I'm looking for more information on what promoter sequence properties affect initiation (i.e. the mechanisms involved rather than descriptions of promoter strength) but found little in Pubmed/Google Scholar along the lines of "promoter sequence affects initiation" as they are quite ubiquitous terms in the field.
I was reading a textbook and came across a paragraph stating that "the exact way in which promoter sequence affects [transcription] initiation is unclear", and am just wondering what the actual status quo is on the topic at the minute.
Take a look at this article:
Promoter Sequence Determines the Relationship between Expression Level and Noise, Carey et al., 2013, PlosBiology
Very interesting article in recent Science (12/13/13), related to your inquiry:
"Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution", by Stergachis, et al. Science 342: 1367-1372 (2013).
See also Perspective there (1325-1326): "The Hidden Codes that Shape Protein Evolution". (Wetheritt and Babu).
Bottom line: there are binding sites WITHIN protein coding regions for transcription factor binding. Not clear to the authors what the role is and how transcription is affected but it seems clear that the sequence of the binding site is critically important.
Hope this helps.
Thanks for that Zev, I'm working in Dr Babu's lab this summer haha so yes I read it! My lecturer pointed me to the relevant paper on the topic (the source of my interest), and from there I just looked at the papers that have cited it since:
U. Deuschle, W. Kammerer, R. Gentz, H. Bujard (1986) Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternate structures. EMBO J., 5, pp. 2987–2994
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