Promoter eukaryotic, location

Archaebacterial RNA polymerases are very different from their eubacterial counterparts and more closely resemble eukaryotic enzymes both in their subunit complexity and in their amino acid sequences (for review, see Puehler et al., 1989). This view is also reflected in the diversity of the DNA sequences that are used by the transcription apparatus as signals for initiation of transcription, namely, the promoters. Many attempts were made to identify a consensus promoter structure (Zillig et al., 1988). However, as more genes are isolated and characterized, the picture becomes less coherent. Earlier identification of two upstream sequences, box A and box B, located around positions — 30 and + 1, respectively, gave way to two elements —DPE (distal promoter element) and PPE (proximal promoter element)—located - 38 to - 25 and — 11 to — 2, respectively (Reiter et al., 1990). The DPE encompasses the box A sequence TTTA(A or T)A, but the PPE sequence seems to depend more on an (A + T)-rich sequence rather than on a specific DNA sequence. 

Additional promoters are located between -40 and -110. Most of these contain a CAAT box [5 GG(C, T)CCA(A, T)CT3 ] and some a GC box (5,GGGCG3, or CCGCCC). Very little is known about eukaryotic mRNA termination. It apparently occurs hundreds or even thousands of nucleotides downstream. The 3 ends of mRNA are produced mainly by processing (see later). 

A third class of sequence elements can either increase or decrease the rate of transcription initiation of eukaryotic genes. These elements are called either enhancers or repressors (or silencers), depending on which effect they have. They have been found in a variety of locations both upstream and downstream of the transcription start site and even within the transcribed portions of some genes. In contrast to proximal and upstream promoter elements, enhancers and silencers can exert their effects when located hundreds or even thousands of bases away from transcription units located on the same chromosome. Surprisingly, enhancers and silencers can function in an orientation-independent fashion. Literally hundreds of these elements have been described. In some cases, the sequence requirements for binding are rigidly constrained in others, considerable sequence variation is... 

The structure and sequence of the catalytic moiety have been determined (06, V6, W6). The enzyme consists of 362 amino acids and 40,638 daltons of the protein predicted by the cDNA sequence. The ADA gene spans 32 kb and consists of 12 exons. The apparent promoter region of the gene lacks the TATA and CAAT sequences often found in eukaryotic promoters and is extremely G/C rich. The location of the ADA gene is on chromosome 20ql2-ql3.11 (Jl). 

Activator proteins (and a few repressors) are important in eukaryotes, as they are in prokaryotes. The DNA sequences to which activator proteins bind in eiikaryotic DNA are called response elements. A few response elements are located within the promoter region (upstream promoter elements [UPE]), but most are outside the promoter and often clustered to form an enhancer region that allows control of gene expression by multiple signals (Figure 1-5-4). 

Eukaryotic ribosomes contain four pieces of RNA (Tables 5-4 and 29-1), which are usually designated by their sedimentation coefficients. Tire 18S, 5.8S, and 28S RNAs are encoded as single transcriptional units with spacers separating the sequences that encode the mature RNAs. A typical animal cell contains several hundred copies of this transcriptional unit, all located in the DNA in the nucleolus (Fig. 28-15), and each having its own set of promoter sequences, enhancers, and transcription factors.47 520 522 The promoter sequences vary substantially among different species.523 The primary transcripts from these units are the sole product of RNA polymerase I. 

In Eukaryotes Promoter Elements Are Located at a Considerable Distance from the Polymerase Binding Site... 

The rRNA promoter consists of a core element which straddles the transcriptional start site (designated as position +1) from residues -31 to +6 plus an upstream control element (UCE) about 50-80 bp in size and located about 100 bp upstream from the start site (i.e. at position -100 Fig. 4b). A transcription factor called upstream binding factor (UBF) binds both to the UCE as well as to a region next to and overlapping with the core element. Interestingly, TATA box binding protein (TBP see Topic G6), also binds to the rRNA promoter (in fact, TBP is required for initiation by all three eukaryotic RNA polymerases). The UBF and TBP transcription factors interact with each other and with RNA Pol I to form a transcription initiation complex. The RNA Pol I then transcribes... 

In eukaryotes, the tRNA genes exist as multiple copies and are transcribed by RNA polymerase III (RNA Pol III). As in prokaryotes, several tRNAs may be transcribed together to yield a single pre-tRNA molecule that is then processed to release the mature tRNAs. The promoters of eukaryotic tRNA genes are unusual in that the transcriptional control elements are located downstream (i.e. on the 3 side) of the transcriptional start site (at position +1). In fact they lie within the gene itself. Two such elements have been identified, called the A box and B box (Fig. 3). Transcription of the tRNA genes by RNA Pol III requires transcription factor IIIC (TFIIIC) as well as TFIIIB. THIIC binds to the A and B boxes whilst TFIIIB binds upstream of the A box. TFIIIB contains three subunits, one of which is TBP (TATA binding protein), the polypeptide required by all three eukaryotic RNA polymerases. 

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. 

As in the TATA box, which is a TATA-rich region located upstream from the RNA-synthesis initiation site in eukaryotes and within the promoter region for the gene in question analogous to the Pribnow box in prokaryotes... 

Promoters for RNA polymerase II, like those for bacterial polymerases, are located on the 5 side of the start site for transcription. The results of mutagenesis experiments, footprinting studies, and comparisons of many higher eukaryotic... 

---