Initiation enhancing sequences

NtrC-P dimerizes and binds to the enhancer sequence, where it appears to catalyze an ATP-depen-dent isomerization of the closed to open forms of the transcription initiation complex (Eq. 28-1).153/154 The isomerization may depend upon looping.152 Other operons that utilize the oN subunit of RNAP often also have upstream or downstream enhancers.155156... 

The presence of an enhancer sequence may cause as much as 100- to 1000-fold increase in the rate of transcription as compared with the same transcriptional emit from which the enhancer has been deleted. A surprising fact is that enhancers as far as 1 -2 kbp upstream or even far downstream of the promoter and in either of the two possible orientations are effective. range conformational alterations in DNA. Alternatively, they might contain points of entry for RNA polymerase or for an initiation factor that could move along the DNA to the promoter region. However, the synthetic DNA molecule shown in Fig. 28-14 contains two copies of an enhancer in opposite orientations in one strand but none in the other strand.354 The... 

Figure 13.11. Conserved ARE (EpRE) enhancer sequences identified in various phase II genes. The negative numbers shown on the 5 and 3 positions of each sequence are nucleotide positions from a transcription initiation site of each gene.

Transcriptional initiation is the most important mode for control of eukaryotic gene expression. Specific factors that exert control include the strength of promoter elements within the DNA sequences of a given gene, the presence or absence of enhancer sequences (which enhance the activity of RNA polymerase at a given promoter by binding specific transcription factors) and the interaction between multiple activator proteins and inhibitor proteins. 

The operation of the proton-enhanced sequences is best understood by reference to the original INEPT-INADEQUATE sequence shown in simplified form in Fig. 5.80 in which the individual component parts have been identified and may be followed in a stepwise manner. Thus, initial transfer from proton to carbon is via the INEPT sequence introduced in Chapter 4 followed by the generation of DQC as for the INADEQUATE above. This again evolves to encode c after which gradient selection begins. The DQ then returns to single quantum, and the C- C-coupling is refocused by the spin-echo. The final step is INEPT in reverse to transfer from carbon back onto proton, followed by... 

Initiation enhancing Kozak consensus sequence Shine-Dalgamo consensus sequence... 

Figure 9.1 The transcriptional elements of a eucaryotic structural gene extend over a large region of DNA. The regulatory sequences can be divided into three main regions (1) the basal promoter elements such as the TATA box, (2) the promoter proximal elements close to the initiation site, and (3) distal enhancer elements far from the initiation site.

Regulatory regions are transcriptional control sequences, which consist of promoters, response elements, enhancers and possibly silencers, located upstream of the start site of transcription. The overall effect on gene transcription is a sum of the contributions of these elements and the activities of proteins recruited to these sites. Promoters are located immediately upstream of the start site and initiate transcription. They often contain tissue- or cell-specific elements if the gene is not ubiquitously expressed. Enhancers are positive regulatory elements which function independently of orientation and distance from the genes they regulate. 

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... 

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