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TATA box
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== Mutations == [[File:Mutation_mechanism.png|thumb|612x612px|'''Figure 3.''' Effects on TBP binding to the TATA box from mutations. Wildtype shows transcription done normally. An insertion or deletion shifts the TATA box recognition site which results in a shifted transcription site.<ref name=":5">{{cite journal | vauthors = Chioin R, Stritoni P, Scognamiglio R, Boffa GM, Daliento L, Razzolini R, Ramondo A, Dalla Volta S | title = [Natural history of coronary disease with and without aortocoronary by-pass operation. Survival curves of 272 patients over a maximum period of 24 months (author's transl)] | journal = Giornale Italiano di Cardiologia | volume = 8 | issue = 4 | pages = 359–64 | date = 1987 | pmc = 306359 | pmid=3671084| doi = 10.1093/nar/15.20.8283 }}</ref> Point mutations risk the TBP being unable to bind for initiation.<ref name=":6">{{cite journal | vauthors = Gaillard J, Haguenauer JP, Romanet P, Boulud B, Gerard JP | title = [Tumors of the olfactory placode. Study of 5 cases] | journal = Journal Français d'Oto-Rhino-Laryngologie; Audiophonologie, Chirurgie Maxillo-Faciale | volume = 26 | issue = 9 | pages = 669–76 | date = November 1977 | pmc = 146060 | pmid=8760900| doi = 10.1093/nar/24.15.3100 }}</ref>]] [[Mutation]]s to the TATA box can range from a [[Deletion (genetics)|deletion]] or [[Insertion (genetics)|insertion]] to a [[point mutation]] with varying effects based on the gene that has been mutated. The [[mutation]]s change the binding of the [[TATA-binding protein|TATA-binding protein (TBP)]] for [[Transcription (biology)|transcription]] initiation. Thus, there is a resulting change in [[phenotype]] based on the gene that is not being [[Gene expression|expressed]] (Figure 3). === Insertions or deletions === One of the first studies of TATA box [[mutation]]s looked at a sequence of DNA from ''[[Agrobacterium tumefaciens]]'' for the octopine type [[Cytokinin signaling and response regulator protein|cytokinin gene]].<ref name=":5" /> This specific gene has three TATA boxes. A [[phenotype]] change was only observed when all three TATA boxes were deleted. An [[Insertion (genetics)|insertion]] of extra base pairs between the last TATA box and the transcription start site resulted in a shift in the start site; thus, resulting in a phenotypic change. From this original [[mutation]] study, a change in transcription can be seen when there is no TATA box to promote transcription, but transcription of a gene will occur when there is an [[Insertion (genetics)|insertion]] to the sequence. The nature of the resulting phenotype may be affected due to the [[Insertion (genetics)|insertion]]. [[Mutation]]s in [[maize]] [[Promoter (genetics)|promoters]] affect the expression of the [[Promoter (genetics)|promoter]] [[gene]]s in a plant-organ-specific manner.<ref name=":19">{{cite journal | vauthors = Kloeckener-Gruissem B, Vogel JM, Freeling M | title = The TATA box promoter region of maize Adh1 affects its organ-specific expression | journal = The EMBO Journal | volume = 11 | issue = 1 | pages = 157–66 | date = January 1992 | pmid = 1740103 | pmc=556436| doi = 10.1002/j.1460-2075.1992.tb05038.x }}</ref> A [[Duplication (chromosomal)|duplication]] of the TATA box leads to a significant decrease in [[Enzyme|enzymatic activity]] in the [[Scutellum (botany)|scutellum]] and [[root]]s, leaving [[pollen]] enzymatic levels unaffected. A [[Deletion (genetics)|deletion]] of the TATA box leads to a small decrease in [[Enzyme|enzymatic activity]] in the [[Scutellum (botany)|scutellum]] and [[root]]s, but a large decrease in [[Enzyme|enzymatic levels]] in [[pollen]].<ref name=":19" /> === Point mutations === Point mutations to the TATA box have similar varying [[Phenotype|phenotypic]] changes depending on the gene that is being affected. Studies also show that the placement of the [[mutation]] in the TATA box sequence hinders the binding of [[TATA-binding protein|TBP]].<ref name=":6" /> For example, a [[mutation]] from TATAAAA to CATAAAA does completely hinder the binding sufficiently to change [[Transcription (biology)|transcription]], the neighboring sequences can affect if there is a change or not.<ref>{{cite journal | vauthors = Fei YJ, Stoming TA, Efremov GD, Efremov DG, Battacharia R, Gonzalez-Redondo JM, Altay C, Gurgey A, Huisman TH | title = Beta-thalassemia due to a T----A mutation within the ATA box | journal = Biochemical and Biophysical Research Communications | volume = 153 | issue = 2 | pages = 741–7 | date = June 1988 | pmid = 3382401 | doi = 10.1016/S0006-291X(88)81157-4 }}</ref> However, a change can be seen in [[HeLa]] cells with a TATAAAA to TATACAA which leads to a 20 fold decrease in [[Transcription (biology)|transcription]].<ref>{{cite journal | vauthors = Bower GC | title = The award of the Will Ross Medal for 1978 | journal = The American Review of Respiratory Disease | year = 1978 | volume = 118 | issue = 3 | pages = 635–636 | pmid= 360896 }}</ref> Some diseases that can be caused due to this insufficiency by specific gene [[Transcription (biology)|transcription]] are: [[Thalassemia]],<ref name="pmid6583702">{{cite journal | vauthors = Antonarakis SE, Irkin SH, Cheng TC, Scott AF, Sexton JP, Trusko SP, Charache S, Kazazian HH | title = beta-Thalassemia in American Blacks: novel mutations in the "TATA" box and an acceptor splice site | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 81 | issue = 4 | pages = 1154–8 | year = 1984 | pmid = 6583702 | pmc = 344784 | doi = 10.1073/pnas.81.4.1154| bibcode = 1984PNAS...81.1154A | doi-access = free }}</ref> [[lung cancer]],<ref>{{cite journal | vauthors = Zienolddiny S, Ryberg D, Maggini V, Skaug V, Canzian F, Haugen A | title = Polymorphisms of the interleukin-1 beta gene are associated with increased risk of non-small cell lung cancer | journal = International Journal of Cancer | volume = 109 | issue = 3 | pages = 353–6 | date = April 2004 | pmid = 14961572 | doi = 10.1002/ijc.11695 | doi-access = free }}</ref> [[Hemolytic anemia|chronic hemolytic anemia]],<ref>{{cite journal | vauthors = Hildebrandt P | title = Subcutaneous absorption of insulin in insulin-dependent diabetic patients. Influence of species, physico-chemical properties of insulin and physiological factors | journal = Danish Medical Bulletin | volume = 38 | issue = 4 | pages = 337–46 | date = August 1991 | pmc = 1914533 | pmid=8571957}}</ref> [[immunosuppression]],<ref>{{cite journal | vauthors = Takahashi K, Ezekowitz RA | title = The role of the mannose-binding lectin in innate immunity | journal = Clinical Infectious Diseases | volume = 41 | pages = S440–4 | date = November 2005 | issue = Suppl 7 | pmid = 16237644 | doi = 10.1086/431987 | doi-access = free }}</ref> [[Haemophilia B|hemophilia B Leyden]],<ref>{{cite journal | vauthors = Sweet D, Golomb H, Desser R, Ultmann JE, Yachnin S, Stein R | title = Letter: Chemotherapy of advanced histocytic lymphomas | journal = Lancet | volume = 1 | issue = 7916 | pages = 6300–3 | date = May 1975 | pmc = 49488 | doi=10.1016/s0140-6736(75)92521-0 | pmid=1631121}}</ref> and [[thrombophlebitis]] and [[myocardial infarction]].<ref>{{cite journal | vauthors = Arnaud E, Barbalat V, Nicaud V, Cambien F, Evans A, Morrison C, Arveiler D, Luc G, Ruidavets JB, Emmerich J, Fiessinger JN, Aiach M | title = Polymorphisms in the 5' regulatory region of the tissue factor gene and the risk of myocardial infarction and venous thromboembolism: the ECTIM and PATHROS studies. Etude Cas-Témoins de l'Infarctus du Myocarde. Paris Thrombosis case-control Study | journal = Arteriosclerosis, Thrombosis, and Vascular Biology | volume = 20 | issue = 3 | pages = 892–8 | date = March 2000 | pmid = 10712418 | doi = 10.1161/01.ATV.20.3.892 | doi-access = free }}</ref> Savinkova et al. has written a simulation to predict the ''[[Dissociation constant|K<sub>D</sub>]]'' value for a selected TATA box sequence and [[TATA-binding protein|TBP]].<ref name=":1">{{cite journal | vauthors = Savinkova L, Drachkova I, Arshinova T, Ponomarenko P, Ponomarenko M, Kolchanov N | title = An experimental verification of the predicted effects of promoter TATA-box polymorphisms associated with human diseases on interactions between the TATA boxes and TATA-binding protein | journal = PLOS ONE | volume = 8 | issue = 2 | pages = e54626 | date = 2013 | pmid = 23424617 | pmc = 3570547 | doi = 10.1371/journal.pone.0054626 | bibcode = 2013PLoSO...854626S | doi-access = free }}</ref> This can be used to directly predict the [[Phenotype|phenotypic]] traits resulting from a selected [[mutation]] based on how tightly [[TATA-binding protein|TBP]] is binding to the TATA box. === Diseases === [[Mutation]]s in the TATA box region affects the binding of the [[TATA-binding protein|TATA-binding protein (TBP)]] for transcription initiation, which may cause carriers to have a [[disease]] [[phenotype]]. [[Stomach cancer|Gastric cancer]] is correlated with TATA box [[Polymorphism (biology)|polymorphism]].<ref>{{cite journal| vauthors = De Re V, Magris R, De Zorzi M, Maiero S, Caggiari L, Fornasarig M, Repetto O, Buscarini E, Di Mario F | title = P.08.10: Interference of PG2 Tata Box Region with the Serum PG2 Level in Gastric Cancer|journal=Digestive and Liver Disease|volume=49|pages=e182–e183 | doi=10.1016/s1590-8658(17)30534-0| year=2017| s2cid = 79101992}}</ref> The TATA box has a binding site for the [[transcription factor]] of the PG2 gene. This gene produces PG2 serum, which is used as a [[biomarker]] for [[Neoplasm|tumours]] in gastric cancer. Longer TATA box sequences correlates with higher levels of PG2 serum indicating gastric cancer conditions. Carriers with shorter TATA box sequences may produce lower levels of PG2 serum. Several [[neurodegenerative disorders]] are associated TATA box mutations.<ref>{{cite journal | vauthors = Roshan R, Choudhary A, Bhambri A, Bakshi B, Ghosh T, Pillai B | title = microRNA dysregulation in polyglutamine toxicity of TATA-box binding protein is mediated through STAT1 in mouse neuronal cells | journal = Journal of Neuroinflammation | volume = 14 | issue = 1 | pages = 155 | date = August 2017 | pmid = 28774347 | doi = 10.1186/s12974-017-0925-3 | pmc=5543588 | doi-access = free }}</ref> Two disorders have been highlighted, [[spinocerebellar ataxia]] and [[Huntington's disease]]. In spinocerebellar ataxia, the disease phenotype is caused by expansion of the polyglutamine repeat in the [[TATA-binding protein|TATA-binding protein (TBP)]]. An accumulation of these polyglutamine-TBP cells will occur, as shown by protein aggregates in brain sections of patients, resulting in a loss of [[Neuron|neuronal cells]]. [[Visual impairment|Blindness]] can be caused by excessive [[cataract]] formation when the TATA box is targeted by [[microRNA]]s to increase the level of oxidative stress genes.<ref>{{cite journal | vauthors = Wu C, Liu Z, Ma L, Pei C, Qin L, Gao N, Li J, Yin Y | title = MiRNAs regulate oxidative stress related genes via binding to the 3' UTR and TATA-box regions: a new hypothesis for cataract pathogenesis | journal = BMC Ophthalmology | volume = 17 | issue = 1 | pages = 142 | date = August 2017 | pmid = 28806956 | doi = 10.1186/s12886-017-0537-9 | pmc=5556341 | doi-access = free }}</ref> MicroRNAs can target the [[Three prime untranslated region|3'-untranslated region]] and bind to the TATA box to activate the [[Transcription (biology)|transcription]] of oxidative stress related genes. [[Single-nucleotide polymorphism|SNPs]] in TATA boxes are associated with [[Thalassemia|B-thalassemia]], [[immunosuppression]], and other [[neurological disorder]]s.<ref>{{cite journal | vauthors = Drachkova I, Savinkova L, Arshinova T, Ponomarenko M, Peltek S, Kolchanov N | title = The mechanism by which TATA-box polymorphisms associated with human hereditary diseases influence interactions with the TATA-binding protein | journal = Human Mutation | volume = 35 | issue = 5 | pages = 601–8 | date = May 2014 | pmid = 24616209 | doi = 10.1002/humu.22535 | s2cid = 19928327 | doi-access = free }}</ref> [[Single-nucleotide polymorphism|SNPs]] destabilize the TBP/TATA complex which significantly decreases the rate at which [[TATA-binding protein|TATA-binding proteins (TBP)]] will bind to the TATA box. This leads to lower levels of [[Transcription (biology)|transcription]] affecting the severity of the disease. Results from studies have shown the interaction in vitro so far, but results may be comparable to that in vivo. [[Gilbert's syndrome]] is correlated with UTG1A1 TATA box [[Polymorphism (biology)|polymorphism]].<ref>{{cite journal | vauthors = Žaja O, Tiljak MK, Štefanović M, Tumbri J, Jurčić Z | title = Correlation of UGT1A1 TATA-box polymorphism and jaundice in breastfed newborns-early presentation of Gilbert's syndrome | journal = The Journal of Maternal-Fetal & Neonatal Medicine | volume = 27 | issue = 8 | pages = 844–50 | date = May 2014 | pmid = 23981182 | doi = 10.3109/14767058.2013.837879 | s2cid = 29893463 }}</ref> This poses a risk for developing jaundice in newborns. [[MicroRNA]]s also play a role in replicating [[virus]]es such as [[Subtypes of HIV|HIV-1]].<ref>{{cite journal | vauthors = Zhang Y, Fan M, Geng G, Liu B, Huang Z, Luo H, Zhou J, Guo X, Cai W, Zhang H | title = A novel HIV-1-encoded microRNA enhances its viral replication by targeting the TATA box region | journal = Retrovirology | volume = 11 | pages = 23 | date = March 2014 | pmid = 24620741 | pmc = 4007588 | doi = 10.1186/1742-4690-11-23 | doi-access = free }}</ref> Novel HIV-1-encoded microRNA have been found to enhance the production of the virus as well as activating HIV-1 latency by targeting the TATA box region.
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