If Promotor Regions are Upstream..........

[Dan]

Hi Annie,

If during transcription, the DNA template strand is read by the RNAP
in the 3' to 5' direction and also moves in that direction on the
template strand, why do the lecture notes and book state the the RNAP
binds upstream at the 5' end of the DNA template strand? Figure 8.7
(and lecture slide) says 'The promoter lies "upstream" (toward the 5'
end) of the initiation point". In the case of the RNAP binding to the
template strand, would not the promoter region be at the 3' end since
the RNAP must move toward the 5' end once transcription begins?

Dan S

[Annie]

hi Dan,

The DNA template strand is read in the 3' to 5' direction by RNAP so
that RNAP can synthesize in the 5' to 3' direction. The key word in
the Figure 8.7 caption is "coding":

"The promoter lies "upstream" (towards the 5' end) of the initiation
point and CODING sequence."

The template strand the the coding (nontemplate) strand are
antiparallel, and it is convention to use the coding (nontemplate)
strand to describe the gene directionality, since the coding strand
has the same sequence (upon replacing T's with U's of course) as the
eventual RNA that is transcribed.

You are right that the promoter would be at the 3' end of the template
strand; however, it is at the 5' of the coding strand.

Hope this helps,
-Annie