Lecture 11 - Basal transcription

Question 1

What genes are transcribed by different RNA polymerases?

Answer 1

RNA Polymerase I: Large rRNA
RNA Polymerase II: mRNA; U1-U5 snRNA splicing factors
RNA Polymerase III: Small rRNA; tRNA;
U6 snRNA, VA1 RNA and some other small RNAs of unknown function

Question 2

Describe RNA polymerase II

Answer 2

Large, multi-subunit complex of proteins.
12 subunits in yeast (highly conserved among eukaryotes)
2 largest carry the catalytic site.
The largest subunit has a carboxy-terminal domain (CTD) that consists of a repeated sequence of 7 amino acids (YSPTSPS). Phosphorylation of this domain is important for transcription initiation and downstream processing steps.
Serines in CTD are phosphorylated

Question 3

What are the differences in the eukaryotic vs prokaryotic mode of transcription?

Answer 3

E. coli genome is circular, super coiled DNA molecule lacking any high order chromatin structure. Therefore, the first step in gene expression (promoter recognition and DNA binding) face no real obstacles. This means in order to regulate transcription it needs to be repressed
Non-restrictive transcription…
In Eukaryotes, DNA is packaged into high order chromatin structure, which keeps genes inactive by preventing RNA polymerase from accessing the promoter. In order to regulate gene expression in eukaryotes it must be activated
Restrictive transcription…

Question 4

Describe the RNA polymerase II promoters

Answer 4

The RNA polymerase II promoter can be divided into two regions:

1) A core promoter region that is located proximal to, and some times over laps with, the start site of txn and is sufficient for low levels of txn in vitro.
2) A regulatory region (usually distal to the start site for activator or repressor binding).

All the transcription factors that need to recruit RNA polymerase directly tend to interact with the core promoter
Doesn’t require any activators - can produce basal levels of gene expression on its own - called basal promoter for this reason. Little bit of activity just on its own - landing pad for RNA polymerase and its factors. Also has a regulatory region which tends to be distal (can be quite a long way away, further from promoter and recruit activators/repressors) and affect core promoter - determine whether it will be expressed or not.