytosine must be linked to guanine, with the guanine occurring at the 3 ′ ("three prime") end of the DNA molecule, in a formation that, in scientific notation , is expressed as 5 ′ -CG-3 ′ and is referred to as a CpG dinucleotide (with the "p" representing a phosphate group). (encyclopedia.com)
The frequency of occurrence of the CpG dinucleotide in the genome is not random, as would be expected. (encyclopedia.com)
Instead, the CpG dinucleotide is greatly under represented in eukaryotic genomes, occurring at approximately 5 to 10 percent of its predicted frequency, according to some estimates. (encyclopedia.com)
Since CpG islands contain multiple CpG dinucleotide sequences, there appear to be more than 20 million CpG dinucleotides in the human genome. (wikipedia.org)
Finally, we show that this mutant PPM1D-induced NAMPT inhibitor sensitivity is driven by hypermethylation of CpG islands throughout the genome, and in particular, the epigenetic silencing of nicotinic acid phosphoribosyltransferase (NAPRT), a key gene involved in nicotinamide adenine dinucleotide (NAD) biosynthesis. (nature.com)
And this is called a CpG dinucleotide. (coursera.org)
CpG dinucleotide. (coursera.org)
DNA methylation is a chemical modification that typically occurs within a CpG dinucleotide region in adult somatic cells ( 7 , 8 ). (spandidos-publications.com)

CpG islands in vertebrate genomes. (nih.gov)
Two theories for the maintenance of a high frequency of CpG dinucleotides in CpG islands were tested: that CpG islands in methylated genomes are maintained, despite a tendency for 5mCpG to mutate by deamination to TpG+CpA, by the structural stability of a high G+C content alone, and that CpG islands associated with exons result from some selective importance of the arginine codon CGX. (nih.gov)
Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes . (ucsc.edu)
CpG islands are usually unmethylated in a genome, especially in the promoter regions [ 2 ], in contrast, ~80% of CpG dinucleotides in the mammalian genomes are methylated [ 2 , 3 ]. (hindawi.com)
BACKGROUND: Majority of CpG dinucleotides in mammalian genomes tend to undergo DNA methylation, but most CpG islands are resistant to such epigenetic modification. (rti.org)
CpG dinucleotides are frequently methylated in vertebrate genomes. (biomedcentral.com)
CpG dinucleotides have long been observed to occur with a much lower frequency in the sequence of vertebrate genomes than would be expected due to random chance. (wikipedia.org)
The frequency of CpG dinucleotides in human genomes is 1%-less than one-quarter of the expected frequency. (wikipedia.org)
It was proposed that the CpG deficiency is due to an increased vulnerability of methylcytosines to spontaneously deaminate to thymine in genomes with CpG cytosine methylation. (wikipedia.org)
Many genes in mammalian genomes have CpG islands associated with the start of the gene [8] ( promoter regions ). (wikipedia.org)
In mammalian genomes, CpG islands are typically 300-3,000 base pairs in length. (chemeurope.com)
High CpG methylation in mammalian genomes has an evolutionary cost because it increases the frequency of spontaneous mutations. (wikipedia.org)
Here we computed cleavage rates of all dinucleotides including the methylated CpG and unmethylated CpG dinucleotides using data of the Whole Genome Sequencing datasets of the 1000 Genomes project. (ist.ac.at)

Higher levels of CpG island hypermethylation are found in CIMP. (wikipedia.org)
Tumors possessing a CIMP usually display concurrent hypermethylation of multiple promoter CpG islands. (grantome.com)

The distribution of methylated and nonmethylated CpG dinucleotides is shown at the bottom (black or white circles, respectively). (els.net)

Approximately 80% of CpG dinucleotides are methylated in the 5′ position of cytosine in the mammalian genome. (els.net)
While the cytosine bases in most CpG dinucleotides are methylated, there are short stretches of DNA known as CpG islands that contain a high proportion of unmethylated CpG dinucleotides. (elifesciences.org)

In this study, a large number of sequences of vertebrate genes were screened for the presence of CpG islands. (nih.gov)
Neither of these theories could account for the distribution of CpG dinucleotides in the sequences analysed. (nih.gov)
To test whether non-methylated CpG-dense sequences are sufficient to establish domains of H3K4me3, we analysed artificial CpG clusters that were integrated into the mouse genome. (pubmedcentralcanada.ca)
Various embodiments of the invention described herein include methods for using single point genome signature tags to analyze the related families present in a sample, methods for analyzing sequences associated with hyper- and hypo-methylated CpG islands, methods for visualizing organismic complexity change in a sampling location over time and methods for generating the genome signature tag profile of a sample of fragmented DNA. (energy.gov)
Six sequences were found to be homologous to known genes having one or more 5′-CpG island(s) (5′-CGI). (ccceh.org)
The CpG notation is used to distinguish this single-stranded linear sequence from the CG base-pairing of cytosine and guanine for double-stranded sequences. (wikipedia.org)
Given the frequency of GC two-nucleotide sequences, the number of CpG dinucleotides is much lower than would be expected. (wikipedia.org)
A 2002 study revised the rules of CpG island prediction to exclude other GC-rich genomic sequences such as Alu repeats . (wikipedia.org)
In mammals, the only exception for this global CpG depletion resides in a specific category of GC- and CpG-rich sequences termed CpG islands that are generally unmethylated and therefore retained the expected CpG content. (wikipedia.org)
There are 28,890 CpG islands in the human genome, (50,267 if one includes CpG islands in repeat sequences). (wikipedia.org)
This was exemplified by young CpG rich lineage-restricted repeat sequences that evaded DNA methylation in the absence of co-evolved mechanisms targeting methylation to these sequences, and species specific DNA binding events that protected against DNA methylation in CpG poor regions. (cam.ac.uk)

Hypermethylation of CpG islands has been described in almost every type of tumor. (wikipedia.org)
The first discovery of methylation in a CpG island of a tumor suppressor gene in humans was that of the Retinoblastoma (Rb) gene in 1989. (wikipedia.org)
Cancer epigenetic silencing in its current state was born in the labs of Baylin and Jones, where it was proven that CpG island hypermethylation was a common inactivation mechanism of the tumor suppressor gene p16INK4a. (wikipedia.org)
The frequent hypermethylation of CpG islands in these tumors as well as their irregularity are ways to determine that hypermethylated CpGs differ by tumor type. (wikipedia.org)
Precise mapping of DNA methylation patterns in CpG islands has become essential for understanding diverse biological processes such as the regulation of imprinted genes, X chromosome inactivation, and tumor suppressor gene silencing in human cancer. (pnas.org)
In cancer cells, several tumor suppressor genes such as p16 INK4a , VHL , hMLH1 , and BRCA1 have been found to have hypermethylation of normally unmethylated CpG islands within the promoter regions. (aacrjournals.org)
The promoter of INK4a resides within a CpG island, and abnormal, tumor-associated hypermethylation has been observed in many tumor types and found to result in silencing of the gene ( 14 , 39 ). (asm.org)
In tumor cells, aberrant methylation of CpG dinucleotides at the 5' end of tumor suppressor genes is frequently associated with gene silencing. (roche.com)
발생 과정과 비슷하게, CpG island는 암 발생 과정에도 관여 하게 되는데, 흔히 암 억제 유전자 (Tumor suppressor gene, TSG)의 CpG island에 과다한 메틸화에 의해 발현이 억제되거나, 암 발생 유전자 (Oncogene)의 발현이 증가되는데, CpG island의 잘못된 메틸화가 관여 할 수 있습니다. (2wordspm.com)
Dnmt3b can induce colon tumor in mice with methylation in specific CpG islands. (umn.edu)
The hypermethylation of promoter CpG islands affects tumor suppressive mRNAs ( 9 - 10 ). (spandidos-publications.com)

We have taken advantage of the fact that many mammalian genes are associated with CpG islands whose distinctive properties allow their physical separation from bulk DNA. (pnas.org)
The α‐globin and the aldose reductase (ADO) genes are associated with CpG islands, as is clearly shown by the high density of CpG dinucleotides around their 5′ ends. (els.net)

Since DNA methylation can repress gene transcription at a distance (1 kb-2 kb) from the promoter region, we have investigated the methylation status of this BRCA1 CpG island. (roche.com)
We identified a 600 bp region of the BRCA1 CpG island that possessed strong promoter activity (~40-fold above control), and determined the cytosine methylation patterns of the 30 CpG sites within this region by sodium bisulfite genomic sequencing. (elsevier.com)
These findings suggest that aberrant cytosine methylation of the BRCA1 CpG island promoter may be one mechanism of BRCA1 repression in sporadic breast cancer. (elsevier.com)
Rice, JC, Massey-Brown, KS & Futscher, BW 1998, ' Aberrant methylation of the BRCA1 CpG island promoter is associated with decreased BRCA1 mRNA in sporadic breast cancer cells ', Oncogene , vol. 17, no. 14, pp. 1807-1812. (elsevier.com)

CpG islands are differentially methylated in imprinted genes and in the inactive X chromosomes. (els.net)
P2 is located within a CpG island that is differentially methylated between males and females and overlaps conserved YY1 binding sites that are only bound on the inactive X chromosome where the sites are unmethylated. (biomedcentral.com)

These observations in the E6-expressing HMEC correlate well with the finding that CpG island methylation is a mechanism of p16 inactivation in the development of human tumors, including breast cancer. (asm.org)

The introduction of methylation-specific PCR and sodium bisulfite modification added tools to the belt of cancer epigenetics research, and the list of candidate genes with aberrant methylation of their CpG islands has been growing since. (wikipedia.org)
Effects of genome architecture and epigenetic factors on susceptibility of promoter CpG islands to aberrant DNA methylation induction. (diagenode.com)
Because a CpG island is found at the 5' end of the BRCA1 gene, we hypothesized that the decreased BRCA1 mRNA in sporadic breast cancer was associated with aberrant cytosine methylation of the CpG island. (elsevier.com)

CpGcluster uses only integer arithmetic, thus being a fast and computationally efficient algorithm able to predict statistically significant clusters of CpG dinucleotides. (ugr.es)

By analyzing methylation data of 25 cell lines from the Encyclopedia of DNA Elements (ENCODE) Consortium, we compared the DNA methylation of CpG islands in genomic regions under selective pressure with the methylation of CpG islands in the remaining part of the genome. (pubmedcentralcanada.ca)
A part of all CpG sites present in the genome are clustered into CpG islands that are defined as genomic regions with increased CpG density. (pubmedcentralcanada.ca)
CpG islands are genomic regions that contain a high frequency of CG dinucleotides. (chemeurope.com)
CpG sites occur with high frequency in genomic regions called CpG islands (or CG islands). (wikipedia.org)

Each CpG island was then analysed in terms of length, nucleotide composition, frequency of CpG dinucleotides, and location relative to the transcription unit of the associated gene. (nih.gov)
CpG islands are short, dispersed regions of unmethylated DNA with a high frequency of CpG dinucleotides relative to the bulk genome. (nih.gov)
First, the theoretical maximum sensitivity for the screening test can only be as high as the frequency of GSTP1 CpG island hypermethylation in the primary cancer tissues. (aacrjournals.org)
Additionally, by analyzing SNP frequency in CpG islands, we demonstrated that CpG islands in regions under selective pressure show lower genetic variation. (pubmedcentralcanada.ca)
CpG islands (or CG islands) are regions with a high frequency of CpG sites. (wikipedia.org)
hence CpG dinucleotides steadily deaminate to TpG dinucleotides, which is evidenced by the under-representation of CpG dinucleotides in the human genome (they occur at only 21% of the expected frequency). (wikipedia.org)
Here, we demonstrate that intragenic CpG frequency and distribution impacts transgene and genomic gene expression levels in mammalian cells. (semanticscholar.org)

CpG islands were generally found in the same position relative to the transcription unit of equivalent genes in different species, with some notable exceptions. (nih.gov)
G/C boxes were located both upstream and downstream from the transcription start site of genes with 5' CpG islands. (nih.gov)
CpG islands are typically common near transcription start sites and may be associated with promoter regions. (ucsc.edu)
All housekeeping and widely expressed genes have a CpG island covering the transcription start, whereas 40% of the genes with a tissue-specific or limited expression are associated with islands. (nih.gov)
In this latter group of genes, the position of the islands was not biased toward the 5' end of the transcription unit. (nih.gov)
The great majority of CpG islands colocalise with transcription initiation sites and the origins of DNA replication. (els.net)
If the CpG island is far away from the promoter or transcriptional start site, it is hard to say whether its methylation has any impact on transcription. (protocol-online.org)
Deaton AM, Bird A (2011) CpG islands and the regulation of transcription. (springer.com)
METHODOLOGY/PRINCIPAL FINDINGS: Using the genome-scale in vivo DNA methylation data from human brain, we investigated the flanking sequence features of methylation-resistant CpG islands, and discovered that there are several over-represented putative Transcription Factor Binding Sites (TFBSs) in methylation-resistant CpG islands, and a specific group of zinc finger protein binding sites are over-represented in boundary regions ( approximately 400 bp) flanking such CpG islands. (rti.org)
CONCLUSIONS/SIGNIFICANCE: Our results suggest a possible mechanism that certain putative zinc finger protein binding sites over-represented in the boundary regions of the methylation-resistant CpG islands may block the spreading of methylation into these islands, and those TFBSs over-represented within the islands may both reinforce the methylation blocking and promote transcription. (rti.org)
These islands contain a large number of cytosine and guanine bases, and they are often found at or near transcription start sites. (elifesciences.org)
The lack of methylation at CpG islands has long been assumed to have a passive role in gene expression, leaving the DNA easily accessible and available for transcription factors to bind and initiate transcription. (elifesciences.org)
It has been well established that the methylation status of CpG islands directly affects the DNA-protein interactions by eliminating the otherwise occurring sequence specific binding of the transcription factors whereas inducing the DNA-bindings of members of the methyl-CpG binding protein family (MBD). (biomedcentral.com)
The features for prediction include those that have been previously demonstrated effective (CpG island specific attributes, DNA sequence composition patterns, DNA structure patterns, distribution patterns of conserved transcription factor binding sites and conserved elements, and histone methylation status) as well as those that have not been extensively explored but are likely to contribute additional information from a biological point of view (nucleosome positioning propensities, gene functions, and histone acetylation status). (biomedcentral.com)
CpG islands typically occur at or near the transcription start site of genes, particularly housekeeping genes, in vertebrates. (chemeurope.com)
These "islands" commonly occur in promoter regions of genes (regions where RNA polymerase binds to start transcription), which are located at the 5 ′ ("five prime") end of the genes. (encyclopedia.com)
일반적으로 CpG island의 메틸화가 되면 유전자 발현에 관여하는 여러 transcription factor의 접근을 막고, 동시에 메틸화된 CpG site에 결합하는 MBD (Methyl-CpG-binding domain proteins) 단백 들이 유전자 발현을 억제 하게 됩니다. (2wordspm.com)
We report that a CpG island close to the UCP1 transcription start site is highly conserved in all 29 vertebrates examined apart from the mouse and xenopus. (frontiersin.org)
CpG islands and the regulation of transcription. (semanticscholar.org)
Methylation of promoter CpG islands present in or near promoter regions may also disrupt the binding of transcription factors ( 11 ). (spandidos-publications.com)

A CpG island is a Cytosine and Guanine linked by a phosphate in a repeated sequence. (wikipedia.org)
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)
CpG sites are DNA regions where a cytosine nucleotide occurs next to a guanine nucleotide. (pubmedcentralcanada.ca)
The CpG sites or CG sites are regions of DNA where a cytosine nucleotide is followed by a guanine nucleotide in the linear sequence of bases along its 5' → 3' direction . (wikipedia.org)
The CpG notation is therefore to be interpreted as the cytosine being 5 prime to the guanine base. (wikipedia.org)
CpG should not be confused with GpC , the latter meaning that a guanine is followed by a cytosine in the 5' → 3' direction of a single-stranded sequence. (wikipedia.org)
[1] [2] The "p" in CpG notation refers to the phosphodiester bond between the cytosine and the guanine . (chemeurope.com)
Cytosine과 Guanine이 phosphate로 연결되어 있기 때문에, 흔히 CpG site 라고 부르기도 합니다. (2wordspm.com)

Possible functions of CpG islands in transcriptional and post-transcriptional regulation of gene expression were discussed, and were related to theories for the maintenance of CpG islands as "methylation-free zones" in germline DNA. (nih.gov)
In particular, it has been shown that specific proteins bind to CpG islands to create chromatin environments that are more favourable for the initiation of gene expression. (elifesciences.org)
Moreover, a subset of CpG islands can also bind polycomb-group proteins, including the polycomb repressive complex 1 (PRC1) that silence gene expression. (elifesciences.org)
The role of DNA methylation in the control of mammalian gene expression has been the subject of intensive research in recent years, partly due to the critical role of CpG island methylation in the inactivation of tumour suppressor genes during the development of cancer. (biochemsoctrans.org)
This observation led to the speculation that methylation of CpG sites in the promoter of a gene may inhibit gene expression. (wikipedia.org)
The lack of methylation in CpG islands leads to a less compact chromatin structure, and generally allows for active gene expression. (encyclopedia.com)
inproceedings{Krinner2014CpGDD, title={CpG domains downstream of TSSs promote high levels of gene expression}, author={Simone Krinner and Asli P. Heitzer and Sarah Daniela Diermeier and Ingrid Obermeier and Gernot L{\'a}ngst and Ralf Dipl. (semanticscholar.org)
CpG dinucleotides are known to play a crucial role in regulatory domains, affecting gene expression in their natural context. (semanticscholar.org)

Recent works have suggested the role of epigenetic modification at a CpG island located in POLG gene, encoding the polymerase responsible for mtDNA synthesis. (bmj.com)
Most of these elements remain protected from CpG methylation, a prevalent epigenetic modification associated with transcriptional silencing. (fpwr.org)
Here we report that the promoter methylation of Plk4 CpG islands increases with age, was more prevalent in males and that Plk4 epigenetic modification and subsequent downregulation of expression was associated with the development of HCC in Plk4 mutant mice. (biomedcentral.com)

We have analyzed 375 genes and 58 pseudogenes from the human entries in the EMBL Database for the presence of CpG islands. (nih.gov)

In fact, about 50 percent of all genes contain a CpG island in their promoter regions. (encyclopedia.com)

In normal tissues, the vast majority of CpG islands are completely unmethylated with some exceptions. (wikipedia.org)

Takai D, Jones PA (2002) Comprehensive analysis of CpG islands in human chromosomes 21 and 22. (springer.com)

This detailed volume examines bioinformatic and molecular biological methods useful to identify and to explore the functions of CpG islands, key navigation points to understand gene regulation in fundamental processes such as development and cell differentiation as well as in diseases like cancer. (springer.com)

Beginning with a historical perspective and important properties of CpG islands, the book continues with sections on computational and wet lab methods related to the study of DNA methylation, and in-depth protocols for the analysis of CpG island functional features including epigenetic profiling and chromatin interactions. (springer.com)
Therefore, none of the main statistical properties of CpG islands (neither G+C content, CpG fraction nor length threshold) are needed as search parameters, which may lead to the high specificity and low overlap with spurious Alu elements observed for CpGcluster predictions. (ugr.es)

Methylated CpG dinucleotides at position 5 of cytosine are associated with transcriptional repression and an inactive chromatin conformation in mammals. (els.net)
DNA methylation of intragenic CpG islands depends on their transcriptional activity during differentiation and disease. (ox.ac.uk)

오늘은 그 연장선에서 Epigenetics의 중심을 이루는 DNA의 메틸화 (Methylation)에 관여하는 분자들과 CpG island, 그 조절 기전에 대해서 조금 더 자세하게 다뤄볼까 합니다. (2wordspm.com)

Controls the plotting of GC content, CpGoe content, CpG islands greater than the minimum island size, and all potential CpG islands for the specified criteria. (mathworks.com)
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)

The majority of CpG pairs in mammals are chemically modified by the covalent attachment of a methyl group to the C5 position of the cytosine ring. (wikipedia.org)
These complexes have an important role in the regulation of genes during early development in animals, but the mechanism by which PRC1 recognizes CpG islands in mammals has remained enigmatic. (elifesciences.org)
In mammals, 70% to 80% of CpG cytosines are methylated. (wikipedia.org)
In plants and other organisms, DNA methylation is found in three different sequence contexts: CG (or CpG ), CHG or CHH (where H correspond to A, T or C). In mammals however, DNA methylation is almost exclusively found in CpG dinucleotides, with the cytosines on both strands being usually methylated. (wikipedia.org)

The Percentage CpG is the ratio of CpG nucleotide bases (twice the CpG count) to the length. (ucsc.edu)

Thus, G/C boxes appeared to be a feature of CpG islands in general, rather than a feature of the promoter region of housekeeping genes. (nih.gov)
I use CpG Island Explorer to predicate CpG islands,but in one gene I did not get CpG island in the promoter region adjacent to exon1 , I only get one CpG island about 4kb upstream the ATG codon, does the CpG region could be representative for study? (protocol-online.org)
The promoter region of around 70% of all genes in the human genome is overlapped by a CpG island (CGI). (springer.com)
This initial reduction of p16 expression was associated with limited methylation of the p16 promoter region CpG island. (asm.org)
Hypermethylation of CpG islands in the promoter region of death-associated protein kinase (DAP-kinase) coupled with the loss of gamma-interferon-induced apoptosis have been reported in B-cell malignancies suggesting a role in pathogenesis or prognosis. (cdc.gov)
In normal lymphocytes, the CpG islands in the promoter region were unmethylated, as were the T-cell lymphoblastic lymphoma and anaplastic LCL. (cdc.gov)
Dynamic CpG island methylation changes were derived primarily from methylation in the promoter region. (spandidos-publications.com)

Cytosines in CpG dinucleotides can be methylated to form 5-methylcytosine. (pubmedcentralcanada.ca)
In the human genome, is DNA methylation mostly restricted to the cytosines of CpG dinucleotides. (biomedcentral.com)

The locations of G/C boxes, composed of the sequence GGGCGG or its reverse complement CCGCCC, were investigated relative to the location of CpG islands. (nih.gov)
Calculate the CpG islands in the sequence and plot the results. (mathworks.com)
The entire genome sequence, masking areas included, was used for the construction of the track Unmasked CpG . (ucsc.edu)
The track CpG Islands is constructed on the sequence after all masked sequence is removed. (ucsc.edu)
Sequence comparison confirms that about 20% of the human CpG islands are absent from the homologous mouse genes. (pnas.org)
I get the DNA sequence 5kb upstream from exon1 and exon1 to predicate CpG islands. (protocol-online.org)
Messenger RNA levels of the reporter gene and targeted gene were assessed by qRT-PCR, and methylation of the promoter CpG islands and LacZ coding sequence were evaluated by sequencing of bisulfitetreated DNA. (elsevier.com)
Within the silenced group, LacZ coding sequence methylation was significantly and positively correlated with CpG Island methylation, while promoter CpG methylation was only weakly correlated with LacZ gene mRNA. (elsevier.com)
[13] Furthermore, non-CpG methylation has also been observed in hematopoietic progenitor cells, and it occurred mainly in a CpApC sequence context. (wikipedia.org)
They also demonstrated that methylation of these CpG islands was dependent on DNA methyltransferase 3α and DNA methyltransferase 3-like, but the methylation changes were not distinct at the sequence level. (spandidos-publications.com)

Detailed understanding of the relationship between these modifications, notably, methylation of the full-length CpG island, the association of methyl-CpG binding proteins (MBPs), and the acetylation and methylation of histones in gene silencing is vitally important. (semanticscholar.org)

Silencing of the E-cadherin invasion-suppressor gene by CpG methylation in human carcinomas. (semanticscholar.org)
The aim of current study was to apply the methylated DNA immunoprecipitation (MeDIP)‑Chip method to investigate dynamic changes in CpG island methylation in human sperm, oocytes and various developmental stages of preimplantation embryos. (spandidos-publications.com)

also find low but appreciable levels of PRC1 at most CpG islands genome-wide, in addition to the high levels of PRC1 at selected islands: this suggests that KDM2B may sample the whole genome to find CpG islands where PRC1 can establish silencing. (elifesciences.org)

We evaluated the methylation status in the CpG islands of four deregulated genes ( Casp3 , Cldn1 , Pex11a and Nox4 ) using methylation-sensitive high-resolution melting technology for the samples obtained from different stages of hepatocarcinogenesis. (biologists.org)

This would imply that colorectal cancer will not necessarily have the same set of hypermethylated CpG islands as in a glioma. (wikipedia.org)
Our data support a possible role of DNMT3B in nonrandom de novo CpG island methylation leading to colorectal cancer. (umn.edu)

Analysis of a selection of genes suggests that both human and mouse are losing CpG islands over evolutionary time due to de novo methylation in the germ line followed by CpG loss through mutation. (pnas.org)
As a result, residual CpG islands are created in areas where methylation is rare, and CpG sites stick (or where C to T mutation is highly detrimental). (wikipedia.org)

In vertebrates, around 60-80% of CpG are methylated in somatic cells [15] and DNA methylation appears as a default state that has to be specifically excluded from defined locations. (wikipedia.org)

CpG islands as gene markers in the human genome. (nih.gov)
Examples of human genes with and without CpG islands. (els.net)
Recently, CpG island methylation within the p16 promoter has been identified as a mechanism to eliminate p16 expression in a variety of human tumors ( 23 , 25 , 38 , 44 , 56 ). (asm.org)
Here we clone and characterize the promoter of the human ARF gene and show that it is a CpG island characteristic of a housekeeping gene which contains numerous Sp1 sites. (asm.org)
We found that this CpG island is highly methylated in human tissues, whatever developmental stages (after 12 weeks) or tissue energy-demand. (bmj.com)
Heterogeneity in the modification and involvement of chromatin components of the CpG island of the silenced human CDH1 gene in cancer cells. (semanticscholar.org)
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. (semanticscholar.org)
Demethylation of this island is correlated with reactivation of XIST in human [ 13 ] and mouse [ 14 ] somatic cells. (biomedcentral.com)
Association of altered DNA methylation patterns of the promoter CpG islands with the expression profile of cancer-related genes, has been found in many human tumors. (biomedcentral.com)
Here, we develop CpGIMethPred, the support vector machine-based models to predict the methylation status of the CpG islands in the human genome under normal conditions. (biomedcentral.com)
The availability of AscI as a restriction landmark for RLGS allows for scanning almost twice as many CpG islands in the human genome compared with using NotI only. (northwestern.edu)
Using methylation sensitive restriction digest and bisulfite mapping we show that the CpG island in both the bovine and human is largely un-methylated and is not related to differences in UCP1 expression between white and BAT. (frontiersin.org)
Unusual features of CpG-rich (HTF) islands in the human alpha globin complex: association with non-functional pseudogenes and presence within the 3' portion of the zeta gene. (ox.ac.uk)
We have characterised a cluster of CpG rich (HTF) islands in the alpha-globin complex and report here two unusual features: The human embryonic zeta 2-globin gene is associated with an HTF island within its 3' portion rather than at the 5' end. (ox.ac.uk)
In conclusion, the current study indicated that CpG island methylation changes in human preimplantation embryos were divided into three stages. (spandidos-publications.com)

However, using GSTP1 CpG island hypermethylation as the only marker for molecular screening and diagnosis of prostate cancer presents some potential limitations. (aacrjournals.org)

Furthermore, CpG island hypermethylation patterns in prostate cancer metastases were very similar to the primary prostate cancers and tended to show greater differences between cases than between anatomical sites of metastasis. (aacrjournals.org)
While some features are common to all Del elements, CpG island patterns within the LTRs were particular to lineage specific clusters. (sigmaaldrich.com)

Hackenberg M, Barturen G, Carpena P et al (2010) Prediction of CpG-island function: CpG clustering vs. sliding-window methods. (springer.com)
Because of this, the presence of a CpG island is used to help in the prediction and annotation of genes. (wikipedia.org)

Anatomy6

Diseases4

Chemicals and Drugs34

Analytical, Diagnostic and Therapeutic Techniques and Equipment10

Phenomena and Processes35

Disciplines and Occupations3

Information Science3

Health Care1

Geographicals13

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

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

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

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

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

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

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

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)

CpG Islands

DNA Methylation

Islands

Dinucleoside Phosphates

Promoter Regions, Genetic

Azacitidine

Gene Silencing

Epigenesis, Genetic

Sulfites

Rhode Island

Indian Ocean Islands

Pacific Islands

DNA (Cytosine-5-)-Methyltransferase

Base Sequence

DNA Modification Methylases

Genome, Human

Sequence Analysis, DNA

Molecular Sequence Data

Gene Expression Regulation, Neoplastic

Methylation

DNA, Neoplasm

Genes, Tumor Suppressor

Genes, p16

Polymerase Chain Reaction

Prince Edward Island

Mediterranean Islands

Microsatellite Instability

Cytosine

Transcription Initiation Site

Deoxyribonuclease HpaII

Long Interspersed Nucleotide Elements

DNA

Cell Line, Tumor

Genomic Imprinting

Cyclin-Dependent Kinase Inhibitor p16

Epigenomics

United States Virgin Islands

5-Methylcytosine

Melanesia

Colorectal Neoplasms

Oligonucleotide Array Sequence Analysis

Cyclin-Dependent Kinase Inhibitor p15

Reverse Transcriptase Polymerase Chain Reaction

Tumor Cells, Cultured

Transcription, Genetic

Micronesia

Oligodeoxyribonucleotides

Glutathione S-Transferase pi

Genes, Neoplasm

Chromatin

Exons

Base Composition

Histones

Geography

Death-Associated Protein Kinases

Proto-Oncogene Proteins B-raf

Channel Islands

Chromosome Mapping

Phenotype

Tumor Suppressor Proteins

Reunion

Falkland Islands

Polynesia

Alu Elements

DNA Primers

RNA, Messenger

Gene Expression Profiling

Gene Expression Regulation

Neoplasm Proteins

Models, Genetic

Core Binding Factor Alpha 3 Subunit

Microsatellite Repeats

Phylogeny

Chromosomes, Human, Pair 21

Cell Line

Genome

X Chromosome

Restriction Mapping

Toll-Like Receptor 9

DNA-Cytosine Methylases