Eukaryotic RNA polymerases and their promoters

1
Chapter 10

Eukaryotic RNA polymerases and their promoters
Page 276-295
2
Initiator --PyPyANT/APyPy -- is sufficient by
itself to direct transcription Downstream
promoter elements (DPE) -- quite common in
fruitfly genes. Found 30 bp downstream of the
transcription initiation site Have the consensus
sequence -- G(A/T)CG -- behave as a TATA-box BRE
-- (G/C)(G/C)(G/A)CGCC -- TFIIB-binding site
Upstream element
3
Why are RNA Pol II promoters so complicated to
have multiple cis-elements?

• RNA polymerase II has more subunits than the
  other two RNA polymerases
• RNA polymerase II has diverse targets that need
  to be differentially regulated
• Other RNA polymerases use specific primers to
  initiate transcription
• Other RNA polymerases are less specific in term
  of their promoter selections
• None of above

B
4
Class I promoter (Pol I promoter)
Relatively simple -- one template (the rRNA
precursor gene)
5
The spacing between the two elements is important
6
Class III promoter (Pol III promoter)
7
Class III promoter (Pol III promoter)
Classical class III promoter
Unlike class I and II promoters, classical class
III promoters locate within the genes.
U6 snRNA, 7SL, and 7SK RNA gene still need
elements 5 of the genes. Their promoters
resemble class II promoters (nonclassical class
III promoter).
8
A promoter must have

• a TATA box
• a GC box
• an element that direct where RNA polymerase
  should start
• An upstream promoter element
• A Box A sequence

C
9
(No Transcript)
10
How do enhancers work?

• An enhancers binds transcription factors
  (activators) to activate transcription
• An enhancer can localize upstream, within, or
  downstream of a gene.

11
How do enhancers work?

• An enhancers binds transcription factors
  (activators) to activate transcription
• An enhancer can localize upstream, within, or
  downstream of a gene.

12
(No Transcript)
13
Chapter 11

• General Transcription Factors in Eukaryotes

Page 303-309
14
Polymerases need help to find the promoters
The factors that attract polymerases to their
respective promoters are called general
transcription factors General transcription
factors combine with an RNA polymerase to form an
open promoter complex or a preinnitiation complex
to activate transcription Class II factors work
with Pol II.
15
Class II preinitiation complex
Six class II factors TFIIA, TFIIB, TFIID, TFIIE,
TFIIF and TFIIH. Preinitiation complex is
assembled in a precise order
D
DA
DAB
DAB-PolF
DAB-PolF-EH
16
Two important assays to examine protein-DNA
interaction DNase I footprint analysis Gel
mobility shift assay or Gel retardation assay
17
DNase I footprint assay
18
Mobility shift assay Gel retardation assay