Explanation needed please

Jens Tornoe imjt at pop.dtu.dk
Sat Nov 13 09:26:32 EST 1999

To the best of my knowledge, that is not an uncommon observation.
Frequently, RNA PolII can initiate transcription from several sites that
might not be of any physiological relevance. How is the sequence around the
2 initiation sites you have identified? Can you find any consensus sequences
for an Initiator element and a TATA box ~30 bp upstream from the initiation
site in either case? One would expect that the TATA and Inr elements giving
rise to the predominant product would be more 'consensus-like' than for the
other product. That is not always the case, though. For instance, the SV40
promoter TATA box and Inr site are not exactly textbook examples.

Depending on the location of the initiation sites, both mRNAs might be
translatable and yield protein. If the weak band represents a longer mRNA I
would just expect it to add to the amount of gene product coming from the
strong mRNA. If it is shorter, it could both be translated or possibly
degraded because of lack of important protecting 5' structures.

If you really wanted to go into the details of the promoter, you could
examine what impact mutation of the areas around either transcription start
site would have on mRNA and protein production.



Jens Tornøe
Pederstrup, Denmark

UIC Network Services Kit User <karthi at CCVAX.SINICA.EDU.TW> wrote in message
news:382B0A59.9A2F2240 at ccvax.sinica.edu.tw...
> Dear netters;
> I am working on a dentin speific promoter. Recently I have done primer
> extension to map the transcription start site for this gene. I found 2
> bands on the autoradiogram with a spacing of 80 bp. However, one of the
> band was much stronger than the other. I would like to request for an
> explanation from anyone who can explain to me some of the importance of
> the presence of two start sites of one being stronger. The expt was
> carried out RNA prepared from cell line.
> Thank you for your time.
> sincerely
> --
> Narayanan Karthikeyan Ph.D.,
> College of Dentistry,
> Department of Oral Biology,
> University of Illinois at Chicago
> Chicago IL 60612
> Tel: 312-413-5375
> Fax: 312-413-6694

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