Question: You are interested in studying eukaryotic transcription factors and have developed an in vitro tr…

You are interested in studying eukaryotic transcription factors
and have developed an in vitro transcription system using a segment
of DNA that includes a transcribed gene and its predicted upstream
regulatory region (see figure below). The transcription of this DNA
occurs in a defined system in which you add purified RNA polymerase
II and basal factors You perform a series of experiments that
compare the efficiency of transcription in your defined system with
the efficiency of transcription in a crude nuclear extract. You
test the two systems with your WT DNA and various deletion mutants
that you have generated (see figure below). The results of your
study are shown in the table:

a) Why is there no transcription from the -11 deletion
template?

b) Why do the results for the WT DNA differ between the nuclear
extract and the defined system?

c) Compare the results obtained for the deletion mutants when
tested in the nuclear extract and the defined system. Propose a
model to explain the differences – be as specific as you can.