Transcript Slide 1

Table 1
Complexes Involved in RNApII PIC assembly.
Protein complex
Functions
RNApII
12 Subunits; catalyzes transcription of all mRNAs and a subset of noncoding RNAs including snoRNAs
and miRNAs
TFIIA
2–3 subunits; functions to counteract repressive effects of negative cofactors like NC2; acts as a
coactivator by interacting with activators and components of the basal initiation machinery
TFIIB
Single subunit; stabilizes TFIID-promoter binding; aids in recruitment of TFIIF/Pol II to the promoter;
directs accurate start site selection
TFIID
14 subunits including TBP and TBP Associated Factors (TAFs); nucleates PIC assembly either through
TBP binding to TATA sequences or TAF binding to other promoter sequences; coactivator activity through
direct interaction of TAFs and gene specific activators
TFIIE
2 subunits; helps recruit TFIIH to promoters; stimulates helicase and kinase activities of TFIIH; binds
ssDNA and is essential for promoter melting
TFIIF
2–3 subunits; tightly associates with RNApII; enhances affinity of RNApII for TBP-TFIIB-promoter
complex; necessary for recruitment of TFIIE/TFIIH to the PIC; aids in start site selection and promoter
escape; enhances elongation efficiency
TFIIH
10 subunits; ATPase/helicase necessary for promoter opening and promoter clearance; helicase activity
for transcription coupled DNA repair; kinase activity required for phosphorylation of RNApII CTD;
facilitates transition from initiation to elongation
Mediator
At least 24 subunits; bridges interaction between activators and basal factors; stimulates both activator
dependent and basal transcription; required for transcription from most RNApII dependent promoters
SAGA
20 subunits; interacts with activators, histone H3, and TBP; histone acetyltransferase activity;
deubiquitinating activity
Trf1
TBP related factor identified in Drosophila; upregulated in CNS and gonads during development; can bind
TATA sequences; mostly found at RNApIII dependent promoters as part of TFIIIB but also required at a
subset of RNApII dependent promoters
Trf2
TBP related factor identified in all metazoans; cannot bind TATA sequences; important for histone gene
expression in Drosophila
Trf3
TBP related factor identified in vertebrates; can bind TATA sequences; important for differentiation of
muscle cells in mammals and for haematopoietic cell development in zebrafish.
TFIIS
1 subunit; stimulates intrinsic transcript cleavage activity of RNApII allowing backtracking to resume RNA
synthesis after transcription arrest; stimulates PIC assembly at some promoters
NC2
2 subunits; binds TBP/DNA complexes and blocks PIC assembly; can have both positive and negative
effects on transcription
Mot1/bTAF1
1 subunit; induces dissociation of TBP/DNA complexes in ATP dependent manner; can have both positive
and negative effects on transcription
PIC = Pre-initiation complex; this is the “business end”
of the transcription apparatus.
Questions:
1. How does the PIC decide where to form?
2. Why isn’t the PIC sufficient for efficient gene expression?
3. How are PIC assembly and transcriptional activation controlled?
Table 1
Complexes Involved in RNApII PIC assembly.
Protein complex
Functions
RNApII
12 Subunits; catalyzes transcription of all mRNAs and a subset of noncoding RNAs including snoRNAs
and miRNAs
TFIIA
2–3 subunits; functions to counteract repressive effects of negative cofactors like NC2; acts as a
coactivator by interacting with activators and components of the basal initiation machinery
TFIIB
Single subunit; stabilizes TFIID-promoter binding; aids in recruitment of TFIIF/Pol II to the promoter;
directs accurate start site selection
TFIID
14 subunits including TBP and TBP Associated Factors (TAFs); nucleates PIC assembly either through
TBP binding to TATA sequences or TAF binding to other promoter sequences; coactivator activity through
direct interaction of TAFs and gene specific activators
TFIIE
2 subunits; helps recruit TFIIH to promoters; stimulates helicase and kinase activities of TFIIH; binds
ssDNA and is essential for promoter melting
TFIIF
2–3 subunits; tightly associates with RNApII; enhances affinity of RNApII for TBP-TFIIB-promoter
complex; necessary for recruitment of TFIIE/TFIIH to the PIC; aids in start site selection and promoter
escape; enhances elongation efficiency
TFIIH
10 subunits; ATPase/helicase necessary for promoter opening and promoter clearance; helicase activity
for transcription coupled DNA repair; kinase activity required for phosphorylation of RNApII CTD;
facilitates transition from initiation to elongation
Mediator
At least 24 subunits; bridges interaction between activators and basal factors; stimulates both activator
dependent and basal transcription; required for transcription from most RNApII dependent promoters
SAGA
20 subunits; interacts with activators, histone H3, and TBP; histone acetyltransferase activity;
deubiquitinating activity
Trf1
TBP related factor identified in Drosophila; upregulated in CNS and gonads during development; can bind
TATA sequences; mostly found at RNApIII dependent promoters as part of TFIIIB but also required at a
subset of RNApII dependent promoters
Trf2
TBP related factor identified in all metazoans; cannot bind TATA sequences; important for histone gene
expression in Drosophila
Trf3
TBP related factor identified in vertebrates; can bind TATA sequences; important for differentiation of
muscle cells in mammals and for haematopoietic cell development in zebrafish.
TFIIS
1 subunit; stimulates intrinsic transcript cleavage activity of RNApII allowing backtracking to resume RNA
synthesis after transcription arrest; stimulates PIC assembly at some promoters
NC2
2 subunits; binds TBP/DNA complexes and blocks PIC assembly; can have both positive and negative
effects on transcription
Mot1/bTAF1
1 subunit; induces dissociation of TBP/DNA complexes in ATP dependent manner; can have both positive
and negative effects on transcription
Image from euchromatin.org
Gnatt et al, (2001) Science, vol 292, 1876-1882
Table 1
Complexes Involved in RNApII PIC assembly.
Protein complex
Functions
RNApII
12 Subunits; catalyzes transcription of all mRNAs and a subset of noncoding RNAs including snoRNAs
and miRNAs
TFIIA
2–3 subunits; functions to counteract repressive effects of negative cofactors like NC2; acts as a
coactivator by interacting with activators and components of the basal initiation machinery
TFIIB
Single subunit; stabilizes TFIID-promoter binding; aids in recruitment of TFIIF/Pol II to the promoter;
directs accurate start site selection
TFIID
14 subunits including TBP and TBP Associated Factors (TAFs); nucleates PIC assembly either through
TBP binding to TATA sequences or TAF binding to other promoter sequences; coactivator activity through
direct interaction of TAFs and gene specific activators
TFIIE
2 subunits; helps recruit TFIIH to promoters; stimulates helicase and kinase activities of TFIIH; binds
ssDNA and is essential for promoter melting
TFIIF
2–3 subunits; tightly associates with RNApII; enhances affinity of RNApII for TBP-TFIIB-promoter
complex; necessary for recruitment of TFIIE/TFIIH to the PIC; aids in start site selection and promoter
escape; enhances elongation efficiency
TFIIH
10 subunits; ATPase/helicase necessary for promoter opening and promoter clearance; helicase activity
for transcription coupled DNA repair; kinase activity required for phosphorylation of RNApII CTD;
facilitates transition from initiation to elongation
Mediator
At least 24 subunits; bridges interaction between activators and basal factors; stimulates both activator
dependent and basal transcription; required for transcription from most RNApII dependent promoters
SAGA
20 subunits; interacts with activators, histone H3, and TBP; histone acetyltransferase activity;
deubiquitinating activity
Trf1
TBP related factor identified in Drosophila; upregulated in CNS and gonads during development; can bind
TATA sequences; mostly found at RNApIII dependent promoters as part of TFIIIB but also required at a
subset of RNApII dependent promoters
Trf2
TBP related factor identified in all metazoans; cannot bind TATA sequences; important for histone gene
expression in Drosophila
Trf3
TBP related factor identified in vertebrates; can bind TATA sequences; important for differentiation of
muscle cells in mammals and for haematopoietic cell development in zebrafish.
TFIIS
1 subunit; stimulates intrinsic transcript cleavage activity of RNApII allowing backtracking to resume RNA
synthesis after transcription arrest; stimulates PIC assembly at some promoters
NC2
2 subunits; binds TBP/DNA complexes and blocks PIC assembly; can have both positive and negative
effects on transcription
Mot1/bTAF1
1 subunit; induces dissociation of TBP/DNA complexes in ATP dependent manner; can have both positive
and negative effects on transcription
Eukaryotic Basal DNA elements:
TATA element (TATA)
Initiator element (INR)
Downstream Promoter element (DPE)
TFIIB recognition element (BRE)
Any given eukaryotic promoter will have
one or more of these elements, but
seldom all of them. The PIC can thus be
recruited to different promoters in different
Ways.
Table 1
Complexes Involved in RNApII PIC assembly.
Protein complex
Functions
RNApII
12 Subunits; catalyzes transcription of all mRNAs and a subset of noncoding RNAs including snoRNAs
and miRNAs
TFIIA
2–3 subunits; functions to counteract repressive effects of negative cofactors like NC2; acts as a
coactivator by interacting with activators and components of the basal initiation machinery
TFIIB
Single subunit; stabilizes TFIID-promoter binding; aids in recruitment of TFIIF/Pol II to the promoter;
directs accurate start site selection
TFIID
14 subunits including TBP and TBP Associated Factors (TAFs); nucleates PIC assembly either through
TBP binding to TATA sequences or TAF binding to other promoter sequences; coactivator activity through
direct interaction of TAFs and gene specific activators
TFIIE
2 subunits; helps recruit TFIIH to promoters; stimulates helicase and kinase activities of TFIIH; binds
ssDNA and is essential for promoter melting
TFIIF
2–3 subunits; tightly associates with RNApII; enhances affinity of RNApII for TBP-TFIIB-promoter
complex; necessary for recruitment of TFIIE/TFIIH to the PIC; aids in start site selection and promoter
escape; enhances elongation efficiency
TFIIH
10 subunits; ATPase/helicase necessary for promoter opening and promoter clearance; helicase activity
for transcription coupled DNA repair; kinase activity required for phosphorylation of RNApII CTD;
facilitates transition from initiation to elongation
Mediator
At least 24 subunits; bridges interaction between activators and basal factors; stimulates both activator
dependent and basal transcription; required for transcription from most RNApII dependent promoters
SAGA
20 subunits; interacts with activators, histone H3, and TBP; histone acetyltransferase activity;
deubiquitinating activity
Trf1
TBP related factor identified in Drosophila; upregulated in CNS and gonads during development; can bind
TATA sequences; mostly found at RNApIII dependent promoters as part of TFIIIB but also required at a
subset of RNApII dependent promoters
Trf2
TBP related factor identified in all metazoans; cannot bind TATA sequences; important for histone gene
expression in Drosophila
Trf3
TBP related factor identified in vertebrates; can bind TATA sequences; important for differentiation of
muscle cells in mammals and for haematopoietic cell development in zebrafish.
TFIIS
1 subunit; stimulates intrinsic transcript cleavage activity of RNApII allowing backtracking to resume RNA
synthesis after transcription arrest; stimulates PIC assembly at some promoters
NC2
2 subunits; binds TBP/DNA complexes and blocks PIC assembly; can have both positive and negative
effects on transcription
Mot1/bTAF1
1 subunit; induces dissociation of TBP/DNA complexes in ATP dependent manner; can have both positive
and negative effects on transcription
TFIID
TFIID is a major player in transcriptional initiation.
Thought to nucleate PIC assembly through TBP binding to DNA.
Its composition can change depending on which subunits are included
(see next fig).
About 10% of genes are dependent on SAGA rather than TFIID. SAGA
TFIID are probably homologous. SAGA also includes TBP.
Is TFIID required for every round of transcription?
Cler et al, (2009) Cell Mol Lif Sci, vol 66, 2123-2134
Table 1
Complexes Involved in RNApII PIC assembly.
Protein complex
Functions
RNApII
12 Subunits; catalyzes transcription of all mRNAs and a subset of noncoding RNAs including snoRNAs
and miRNAs
TFIIA
2–3 subunits; functions to counteract repressive effects of negative cofactors like NC2; acts as a
coactivator by interacting with activators and components of the basal initiation machinery
TFIIB
Single subunit; stabilizes TFIID-promoter binding; aids in recruitment of TFIIF/Pol II to the promoter;
directs accurate start site selection
TFIID
14 subunits including TBP and TBP Associated Factors (TAFs); nucleates PIC assembly either through
TBP binding to TATA sequences or TAF binding to other promoter sequences; coactivator activity through
direct interaction of TAFs and gene specific activators
TFIIE
2 subunits; helps recruit TFIIH to promoters; stimulates helicase and kinase activities of TFIIH; binds
ssDNA and is essential for promoter melting
TFIIF
2–3 subunits; tightly associates with RNApII; enhances affinity of RNApII for TBP-TFIIB-promoter
complex; necessary for recruitment of TFIIE/TFIIH to the PIC; aids in start site selection and promoter
escape; enhances elongation efficiency
TFIIH
10 subunits; ATPase/helicase necessary for promoter opening and promoter clearance; helicase activity
for transcription coupled DNA repair; kinase activity required for phosphorylation of RNApII CTD;
facilitates transition from initiation to elongation
Mediator
At least 24 subunits; bridges interaction between activators and basal factors; stimulates both activator
dependent and basal transcription; required for transcription from most RNApII dependent promoters
SAGA
20 subunits; interacts with activators, histone H3, and TBP; histone acetyltransferase activity;
deubiquitinating activity
Trf1
TBP related factor identified in Drosophila; upregulated in CNS and gonads during development; can bind
TATA sequences; mostly found at RNApIII dependent promoters as part of TFIIIB but also required at a
subset of RNApII dependent promoters
Trf2
TBP related factor identified in all metazoans; cannot bind TATA sequences; important for histone gene
expression in Drosophila
Trf3
TBP related factor identified in vertebrates; can bind TATA sequences; important for differentiation of
muscle cells in mammals and for haematopoietic cell development in zebrafish.
TFIIS
1 subunit; stimulates intrinsic transcript cleavage activity of RNApII allowing backtracking to resume RNA
synthesis after transcription arrest; stimulates PIC assembly at some promoters
NC2
2 subunits; binds TBP/DNA complexes and blocks PIC assembly; can have both positive and negative
effects on transcription
Mot1/bTAF1
1 subunit; induces dissociation of TBP/DNA complexes in ATP dependent manner; can have both positive
and negative effects on transcription
TFIIH
TFIIH has three enzymatic activities:
2 helicases (for promoter opening and for DNA repair)
1 kinase (for phosphorylating CTD of RNA pol II)
Involved in transitioning from initiation to elongation.
Keep in mind:
Basal transcription factors (ie PIC) don’t transcribe chromatin templates.
Basal transcription factors don’t respond to activators.
This raises the level of complexity, and provides avenues for regulation,
in two ways.
See upcoming lectures by:
Whitehouse (chromatin)
DiGregorio and Pertsinidis (activators and regulatory modules)
Table 1
Complexes Involved in RNApII PIC assembly.
Protein complex
Functions
RNApII
12 Subunits; catalyzes transcription of all mRNAs and a subset of noncoding RNAs including snoRNAs
and miRNAs
TFIIA
2–3 subunits; functions to counteract repressive effects of negative cofactors like NC2; acts as a
coactivator by interacting with activators and components of the basal initiation machinery
TFIIB
Single subunit; stabilizes TFIID-promoter binding; aids in recruitment of TFIIF/Pol II to the promoter;
directs accurate start site selection
TFIID
14 subunits including TBP and TBP Associated Factors (TAFs); nucleates PIC assembly either through
TBP binding to TATA sequences or TAF binding to other promoter sequences; coactivator activity through
direct interaction of TAFs and gene specific activators
TFIIE
2 subunits; helps recruit TFIIH to promoters; stimulates helicase and kinase activities of TFIIH; binds
ssDNA and is essential for promoter melting
TFIIF
2–3 subunits; tightly associates with RNApII; enhances affinity of RNApII for TBP-TFIIB-promoter
complex; necessary for recruitment of TFIIE/TFIIH to the PIC; aids in start site selection and promoter
escape; enhances elongation efficiency
TFIIH
10 subunits; ATPase/helicase necessary for promoter opening and promoter clearance; helicase activity
for transcription coupled DNA repair; kinase activity required for phosphorylation of RNApII CTD;
facilitates transition from initiation to elongation
Mediator
At least 24 subunits; bridges interaction between activators and basal factors; stimulates both activator
dependent and basal transcription; required for transcription from most RNApII dependent promoters
SAGA
20 subunits; interacts with activators, histone H3, and TBP; histone acetyltransferase activity;
deubiquitinating activity
Trf1
TBP related factor identified in Drosophila; upregulated in CNS and gonads during development; can bind
TATA sequences; mostly found at RNApIII dependent promoters as part of TFIIIB but also required at a
subset of RNApII dependent promoters
Trf2
TBP related factor identified in all metazoans; cannot bind TATA sequences; important for histone gene
expression in Drosophila
Trf3
TBP related factor identified in vertebrates; can bind TATA sequences; important for differentiation of
muscle cells in mammals and for haematopoietic cell development in zebrafish.
TFIIS
1 subunit; stimulates intrinsic transcript cleavage activity of RNApII allowing backtracking to resume RNA
synthesis after transcription arrest; stimulates PIC assembly at some promoters
NC2
2 subunits; binds TBP/DNA complexes and blocks PIC assembly; can have both positive and negative
effects on transcription
Mot1/bTAF1
1 subunit; induces dissociation of TBP/DNA complexes in ATP dependent manner; can have both positive
and negative effects on transcription
Mediator
Basal Factor or not? Not required for basal activity in vitro, but it can
stimulate this activity.
It has been proposed to stimulate phosphorylation of the CTD of
RNA pol II (see Shuman lecture).
Its composition can change depending on which subunits are included
(again……).
Might also act by stimulating reinitiation.
D’Alessio et al, (2009) Mol Cell, vol 36, 924-931
Table 1
Complexes Involved in RNApII PIC assembly.
Protein complex
Functions
RNApII
12 Subunits; catalyzes transcription of all mRNAs and a subset of noncoding RNAs including snoRNAs
and miRNAs
TFIIA
2–3 subunits; functions to counteract repressive effects of negative cofactors like NC2; acts as a
coactivator by interacting with activators and components of the basal initiation machinery
TFIIB
Single subunit; stabilizes TFIID-promoter binding; aids in recruitment of TFIIF/Pol II to the promoter;
directs accurate start site selection
TFIID
14 subunits including TBP and TBP Associated Factors (TAFs); nucleates PIC assembly either through
TBP binding to TATA sequences or TAF binding to other promoter sequences; coactivator activity through
direct interaction of TAFs and gene specific activators
TFIIE
2 subunits; helps recruit TFIIH to promoters; stimulates helicase and kinase activities of TFIIH; binds
ssDNA and is essential for promoter melting
TFIIF
2–3 subunits; tightly associates with RNApII; enhances affinity of RNApII for TBP-TFIIB-promoter
complex; necessary for recruitment of TFIIE/TFIIH to the PIC; aids in start site selection and promoter
escape; enhances elongation efficiency
TFIIH
10 subunits; ATPase/helicase necessary for promoter opening and promoter clearance; helicase activity
for transcription coupled DNA repair; kinase activity required for phosphorylation of RNApII CTD;
facilitates transition from initiation to elongation
Mediator
At least 24 subunits; bridges interaction between activators and basal factors; stimulates both activator
dependent and basal transcription; required for transcription from most RNApII dependent promoters
SAGA
20 subunits; interacts with activators, histone H3, and TBP; histone acetyltransferase activity;
deubiquitinating activity
Trf1
TBP related factor identified in Drosophila; upregulated in CNS and gonads during development; can bind
TATA sequences; mostly found at RNApIII dependent promoters as part of TFIIIB but also required at a
subset of RNApII dependent promoters
Trf2
TBP related factor identified in all metazoans; cannot bind TATA sequences; important for histone gene
expression in Drosophila
Trf3
TBP related factor identified in vertebrates; can bind TATA sequences; important for differentiation of
muscle cells in mammals and for haematopoietic cell development in zebrafish.
TFIIS
1 subunit; stimulates intrinsic transcript cleavage activity of RNApII allowing backtracking to resume RNA
synthesis after transcription arrest; stimulates PIC assembly at some promoters
NC2
2 subunits; binds TBP/DNA complexes and blocks PIC assembly; can have both positive and negative
effects on transcription
Mot1/bTAF1
1 subunit; induces dissociation of TBP/DNA complexes in ATP dependent manner; can have both positive
and negative effects on transcription
SAGA
Our first mention of histone modifying activity.
As mentioned earlier, can substitute (and might be related to) TFIID.
Like Mediator, it can interact with both activators and TBP, acting as
a bridging molecule.
Baker and Grant, (2007) Oncogene, vol 26, 5329-5340
Table 1
Complexes Involved in RNApII PIC assembly.
Protein complex
Functions
RNApII
12 Subunits; catalyzes transcription of all mRNAs and a subset of noncoding RNAs including snoRNAs
and miRNAs
TFIIA
2–3 subunits; functions to counteract repressive effects of negative cofactors like NC2; acts as a
coactivator by interacting with activators and components of the basal initiation machinery
TFIIB
Single subunit; stabilizes TFIID-promoter binding; aids in recruitment of TFIIF/Pol II to the promoter;
directs accurate start site selection
TFIID
14 subunits including TBP and TBP Associated Factors (TAFs); nucleates PIC assembly either through
TBP binding to TATA sequences or TAF binding to other promoter sequences; coactivator activity through
direct interaction of TAFs and gene specific activators
TFIIE
2 subunits; helps recruit TFIIH to promoters; stimulates helicase and kinase activities of TFIIH; binds
ssDNA and is essential for promoter melting
TFIIF
2–3 subunits; tightly associates with RNApII; enhances affinity of RNApII for TBP-TFIIB-promoter
complex; necessary for recruitment of TFIIE/TFIIH to the PIC; aids in start site selection and promoter
escape; enhances elongation efficiency
TFIIH
10 subunits; ATPase/helicase necessary for promoter opening and promoter clearance; helicase activity
for transcription coupled DNA repair; kinase activity required for phosphorylation of RNApII CTD;
facilitates transition from initiation to elongation
Mediator
At least 24 subunits; bridges interaction between activators and basal factors; stimulates both activator
dependent and basal transcription; required for transcription from most RNApII dependent promoters
SAGA
20 subunits; interacts with activators, histone H3, and TBP; histone acetyltransferase activity;
deubiquitinating activity
Trf1
TBP related factor identified in Drosophila; upregulated in CNS and gonads during development; can bind
TATA sequences; mostly found at RNApIII dependent promoters as part of TFIIIB but also required at a
subset of RNApII dependent promoters
Trf2
TBP related factor identified in all metazoans; cannot bind TATA sequences; important for histone gene
expression in Drosophila
Trf3
TBP related factor identified in vertebrates; can bind TATA sequences; important for differentiation of
muscle cells in mammals and for haematopoietic cell development in zebrafish.
TFIIS
1 subunit; stimulates intrinsic transcript cleavage activity of RNApII allowing backtracking to resume RNA
synthesis after transcription arrest; stimulates PIC assembly at some promoters
NC2
2 subunits; binds TBP/DNA complexes and blocks PIC assembly; can have both positive and negative
effects on transcription
Mot1/bTAF1
1 subunit; induces dissociation of TBP/DNA complexes in ATP dependent manner; can have both positive
and negative effects on transcription
TFIIS
Originally characterized as an elongation factor, however more recently
shown to play a role in initiation and PIC formation as well.
Prather et al, (2005) Mol Cell Biol, vol 25, 2650-2659
Table 1
Complexes Involved in RNApII PIC assembly.
Protein complex
Functions
RNApII
12 Subunits; catalyzes transcription of all mRNAs and a subset of noncoding RNAs including snoRNAs
and miRNAs
TFIIA
2–3 subunits; functions to counteract repressive effects of negative cofactors like NC2; acts as a
coactivator by interacting with activators and components of the basal initiation machinery
TFIIB
Single subunit; stabilizes TFIID-promoter binding; aids in recruitment of TFIIF/Pol II to the promoter;
directs accurate start site selection
TFIID
14 subunits including TBP and TBP Associated Factors (TAFs); nucleates PIC assembly either through
TBP binding to TATA sequences or TAF binding to other promoter sequences; coactivator activity through
direct interaction of TAFs and gene specific activators
TFIIE
2 subunits; helps recruit TFIIH to promoters; stimulates helicase and kinase activities of TFIIH; binds
ssDNA and is essential for promoter melting
TFIIF
2–3 subunits; tightly associates with RNApII; enhances affinity of RNApII for TBP-TFIIB-promoter
complex; necessary for recruitment of TFIIE/TFIIH to the PIC; aids in start site selection and promoter
escape; enhances elongation efficiency
TFIIH
10 subunits; ATPase/helicase necessary for promoter opening and promoter clearance; helicase activity
for transcription coupled DNA repair; kinase activity required for phosphorylation of RNApII CTD;
facilitates transition from initiation to elongation
Mediator
At least 24 subunits; bridges interaction between activators and basal factors; stimulates both activator
dependent and basal transcription; required for transcription from most RNApII dependent promoters
SAGA
20 subunits; interacts with activators, histone H3, and TBP; histone acetyltransferase activity;
deubiquitinating activity
Trf1
TBP related factor identified in Drosophila; upregulated in CNS and gonads during development; can bind
TATA sequences; mostly found at RNApIII dependent promoters as part of TFIIIB but also required at a
subset of RNApII dependent promoters
Trf2
TBP related factor identified in all metazoans; cannot bind TATA sequences; important for histone gene
expression in Drosophila
Trf3
TBP related factor identified in vertebrates; can bind TATA sequences; important for differentiation of
muscle cells in mammals and for haematopoietic cell development in zebrafish.
TFIIS
1 subunit; stimulates intrinsic transcript cleavage activity of RNApII allowing backtracking to resume RNA
synthesis after transcription arrest; stimulates PIC assembly at some promoters
NC2
2 subunits; binds TBP/DNA complexes and blocks PIC assembly; can have both positive and negative
effects on transcription
Mot1/bTAF1
1 subunit; induces dissociation of TBP/DNA complexes in ATP dependent manner; can have both positive
and negative effects on transcription
Repressors: Mot1/bTAF1 and NC2
These proteins affect TBP/DNA binding by either blocking PIC assembly
or inducing dissociation of TBP from the DNA.
Counter-intuitively, these can act as activators by preventing or reducing
in appropriate binding of PIC to cryptic promoters, thus making
more PIC available for activation of appropriate promoters.
van Werven et al, (2009) Genes and Development, vol 22, 2259-2369
D’Alessio et al, (2009) Mol Cell, vol 36, 924-931
Model of “Regulated Recruitment”
Potential mechanisms of transcriptional activation:
1. Regulated Recruitment: proteins bind to DNA and recruit an active
polymerase complex to the promoter.
2. Polymerase Activation: proteins bind to DNA and activate a pre-bound,
inactive polymerase complex, thus initiating transcription.
3. Promoter Activation: proteins bind to DNA and induce a conformational
change in the DNA, twisting it into a active state that allows a
transcriptionally active polymerase can bind.
(Figures and concepts taken from Ptashne, M. and Gann, A. (2002) Genes and Signals. Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, New York, USA.)