The TATA box is considered a non-coding DNAsequence (also known as a cis-regulatory element). It was termed the "TATA box" as it contains a consensus sequence characterized by repeating T and A base pairs.[3] How the term "box" originated is unclear. In the 1980s, while investigating nucleotide sequences in mousegenomeloci, the Hogness box sequence was found and "boxed in" at the -31 position.[4] When consensusnucleotides and alternative ones were compared, homologous regions were "boxed" by the researchers.[4] The boxing in of sequences sheds light on the origin of the term "box".
The TATA box was first identified in 1978[1] as a component of eukaryotic promoters. Transcription is initiated at the TATA box in TATA-containing genes. The TATA box is the binding site of the TATA-binding protein (TBP) and other transcription factors in some eukaryotic genes. Gene transcription by RNA polymerase II depends on the regulation of the core promoter by long-range regulatory elements such as enhancers and silencers.[5] Without proper regulation of transcription, eukaryotic organisms would not be able to properly respond to their environment.
The TATA box was the first eukaryotic core promoter motif to be identified in 1978 by American biochemist David Hogness[1] while he and his graduate student, Michael Goldberg were on sabbatical at the University of Basel in Switzerland.[7] They first discovered the TATA sequence while analyzing 5' DNApromoter sequences in Drosophila,mammalian, and viral genes.[8][2] The TATA box was found in protein coding genes transcribed by RNA polymerase II.[2]
Evolutionary history
Most research on the TATA box has been conducted on yeast, human, and Drosophila genomes, however, similar elements have been found in archaea and ancient eukaryotes.[2] In archaea species, the promoter contains an 8 bp AT-rich sequence located ~24 bp upstream of the transcription start site. This sequence was originally called Box A, which is now known to be the sequence that interacts with the homologue of the archaeal TATA-binding protein (TBP). Also, even though some studies have uncovered several similarities, there are others that have detected notable differences between archaeal and eukaryotic TBP. The archaea protein exhibits a greater symmetry in its primary sequence and in the distribution of electrostatic charge, which is important because the higher symmetry lowers the protein's ability to bind the TATA box in a polar manner.[2]
Even though the TATA box is present in many eukaryotic promoters, it is not contained in the majority of promoters. One study found less than 30% of 1031 potential promoter regions contain a putative TATA box motif in humans.[9] In Drosophila, less than 40% of 205 core promoters contain a TATA box.[8] When there is an absence of the TATA box and TBP is not present, the downstream promoter element (DPE) in cooperation with the initiator element (Inr) bind to the transcription factor II D (TFIID), initiating transcription in TATA-less promoters. The DPE has been identified in three Drosophila TATA-less promoters and in the TATA-less human IRF-1 promoter.[10]
Features
Location
Promoter sequences vary between bacteria and eukaryotes. In eukaryotes, the TATA box is located 25 base pairsupstream of the start site that Rpb4/Rbp7 use to initiate transcription. In metazoans, the TATA box is located 30 base pairs upstream of the transcription start site.[5] While in yeast, S. cerevisiae, the TATA box has a variable position which can range from 40 to 100 bp upstream of the start site. The TATA box is also found in 40% of the core promoters of genes that code for the actin cytoskeleton and contractile apparatus in cells.[5]
The type of core promoter affects the level of transcription and expression of a gene. TATA-binding protein (TBP) can be recruited in two ways, by SAGA, a cofactor for RNA polymerase II, or by TFIID.[11] When promoters use the SAGA/TATA box complex to recruit RNA polymerase II, they are more highly regulated and display higher expression levels than promoters using the TFIID/TBP mode of recruitment.[11]
Analogous sequences
In bacteria, promoter regions may contain a Pribnow box, which serves an analogous purpose to the eukaryotic TATA box. The Pribnow box has a 6 bp region centered around the -10 position and an 8-12 bp sequence around the -35 region that are both conserved.[10]
A CAAT box (also CAT box) is a region of nucleotides with the following consensus sequence: 5’ GGCCAATCT 3’. The CAAT box is located about 75-80 bases upstream of the transcription initiation site and about 150 bases upstream of the TATA box. It binds transcription factors (CAAT TF or CTFs) and thereby stabilizes the nearby preinitiation complex for easier binding of RNA polymerases. CAAT boxes are rarely found in genes that express proteins ubiquitous in all cell types.[10]
Structure
Sequence and prevalence
Figure 2. Mechanism for transcription initiation at the TATA box. Transcription factors, TATA binding protein (TBP), and RNA polymerase II are all recruited to begin transcription.
The TATA box is a component of the eukaryotic core promoter and generally contains the consensus sequence 5'-TATA(A/T)A(A/T)-3'.[3] In yeast, for example, one study found that various Saccharomyces genomes had the consensus sequence 5'-TATA(A/T)A(A/T)(A/G)-3', yet only about 20% of yeast genes even contained the TATA sequence.[12] Similarly, in humans only 24% of genes have promoter regions containing the TATA box.[13] Genes containing the TATA-box tend to be involved in stress-responses and certain types of metabolism and are more highly regulated when compared to TATA-less genes.[12][14] Generally, TATA-containing genes are not involved in essential cellular functions such as cell growth, DNA replication, transcription, and translation because of their highly regulated nature.[14]
The TATA box is usually located 25-35 base pairs upstream of the transcription start site. Genes containing the TATA box usually require additional promoter elements, including an initiator site located just upstream of the transcription start site and a downstream core element (DCE).[3] These additional promoter regions work in conjunction with the TATA box to regulate initiation of transcription in eukaryotes.
Function
Role in transcription initiation
The TATA-box is the site of preinitiation complex formation, which is the first step in transcription initiation in eukaryotes. Formation of the preinitiation complex begins when the multi-subunit transcription factor II D (TFIID) binds to the TATA box at its TATA-binding protein (TBP) subunit.[3] TBP binds to the minor groove[15] of the TATA box via a region of antiparallel β sheets in the protein.[16] Three types of molecular interactions contribute to TBP binding to the TATA box:
Four phenylalanine residues(Phe57, Phe74, Phe148, Phe 165) on TBP bind to DNA and form kinks in the DNA, forcing the DNA minor groove open.[16][17][18]
Additionally, binding of TBP is facilitated by stabilizing interactions with DNA flanking the TATA box, which consists of G-C rich sequences.[19] These secondary interactions induce bending of the DNA and helical unwinding.[20] The degree of DNA bending is species and sequence dependent. For example, one study used the adenovirus TATA promoter sequence (5'-CGCTATAAAAGGGC-3') as a model binding sequence and found that human TBP binding to the TATA box induced a 97° bend toward the major groove while the yeast TBP protein only induced an 82° bend.[21]X-ray crystallography studies of TBP/TATA-box complexes generally agree that the DNA goes through an ~80° bend during the process of TBP-binding.[16][17][18]
The conformational changes induced by TBP binding to the TATA box allows for additional transcription factors and RNA polymerase II to bind to the promoter region. TFIID first binds to the TATA box, facilitated by TFIIA binding to the upstream part of the TFIID complex.[22][23]TFIIB then binds to the TFIID-TFIIA-DNA complex through interactions both upstream and downstream of the TATA box.[24]RNA polymerase II is then recruited to this multi-protein complex with the help of TFIIF.[24] Additional transcription factors then bind, first TFIIE and then TFIIH.[24] This completes the assembly of the preinitiation complex for eukaryotic transcription.[3] Generally, the TATA box is found at RNA polymerase II promoter regions, although some in vitro studies have demonstrated that RNA polymerase III can recognize TATA sequences.[25]
This cluster of RNA polymerase II and various transcription factors is known as the basal transcriptional complex (BTC). In this state, it only gives a low level of transcription. Other factors must stimulate the BTC to increase transcription levels.[2] One such example of a BTC stimulating region of DNA is the CAAT box. Additional factors, including the Mediator complex, transcriptional regulatory proteins, and nucleosome-modifying enzymes also enhance transcriptionin vivo.[3]
Interactions
In specific cell types or on specific promoters TBP can be replaced by one of several TBP-related factors (TRF1 in Drosophila, TBPL1/TRF2 in metazoans, TBPL2/TRF3 in vertebrates), some of which interact with the TATA box similar to TBP.[26] Interaction of TATA boxes with a variety of activators or repressors can influence the transcription of genes in many ways[citation needed]. Enhancers are long-range regulatory elements that increase promoter activity while silencers repress promoter activity.
Mutations
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.[27] Point mutations risk the TBP being unable to bind for initiation.[28]
One of the first studies of TATA box mutations looked at a sequence of DNA from Agrobacterium tumefaciens for the octopine type cytokinin gene.[27] This specific gene has three TATA boxes. A phenotype change was only observed when all three TATA boxes were deleted. An 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 to the sequence. The nature of the resulting phenotype may be affected due to the insertion.
Savinkova et al. has written a simulation to predict the KD value for a selected TATA box sequence and TBP.[38] This can be used to directly predict the phenotypic traits resulting from a selected mutation based on how tightly TBP is binding to the TATA box.
Gastric cancer is correlated with TATA box polymorphism.[39] 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 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.[40] 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 (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 neuronal cells.
Blindness can be caused by excessive cataract formation when the TATA box is targeted by microRNAs to increase the level of oxidative stress genes.[41] MicroRNAs can target the 3'-untranslated region and bind to the TATA box to activate the transcription of oxidative stress related genes.
SNPs in TATA boxes are associated with B-thalassemia, immunosuppression, and other neurological disorders.[42]SNPs destabilize the TBP/TATA complex which significantly decreases the rate at which TATA-binding proteins (TBP) will bind to the TATA box. This leads to lower levels of 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.
MicroRNAs also play a role in replicating viruses such as HIV-1.[44] 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.
Clinical significance
Technology
Many of the studies so far have been performed in vitro, providing only a prediction of what may happen not a real-time representation of what is happening in the cells. Recent studies in 2016 have been done to demonstrate TATA-binding activity in vivo. Core promoter-specific mechanisms for transcription initiation by the canonical TBP/TFIID-dependent basal transcription machinery has recently been documented in vivo showing the activation by SRF-dependent upstream activating sequence (UAS) of the human ACTB gene involved in TATA-binding.[5]
Evolutionary changes have pushed plants to adapt to the changing environmental conditions. In the history of Earth, the development of Earth's aerobic atmosphere resulted in an iron deficiency in plants.[46] Compared to other members of the same species, Malus baccata var. xiaojinensis has a TATA box inserted in the promoter upstream of the iron-regulated transporter 1 (IRT1) promoter. As a result, the promoter activity levels are enhanced, increasing TFIID activity and subsequently transcription initiation, resulting in a more iron-efficient phenotype.[46]
^ abcLifton RP, Goldberg ML, Karp RW, Hogness DS (1978). "The organization of the histone genes in Drosophila melanogaster: functional and evolutionary implications". Cold Spring Harbor Symposia on Quantitative Biology. 42 (2): 1047–51. doi:10.1101/sqb.1978.042.01.105. PMID98262.
^ abcdefWatson, James D. (2014). Molecular biology of the gene. Watson, James D., 1928- (Seventh ed.). Boston. ISBN9780321762436. OCLC824087979.{{cite book}}: CS1 maint: location missing publisher (link)
^Fei YJ, Stoming TA, Efremov GD, Efremov DG, Battacharia R, Gonzalez-Redondo JM, Altay C, Gurgey A, Huisman TH (June 1988). "Beta-thalassemia due to a T----A mutation within the ATA box". Biochemical and Biophysical Research Communications. 153 (2): 741–7. doi:10.1016/S0006-291X(88)81157-4. PMID3382401.
^Bower GC (1978). "The award of the Will Ross Medal for 1978". The American Review of Respiratory Disease. 118 (3): 635–636. PMID360896.
^De Re V, Magris R, De Zorzi M, Maiero S, Caggiari L, Fornasarig M, Repetto O, Buscarini E, Di Mario F (2017). "P.08.10: Interference of PG2 Tata Box Region with the Serum PG2 Level in Gastric Cancer". Digestive and Liver Disease. 49: e182–e183. doi:10.1016/s1590-8658(17)30534-0. S2CID79101992.
^Žaja O, Tiljak MK, Štefanović M, Tumbri J, Jurčić Z (May 2014). "Correlation of UGT1A1 TATA-box polymorphism and jaundice in breastfed newborns-early presentation of Gilbert's syndrome". The Journal of Maternal-Fetal & Neonatal Medicine. 27 (8): 844–50. doi:10.3109/14767058.2013.837879. PMID23981182. S2CID29893463.
^ abcHurley LH (March 2002). "DNA and its associated processes as targets for cancer therapy". Nature Reviews. Cancer. 2 (3): 188–200. doi:10.1038/nrc749. PMID11990855. S2CID24209612.
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