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This, combined with the portions that are homologous to chicken Z and human 9 chromosomes imply that this level of incomplete silencing may be the ancestral form of dosage compensation. Regardless of their ambiguous evolutionary history, platypuses have been empirically determined to follow an XY sex-determination syst... | Wikipedia - Sex-chromosome dosage compensation - Other species-specific methods > Monotremes | 341 | 1,699 | null |
Section: Other species-specific methods > Plants. In addition to humans and flies, some plants also make use of the XX/XY dosage compensation systems. Silene latifolia plants are also either male (XY) or female (XX), with the Y chromosome being smaller, with fewer genes expressed, than the X chromosome. Two separate st... | Wikipedia - Sex-chromosome dosage compensation - Other species-specific methods > Plants | 244 | 1,112 | null |
Section: Other species-specific methods > Reptiles. Research into dosage compensation has been carried out in six species of toxicoferan reptiles and in one species of softshell turtle. Two species of caenophidian snake (one which belongs to the family Viperidae and the other to the family Colubridae) have been investi... | Wikipedia - Sex-chromosome dosage compensation - Other species-specific methods > Reptiles | 253 | 1,112 | null |
Section: X chromosome inactivation and embryonic stem cells. XCI is initiated very early during female embryonic development or upon differentiation of female embryonic stem (ES) cells and results in inactivation of one X chromosome in every female somatic cell. This process is initiated very early during development, ... | Wikipedia - Sex-chromosome dosage compensation - X chromosome inactivation and embryonic stem cells | 313 | 1,466 | null |
Section: Xist, Xite, and Tsix and their roles in X-inactivation. Xite and Xist, are both long non-coding RNAs that regulate and facilitate the process of X-inactivation and are important in the silencing of genes within the X chromosome that is being inactivated. These work in combination with Tsix, which is non-coding... | Wikipedia - Sex-chromosome dosage compensation - Xist, Xite, and Tsix and their roles in X-inactivation | 301 | 1,311 | null |
Section: Plumage appearance. The presence of a white bar on a dark background is distinguishing sex-linked barring from Autosomal barring, another plumage pattern in chickens which is created by a black bar on a light color background (white/ beige or brown) as exemplified by the breed Egyptian Fayoumi. The absence of ... | Wikipedia - Sex-linked barring - Plumage appearance | 228 | 1,124 | null |
Section: Genetics. Sex-linked barring has been established as the dominant locus B by traditional mendelian genetics in the beginning of the 20th century. The responsible gene was predicted to be located on the Z chromosome and since male birds are homogametic (ZZ), they can be either hetero- or homozygous for sex-link... | Wikipedia - Sex-linked barring - Genetics | 348 | 1,594 | null |
The B0 allele only carries the two non-coding mutations and its contribution to the barring pattern remained unknown as it only occurred in breeds that also carry the Dominant white mutation which is masking the effect at the B locus.). Recently scientists have removed the Dominant white mutation from chickens of those... | Wikipedia - Sex-linked barring - Genetics | 183 | 928 | null |
Section: Molecular pattern formation in the feather follicle. Scientists were able to show that either both or one of the non-coding mutations present in all B alleles, cause an up-regulation of the activity of CDKN2A. ). With more of the gene product, which is called ARF (Alternate Reading frame Protein) in the cell, ... | Wikipedia - Sex-linked barring - Molecular pattern formation in the feather follicle | 342 | 1,597 | null |
Section: Sex-linked barring mutations and melanoma. Mutations in CDKN2A have been associated with the occurrence of familial melanoma in humans. Changes in its gene product ARF often cause the cell to lose their ability for self-induced cell death or cell cycle arrest, which are mechanisms of cells to manage uncontroll... | Wikipedia - Sex-linked barring - Sex-linked barring mutations and melanoma | 162 | 753 | null |
Article: Shadow effect. The shadow effect is a phenomenon seen in genetic studies that use noninvasive genetic data collection methods. It occurs when there are not enough loci and/or loci that have low variance of alleles within the population. As a result, researchers can capture two separate individuals and mistaken... | Wikipedia - Shadow effect - Summary | 153 | 791 | null |
Section: Background. There are several types of rarefaction methods that can be used to estimate the size of a hard monitor species. The study of population size and density falls under demography, the study of populations of any kind of organism. Mark and recapture is a common form of data collection involving species... | Wikipedia - Shadow effect - Background | 320 | 1,625 | null |
Article: Somatic mutation. A somatic mutation is a change in the DNA sequence of a somatic cell of a multicellular organism with dedicated reproductive cells; that is, any mutation that occurs in a cell other than a gamete, germ cell, or gametocyte. Unlike germline mutations, which can be passed on to the descendants o... | Wikipedia - Somatic mutation - Summary | 172 | 821 | null |
Section: Fraction of cells affected. The term somatic generally refers to the cells of the body, in contrast to the reproductive (germline) cells, which give rise to the egg or sperm. For example, in mammals, somatic cells make up the internal organs, skin, bones, blood, and connective tissue. In most animals, separati... | Wikipedia - Somatic mutation - Fraction of cells affected | 258 | 1,256 | null |
Section: Fraction of cells affected > Exceptions to inheritance. There are many exceptions to the rule that somatic mutations cannot be inherited by offspring. Many organisms simply do not dedicate a separate germline during early development. Plants and basal animals such as sponges and corals instead generate gametes... | Wikipedia - Somatic mutation - Fraction of cells affected > Exceptions to inheritance | 257 | 1,293 | null |
Section: Causes. As with germline mutations, mutations in somatic cells may arise due to endogenous factors, including errors during DNA replication and repair, and exposure to reactive oxygen species produced by normal cellular processes. Mutations can also be induced by contact with mutagens, which can increase the r... | Wikipedia - Somatic mutation - Causes | 217 | 1,044 | null |
Section: Mutation frequency. Research suggests that the frequency of mutations is generally higher in somatic cells than in cells of the germline; furthermore, there are differences in the types of mutation seen in the germ and in the soma. There is variation in mutation frequency between different somatic tissues with... | Wikipedia - Somatic mutation - Mutation frequency | 350 | 1,561 | null |
Section: Disease. Somatic mutations accumulate within an organism's cells as it ages and with each round of cell division; the role of somatic mutations in the development of cancer is well established, and the accumulation of somatic mutations is implicated in the biology of aging. Mutations in neuronal stem cells (es... | Wikipedia - Somatic mutation - Disease | 205 | 1,007 | null |
Article: State switching. State switching (a.k.a. phenotypic switching) is a fundamental physiological process in which a cell/organism undergoes spontaneous, and potentially reversible, transitions between different phenotypes. Thus, the ability to switch states/phenotypes (phenotypic plasticity) is a key feature of d... | Wikipedia - State switching - Summary | 308 | 1,520 | null |
Section: Intrinsically Disordered Proteins (IDPs) and state switching. A hallmark of the factors implicated in phenotypic switching whether in cancer or in normal cells is that they are Intrinsically disordered proteins (IDPs). That is, they lack a rigid 3D-structure under physiological conditions at least in vitro and... | Wikipedia - State switching - Intrinsically Disordered Proteins (IDPs) and state switching | 273 | 1,158 | null |
Section: Scale-free Networks. Until the 1990s, it was tacitly assumed that most networks adopt a random architecture wherein an edge (connection) between each pair of nodes has equal probability, independent of the other edges (Erdős–Rényi model). However, pioneering work by Barabási and colleagues (Barabási–Albert mod... | Wikipedia - State switching - Scale-free Networks | 232 | 1,064 | null |
Section: The MRK Model explaining state switching. The authors proposed a theoretical model (hereby named the ‘MRK model’ after the main proponents- Gita Mahmoudabadi, Govindan Rangarajan, and Prakash Kulkarni) which envisaged that because IDPs have multiple conformational states and rapid conformational dynamics, they... | Wikipedia - State switching - The MRK Model explaining state switching | 333 | 1,626 | null |
Rather, the model emphasizes that IDPs could likely relay, and perhaps, even amplify, other intrinsic and extrinsic types of noise and perturbations in the system. Consistent with this argument, there are now numerous examples of remodeling of the IDP conformational ensemble in response to binding and/or post-translati... | Wikipedia - State switching - The MRK Model explaining state switching | 271 | 1,276 | null |
Section: Learning and evolution. It seems quite reasonable to assume that organisms acquire useful adaptations during their lifetime. Such adaptations are the result of an exploratory search which samples various iterations of potential outputs in order to discern and select the most appropriate ones. Thus, it is plaus... | Wikipedia - State switching - Learning and evolution | 294 | 1,554 | null |
In 1987, Hinton & Nowlan using a computer simulation demonstrated that indeed, learning (they actually meant phenotypic plasticity) can be very effective in guiding the evolutionary search. In fact, the authors observed that learning alters (smoothens) the shape of the search space in which evolution operates and predi... | Wikipedia - State switching - Learning and evolution | 333 | 1,724 | null |
While cancer cells are not protists per se, they exhibit several characteristics that are typical of these simple forms of life. In fact, cancer has been postulated to represents some sort of reversion to a more primitive phenotype – an atavism. In the atavistic model of cancer progression, tumor cell dedifferentiation... | Wikipedia - State switching - Learning and evolution | 344 | 1,745 | null |
Section: Inheritance of adaptive learning or phenotypic plasticity: Can information transfer be reversed (from phenotype to genotype)?. For adaptive learning to be inherited, one would anticipate that changes in the genome, whether genetic or epigenetic, would be necessary implying a reversal of information flow from p... | Wikipedia - State switching - Inheritance of adaptive learning or phenotypic plasticity: Can information transfer be reversed (from phenotype to genotype)? | 341 | 1,742 | null |
Insofar as genetic changes are concerned, emerging evidence suggests that a nexus between transcription factors and chromatin remodelers, and between transcription factors and DNA repair proteins that are part of large PINs, can facilitate such changes. With regard to genetic assimilation, Waddington proposed that it i... | Wikipedia - State switching - Inheritance of adaptive learning or phenotypic plasticity: Can information transfer be reversed (from phenotype to genotype)? | 330 | 1,817 | null |
However, in either case, mutations that hold the key arise by chance and without foresight for the potential advantage or disadvantage of the mutation. Furthermore, the underlying implication would be a unidirectional flow of information from genotype to phenotype. On the other hand, in the scenario resulting from the ... | Wikipedia - State switching - Inheritance of adaptive learning or phenotypic plasticity: Can information transfer be reversed (from phenotype to genotype)? | 264 | 1,354 | null |
In fact, the inheritance of characteristics induced by the environment has often been opposed to the theory of evolution by natural selection. However, it is important to note that the emergence of non-conventional modes and the diversity of mechanisms for generating and transmitting variations such as the transmission... | Wikipedia - State switching - Inheritance of adaptive learning or phenotypic plasticity: Can information transfer be reversed (from phenotype to genotype)? | 305 | 1,627 | null |
The adaptation of the different schemes for processing variations is quantified for a range of fluctuating environments, following an approach that links quantitative genetics with stochastic control theory. When the authors conducted a Gedankenexperiment (German for a thought-experiment) that allowed them to compare t... | Wikipedia - State switching - Inheritance of adaptive learning or phenotypic plasticity: Can information transfer be reversed (from phenotype to genotype)? | 164 | 896 | null |
Article: Sterility (physiology). Sterility is the physiological inability to effect sexual reproduction in a living thing, members of whose kind have been produced sexually. Sterility has a wide range of causes. It may be an inherited trait, as in the mule; or it may be acquired from the environment, for example throug... | Wikipedia - Sterility (physiology) - Summary | 266 | 1,249 | null |
Section: Mechanisms of sterility. Hybrid sterility can be caused by different closely related species breeding and producing offspring. These animals are usually sterile due to the different numbers of chromosomes between the two parents. The imbalance results in offspring that is viable but not fertile, as is the case... | Wikipedia - Sterility (physiology) - Mechanisms of sterility | 233 | 1,146 | null |
Section: Economic uses of sterility. Economic uses of sterility include: The production of certain kinds of seedless fruit, such as seedless tomato or watermelon (though sterility is not the only available route to fruit seedlessness); Terminator technology, methods for restricting the use of genetically modified plant... | Wikipedia - Sterility (physiology) - Economic uses of sterility | 173 | 878 | null |
Section: Naming convention > Human Y-DNA. The Y Chromosome Consortium (YCC) developed a system of naming major human Y-DNA haplogroups with the capital letters A through T, with further subclades named using numbers and lower case letters (YCC longhand nomenclature). YCC shorthand nomenclature names Y-DNA haplogroups a... | Wikipedia - Subclade - Naming convention > Human Y-DNA | 187 | 889 | null |
Article: Synaptic tagging. Synaptic tagging, or the synaptic tagging hypothesis, has been proposed to explain how neural signaling at a particular synapse creates a target for subsequent plasticity-related product (PRP) trafficking essential for sustained LTP and LTD. Although the molecular identity of the tags remains... | Wikipedia - Synaptic tagging - Summary | 189 | 904 | null |
Section: History. Frey, a researcher at the Leibniz Institute for Neurobiology (later at the Medical College of Georgia and the Lund University), and Morris, a researcher at the University of Edinburgh, laid the groundwork for the synaptic tagging hypothesis, stating: "We propose that LTP initiates the creation of a sh... | Wikipedia - Synaptic tagging - History | 335 | 1,574 | null |
However, as Frey and Morris discovered, the tag is temporary and will disappear if no protein presents itself for capture. Therefore, the tag and protein production must overlap if L-LTP is to be induced by the high-frequency stimulation. The experiment performed by Frey and Morris involved the stimulation of two diffe... | Wikipedia - Synaptic tagging - History | 332 | 1,553 | null |
It involves late-associative interactions between LTP and LTD induced in sets of independent synaptic inputs: late-LTP induced in one set of synaptic inputs can transform early-LTD into late-LTD in another set of inputs. The opposite effect also occurs: early LTP induced in the first synapse can be transformed into lat... | Wikipedia - Synaptic tagging - History | 259 | 1,191 | null |
Section: mRNA trafficking to the dendritic spine and cytoskeleton. Synaptic tagging/ tag-and-capture theory potentially addresses the significant problem of explaining how mRNA, proteins, and other molecules may be specifically trafficked to certain dendritic spines during late phase LTP. It has long been known that th... | Wikipedia - Synaptic tagging - mRNA trafficking to the dendritic spine and cytoskeleton | 327 | 1,609 | null |
The alternate splicing mechanisms allow cells to produce a diverse set of proteins from a single gene within the genome. Recent developments in next-generation sequencing have allowed for greater understanding of the diversity eukaryotic cells achieve through splice variants. Transcribed mRNA must reach the intended de... | Wikipedia - Synaptic tagging - mRNA trafficking to the dendritic spine and cytoskeleton | 348 | 1,628 | null |
Section: Local protein synthesis. Since the 1980s, it has become more and more clear that the dendrites contain the ribosomes, proteins, and RNA components to achieve local and autonomous protein translation. Many mRNAs shown to be localized in the dendrites encode proteins known to be involved in LTP, including AMPA r... | Wikipedia - Synaptic tagging - Local protein synthesis | 348 | 1,616 | null |
Section: Possible tag models. Synaptic tagging is likely to involve the acquisition of molecular maintenance mechanisms by a synapse that would then allow for the conservation of synaptic changes. There are several proposed processes through which synaptic tagging functions. One model suggests that the tag allows for l... | Wikipedia - Synaptic tagging - Possible tag models | 342 | 1,743 | null |
Section: Behavioral tagging. While the concept of the synaptic tagging hypothesis mainly resulted from experiments applying stimulation to synapses, a similar model can be established considering the process of learning in a broader - behavioral - sense. Fabricio Ballarini and colleagues developed this behavioral taggi... | Wikipedia - Synaptic tagging - Behavioral tagging | 247 | 1,286 | null |
Article: Syntelic. Syntelic attachment occurs when both sister chromosomes are attached to a single spindle pole. Normal cell division distributes the genome equally between two daughter cells, with each chromosome attaching to an ovoid structure called the spindle. During the division process, errors commonly occur in... | Wikipedia - Syntelic - Summary | 151 | 789 | null |
Section: Causes. Microtubules extend from the spindle poles and attach to the first kinetochore they encounter. Because this process is stochastic and not facilitated or directed, the first microtubules to come into contact with a kinetochore may not have originated at the correct spindle pole. Normally, the sister kin... | Wikipedia - Syntelic - Causes | 317 | 1,559 | null |
Section: Error correction. Error correction is closely tied to the spindle assembly checkpoint (SAC), which oversees the progression through mitosis and can halt the cell in metaphase until proper bi-orientation of all chromosomes is achieved. Initial attachments occur randomly, and the cell destabilizes any incorrect ... | Wikipedia - Syntelic - Error correction | 309 | 1,441 | null |
Correct attachments that induce tension are more likely to occur when the kinetochores are geometrically positioned on opposite sides of the centromere. Robust destabilization by Ipl1/Aurora B in the absence of tension leads to a specific challenge: the initial establishment of bi-orientation, prior to the buildup of t... | Wikipedia - Syntelic - Error correction | 194 | 885 | null |
Section: Consequences. Syntelic attachment is not uncommon in early metaphase, and can often be resolved by error correction mechanisms that are well-conserved across metazoans. If syntelic attachment is left uncorrected, for example if the spindle assembly checkpoint does not successfully pause cells in metaphase, the... | Wikipedia - Syntelic - Consequences | 154 | 726 | null |
Article: Synthesis-dependent strand annealing. Synthesis-dependent strand annealing (SDSA) is a major mechanism of homology-directed repair of DNA double-strand breaks (DSBs). Although many of the features of SDSA were first suggested in 1976, the double-Holliday junction model proposed in 1983 was favored by many rese... | Wikipedia - Synthesis-dependent strand annealing - Summary | 325 | 1,560 | null |
After the transient RNA-DNA hybrid intermediate is formed the RNA strand is replaced by the Rad51 protein which catalyzes the subsequent stage of strand invasion. In the SDSA model, repair of double-stranded breaks occurs without the formation of a double Holliday junction, so that the two processes of homologous recom... | Wikipedia - Synthesis-dependent strand annealing - Summary | 307 | 1,419 | null |
Section: Enzymes employed in SDSA during meiosis. Assembly of a nucleoprotein filament comprising single-stranded DNA (ssDNA) and the RecA homolog, Rad51, is a key step necessary for homology search during recombination. In the budding yeast Saccharomyces cerevisiae, Srs2 translocase dismantles Rad51 filaments during m... | Wikipedia - Synthesis-dependent strand annealing - Enzymes employed in SDSA during meiosis | 340 | 1,271 | null |
Similarly, S. cerevisiae Sgs1, an ortholog of BLM, appears to be a central regulator of most of the recombination events that occur during S. cerevisiae meiosis. Sgs1(BLM) may disassemble D-loop structures analogous to early strand invasion intermediates and thus promote NCO formation by SDSA. The Sgs1 helicase forms a... | Wikipedia - Synthesis-dependent strand annealing - Enzymes employed in SDSA during meiosis | 336 | 1,277 | null |
Data based on tetrad analysis from several species of fungi show that only a minority (on average about 34%) of recombination events during meiosis are COs (see Whitehouse, Tables 19 and 38 for summaries of data from S. cerevisiae, Podospora anserina, Sordaria fimicola and Sordaria brevicollis). In the fruit fly D. mel... | Wikipedia - Synthesis-dependent strand annealing - Enzymes employed in SDSA during meiosis | 156 | 594 | null |
Article: Synthetic genetic array. Synthetic genetic array analysis (SGA) is a high-throughput technique for exploring synthetic lethal and synthetic sick genetic interactions (SSL). SGA allows for the systematic construction of double mutants using a combination of recombinant genetic techniques, mating and selection s... | Wikipedia - Synthetic genetic array - Summary | 247 | 1,230 | null |
Section: Procedure. Synthetic genetic array analysis is generally conducted using colony arrays on petriplates at standard densities (96, 384, 768, 1536). To perform a SGA analysis in S.cerevisiae, the query gene deletion is crossed systematically with a deletion mutant array (DMA) containing every viable knockout ORF ... | Wikipedia - Synthetic genetic array - Procedure | 155 | 719 | null |
Article: Synthetic lethality. Synthetic lethality is defined as a type of genetic interaction where the combination of two genetic events results in cell death or death of an organism. Although the foregoing explanation is wider than this, it is common when referring to synthetic lethality to mean the situation arising... | Wikipedia - Synthetic lethality - Summary | 279 | 1,425 | null |
Section: Background. The phenomenon of synthetic lethality was first described by Calvin Bridges in 1922, who noticed that some combinations of mutations in the model organism Drosophila melanogaster (the common fruit fly) confer lethality. Theodore Dobzhansky coined the term "synthetic lethality" in 1946 to describe t... | Wikipedia - Synthetic lethality - Background | 299 | 1,620 | null |
Section: High-throughput screens. High-throughput synthetic lethal screens may help illuminate questions about how cellular processes work without previous knowledge of gene function or interaction. Screening strategy must take into account the organism used for screening, the mode of genetic perturbation, and whether ... | Wikipedia - Synthetic lethality - High-throughput screens | 219 | 1,089 | null |
Section: DDR deficiencies > DNA mismatch repair deficiency. Mutations in genes employed in DNA mismatch repair (MMR) cause a high mutation rate. In tumors, such frequent subsequent mutations often generate "non-self" immunogenic antigens. A human Phase II clinical trial, with 41 patients, evaluated one synthetic lethal... | Wikipedia - Synthetic lethality - DDR deficiencies > DNA mismatch repair deficiency | 241 | 1,105 | null |
Section: DDR deficiencies > Werner syndrome gene deficiency. The analysis of 630 human primary tumors in 11 tissues shows that WRN promoter hypermethylation (with loss of expression of WRN protein) is a common event in tumorigenesis. The WRN gene promoter is hypermethylated in about 38% of colorectal cancers and non-sm... | Wikipedia - Synthetic lethality - DDR deficiencies > Werner syndrome gene deficiency | 345 | 1,537 | null |
Section: DDR deficiencies > Clinical and preclinical PARP1 inhibitor synthetic lethality. As reviewed by Murata et al., five different PARP1 inhibitors are now undergoing Phase I, II and III clinical trials, to determine if particular PARP1 inhibitors are synthetically lethal in a large variety of cancers, including th... | Wikipedia - Synthetic lethality - DDR deficiencies > Clinical and preclinical PARP1 inhibitor synthetic lethality | 188 | 750 | null |
Section: DDR deficiencies > Preclinical ARID1A synthetic lethality. ARID1A, a chromatin modifier, is required for non-homologous end joining, a major pathway that repairs double-strand breaks in DNA, and also has transcription regulatory roles. ARID1A mutations are one of the 12 most common carcinogenic mutations. Muta... | Wikipedia - Synthetic lethality - DDR deficiencies > Preclinical ARID1A synthetic lethality | 155 | 680 | null |
Section: Motivation. The rise of systems biology, seeking to comprehend biological processes as a whole, highlighted the need to not only develop corresponding quantitative models but also to create standards allowing their exchange and integration. This concern drove the community to design common data formats, such a... | Wikipedia - Systems Biology Ontology - Motivation | 254 | 1,296 | null |
Section: SBO and SBML. Since Level 2 Version 2 SBML provides a mechanism to annotate model components with SBO terms, therefore increasing the semantics of the model beyond the sole topology of interaction and mathematical expression. Modelling tools such as SBMLsqueezer interpret SBO terms to augment the mathematics i... | Wikipedia - Systems Biology Ontology - SBO and SBML | 227 | 1,095 | null |
Article: Three-point cross. In genetics, a three-point cross is used to determine the loci of three genes in an organism's genome. An individual heterozygous for three mutations is crossed with a homozygous recessive individual, and the phenotypes of the progeny are scored. The two most common phenotypes that result ar... | Wikipedia - Three-point cross - Summary | 314 | 1,432 | null |
Article: Transcription bubble. A transcription bubble is a molecular structure formed during the initialization of DNA transcription, when a limited portion of the DNA double helix is unwound, providing enough space for RNA polymerase (RNAP) to bind to the template strand and begin RNA synthesis. The transcription bubb... | Wikipedia - Transcription bubble - Summary | 256 | 1,255 | null |
Section: Formation > Prokaryotic initiation. In prokaryotes, three mechanisms of RNAP's promoter search have been observed to various extents: 1D sliding, intersegment transfer (1D diffusion mechanisms), and hopping (3D diffusion mechanism). While the extent that each mechanism contributes is uncertain, mechanism which... | Wikipedia - Transcription bubble - Formation > Prokaryotic initiation | 348 | 1,534 | null |
Section: Formation > Eukaryotic initiation. In eukaryotes, the search for loci to open transcription bubbles occur through the recruitment of general transcription factors to a promoter region and formation of the preinitiation complex (PIC). Once the PIC forms, the DNA duplex is melted, forming the transcription bubbl... | Wikipedia - Transcription bubble - Formation > Eukaryotic initiation | 333 | 1,550 | null |
Section: Termination > Prokaryotic termination. In Escherichia coli, the process of transcription termination via dissociation of the RNA polymerase have been found to depend on 3 possible mechanisms: an interaction between the polymerase and an intrinsic terminator sequence found on the hairpin loops of completed RNA,... | Wikipedia - Transcription bubble - Termination > Prokaryotic termination | 345 | 1,703 | null |
Section: Termination > Eukaryotic termination. Transcription termination by eukaryotic RNA polymerase I (Pol I) requires transcription termination factors similar to rho-dependent termination in prokaryotes. In mice, repeated terminators encoded on DNA are exposed as single-stranded binding sites for protein TTF-I once... | Wikipedia - Transcription bubble - Termination > Eukaryotic termination | 342 | 1,701 | null |
Section: Regulation > DNA sequence and supercoiling effects. Molecular dynamic simulations have found that the lifetime of the transcription bubble is sequence-dependent, and longer bubble lifetimes are associated with A-T rich core promoter sequences. The weaker A-T base interactions enable transcription bubbles to fo... | Wikipedia - Transcription bubble - Regulation > DNA sequence and supercoiling effects | 199 | 1,092 | null |
Section: Regulation > Role of transcription factors. The general transcription factors (GTFs) TFIIH function as key elements for transcription initiation in eukaryotic cells. The XPB and XPD helicase subunits of TFIIH enable DNA unwinding through DNA duplex translocation which produces single-stranded regions needed fo... | Wikipedia - Transcription bubble - Regulation > Role of transcription factors | 260 | 1,354 | null |
Section: Regulation > Epigenetic modifications and chromatin structure. Epigenetic modifications significantly influence chromatin structure and transcriptional activity. The acetylation of lysine 27 on histone 3 (H3K27ac) creates a less stable nucleosome structure, which leads to the formation of essential transcripti... | Wikipedia - Transcription bubble - Regulation > Epigenetic modifications and chromatin structure | 167 | 859 | null |
Section: Role in gene expression. In both eukaryotes and prokaryotes, multiple transcription start sites have been observed within the same promoter, and transcription bubble dynamics—such as expansion ("scrunching") and contraction ("unscrunching")—have been shown to play a role in the positioning of these variable tr... | Wikipedia - Transcription bubble - Role in gene expression | 332 | 1,622 | null |
Section: Evolutionary origins. The first DNA replication origins were hypothesized to be promoters for the 2-double-Ψ-β-barrel (2-DPBB) domains of RNAP. Replication was initiated using 2-DPBB type RNAPs followed by DNA synthesis with reverse transcriptase, providing the earliest known instances of transcription bubbles... | Wikipedia - Transcription bubble - Evolutionary origins | 328 | 1,635 | null |
Section: Pharmaceutical significance > Dactinomycin (Actinomycin D). Dactinomycin is a potent intercalating agent and chemotherapeutic drug that works by inhibiting RNA synthesis. It binds directly to single-stranded DNA in the transcription bubble, the region of DNA where transcription is actively occurring.First isol... | Wikipedia - Transcription bubble - Pharmaceutical significance > Dactinomycin (Actinomycin D) | 342 | 1,604 | null |
Section: Pharmaceutical significance > Rifampicin. Rifampicin is a widely used antibiotic that targets bacterial RNA polymerase, inhibiting its ability to synthesize RNA. It is particularly effective against Mycobacterium tuberculosis, the bacterium responsible for tuberculosis, and has been commonly used in combinatio... | Wikipedia - Transcription bubble - Pharmaceutical significance > Rifampicin | 181 | 952 | null |
Section: Mechanisms of transcriptional amplification. Gene expression is regulated by numerous types of proteins that directly or indirectly influence transcription by RNA Polymerase II. As opposed to transcriptional activators or repressors that selectively activate or repress specific genes, amplifiers of transcripti... | Wikipedia - Transcriptional amplification - Mechanisms of transcriptional amplification | 155 | 778 | null |
Section: Identifying and measuring transcriptional amplification. Commonly used gene expression experiments interrogate the expression of one gene (qPCR) or many genes (microarray, RNA-Seq). These techniques generally measure relative mRNA levels and employ normalization methods that assume only a small number of genes... | Wikipedia - Transcriptional amplification - Identifying and measuring transcriptional amplification | 167 | 924 | null |
Section: Role in disease. Transcriptional amplification has been implicated in cancer, Rett syndrome, heart disease, Down syndrome, and cellular aging. In cancer, Myc-driven transcriptional amplification is posited to help tumor cells overcome rate-limiting constraints in growth and proliferation. Drugs that target the... | Wikipedia - Transcriptional amplification - Role in disease | 197 | 967 | null |
Article: Transcriptome-wide association study. Transcriptome-wide association study (TWAS) is a genetic methodology that can be used to compare the genetic components of gene expression and the genetic components of a trait to determine if an association is present between the two components. TWAS are useful for the id... | Wikipedia - Transcriptome-wide association study - Summary | 177 | 994 | null |
Section: Transcriptome Analysis. A transcriptome is the sum of all RNA transcripts that are present in a given cell, tissue, or organ within an organism. Transcriptomes include both mRNA, which functions as an intermediate to the central dogma; as well as noncoding RNAs that may play other roles in protein synthesis. I... | Wikipedia - Transcriptome-wide association study - Transcriptome Analysis | 350 | 1,928 | null |
Section: Methods. A genome-wide association study, or GWAS, is a genetic tool that uses single nucleotide polymorphisms, or SNPs, to identify if a trait or disease is linked to a specific genetic variant. By observing if frequencies of a specific variant are more commonly associated, or higher than expected, with the g... | Wikipedia - Transcriptome-wide association study - Methods | 339 | 1,760 | null |
By predicting the levels of gene expression within a tissue, other variables such as environment and epigenetic effects are eliminated as this prediction is solely based on the variant present and the expected level of gene expression. However, this can lead to inaccuracies with gene expression predictions as both the ... | Wikipedia - Transcriptome-wide association study - Methods | 346 | 1,726 | null |
The Manhattan plot is named as such as the statistically significant genes appear to show up as "skyscrapers" on the plot, and when there are many genes that are associated with the trait, the plot resembles the Manhattan skyline. Although the Manhattan plot image is for a GWAS study, TWAS results are shown the same wa... | Wikipedia - Transcriptome-wide association study - Methods | 275 | 1,436 | null |
Section: Advantages. The advantages of this methodology are through the insight it gives researchers into the function of genes and the association between gene functions and gene expression. TWAS has the potential to take results from GWAS and extend the results to aid in the understanding of disease mechanisms. Addit... | Wikipedia - Transcriptome-wide association study - Advantages | 326 | 1,768 | null |
Section: Limitations. Many of the disadvantages of TWAS are implications of the prediction capabilities of the model used to predict gene expression levels based on genotypes. One disadvantage of TWAS is that it mainly looks at cis-genetic components for imputation and for in most studies, does not identify any trans-g... | Wikipedia - Transcriptome-wide association study - Limitations | 347 | 1,849 | null |
Even though a statistically significant association can be seen between the gene or loci of interest and the trait or disease, no causal relationship can be derived. In order to establish a causal relationship, further studies utilizing a reverse genetics approach for knock-outs of genes or site-directed mutagenesis wo... | Wikipedia - Transcriptome-wide association study - Limitations | 201 | 1,092 | null |
Section: Applications > Schizophrenia. A TWAS study was performed following a GWAS investigating loci associated with schizophrenia. From the GWAS results, over 100 risk loci were located. A TWAS was then used to identify 157 significant loci using expression data, and 35 of the identified loci from the TWAS did not al... | Wikipedia - Transcriptome-wide association study - Applications > Schizophrenia | 155 | 747 | null |
Section: Applications > Breast Cancer. In 2018, a TWAS was used to identify candidate causal genes for breast cancer. Data was collected from The Cancer Genome Atlas to establish genetic models as well as 229,000 women of European ancestry. In this study, 8,597 genes were evaluated. Through GWAS studies, around 170 loc... | Wikipedia - Transcriptome-wide association study - Applications > Breast Cancer | 272 | 1,271 | null |
Article: Transfer DNA binary system. A transfer DNA (T-DNA) binary system is a pair of plasmids consisting of a T-DNA binary vector and a vir helper plasmid. The two plasmids are used together (thus binary) to produce genetically modified plants. They are artificial vectors that have been derived from the naturally occ... | Wikipedia - Transfer DNA binary system - Summary | 286 | 1,164 | null |
Section: Background of Agrobacterium-mediated transformation > Ti plasmid. Agrobacterium contains a plasmid, a circular piece of DNA, called the "Tumor-inducing plasmid" ("Ti plasmid" for short). The Ti plasmid contains the following elements: The "T-DNA" region: The T-DNA region is the section of the plasmid that beco... | Wikipedia - Transfer DNA binary system - Background of Agrobacterium-mediated transformation > Ti plasmid | 331 | 1,404 | null |
Opine genes: The opine genes encode and force the plant cell to express enzymes that synthesize opine, a carbon- and nitrogen-rich compound that acts as a food source for Agrobacterium. After synthesis, the opines are secreted into the intercellular space and surrounding environment, allowing them to be taken-up by nea... | Wikipedia - Transfer DNA binary system - Background of Agrobacterium-mediated transformation > Ti plasmid | 347 | 1,381 | null |
Mechanisms of and machinery involved in gene expression differs in prokaryotic and eukaryotic organisms. Agrobacterium has evolved to contain eukaryotic gene elements in the T-DNA region which allows for the genes encoded in the region to be expressed by the plant cells. The remaining Ti plasmid adheres to regular prok... | Wikipedia - Transfer DNA binary system - Background of Agrobacterium-mediated transformation > Ti plasmid | 163 | 683 | null |
Section: Background of Agrobacterium-mediated transformation > Infection mechanism. The natural mechanism of Agrobacterium infection of plant cells is mediated via the 6 vir genes located on the Ti plasmid. The process of infection occurs in 2 general steps: Plant cell recognition and activation of vir gene expression:... | Wikipedia - Transfer DNA binary system - Background of Agrobacterium-mediated transformation > Infection mechanism | 323 | 1,465 | null |
This new strand pushes the original T-DNA strand away. As this occurs, single-stranded DNA binding proteins (ssDNA binding proteins), encoded by virE, bind along the length of the original T-DNA to stabilize it and prevent it from being degraded. Another virD endonuclease recognizes and cuts a strand in the LB, releasi... | Wikipedia - Transfer DNA binary system - Background of Agrobacterium-mediated transformation > Infection mechanism | 188 | 834 | null |
Section: Components of the binary vector system > Binary vector. A binary vector is used in plant genetic engineering to transfer foreign genes into plant cells. The reason for having two separate plasmids is because it is easier to clone and manipulation of genes of interest in E. coli using the T-DNA vector because i... | Wikipedia - Transfer DNA binary system - Components of the binary vector system > Binary vector | 305 | 1,475 | null |
A promoter is also introduced which drives the expression of the gene of interest within the plant cells. Commonly used promoters include the CaMV 35S promoter and the UBQ10 promoter for constitutive expression.Finally, a terminator sequence signals the end of transcription, ensuring that the gene is expressed properly... | Wikipedia - Transfer DNA binary system - Components of the binary vector system > Binary vector | 315 | 1,520 | null |
coli cells divide. Additionally, the binary vector contains an origin of replication for Agrobacterium, which is required to ensure that the plasmid can replicate within Agrobacterium cells. After cloning and amplification in E. coli, the plasmid is transferred into Agrobacterium for plant transformation. The origin of... | Wikipedia - Transfer DNA binary system - Components of the binary vector system > Binary vector | 171 | 824 | null |
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