36 Questions
What is the purpose of forming the pre-initiation complex (PIC)?
To mark the TSS site
What is recognized by the TBP in the promoter region?
The TATA box
In what percentage of genes does the TBP act as a true TBP?
20%
What is the order of recruitment of factors to form the PIC?
TBP, TFIIA, TFIIB, RNA Pol II
What is the function of the TAFs in the promoter region?
To incorporate into TFIID
What happens to the PIC in promoters with multiple TSS sites?
The PIC forms randomly in a large region
What is the name of the complex formed after the incorporation of the necessary factors?
Pre-initiation complex (PIC)
What is the role of the helicase activity in the PIC?
To open the DNA double helix
What happens to the transcription factors after the RNA polymerase has moved?
Some remain bound to the promoter, while others are released
What is the role of TFIIS in the transcription process?
To solve polymerase pauses
What is the purpose of the reiniciation of RNA Pol II?
To initiate a new transcription cycle
How does the RNA Pol II locate the promoter region?
Through the interaction with the transcription factors
What is the role of the CTD in the RNA Pol II?
To facilitate the reiniciation of the polymerase
What is the structural difference between the PIC and the open complex?
The PIC has a closed DNA structure, while the open complex has an open DNA structure
What is the function of the TFIIH subunit Ssl2?
To have helicase activity
How does the RNA Pol II interact with the DNA?
Indirectly, through the interaction with the transcription factors
What is the primary function of Ssl2 in the process of transcription?
To separate the template strand from the complementary strand
What is the difference between the closed complex and the open complex in transcription?
The DNA is not separated in the closed complex, but is separated in the open complex
What is the role of the TFIIH complex in transcription?
To phosphorylate the RNA polymerase
What is the purpose of the promoter proximal in gene transcription?
To facilitate the binding of general transcription factors to the promoter
What is the difference between the initial transcribing complex and the elongation complex?
The RNA polymerase is not active in the initial transcribing complex, but is active in the elongation complex
What is the role of the mediator complex in transcription?
To bridge the gap between the promoter proximal and promoter basal regions
What is the primary function of the promoter region in gene transcription?
To regulate the level of transcription
What is the difference between the pre-initiation complex and the open complex?
The DNA is not separated in the pre-initiation complex, but is separated in the open complex
What is the role of the TFIIA complex in transcription?
To facilitate the binding of general transcription factors to the promoter
What is the purpose of the promoter distal region in gene transcription?
This region is not involved in gene transcription
What is the primary function of the mediator complex in gene transcription?
To facilitate the entry of general transcription factors into the promoter region
What is the characteristic of remodeler complexes that allows them to recognize specific types of nucleosomes?
Presence of a bromodomain that recognizes acetylated lysines
What is the effect of remodeler complexes on nucleosomes during transcription initiation?
They can either move or remove nucleosomes to create space for the PIC
What is the role of the mediator complex in promoters without a TATA box?
It is replaced by the TFIID complex
What is the function of the ATPase activity in remodeler complexes?
To open up the double helix and disorganize chromatin
What is the effect of histone acetylation on remodeler complexes?
It allows remodeler complexes to recognize specific types of nucleosomes
What is the role of the mediator complex in the formation of the PIC?
It acts as a co-regulator to facilitate the entry of general transcription factors
What is the characteristic of the mediator complex in terms of its size?
It is similar in size to the RNA polymerase II enzyme
What is the effect of remodeler complexes on chromatin structure?
They can either compact or loosen chromatin, depending on the context
What is the role of the TBP in promoters with a TATA box?
It is the contact between the mediator and activators
Study Notes
Formation of the Pre-initiation Complex (PIC)
- The PIC is formed through a sequential model, where several factors bind to the promoter region of the DNA.
- The process begins with the recognition of the TATA box by TBP (TATA-binding protein) accompanied by the SAGA complex (in SP promoters) or TFIID (in non-TATA promoters).
- TFIID incorporates TBP and TAFs (TBP-associated factors) to bind to the promoter region.
- Not all promoters are recognized directly by TBP; some are recognized by other factors that form TFIIB.
- The PIC is formed through the recruitment of several factors, including TFIIA, TFIIB, TFIIE, TFIIH, and TFIIJ.
Structure of the PIC
- The PIC is a large complex that includes RNA polymerase II, TBP, TFIIA, TFIIB, and TFIIH.
- The DNA is positioned in the center, and the polymerase is located on one side, while the other factors are positioned on the other side.
- The PIC is held together by protein-protein interactions, allowing the polymerase to access the DNA.
- The complex is dynamic, with factors entering and leaving as transcription proceeds.
Initiation of Transcription
- The transition from the PIC to the open complex (OC) involves the unwinding of the DNA and the binding of the polymerase to the template strand.
- This process requires the activity of TFIIH, which has a helicase subunit that unwinds the DNA.
- The polymerase begins transcription by adding nucleotides to the growing RNA chain.
- As transcription proceeds, the polymerase moves along the DNA, and the factors that made up the PIC dissociate and reassociate with the promoter.
Elongation of Transcription
- The transition from the OC to the elongation complex (EC) occurs when the polymerase begins to synthesize RNA at a high rate.
- During elongation, the polymerase moves rapidly along the DNA, and the RNA grows in size.
- The polymerase may encounter obstacles, such as pauses or roadblocks, which can cause it to stall or backtrack.
Regulation of Transcription
- Transcriptional regulation occurs at multiple levels, including the recruitment of general transcription factors, the binding of specific transcription factors, and the modification of chromatin structure.
- Chromatin remodeling complexes, such as the SWI/SNF complex, play a crucial role in accessing the promoter region by reorganizing the nucleosomes.
- These complexes can either relax or compact chromatin, allowing or blocking access to the promoter region.
Chromatin Remodeling Complexes
- Chromatin remodeling complexes are multi-protein complexes that use ATP to reorganize the nucleosomes and facilitate transcription.
- These complexes often have helicase activity and can recognize specific histone modifications, such as acetylation.
- Examples of chromatin remodeling complexes include the SWI/SNF complex, the RSC complex, and the Mi-2/NuRD complex.
Learn about the sequential classical model of PIC formation, a crucial step in transcription initiation. This process involves the assembly of various factors to form the pre-initiation complex. Understand the classic model and how it differs from other models.
Make Your Own Quizzes and Flashcards
Convert your notes into interactive study material.
Get started for free
