TATA sequences

Figure 9.7 Sequence specific interactions between TBP and the TATA box. Asn 69 and Thr 124 from one domain and the equivalent residues Asn 159 and Thr 215 from the second domain interact with the palindromic TATA sequence of the central region of the TATA box.

These discontinuities in the TATA region may be an expression of structural features which are an inherent part of the TATA sequence possibly associated with stacking modifications. This might be of biological interest, since the base sequence TATA is one of the common signals which is used in the initiation of transcription by SNA polymerase. 

The TATA binding protein and general transcription initiation factors. A slow basal level of transcription can be observed when all but a small part of the control region at the 5 end of a gene is deleted.325 This minimum promoter, which includes the TATA sequence, is the binding site of both the RNA... 

Figure 28-13 (A) Stereoscopic ribbon drawing of the phyloge-netically conserved 180-residue C-terminal portion of the TATA-binding protein (TBP) from Arabidopsis thaliana. The sequence consists of two direct repeats, giving the protein an approximate twofold symmetry. From Nikolov et al.337 (B) Structure of the corresponding C-terminal core (residues 155-335) of the human TATA-binding protein (TBP) bound to the TATA sequence of a promoter in adenovirus DNA. From Nikolov et al.327 (C) Structure of human transcription factor IIB bound to a TBP from Arabidopsis thaliana, which, in turn, is bound to an adenovirus TATA sequence. Hypothetical B DNA extensions have been modeled at both ends of the DNA segment. The +1 at the left end is the transcription start site and the —43 upstream end is to the right. From Nikolov et al.338 Courtesy of Stephen K. Burley.

The first of these contains a TATA sequence, and both promoters also depend upon a 21-bp repeat segment as well as the SV40 enhancer. At least two proteins, one that binds to the enhancer and one that binds to the 21-bp repeat, are needed for initiation of early transcription. The early-late promoter lacks the TATA sequence but requires the 21-bp repeat and enhancer. 

Translation Initiation Site. In eukaryotes, if the transcription start site is known, and there is no intron interrupting the 5 UTR, Kozak s rule (Kozak, 1996) probably will locate the correct initiation codon in most cases. Splicing is normally absent in prokaryotes, yet because of the existence of multicitronic operons, promoter location is not the key information. Rather, the key is reliable localization of the ribosome binding site. The TATA sequence about 30 bp from the transcription start site may be used as a possible resource. 

It seems that this motif of hydration depends on the TATA sequence because the methyl groups are required for formation of the large rings consisting of water and 0(1) atoms. In other sequences like TTAA or in G/C sequences, such pentagons are unlikely to occur, and they have not thus far been observed. 

Moreover, the behavior of TATA sequences duplicated in different simulations appears to remain consistent. 

A simplified diagram of transcription is shown here. Double-stranded DNA (dsDNA) is shown as a long rectangle. RNA polymerase binds to a region of DNA called a core promoter The core promoter consists of all the DNA between the TATA sequence and the transcription start site. The core promoter is a short stretch of DNA that serves to bind and orient RNA polymerase, and the basal transcription factors. The TATA sequence, which is composed of only four nucleotides T A, T, and A), usually occurs about 25 base pairs upstream of the transcription start site. The TATA-binding protein is a special protein that binds to the TATA sequence prior to initiating transcription. 

The promoter has a sequence that is variable and indistinct. Not all promoters contain the TATA sequence. Some promoters contain the GC sequence, or other simple sequences. To highlight the important funebon of these simple sequences, they are usually called boxes," i.e., the TATA box or GC box. The GC box, which is only two nucleotides long, usually occurs 40-70 base pairs upstream of the transcription start site. The GC box is recognized by a special transcription factor called SPl. 

These events are illustrated in the simple diagram that follows. The region called the promoter consists of about 20 base pairs The promoter binds RNA polymerase. The transcription start site begins a few base pairs downstream of the promoter. The TATA sequence occurs about 30 base pairs upstream of the transcription start site. Response elements can reside a bit further, or quite a bit further, upstream of the TATA sequence. The sizes of the various regions in the diagram are not to scale ... 

Initiation of transcription ultimately leads to production of a primary transcript, which in higher eukaryotes is processed to form an mRNA. Alternative processing patterns can yield different mRNAs. One example comes from chicken skeletal muscle in which two forms of the muscle protein myosin, LCl and LC3, are produced. The myosin gene has two different TATA sequences that yield two different primary transcripts. These two transcripts are processed differently to form mRNA molecules encoding distinct forms of the protein (Figure 26-10). 

Chicken LC1/LC3 gene. Two distinct TATA sequences lead to production of different primary transcripts, which contain the same coding sequences. Two modes of intron excision lead to the formation of distinct mRNA molecules that encode proteins having different amino terminal regions and the same carboxy terminal regions. 

Before RNA polymerase II can begin transcribing a gene, transcription factors must assemble into a complex. The process begins when TFIID binds to a TATA sequence. TFIID, which consists of TBP (a TATA binding protein) and several associated proteins, binds to and unwinds the DNA duplex in the TATA sequence. Then TFHB binds and, later, TFIIE, TFIIH, and TFIU. TFIIF binds directly to RNA polymerase n. Because of phosphorylation reactions catalyzed by TFIIH, the RNA polymerase II becomes active and begins transcription. 

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