Upstream conserved region

Another conserved region is centered 35 base pairs (bp) upstream of the start site (i.e., at -35 bp). The consensus sequence is TTGACA in more detailed form, the sequence is ... 

Archaeal promoters resemble the RNAIl promoters of the eucarya [40,161] and are different from those in the bacteria [162]. Analysis of the promoters of archaeal r-protein genes shows the presence of two conserved regions a hexanucleotide sequence (TTTAAA/T) located 20-30 nucleotides upstream of the transcription initiation site and two conserved nucleotides around the transcription initiation site (shown in lower case (Ta/gT/G)) [9,114,120,141,144,145,148,150]. Transcription in the archaea usually starts at a purine residue as is the case in the other two domains [161,162]. The presence of several initiation sites is common among the extreme thermophiles [120,141,148], a situation similar to that found for yeast r-proteins genes [156]. 

Liu, X., Brutlag, D. L., and Liu, J. S. (2001) BioProspector discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput. 127-138. 

The methods utilized here have been developed to provide a broad-based or universal genotyping system for all bacteria. As we have demonstrated with the fla-viviruses, the approach is readily adapted to broad viral typing as well, if well-conserved regions can be identified for PCR priming across the strains of interest. We are presently working on upstream steps for separation of complex bacterial communities as well as algorithmic approaches to nonclonal samples. 

Bacterial promoters are approximately 40 nucleotides (40 bp or four turns of the DNA double helix) in length, a region small enough to be covered by an E coli RNA holopolymerase molecule. In this consensus promoter region are two short, conserved sequence elements. Approximately 35 bp upstream of the transcrip-... 

G-CSF expression is controlled at both the transcriptional and posttranscrip-tional levels. A sequence of 300 nucleotides upstream of the initiation codon is conserved in both the murine and human genes, and this appears to contain three regulatory sites. G-CSF (and some other cytokine genes) may be constitutively transcribed by cells such as blood monocytes, fibroblasts and endothelial cells, but the mRNA may be short-lived (fi/2 < 15 min). The mRNA contains poly-AUUUA sequences in the untranslated region, and this motif is usually associated with mRNA instability. Indeed, such regions have also been identified in mRNA for GM-CSF, IL-1, IL-6, interferons, TNF, some growth factors, c-jun, c-fos, c-myc and c-myb. Upon the addi-... 

Promoter sequences. In 1975, Pribnow pointed out46 that a series of six known promoters had a conserved 7-base sequence beginning six nucleotides upstream from the initiation site for transcription. Although this sequence varies somewhat from one promoter to another, it has been found in hundreds of E. coli promoters. This is called the -10 region, the Pribnow sequence, or Pribnow box (the last in recognition of the fact that people like to draw boxes around these special sequences). A typical 6-base consensus Pribnow sequence is 5-TATAAT as written for the coding strand, whose sequence corresponds to that of the rnRNA. Only three of these bases are highly... 

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