Transcription Initiation in Eukaryotes Flashcards
What is the other name for RNA polymerase
Holenzyme
After initiation what happens to the closed complex
Forms a open complex which goes on to be elongated
what are promoters
cis acting DNA regulatory element through which transcription is initiated and controlled
At what position are the consensus sequences
-35 to -10
what are the four core (basal) promoter elements
TATA box, Initiator (Inr), DPE and BRE
at what position is the TATA box located
-31 to -26
at what position is the Initiator (Inr) located
-2 to +4
what % of protein coding genes in mammals lack an obvious TATA & Inr
60-70%
how does transcription initiation occur
at a lower rate
at several start sites
start sites are associated with regions with a high frequency of -
CG sequences - CpG islands
most C residues are followed by G are
methylated
generally C residues in CpG islands -
escaped methylation (hypomethylated)
What is the effect of methylation of CpG islands
silencing
UAS & enhancers =
activator binding sites
URS & silencer =
repressor binding sites
how does sequence comparison identify promoter elements
identification of the TATA box
examples of reporter genes are
GFP, luciferase, LacZ (B-glactosidase)
what are the target genes and location
mRNA and Nucleus
what is the structure of bacterial RNA polymerase
ß subunit
ß’ subunit
α subunit (x2)
ω subunit
how many subunits are in yeast RNA polymerase II
12
what are general transcription factors (GTF’s)
In eukaryotes, there are sigma factors which are RNA pol specific.
where does GTF form a complex, and what does it do
on TATA box, recruits RNA pol II to the promoter and direct initiation at start site
how many GTFs and name them
6 - TFIIA,B,D,E,F,H
the helicase activity of which TFII seperates the template strand at the start site
TFIIH
what does the helicase activity of TFIIH require?
requires ATP hydrolysis
Pol II beginning transcribing is called
promoter clearance
what occurs to C-terminal domain during promoter clearance
extensively phosphorylated
what is the C-terminal domain
series of repeats located at the C-terminal end of the largest (B’ homologous subunit of pol II
Which two TFII s stay behind on the TATA box
TFIID, TFIIA
which TFII are released
TFIIB, TFIIE, and TFIIH
which TFII moves with Pol II
TFIIF
what are the property of TFIID
binds to TATA box and recruits TFIIB
what are the properties of TFIIA
stabilises TFIID binding
Anti-repression function
what are the properties of TFIIB
- recruits RNA pol II-TFIIF
- Important for start site selection
what are the properties of TFIIF
- stimulates elongation
- destabilises non -specific RNA pol II-DNA interactions
what are the properties of TFIIE
recruits TFIIH and modulates TFIIH activity
what are the properties of TFIIH
- promoter melting and clearance
- CTD kinase activity
- DNA repair coupling
How many subunits are TFIIH made from
9-10 subunits
what are the two modules that TFIIH can be divided into
CORE and CAK
what phosphorylates the CTD of RNAP II
a kinases contained into the CAK module
what is XPB (found in TFIIH) and what does it do
- ATPase which aids promoter melting
what two parts make up TFIID
TATA binding protein (TBP) which is attached to TAF1. There are Multiple TAFs (TBP associated factors)
what shape is the TBP
curve - molecular saddle
what are the differences between TBP vs TFIID
- TBP can direct the assembly of teh PIC on a TATA-containing promoter
- however TBP alone cant direct PIC assembly on a TATA-less promoter
TBP can not support _ transcription
activated
what do TAFs do
-Promote the interaction of TFIID with the basal promoter
- interact with activators
