Eukaryotic Transcription 1 Flashcards
basal transcription factors
proteins that bind to the core promoter near the start point for transcription and are required to recruit RNA polymerase
core promoter
region of DNA (that includes the start point of transcription) that binds the basal factors. usually consists of sequences around start and 100 bp upstream
start point of transcription
DNA of the promoter that corresponds to the first nucleotides transcribed. RNA pol contacts it directly but does not select it
enhancers
- contains several closely arranged sequence elements that bind to transcription factors
- where transactivators and coactivators bind, which recruit HATs to open chromatin
- contain modules or domains which consists of cis-elements. may be all the same or a combination of different elements
- enhancers and individual cis-elements may be over 1,000 pb distant and can function in either orientation
basal transcription
- low level background activity, not regulated, only requires a minimal promoter, no involvement of upstream elements or transactivator proteins
transactivators
recognize DNA and recruit complexes that have enzymatic activity that affect the histone code
- recruit co-activators, which aren’t considered transactivators because it does not recognize DNA and has enzymatic activity
repressors
- HDAC
- bind to a silencer that is separate from a promoter
inducible factors
- a type of upstream factor that control highly regulated genes (inducible transcription, binds to a response element)
- activation state of the factor itself is inducible
non-inducible factors
x
what kinds of genes does RNA pol 1 read?
- ribosomal genes
- most amount of activity in RNA synthesis
- in the nucleolus
what kinds of genes does RNA pol 2 read?
- genes encoding proteins
- accounts for most of the remaining activity in the cell
- in the nucleoplasm
what kinds of genes are read by RNA pol 3?
- tRNA genes and other small RNAs
- minor activity in the cell
what is the basic promoter structure of RNA pol 1?
- bipartite promoter consisting of a core promoter and an upstream promoter element (UPE)
- associated with two proteins: SL1 and upstream binding factor (UBF)
what are the major transcription factors associated with RNA pol 1?
- SL1 and UBF
SL1
- transcription factor in RNA pol 1
- core binding factor
- consists of TBF and 3 other proteins
- positions RNA pol 1
- low levels of constitutive transcription
UBF
- upstream binding factor
- single peptide
- ensure high frequency initiation
what is the commitment factor in RNA pol 1?
SL1
what is the basic promoter structure of RNA pol 3?
- consists of three types
- internal and upstream
internal promoter
- have short consensus sequences located within the transcription unit to occur a fixed distance upstream
upstream promoters
- contain 3 short consensus sequences upstream of the start point that are bounded by transcription factors
what are the major transcription factors associated with RNA pol 3?
- TF3B
- the other factors are assembly factors
type 1 promoter
- uses TF3A/C
- bind to the consensus sequences and enable TF3B to bind at the start point
- TF3B delivers TBP to preinitiation complex
- box A and box C
type 2 promoter
- only uses TF3C and Tf3B
- box A and box C
assembly factors
- TF3A and TF3C
- only role is to direct TF3B to the right location
- can be removed once TF3B has bounded
TF3C
- assembly factor
- 6 subunits more than 500 kD
- same size as RNA polymerase
TF3A
- assembly factor
- contains a zinc finger DNA binding domain
what is the commitment factor for RNA pol 3?
TF3B
where is TBP found in RNA pol 3?
- within TF3B (subunit)
TF3B
- contains TBP and Brf, and B’
- B’ seems to assist in melting the promoter
what is the relationship between archaeal RNA polymerases and eukaryotic RNA polymerases?
- archaea have the same RNA polymerase except that its beta prime is in 2 parts
- no sigma in eukaryotes
what is the common structure of RNA polymerases in eukaryotes?
- have 12 subunits
- roughly 500 kD
- some of the subunits are common between the 3
- all can transcribe DNA non-specifically in vitro but promoter recognition depends on transcription factors
what is the largest subunit of RNA pol 2?
- CTD consisting of multiple repeats of a heptamer (7 amino acids)
- 26 CTD in yeast but 50 in mammals
where does RNA polymerase bind?
UBF1-SL1 complex at the core promoter
Which RNA polymerase is most sensitive to the fungal toxin alpha-amanitin?
RNA polymerase 2
Which enzymatic activities are associated with co-activators? With repressors?
- enhancers w/ co-activators
- silencers w/ repression
Understand the steps that lead to activated transcription.
- transactivators bind to the enhancer region
- transactivators open chromatin with HAT
- tranactivators recruit basal factors
- basal factors recruit RNA pol 2
- start point begins at +1
What is the difference between a basal factor and a transactivator or a repressor?
- basal factors are involved in initiation of RNA synthesis of all RNA pol 2 promoters and form the preintiation complex
- a transactivator or repressor bind to upstream elements specific to different promoters which in turn recruit basal factors
Name the three control elements located in the core promoter, or immediately downstream.
TATAA, Initiator and the DPE
Which element can be present in both TATAA-less and in TATAA-containing promoters?
the Initiator
Which element is common in Drosophila, but only occasionally present in human genes?
the downstream promoter element; DPE
What is the difference between the “minimal promoter” and the “core promoter”?
- both are the same thing
- consists of the InR and a TATA box/DPE
What is the difference between an inducible versus a noninducible upstream factor?
Once synthesized, the activity of Inducible Factors can be regulated. For Noninducible Factors, after they are made, their activity remains constant. This concept refers to their activity after they have been produced, not the regulation of their abundance in the cell.
Know the difference between basal and activated transcription.
The distinction is simple: activated transcription must have involvement of upstream factors, not just the basal factors. The distinction has nothing to do with whether activity is inducible or noninducible.
how is the start point for RNA polymerase 2 determined?
- RNA polymerase requires general transcription factors to initiate transcription (also called basal factors) that nucleate at the core promoter
- RNA polymerase 2 promoters have a short conserved (Py2CAPy5) initiator region (InR) overlapping the start point
TATA box
- common component of RNA polymerase 2 promoters
- consists of an AA-T rich octamer located 25 bp upstream of the startpoint
DPE
- a common component of RNA polymerase 2 promoters that do not contain a TATA box
upstream factors
- transactivators/transfactors
- bind upstream elements, specific to different promoters
what is the organization of cis-acting elements?
- cis-elements may be located upstream, downstream, or in introns (commonly upstream)
- elements may be scattered in distribution or organized in clusters called enhancers
activated transcription
- requires upstream (or other locations) cis-elements, usually much higher levels of activity than basal transcription
what is the process of the recruitment of basal factors to the core promoter?
- key steps in activated transcription are performed by transactivator proteins
- transactivator proteins open the chromatin and recruit basal factors
- the preinitiation complex forms near the start site
- transactivator proteins open the chromatin and recruit basal factors
- after the CTD is phosphorylated, initiation occurs
- transcriptional initiation is followed by a pause
- during the pause, the CTD loads RNA processing complexes before the elongation phase
- TF2D remains at the promoter for next round of initiation
