Structural Biochemistry/TATA-Binding Protein

Overview
RNA polymerase II accurately transcribes because of the TATA box's directions. TATA box is the core promoter's predominant DNA element. TATA-binding protein is what recognizes the TATA box. TATA-binding protein is found to have strong preferences for the TATA, shown through structural experiments and in vitro binding. Severe DNA bending is also induced by the TATA-binding protein. NC2 and Mot1p regulate the TATA-binding protein turnover at TATA boxes. It is proposed that the TATA-binding protein acts with NC2 and Mot1p to bend TATA and releases the TATA-binding protein at a more rapid pace from promoters of TATA. This occurs in vivo.

RNA polymerase II transcription: TATA, TFIID, and TATA-binding protein discovery
Using Drosophila melanogaster genes, David Hogness and Michael Goldberg discovered that the DNA sequences was found to be rich in A and T. This was also later found in many eukaryotic and viral genes. In eukaryotic genes, the sequences rich in A and T are present on the 5’ start site of mRNA. The TATA box was known as the ‘Goldberg-Hogness’ box, due to its discoverers. The TATA box is really important in the initiation of accurate transcription, which was underscored by mutational analysis. The first steps in assembling pol II pre-initiation complex was marked by the basal transcription factor recognizing the TATA box because of the TATA-binding protein. TATA and TATA-binding protein characterizes an unusual DNA-protein complex. TATA-promoters is a core promoter, which control viral genes, representing cellular promoter minorities. Five general factors that is required for in vitro transcription has been identified from the strong promoters of TATA box. TATA-binding protein and TFIID were the first to stably bind to the template in directing the assembly of pol II.


 * Based on the quality of TATA box, TATA-binding protein and TATA sequences can form stable complexes in vitro. This selects the pol II promoters to use in transcription.  TATA minor groove binding is mediated by the concave hydrophobic surfaces of TATA-binding surfaces.
 * The minor groove widens as the beta form goes in and out of the complex
 * The first T A step and in between the last 2 base pairs is inserted by two pairs of phenylalanine.  This creates sharp kinds and bending towards the major groove.
 * TATA-binding protein is enhanced because of the bending towards major groove.
 * Reduced bending is due to the sequence TATAAAAG.
 * A stable complex is yielded by slower isomerization.
 * TATA-binding protein and TATA dissociates slowly.
 * In vitro, compared to TATA sequences, TATA-binding protein shows less affinity to non-specific DNA.

In eukaryotic cells, few free TATA-binding proteins are found. TATA-binding protein can also be found in other complexes besides TFIID. Other elements, such as INR, MTE, DCE, and DPE do not contact TATA-binding protein, but they contact TAF of TFIID.

It is proposed that the role of in vivo TATA box for transcription of pol II is to help in dissociating TATA-binding protein of pol II promoters. NC2, ATPases BTAF1, or Mot1p regulators can regulate TATA-binding proteins to release TATA-binding protein quickly from TATA.

TATA-binding protein activity regulation
Gene specific regulators, basal transcription, and cofactors regulate TATA-binding protein activities. TFIIA is related to NC2 inhibition relief of basal transcription and activated transcription. TFIIA and TFIIB basal factors are blocked by NC2 and TATA-binding protein – TATA complex binding. Non-TATA sequences can be recognized by TATA-binding protein by structural changes due to NC2.

MOT1 is shown to positively and negatively regulate pol II transcription. Yeast genes encode Mot1p and NC2 subunits. Mot1p and TATA-binding protein complexes have a large affinity to DNA while it has a relaxed one for TATA. NC2 and TATA-binding protein complexes do not really prefer TATA sequences. NC2 and TATA-binding protein does not have BTAF1 in human chromatin. TATA-binding protein in pol II transcription is regulated by the collaboration of BTAF1 and NC2.

in vivo Dynamic Regulation of TATA-Binding Protein Mobility
Chromatin structures allow for cells to have TATA-binding protein activity. This activity is regulated by core promoters’ restricted access. Barriers from nucleosome promoters must be defeated. Experiments have shown that TATA binding sites are competed for by nucleosomes and TATA-binding protein. Some observations have shown that nucleosomes have low density in promoters.

Promoters containing TATA have highly regulated transcription and it is usually tissue-specific. In cells, it is very unlikely that TATA is the function that directs TATA-binding protein to PIC assembly. Van Werven et al. demonstrated that the turnover of TATA-binding protein to TATA promoters is largely significant, compared to promoters of non-TATA. This turnover is really dependent on Mo1p, as well as NC2, and SAGA action. Lacking in TATA sequences compared to promoters of pol II, promoters of pol I and pol III have lower TATA-binding protein turnover. These findings indicate that the TATA-binding protein turnover of pol II promoters is contributed by the sequence TATA.

Rapid TATA-Binding Protein Dissociation in vivo, Main Player: TATA
The bending of DNA is really important in distinguishing the functionality of TATA-binding protein between the promoters that contain TATA and the promoters that do not contain TATA. TATA box binding by TATA-binding protein is key in creating the DNA bent conformation. DNA's strained conformation can be released by BTAF1 and NC2, helping the TATA-binding protein dissociation with TATA. In humans, in vitro experiments have shown that NC2 can reduce this bending alone at sequences of TATA box.

It has been proposed that TATA-binding protein cannot be released as quickly as the promoters containing TATA, with the activities of BTAF1 and NC2. SAGA complexes may be involved in the removal of TATA-binding protein from promoters, which can inhibit the TATA-binding protein binding promoter in vitro.

Two Functional Classes, Eukaryotic Core Promoters Dissection
It has been shown that Mot1 and NC2 can repress TATA dependent transcription and activate DPE dependent transcription in insect cells. In yeast, TATA promoters are repressed by Mot1p and NC2. Yeast needs the SAGA complex for promoters containing TATA and recruitment of TATA-binding proteins. Developmentally regulated genes are promoted by promoters that contain TATA to initiate direct transcription at a specific site in mammalian cells. Yeast promoters that do not contain TATA are TFIID dependent.