How reliable are promoter element identities? - (Sep/19/2007 )

Just that, really. If I have a group of co-expressed genes and I am looking for common promoter elements (on the assumption that co-expressed genes may be co-regulated, and that this might be at the level of the promoter), how confident can I be that the promoter element identity is correct? For example, if I have something which is described as responsive to lactate, how can I be sure that it's not pH responsive, or a light-responsive element which might be really be carbohydrate responsive.

I know I could look at the original papers, but I have a lot of potential elements in my analysis.

Can anyone recommend a reference which looks at how cross-talk in signalling pathways might lead to 'mis-labelling' of promoter elements?

Thanks in advance for any help.

well, how are you identifying these elements?

if it's entirely sequence-based, not reliable at all

there has to be data to back it up. unless you're making knockouts of that particular part of the promoter just for your gene...even then, the DNA you change may involve another promoter element

one thing is this - start with sequence, then prove it. do chip and/or emsa, use an inhibitor and see if expression goes down; use and inducer and see if it goes up. purify the dna/protein complex when it's bound together and sequence. anyways, that's a big can of worms and it's very difficult to say with certainty what is / isn't the primary element involved in regulation of a given gene under a given stimulus

oh, and I hope I wasn't overly discouraging? I read my post and thought it was kind of disheartening. I hope yours is easy to sort out