Upstream Sequences

As each of these identified immediate upstream sequences seems to be unique (although potential homologies can be identified), each will be independently discussed. Finally, we will only deal with those sequences which have been demonstrated by mutational analysis to have effects on transcription. 

Herpes simplex virus thymidine kinase -105 to -81 -61 to -48 Simian virus 40 early -113 to -93 -92 to -72 -71 to -50 Simian virus 40 late -285 to -264 -263 to -243 -242 to -222 Human ai-globin  

Herpes Simplex Virus Thymidine Kinase Promoter 

The italicized bases are those shown to be required for full activity. 

Both the -100 and - 50 regions consist in part of stretches of GC base pairs. In fact, the sequences are largely inverted repeats of one another. The GC-rich portions show some homology to the -100 region of (3-globin control region (see Table 1). However, sequences beyond the GC-rich stretches are definitely required for activity. 

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Gurley, W.B., Czarnecka, E., Nagao, R.T. Key, J.L. (1986). Upstream sequences required for efficient expression of a soybean heat shock gene. Molecular and Cellular Biology, 6, 559-65. 

Kim, C. H., Kim, H. S., Cubells, J. F., 8c Kim, K. S. (1999). A previously undescribed intron and extensive 5 upstream sequence, but not Phox2a-mediated transactivation, are necessary for high level cell type-specific expression of the human norepinephrine transporter gene. /. Biol. Chem., 274, 6507-18. 

Kress, C., Vogels, R DeGraff, W Bonnerot, C., Meijlink, F and Deschamps, J. (1990). Hox 2.3 upstream sequences mediate lacZ expression in intermediate mesoderm derivatives of transgenic mice. Development 109 775-786. 

It should be noted that the NRE defined in these experiments is distinct from the previously described c-mos UMS sequence (Blair et al., 1984 Wood et al., 1984). The UMS is located approximately 1.4 kb upstream of the c-mos spermatocyte promoter and was identified because it blocked activation of c-mos transforming potential by insertion of retroviral promoters. It is thought to act as a transcriptional terminator, blocking transcription of c-mos initiated at upstream sequences. However, both the spermatocyte and oocyte transcription initiation sites are substantially downstream of the UMS. Moreover, the presence or absence of the UMS does not affect c-mos expression in either microin-jected oocytes (Pal et al., 1991) or transfected NIH 3T3 cells (Zinkel et al., 1992). It thus appears unlikely that the UMS functions as a negative regulator of c-mos transcription from either the spermatocyte or oocyte promoters in somatic cells. 

Millar, S. E., Lader, E., Liang, L-F., and Dean, J. (1991). Oocyte-specific factors bind a conserved upstream sequence required for mouse zona pellucida promoter activity. Mol. Cell. Biol. 11 6197-6204. 

Wood, T. G., McGeady, M. L., Baroudy, B. M., Blair, D. G., and Vande Woude, G. F. (1984). Mouse c-mos oncogene activation is prevented by upstream sequences. Proc. Natl. Acad. Sci. USAS/ 7817-7821. 

The 5 upstream region of the MnP-1 gene contains a TATAAA element 81 bp upstream of the translation initiation codon. In addition, three inverted CCAAT elements (ATTGG) ( ) are found at positions -181, -195, and -304 with respect to the initiation codon. We are analyzing the 5 upstream sequence of the MnP-1 gene for other possible regulatory sequence elements. 

Ishidoh, K., Kominami, E., Suzuki, K. and Katsunuma, N. (1989) Gene structure and 5 -upstream sequence of rat cathepsin L. FEBS Letters 259, 71-74. 

For the pea and maize genes, the upstream sequences of genomic clones have been examined (Evans et al., 1990 de Framond, 1991). In maize, no sequence matching the consensus MRE of animal MT genes was found, whereas in pea a related sequence was found between -241 and -248 upstream of the transcription start site. As yet, there is no evidence that this element is active. 

Hatzopoulos, P., Franz, G., Choy, L. Sung, R.Z. (1990). Interaction of nuclear factors with upstream sequences of a lipid body membrane protein gene from carrot. The Plant Cell 2, 457-67. 

Native 5 upstream sequences flanking soybean hs promoter regions have pronounced effects on the level of transcription of Gmhspl7.3-B (Baumann et al., 1987) and Gmhspl7.5-E (Czarnecka et al., 1989) in transgenic plants. One common structural feature of these regions is the occurrence of A- and T-rich sequences which seem to interact with... 

Rieping, M. Schoffl, F. (1992). Synergistic effect of upstream sequences, CAAT box elements, and HSE sequences for enhanced expression of chimaeric heat shock genes in transgenic tobacco. Molecular and General Genetics 231, 226-32. 

Carswell, S. and Alwine, J.C. (1989) Efficiency of utilization of the simian virus 40 late polyadenylation site effects of upstream sequences. Mol. Cell, 9,4248 1258. 

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. 

In vitro methylation of the upstream site of a cloned y-globulin gene prevents transcription. Methylation outside the upstream sequence does not inhibit transcription. 

Key elements of dependent promotors are the TATA box, with the consensus sequence TATAAT 10 bp upstream from the transcription initiation site (pos. -10), and the sequence TTGACA at the position -35 (Fig. 1.18). Both sequences are necessary for the recognition of the promotor by a70. Structural analysis of the Thermus aquaticus RNA polymerase holoenzyme bound to DNA shows that all sequence-specific contacts with the core promotor are mediated by the sigma subunit (Murakami et al. 2002). This archaeal RNA polymerase has a subunit structure (a ji/i oxr) similar to that of the eubacterial enzyme. The intervening sequences, as well as other upstream sequences, can also influence the efficiency of transcription initiation. It is not possible to define consensus sequences at these positions. An optimal dependent promotor can be defined as a sequence with the - 35 hexamer as well as the -10 hexamer 17 bp away. The latter lies 7 bp upstream from the transcription initiation site. 

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