Download What is the difference between basal and activated transcription?

What is the difference between
basal and activated transcription?
Regulation of Transcription
I. Basal vs. activated transcription for
mRNA genes
A. General transcription factor (TF) vs. promoterspecific
1. general TFs are required by all mRNA genes
a. an absolute requirement
b. transcription can occur alone with these
factors is by definition the basal level of transcription
2. promoter-specific TFs are different for each gene
3. the promoter-specific TFs are required for
maximal level of transcription or for activated
transcription (induction)
B. a third state is that of a repressed state
Regulation of Transcription
What is the role of the response
elements and associated factors
How Can You Test the
Functional Activity of an
Activation Domain?
Targets of Activation Domains
• General Transcription Factors
– TBP (TFIID)
– TFIIB
– TFIIA
• RNA polymerase II
• Coactivators
– Mediator
– TFIID
Role of Activation Domains
1.
Recruitment
•
•
2.
Conformational change
•
•
3.
Bind Faster
Remain bound longer
Active vs. inactive configuration
Blocked vs. accessible
Covalent modification
Coactivator versus
Repressor (corepressor)
Activation and Repression of
Transcription
Regulation of Transcription
II. Question of Activation
A. diversity of response - combinatorial effect
1. properties of response elements (RE)
2. relatedness of RE and enhancers
3. trans acting factors
induction: heat shock, heavy metals, viral infection, growth
factors, steroids
4. greater multiplicity with combinatorial approach
B. Master gene regulatory proteins
1. response elements shared
2. example of homeodomains
Regulation of Transcription
II. Question of Activation
A. diversity of response - combinatorial effect
1. properties of response elements (RE)
2. relatedness of RE and enhancers
3. trans acting factors
induction: heat shock, heavy metals, viral infection, growth
factors, steroids
4. greater multiplicity with combinatorial approach
B. Master gene regulatory proteins
1. response elements shared
2. example of homeodomains
C. regulating the activity of the transcription factors
What are the DNA binding
domains of the TFs?
DNA binding domains
A. Zinc fingers
1. Cys2-His2 fingers: Cys-X2-4-Cys-X3-Phe-X5-Leu-X2-His-X-His
a. example is TFIIIA has 9 Zn finger repeat
b. typically the number of fingers range from 2-9
c. can be involved in binding to RNA
d. not all Zn fingers are used to bind DNA, nor are they always
part of a transcription factor
2. Cys2-Cys2 fingers: Cys-X2-Cys-X13-Cys-X2-Cys
a. found in steroid receptors
b. typically nonrepetitive
c. binding sites are short palindromes
d. bind as dimers
3. Binuclear Cys6 finger: Gal4 DNA binding domains
DNA binding domains
B. Steroid receptors
DNA binding domains
B. Steroid receptors
1. Ligand mediated activation
2. Functional Domains
a. DNA binding
b. ligand binding - hormone
c. activation domain
3. Two classes
a. form homodimers: bind consensus half
site (TGTTCT, except for ER is TGACCT)
b. form heterodimers: bind half sites of
TGACCT, direct repeats
c. spacing of the half sites is crucial for the
degree of specificity
DNA binding domains
C. Leucine zippers - dimer formation
1. brings 2 DNA binding domains
in close juxtaposition
example is Gal4
2. amphipathic alpha helices with
Leu residues on one face
Leu repeats every 7 amino acid
3. interface forms a coiled coil
DNA binding domains
D. bZIP example is GCN5
1. basic region attached to a leucine zipper
2. is a dimer kept together by the leucine
zipper
3. an alpha helic containing basic residues
contacts the major groove of DNA
4. contacts are made with the portion of the
bases exposed in the major groove and some
phosphate backbone contacts
DNA binding domains
E. bHLH domain
1. basic helix loop helix motif
2. positively charged alpha helix binds
to major groove
3. two other alpha helices form a four
helix bundle in dimer
4. many will also contain a leucine
zipper
DNA binding domains
Dimer formation regulates the
activity of the transcription factor
Activation Domains
A. Acidic activators - example of Gal4p
B. Glutamine rich domain
C. Proline rich domain
Transcription Elongation
A. General
1. in vivo rates are 1200-2000
nucleotides/min
2. in vitro rates are 100-300 nucleotides/min
3. elongation is not a monotonic continuous
process
a. there are strong pause sites
b. effects of chromatin on
process
4. pausing versus arrest (definition of)
Transcription Elongation
B. Negative elongation factors (N-TEFs)
1. DSIF
2. factor 2
C. Positive elongation factors (P-TEFs)
1. prevent sequence dependent arrest
(i.e. TFIIS or SII)
nucleolytic cleavage/ backtracking
2. catalytic activity (TFIIF, elongin,
ELL complex)
3. regulates the rate of elongation
through chromatin (FACT)