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Paired-end Tag
Paired-end tags (PET) (sometimes "Paired-End diTags", or simply "ditags") are the short sequences at the 5’ and 3' ends of a DNA fragment which are unique enough that they (theoretically) exist together only once in a genome, therefore making the sequence of the DNA in between them available upon search (if full-genome sequence data is available) or upon further sequencing (since tag sites are unique enough to serve as primer annealing sites). Paired-end tags (PET) exist in PET libraries with the intervening DNA absent, that is, a PET "represents" a larger fragment of genomic or cDNA by consisting of a short 5' linker sequence, a short 5' sequence tag, a short 3' sequence tag, and a short 3' linker sequence. It was shown conceptually that 13 base pairs are sufficient to map tags uniquely.Fullwood MJ, Wei CL, Liu ET, Ruan Y. 2009. Next-Generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Research. 19:521–532. {{PMID, 19339662 However ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
5' End
Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. In a single strand of DNA or RNA, the chemical convention of naming carbon atoms in the nucleotide pentose-sugar-ring means that there will be a 5′ end (usually pronounced "five-prime end"), which frequently contains a phosphate group attached to the 5′ carbon of the ribose ring, and a 3′ end (usually pronounced "three-prime end"), which typically is unmodified from the ribose -OH substituent. In a DNA double helix, the strands run in opposite directions to permit base pairing between them, which is essential for replication or transcription of the encoded information. Nucleic acids can only be synthesized in vivo in the 5′-to-3′ direction, as the polymerases that assemble various types of new strands generally rely on the energy produced by breaking nucleoside triphosphate bonds to attach new nucleoside monophosphates to t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene Duplication
Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements. Common sources of gene duplications include ectopic recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage. Mechanisms of duplication Ectopic recombination Duplications arise from an event termed unequal crossing-over that occurs during meiosis between misaligned homologous chromosomes. The chance of it happening is a function of the degree of sharing of repetitive elements between two chromosomes. The products of this recombination are a duplication at the site of the exchange and a reciprocal deletion. Ectopic recombinatio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polyadenylation
Polyadenylation is the addition of a poly(A) tail to an RNA transcript, typically a messenger RNA (mRNA). The poly(A) tail consists of multiple adenosine monophosphates; in other words, it is a stretch of RNA that has only adenine bases. In eukaryotes, polyadenylation is part of the process that produces mature mRNA for translation. In many bacteria, the poly(A) tail promotes degradation of the mRNA. It, therefore, forms part of the larger process of gene expression. The process of polyadenylation begins as the transcription of a gene terminates. The 3′-most segment of the newly made pre-mRNA is first cleaved off by a set of proteins; these proteins then synthesize the poly(A) tail at the RNA's 3′ end. In some genes these proteins add a poly(A) tail at one of several possible sites. Therefore, polyadenylation can produce more than one transcript from a single gene (alternative polyadenylation), similar to alternative splicing. The poly(A) tail is important for the nuc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transcriptome
The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes be used to refer to all RNAs, or just mRNA, depending on the particular experiment. The term ''transcriptome'' is a portmanteau of the words ''transcript'' and ''genome''; it is associated with the process of transcript production during the biological process of transcription. The early stages of transcriptome annotations began with cDNA libraries published in the 1980s. Subsequently, the advent of high-throughput technology led to faster and more efficient ways of obtaining data about the transcriptome. Two biological techniques are used to study the transcriptome, namely DNA microarray, a hybridization-based technique and RNA-seq, a sequence-based approach. RNA-seq is the preferred method and has been the dominant transcriptomics technique since the 2010s. Single-cell transcriptomics allows tracking of transcript chang ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fusion Genes
A fusion gene is a hybrid gene formed from two previously independent genes. It can occur as a result of translocation, interstitial deletion, or chromosomal inversion. Fusion genes have been found to be prevalent in all main types of human neoplasia. The identification of these fusion genes play a prominent role in being a diagnostic and prognostic marker. History The first fusion gene was described in cancer cells in the early 1980s. The finding was based on the discovery in 1960 by Peter Nowell and David Hungerford in Philadelphia of a small abnormal marker chromosome in patients with chronic myeloid leukemia—the first consistent chromosome abnormality detected in a human malignancy, later designated the Philadelphia chromosome. In 1973, Janet Rowley in Chicago showed that the Philadelphia chromosome had originated through a translocation between chromosomes 9 and 22, and not through a simple deletion of chromosome 22 as was previously thought. Several investigators i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chromosome Conformation Capture
Chromosome conformation capture techniques (often abbreviated to 3C technologies or 3C-based methods) are a set of molecular biology methods used to analyze the spatial organization of chromatin in a cell. These methods quantify the number of interactions between genomic loci that are nearby in 3-D space, but may be separated by many nucleotides in the linear genome. Such interactions may result from biological functions, such as promoter- enhancer interactions, or from random polymer looping, where undirected physical motion of chromatin causes loci to collide. Interaction frequencies may be analyzed directly, or they may be converted to distances and used to reconstruct 3-D structures. The chief difference between 3C-based methods is their scope. For example, when using PCR to detect interaction in a 3C experiment, the interactions between two specific fragments are quantified. In contrast, Hi-C quantifies interactions between all possible pairs of fragments simultaneously. D ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Adenocarcinoma
Adenocarcinoma (; plural adenocarcinomas or adenocarcinomata ) (AC) is a type of cancerous tumor that can occur in several parts of the body. It is defined as neoplasia of epithelial tissue that has glandular origin, glandular characteristics, or both. Adenocarcinomas are part of the larger grouping of carcinomas, but are also sometimes called by more precise terms omitting the word, where these exist. Thus invasive ductal carcinoma, the most common form of breast cancer, is adenocarcinoma but does not use the term in its name—however, esophageal adenocarcinoma does to distinguish it from the other common type of esophageal cancer, esophageal squamous cell carcinoma. Several of the most common forms of cancer are adenocarcinomas, and the various sorts of adenocarcinoma vary greatly in all their aspects, so that few useful generalizations can be made about them. In the most specific usage (narrowest sense), the glandular origin or traits are exocrine; endocrine gland tumor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Estrogen Receptor
Estrogen receptors (ERs) are a group of proteins found inside cells. They are receptors that are activated by the hormone estrogen (17β-estradiol). Two classes of ER exist: nuclear estrogen receptors ( ERα and ERβ), which are members of the nuclear receptor family of intracellular receptors, and membrane estrogen receptors (mERs) (GPER (GPR30), ER-X, and Gq-mER), which are mostly G protein-coupled receptors. This article refers to the former (ER). Once activated by estrogen, the ER is able to translocate into the nucleus and bind to DNA to regulate the activity of different genes (i.e. it is a DNA-binding transcription factor). However, it also has additional functions independent of DNA binding. As hormone receptors for sex steroids ( steroid hormone receptors), ERs, androgen receptors (ARs), and progesterone receptors (PRs) are important in sexual maturation and gestation. Proteomics There are two different forms of the estrogen receptor, usually referred to as ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ChIA-PET
Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET or ChIA-PETS) is a technique that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and High-throughput sequencing to determine ''de novo'' long-range chromatin interactions genome-wide. Genes can be regulated by regions far from the promoter such as regulatory elements, insulators and boundary elements, and transcription-factor binding sites (TFBS). Uncovering the interplay between regulatory regions and gene coding regions is essential for understanding the mechanisms governing gene regulation in health and disease (Maston et al., 2006). ChIA-PET can be used to identify unique, functional chromatin interactions between distal and proximal regulatory transcription-factor binding sites and the promoters of the genes they interact with. ChIA-PET can also be used to unravel the mechanisms of genome control during processes such as cell differen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chip-sequencing
ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. It can be used to map global binding sites precisely for any protein of interest. Previously, ChIP-on-chip was the most common technique utilized to study these protein–DNA relations. Uses ChIP-seq is primarily used to determine how transcription factors and other chromatin-associated proteins influence phenotype-affecting mechanisms. Determining how proteins interact with DNA to regulate gene expression is essential for fully understanding many biological processes and disease states. This epigenetic information is complementary to genotype and expression analysis. ChIP-seq technology is currently seen primarily as an alternative to ChIP-chip which requires a hybridization array. This introduces some bias, as an array is restr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ChIP-on-chip
ChIP-on-chip (also known as ChIP-chip) is a technology that combines chromatin immunoprecipitation ('ChIP') with DNA microarray (''"chip"''). Like regular ChIP, ChIP-on-chip is used to investigate interactions between proteins and DNA ''in vivo''. Specifically, it allows the identification of the cistrome, the sum of binding sites, for DNA-binding proteins on a genome-wide basis. Whole-genome analysis can be performed to determine the locations of binding sites for almost any protein of interest. As the name of the technique suggests, such proteins are generally those operating in the context of chromatin. The most prominent representatives of this class are transcription factors, replication-related proteins, like origin recognition complex protein (ORC), histones, their variants, and histone modifications. The goal of ChIP-on-chip is to locate protein binding sites that may help identify functional elements in the genome. For example, in the case of a transcription factor as ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Immunoprecipitation
Immunoprecipitation (IP) is the technique of precipitating a protein antigen out of solution using an antibody that specifically binds to that particular protein. This process can be used to isolate and concentrate a particular protein from a sample containing many thousands of different proteins. Immunoprecipitation requires that the antibody be coupled to a solid substrate at some point in the procedure. Types Individual protein immunoprecipitation (IP) Involves using an antibody that is specific for a known protein to isolate that particular protein out of a solution containing many different proteins. These solutions will often be in the form of a crude lysate of a plant or animal tissue. Other sample types could be body fluids or other samples of biological origin. Protein complex immunoprecipitation (Co-IP) Immunoprecipitation of intact protein complexes (i.e. antigen along with any proteins or ligands that are bound to it) is known as co-immunoprecipitation (Co-I ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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