Eukaryotic Transcription: L13

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Questions and Answers

What element facilitates the binding of TFIID in a core promoter?

Upstream sequence element (USE)

Downstream promoter element (DPE)

Initiator element (INR) (correct)

TATA box

Which of the following correctly describes the TATA box in a core promoter?

Always present in all eukaryotic promoters

Located only downstream of the initiator

Contains a conserved sequence TATAAAA (correct)

Present in 70% of all promoters

What is the typical distance of the DPE from the transcription start site?

+28 to +32 bp (correct)

+1 bp

-100 bp

-30 bp

Which type of core promoter can initiate transcription in the absence of a TATA box?

TATA-less core promoter Signup and view all the answers

What is the consensus sequence for the INR element in humans?

YYANWYY Signup and view all the answers

In which eukaryotic transcription factor is the TATA box recognized?

TATA-binding protein Signup and view all the answers

How does the complexity of the eukaryotic system compare to prokaryotic initiation of transcription?

Eukaryotic promoters have additional upstream elements Signup and view all the answers

Which RNA polymerase is responsible for transcribing all genes that produce mRNA in eukaryotes?

RNA polymerase II Signup and view all the answers

What is the role of TFIID in the transcription initiation process for RNA Pol II?

It binds to the TATA box to initiate transcription. Signup and view all the answers

Which component of the TFIID complex interacts directly with the TATA box?

TBP (TATA binding protein). Signup and view all the answers

What is the purpose of TAFs in the TFIID complex?

To assist in the recruitment of RNA polymerase II. Signup and view all the answers

What is the significance of the TATA box in eukaryotic transcription?

It is where the RNA synthesis begins. Signup and view all the answers

Which general transcription factor recruits RNA polymerase II to the TATA box?

TFIIB. Signup and view all the answers

What is the primary function of RNA polymerase II in eukaryotic transcription?

Transcribes all genes that encode proteins Signup and view all the answers

Which of the following best describes the role of general transcription factors in eukaryotic transcription?

They are required for the initiation of transcription by RNA polymerase II. Signup and view all the answers

What characterizes eukaryotic transcription compared to prokaryotic transcription?

Eukaryotic DNA is packaged into nucleosomes, complicating initiation. Signup and view all the answers

What components help regulate transcription in eukaryotes?

Core promoters and upstream regulatory elements Signup and view all the answers

Which of the following explains the significance of the pre-initiation complex (PIC) in transcription?

It assembles to initiate the transcription process. Signup and view all the answers

What is the role of TFIIF in the initiation of transcription?

It stabilizes RNA Pol II. Signup and view all the answers

Which of the following components is part of the pre-initiation complex (PIC)?

TFIIE Signup and view all the answers

What activity is performed by TFIIH during the transcription initiation phase?

Melting the DNA Signup and view all the answers

Which statement best describes the function of TFIIH in elongation?

It phosphorylates the C terminal domain of RNA Pol II. Signup and view all the answers

What occurs after the phosphorylation of RNA Pol II during transcription elongation?

TFs are released from the complex. Signup and view all the answers

Which transcription factor is required for both initiation and elongation?

TFIIH Signup and view all the answers

What is the primary function of RNA Pol II during transcription?

To synthesize RNA from the DNA template. Signup and view all the answers

Which part of the transcription process is considered the 'elongation' phase?

Synthesis of RNA after initiation. Signup and view all the answers

During the transcription process, which modification occurs to the C terminal domain of RNA Pol II?

Phosphorylation. Signup and view all the answers

How does TFIIH contribute to transcription regulation?

By controlling the phosphorylation of RNA Pol II. Signup and view all the answers

What is the primary function of enhancer elements in eukaryotic promoters?

They enhance the binding of RNA polymerase II. Signup and view all the answers

Which property allows enhancer elements to function effectively in eukaryotic transcription?

They can activate transcription from a distance of up to 1Mb. Signup and view all the answers

What is the consequence of deleting a specific 72 bp sequence from the SV40 promoter?

A 100-fold decrease in expression is seen. Signup and view all the answers

In which location can enhancer elements act?

Either upstream or downstream of the TATA box, or within an intron. Signup and view all the answers

Which of the following is NOT a characteristic of enhancer elements?

They permanently alter the genetic code. Signup and view all the answers

What limitation is noted about upstream sequence elements like the Sp1 site?

They must be placed within 100 bp of the TATA box to function. Signup and view all the answers

The term 'cis-acting' in the context of enhancers refers to what?

Their interaction with transcription factors from the same DNA molecule. Signup and view all the answers

Which statement about the orientation of enhancer elements is accurate?

Enhancers can function regardless of their orientation. Signup and view all the answers

What is the main role of the Pre-initiation complex (PIC) in transcription?

It directs only a very low level of transcription. Signup and view all the answers

Which transcription factor is known to bind to the GC box?

SP1 Signup and view all the answers

What is the significance of the position of upstream sequence elements (USE) in relation to RNA Pol II?

They must be in the same orientation as the RNA Pol II initiation site. Signup and view all the answers

Which of the following is a characteristic of the CAAT box?

It contains the consensus sequence GG(T/C)CAATCT. Signup and view all the answers

Which statement about tissue-specific transcription factors is true?

They are present in all cell types but only functional in certain tissues. Signup and view all the answers

What role do enhancers play in transcription?

They enhance transcription by recruiting transcription factors. Signup and view all the answers

What does the CANNTG motif represent in transcription regulation?

A sequence specifically bound by muscle-specific transcription factors. Signup and view all the answers

Which of the following provides tissue-specific enhancement of transcription?

Upstream sequence elements such as GC and CAAT boxes. Signup and view all the answers

Study Notes

Eukaryotic Transcription Initiation

Eukaryotic transcription is more complex than prokaryotic transcription, primarily due to DNA packaging into nucleosomes.
Transcription initiation involves assembling a pre-initiation complex (PIC).
The PIC positions RNA polymerase II over transcription start sites.
General transcription factors (TFII) bind to the TATA box.
The first factor, TFIID, binds to the TATA box.
TFIID is a complex of TBP (TATA binding protein) and TAFs (TBP associated factors).
The TAFs help other TFs attach to DNA and unwind the chromatin structure.
TFIIB recruits RNA polymerase II to the TATA box.
TFIIA stabilizes the complex.
TFIIE and TFIIH bind and complete the PIC.
TFIIH has helicase activity, which unwinds the DNA.
The PIC is assembled, facilitating the start of transcription.

Eukaryotic Transcription Elongation

TFIIH phosphorylation of RNA polymerase II's C-terminal domain (CTD) occurs.
This phosphorylation signals the release of other transcription factors (TFs).
TFIIH is vital for the elongation process.
There's a conformational change, and RNA polymerase II tightens its grip.
New proteins, including elongation factors, aid in RNA processing and increased elongation rate.

Regulatory Elements in Eukaryotic Promoters

Upstream regulatory elements (like enhancers and silencers) greatly influence transcription.
Enhancers are regulatory elements acting at a distance, up to 1 Mb away, from the promoter.
Enhancers can activate transcription, regardless of orientation or placement (upstream/downstream/within introns).
Enhancers function by binding to specific activator proteins that influence mediator interactions with RNA polymerase.

Core Promoters

Core promoters are the DNA sequences immediately upstream of a gene's coding region.
They contain essential elements that position and stabilize the RNA polymerase II pre-initiation complex (PIC).
TATA box is a core promoter element, frequently found in promoters (approximately 30%) of protein-coding genes.
The Initiator (INR) is a core promoter element.
The Downstream Promoter Element (DPE) is a core promoter element; often located downstream of the transcription initiation site.
Core promoter elements position the transcription machinery appropriately for efficient binding to the promoter.

Introns

Introns are non-coding DNA sequences within a gene.
Transcription involves removing introns and joining exons.
Intron polymorphisms, although not affecting the encoded protein, can impact gene expression.

Upstream Sequence Elements

Upstream sequences are the DNA segments located upstream of the core promoter.
These sequences can strongly influence the rate of transcription.
Specific transcription factors bind to these elements, which are important in modulating transcription in response to stimuli or specific cell types.
Examples include the GC box and the CAAT box.

Factors Affecting Transcription Rate

Gene expression is also influenced by cell-cell or cell-matrix interactions and external factors such as hormones.
Unique sets of transcription factors for various cell types are crucial to determining their fates.

Importance of Eukaryotic Transcriptional Machinery

Both core promoters and upstream sequences are pivotal for regulating gene expression.
Appropriate transcription factor binding is vital for proper transcription initiation and elongation.

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