DNA Transcription Basics Quiz

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27 Questions

Which technique is best suited for studying transcription dynamics in a single cell?

Single cell RNA seq

What is the key limitation of using Single molecule FISH for studying transcription?

Low sequencing depth due to low RNA amount per cell

Which technique involves the extraction of DNA using trysol?

Reverse transcription PCR

In which cellular location does reverse transcription occur in the context of studying transcription?

Cytosol

Which technique is commonly used for measuring transcription output?

RNA-seq

What is a characteristic of all the mentioned techniques (gel, Northern blot, RT-PCR, RNA-seq) for studying transcription?

They are population-based rather than single-cell techniques

What do viruses have the ability to do in the context of gene expression?

Reverse transcribe DNA

What is a defining feature of the transcription process in terms of DNA strands used for transcription?

The choice of DNA strand for transcription depends on where the gene body is located

What is the main drawback of using C-fos* GFP labelled C-fos for studying transcription dynamics?

Low sequencing depth due to low RNA amount per cell

What is a key outcome of understanding and recapitulating the steps involved from DNA to mature mRNA?

Understanding the dynamics of transcription in a single cell

Which enzyme is responsible for adding As to the 3’ end of the mRNA during polyadenylation?

PolyA polymerase (PAP)

What is the role of TFIID in transcription initiation?

Binds to the TATA box and marks the promoter as active

What is the function of CTD of RNA polymerase II during transcription initiation?

Phosphorylates RNA polymerase II

What does PAF1 recruit during transcription elongation?

MLL to trimethylate a histone

What is the role of TFIIH during transcription initiation?

Unwinds the DNA using helicase activity

What is the function of CPSF during transcription termination?

Recognizes the polyadenylation sequence in the 3' UTR

What is the main role of enhancers and silencers in gene transcription regulation?

Enhancers activate gene expression, while silencers repress gene expression

How does cohesin contribute to gene transcription regulation?

Loops DNA to bring enhancers closer to the promoter

Which complex is responsible for recruiting polyA polymerase (PAP) during polyadenylation?

RNA cleavage complex

What modification occurs at the 5’ end of pre-mRNA during transcription elongation?

Capping with a methylated guanine, followed by removal of gamma phosphate and addition of a normal guanine

What is one of the functions of mRNA maturation?

Stabilizes the pre-mRNA molecule

Which of the following is a characteristic of the precatalytic splicesome?

Contains U3

What is the function of the 5'GU sequence in splicing?

Recruits U2 through BBP and U2AF

Why do we have over 2 million proteins in our body despite having only around 20,000 protein coding genes?

Resulting from alternative splicing

What can cause transcription deregulation in the context of cancer?

Alterations in CREs/TREs

How are alterations to alternative splicing linked to cancer cells?

Leading to alterations in splice sites

What is one approach for targeting de-regulated splicing in cancer therapy?

Small molecule compounds modulating the activity of splicing factors

Study Notes

Transcription Dynamics

  • Single-molecule FISH is best suited for studying transcription dynamics in a single cell.
  • The key limitation of using Single molecule FISH is that it is only able to detect RNA in fixed cells.

DNA Extraction

  • The technique that involves the extraction of DNA using trysol is not specific to transcription studies, but rather a general method for DNA extraction.

Reverse Transcription

  • Reverse transcription occurs in the cytoplasm in the context of studying transcription.

Transcription Output Measurement

  • The technique commonly used for measuring transcription output is RT-PCR.

Characteristics of Transcription Techniques

  • A characteristic of all the mentioned techniques (gel, Northern blot, RT-PCR, RNA-seq) for studying transcription is that they are all used to measure RNA levels or transcription output.

Viruses and Gene Expression

  • Viruses have the ability to hijack cellular machinery to express their own genes.

Transcription Process

  • A defining feature of the transcription process is that it occurs on the template DNA strand.

Studying Transcription Dynamics

  • Using C-fos* GFP labelled C-fos to study transcription dynamics has a main drawback of being an indirect measure of transcription.

Transcription and mRNA Maturation

  • Understanding and recapitulating the steps involved from DNA to mature mRNA allows for the manipulation of gene expression.
  • The key outcome of understanding and recapitulating the steps involved from DNA to mature mRNA is the ability to manipulate gene expression.

Polyadenylation

  • The enzyme responsible for adding As to the 3’ end of the mRNA during polyadenylation is polyA polymerase (PAP).
  • CPSF is involved in polyadenylation, and its function is to add As to the 3’ end of the mRNA.

Transcription Initiation

  • TFIID plays a role in transcription initiation by recognizing and binding to the core promoter region.
  • The function of the CTD of RNA polymerase II during transcription initiation is to interact with general transcription factors.
  • TFIIH is involved in transcription initiation and plays a role in unwinding DNA.

Transcription Elongation

  • PAF1 recruits transcription elongation factors during transcription elongation.

Transcription Termination

  • CPSF is involved in transcription termination, and its function is to cleave the RNA transcript.

Gene Regulation

  • Enhancers and silencers are involved in gene transcription regulation by either enhancing or silencing gene expression.
  • Cohesin contributes to gene transcription regulation by looping enhancers to promoters.

Polyadenylation Complex

  • The complex responsible for recruiting polyA polymerase (PAP) during polyadenylation is CPSF.

mRNA Maturation

  • The modification that occurs at the 5’ end of pre-mRNA during transcription elongation is the addition of a 7-methylguanosine cap.
  • One of the functions of mRNA maturation is to protect the mRNA from degradation.

Splicing

  • A characteristic of the precatalytic spliceosome is that it is a large RNA-protein complex.
  • The 5'GU sequence plays a role in splicing by serving as a binding site for the spliceosome.

Proteome Diversity

  • Having over 2 million proteins in our body despite having only around 20,000 protein coding genes is possible due to alternative splicing and post-translational modifications.

Cancer and Transcription

  • Transcription deregulation in the context of cancer can be caused by genetic mutations.
  • Alterations to alternative splicing are linked to cancer cells by allowing for the production of oncogenic proteins.
  • One approach for targeting de-regulated splicing in cancer therapy is to use splice-switching oligonucleotides.

Test your knowledge on the basics of DNA transcription and splicing. This quiz covers the steps involved from DNA to mature mRNA, key transcription terms, and the dynamics of transcription in a single cell.

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