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My book keeps giving different indicators as to whether the promoters are on the coding or template strand.

  • It says the -35 region in prokaryotes must be on the coding strand. It also mentions, that the -10 and -35 regions are binding sites for RNA polymerase.

  • It also says that CAAT and GC, unlike -35 in prokaryotes, can also be on the template strand. Which implies that they are still most common on the coding strand. And then it shows me a figure, where a promoter sequence is shown in the template strand, with the transcription complex attached.

All the sequences are written 5'-TATAAA-3' (for example). This also implies they are on the coding strand, since the template strand will then be 3'->5' which is the direction that transcription happens in.

Obviously I'm confused, and hope someone can clarify this. In which strand can I find the promoters? Does stuff act on the promoter sequence itself, or its complementary sequence? If the promoter can also be on the other strand, should it be reversed?

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The promoters are usually on the coding strand (which is the one which is transcribed) in front of the transcription start site. –  Chris Jan 6 at 20:07
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@Chris I don't think it is correct to say that the coding strand is transcribed - the coding strand of the DNA has the same sequence as the RNA produced by transcription (except T>U). The other strand of the DNA is the template for the synthesis of the RNA. –  Alan Boyd Jan 6 at 22:14
    
You are right. I still get confused by this every now and then. Thanks for correcting. –  Chris Jan 6 at 22:28

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The answer to this question depends upon the definition of the word 'promoter'.

In the simplest possible model of prokaryotic transcription the promoter is the site where RNA polymerase binds to the DNA before initiating RNA synthesis. In this process the σ factor recognises the core promoter elements directing the polymerase to bind to the DNA to form the closed complex. The next step is the switch to the open complex involving separation of the DNA strands.

Articles describing investigating the interaction of the σ factor with the DNA (e.g. here) refer to the protein making contacts with base pairs. I conclude therefore that the original question doesn't make sense - a promoter is a dsDNA entity even though we might describe it in terms of the sequence on one or other of those strands. So, for example, in a promoter the consensus -35 sequence - 5'-TTGACA - would be present on the coding strand (upstream of the coding sequence), but the promoter property of the sequence is due to the presence of this sequence and its complement on the other strand.

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Promoter doesn't sit anywhere.. it is just present .. the transcription factor sits on it :P

Jokes apart.. Adding a little more information to Alan Boyd's answer:

As Alan Boyd points out, the terms coding or template refers to the region that is being transcribed. Usually the Transcription Factors (TF) that bind to DNA have a dsDNA binding domain and therefore bind to both the strands. However, the sequence recognition domains are specific and usually scan the DNA 5'-> 3', subsequently recruiting RNA-polymerase in the same orientation. But there are additional aspects to this:

  • Promoter/regulatory elements are usually upstream but are also downstream of the TSS in several cases
  • The activity of a promoter element depends on the TF that binds to it. Some TFs can control the entire genomic locus i.e they affect several genes- both upstream and downstream.
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