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I don't know if this might have been highlighted in recent research, but a textbook I have states that "the exact way in which promoter sequence affects [transcription] initiation is unclear"

I'm wondering if anyone can suggest sources for more information, or perhaps has seen recent research papers highlighting the properties that cause such variation between strong promoters and the weakest?

I've tried researching but the older research is descriptive rather than mechanistic and the search terms involved are quite ubiquitous so it's hard to actually find more on this specific point.

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2 Answers 2

I agree that it is hard to search for papers but from graduate level classes this is some of the additional insight I have gained. Sequence context of promoters is important. Specific DNA sequences (motifs) can act as binding sites for specific transcription factors and combinations of these transcription factors help recruit RNA pol II to the promoter. These combinations of proteins are spatially and temporally regulated and will help decide if gene that is next to promoter will be activated. A luciferase reporter assay is often used to determine the strength of a promoter.

An example is as follows: A strong promoter might have certain histone marks that would recruit proteins to remodel the chromatin to be more accessible exposing binding sites of transcription factors that help recruit RNA Pol II. A weaker promoter might have less transcription factor binding sites or less chromatin accessibility and thus it is harder for RNA Pol II to be recruited. There are also some kinetics aspects you must keep in mind.

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Echoing what was already mentioned: the DNA sequence directly affects the ability to bind sigma factors (http://en.wikipedia.org/wiki/Sigma_factor). Sequence --> bonding --> how often sigmas bind and for how long they bind --> initiation of transcription

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