Eukaryotic Transcription Regulation

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Questions and Answers

What is the effect of histone acetyltransferase on histone proteins?

It eliminates the presence of histones.

It increases the binding of histones to DNA.

It reduces the binding of histones to DNA. (correct)

It prevents histones from being replaced.

How does DNA methylation typically affect gene transcription?

It enhances transcription by attracting transcription factors.

It promotes the binding of RNA polymerase to the promoter.

It has no effect on transcription.

It inhibits transcription by preventing activator binding. (correct)

Which process is most closely associated with changes in nucleosome positions?

Intronic splicing

Histone deacetylation

DNA replication

Chromatin remodeling (correct)

What defines the difference between euchromatin and heterochromatin?

Euchromatin is loosely packed and often associated with active genes. Signup and view all the answers

What is the role of chromatin-remodeling complexes in histone replacement?

They replace standard histones with variant histones. Signup and view all the answers

What is the role of the TATA box in eukaryotic promoters?

To serve as the primary binding site for RNA polymerase II Signup and view all the answers

Which of the following statements about euchromatin and heterochromatin is TRUE?

Euchromatin is associated with active gene transcription. Signup and view all the answers

What must be present for transcription initiation in eukaryotes?

RNA polymerase II and general transcription factors Signup and view all the answers

Histone modifications primarily affect which aspect of gene regulation?

Chromatin structure and accessibility Signup and view all the answers

Which statement accurately describes enhancer-promoter interactions?

Enhancers can significantly increase the transcription of genes even when located far away. Signup and view all the answers

What is a key difference in transcription regulation between eukaryotes and prokaryotes?

Eukaryotic transcription initiation is typically more complex. Signup and view all the answers

Which factor is NOT necessary for the initiation of transcription in eukaryotes?

RNA polymerase I Signup and view all the answers

What role do small effector molecules play in gene regulation in eukaryotes?

They activate or inhibit transcription factors. Signup and view all the answers

What role does TFIID play in the transcription initiation process?

It promotes the assembly of the preinitiation complex. Signup and view all the answers

Which statement accurately describes the function of enhancers in transcription regulation?

They stimulate mediators to enable faster initiation of transcription. Signup and view all the answers

What effect does chromatin condensation have on gene expression?

It regulates gene expression by controlling accessibility to DNA. Signup and view all the answers

Which modification on histone proteins is primarily associated with promoting gene expression?

Acetylation of lysine residues. Signup and view all the answers

What is the primary function of insulators in the context of transcription regulation?

To prevent the activity of enhancers and restrict their influence. Signup and view all the answers

How does the 'histone code' influence transcription?

Through specific patterns of modifications that alter chromatin compaction. Signup and view all the answers

Which term is used to describe the loosely packed form of chromatin that allows for transcription?

Euchromatin Signup and view all the answers

What is the role of coactivators in transcription regulation?

To enhance the interaction between activators and the mediator. Signup and view all the answers

Which factor inhibits the progression of RNA polymerase II during transcription?

Repressors Signup and view all the answers

What is the primary characteristic of heterochromatin?

It is tightly packed, resulting in limited transcription capability. Signup and view all the answers

Which amino acid modification is associated with transcriptional repression?

Methylation of lysine residues. Signup and view all the answers

Which component is essential for the assembly of the preinitiation complex in transcription initiation?

TFIID Signup and view all the answers

What is the primary function of activators in the transcription process?

To facilitate the transcription machinery's access to the gene. Signup and view all the answers

Which element acts as a barrier preventing inappropriate enhancer activity?

Insulator Signup and view all the answers

What effect does the addition of phosphate groups generally have on histones?

It can either promote or inhibit transcription depending on the context. Signup and view all the answers

What is one consequence of histone acetyltransferase activity on histone proteins?

Histones do not bind DNA as tightly Signup and view all the answers

Which of the following mechanisms can lead to transcription inhibition via DNA methylation?

Inhibition of enhancer binding Signup and view all the answers

What is the primary function of chromatin-remodeling complexes?

To change the positioning of nucleosomes Signup and view all the answers

What is a characteristic of methylated CpG islands?

They restrict transcription factor access Signup and view all the answers

Which statement accurately reflects the role of ATP in chromatin remodeling?

It provides energy for repositioning nucleosomes Signup and view all the answers

What is the primary function of methyl-CpG-binding proteins in chromatin regulation?

To recruit proteins that condense chromatin Signup and view all the answers

How do miRNAs and siRNAs primarily function in gene regulation?

By silencing the expression of mRNAs Signup and view all the answers

What is the role of the RISC complex in the process of RNA interference?

To degrade one of the RNA strands in the duplex Signup and view all the answers

What is released by dicer during the processing of pre-miRNA or pre-siRNA?

A 22-bp RNA molecule Signup and view all the answers

In the process of mRNA silencing, what is the first step after pre-miRNA is synthesized?

It is cut by RNA endonuclease Signup and view all the answers

What is a characteristic unique to eukaryotic gene regulation compared to prokaryotic regulation?

Gene regulation often involves a combination of mechanisms. Signup and view all the answers

What is the location of the TATA box in relation to the transcriptional start site?

Positioned 25 base pairs upstream. Signup and view all the answers

What is necessary for the assembly of the transcription initiation complex in eukaryotes?

A combination of general transcription factors and RNA polymerase II. Signup and view all the answers

Which of the following is NOT a feature of most eukaryotic promoters?

Isolation from regulatory factors downstream. Signup and view all the answers

How do activator and repressor proteins function in eukaryotic transcription regulation?

They influence RNA polymerase's ability to bind to DNA. Signup and view all the answers

Which statement accurately reflects the role of proximal promoter elements in eukaryotic gene regulation?

They interact with general transcription factors to facilitate transcription initiation. Signup and view all the answers

What defines the core promoter in eukaryotic transcription?

The area containing the TATA box and the transcriptional start site. Signup and view all the answers

Which of the following statements is true regarding small effector molecules in eukaryotic gene regulation?

They bind to regulatory proteins and modify their activity. Signup and view all the answers

What is the primary function of the mediator complex in transcription regulation?

Facilitates the interaction between transcription factors and RNA polymerase II Signup and view all the answers

How do activators influence the action of general transcription factors on RNA polymerase II?

They enhance the ability of general transcription factors to bind to the core promoter Signup and view all the answers

Which statement best describes the role of repressors in transcription?

They bind to regulatory DNA regions to inhibit transcription Signup and view all the answers

What are enhancers and their role in transcription regulation?

Regulatory sequences that increase the transcription rate when activated by proteins Signup and view all the answers

How can the rate at which transcription is initiated by RNA polymerase II be regulated?

Through the binding of activators and repressors to specific DNA regions Signup and view all the answers

What is a characteristic feature of the preinitiation complex formed at the TATA box?

It comprises general transcription factors and RNA polymerase II Signup and view all the answers

What is the significance of DNA bending in transcription regulation?

It facilitates interactions between distant regulatory factors and the core promoter Signup and view all the answers

Which mechanism does NOT play a role in regulating RNA polymerase II activity?

Direct interaction of RNA polymerase II with enhancers in regulatory regions Signup and view all the answers

What is the primary role of the mediator in transcription regulation?

To act as a bridge between transcription factors and RNA polymerase II Signup and view all the answers

Which modification on histone proteins is associated with reducing chromatin compaction?

Acetylation of lysine residues Signup and view all the answers

How do insulators function in the context of transcription regulation?

By preventing enhancer interactions with non-target promoters Signup and view all the answers

What is an effect of chromatin condensation on transcription initiation?

Inhibits the access of RNA polymerase II to the DNA Signup and view all the answers

Which component is crucial for the assembly of the preinitiation complex during transcription initiation?

TFIID Signup and view all the answers

Which type of regulation is primarily associated with repressors binding to silencer regions?

Negative control of transcription Signup and view all the answers

What is the significance of the histone code in gene regulation?

It influences the degree of chromatin compaction affecting gene expression Signup and view all the answers

In what way do activators enhance transcription initiation?

By allowing faster formation of the preinitiation complex Signup and view all the answers

What type of modifications are the amino terminal tails of histone proteins mainly subject to?

Covalent modifications Signup and view all the answers

What is the role of chromatin remodeling complexes in gene expression?

To alter nucleosome positioning and accessibility to DNA Signup and view all the answers

Which amino acid is typically associated with transcriptional repression when modified?

Lysine Signup and view all the answers

Which statement best describes the TATA box's role in transcription regulation?

It is essential for the binding of TFIID to initiate transcription Signup and view all the answers

How does the binding of transcriptional repressors affect mediator activity?

Inhibits mediator function, preventing elongation of RNA polymerase II Signup and view all the answers

Study Notes

Histone Acetylation

Histone acetyltransferases (HATs) add acetyl groups to histone proteins, making them less tightly bound to DNA.
Histone deacetylases (HDACs) remove acetyl groups, making histone binding to DNA tighter.

Chromatin Remodeling

Chromatin remodeling enzymes use ATP to alter DNA compaction.
These enzymes can change the position of nucleosomes, remove histones, or replace standard histones with variant histones.

DNA Methylation

DNA methyltransferases attach methyl groups to cytosine bases in DNA.
Methylation often inhibits transcription.
In mammals, about 5% of DNA is methylated.
CpG islands are regions of DNA with frequent cytosine-guanine dinucleotides.
Unmethylated CpG islands are often associated with active genes, while methylated CpG islands are typically found near repressed genes.

Transcriptional Regulation in Eukaryotes

Methylation can inhibit transcription by preventing activator proteins from binding to enhancers or by interfering with transcription factor assembly at promoters.
Transcription factors (TFs) bind to DNA at promoters and can either activate or repress transcription.
Some TFs bind to enhancer regions and can influence transcription at a distance.

Enhancer Action

Enhancers are DNA sequences that can activate transcription of genes located far away.
They have binding sites for TFs and can influence transcription initiation by recruiting coactivator proteins.

Insulator Function

Insulators are DNA sequences that block the activity of enhancers and can redirect enhancer activity to different genes.

Chromatin Condensation and Gene Regulation

Chromatin condensation, the packing of DNA and proteins, plays a crucial role in regulating gene expression.
Open chromatin (euchromatin) allows easier access to DNA for transcription.
Closed chromatin (heterochromatin) is tightly packed and restricts access to DNA, making transcription difficult.

Histone Modification

Histone proteins have amino-terminal tails that are subject to various covalent modifications.
These modifications include acetylation, methylation, and phosphorylation.
The pattern of histone modifications, known as the histone code, influences chromatin compaction and gene expression.

Gene Regulation in Eukaryotes (General)

Eukaryotic gene regulation is more complex than prokaryotic regulation and often involves multiple mechanisms.
Genes in eukaryotic cells are typically regulated individually.
Eukaryotic promoters often contain a TATA box, a transcriptional start site, and proximal promoter elements.

Transcription Initiation in Eukaryotes

Transcription initiation requires RNA polymerase II and five general transcription factors (GTFs).
The core promoter, including the TATA box and transcriptional start site, is essential for initiation.
The preinitiation complex forms at the core promoter and is responsible for the first steps of transcription.

Gene Regulation in Eukaryotes

Eukaryotic gene regulation is similar to prokaryotes in some ways, but there are significant differences.
Activator and repressor proteins control RNA polymerase activity, influenced by small effector molecules.
Eukaryotic genes are typically regulated individually unlike prokaryotes, and regulation is more complex.

Features of Most Eukaryotic Promoters

TATA box: Located 25 base pairs upstream from the transcriptional start site, it has the sequence 5’-TATAAAA-3’.
Transcriptional start site: The site (+1) where transcription begins.
Proximal promoter elements: Found upstream from the TATA box, recognized by regulatory proteins (TFs) that control transcription initiation.

Transcription Initiation in Eukaryotes

Requires three components:
- RNA polymerase II
- 5 General Transcription Factors (GTFs)
- Large mediator protein complex

Regulation of Transcription Initiation

GTFs and RNA polymerase II must assemble at the core promoter (TATA box) before transcription can start.
Mediator is a multi-protein complex that partially wraps around GTFs and RNA polymerase II.
Mediator regulates the rate of transcription initiation by mediating interactions with activators or repressors.

Activators and Repressors

Activators bind to regulatory DNA regions and stimulate gene expression.
Repressors bind to regulatory DNA regions and suppress gene expression.
They influence transcription by interacting with promoter elements and inducing DNA bends.

Ways to Control RNA Polymerase II

Activators and repressors regulate RNA polymerase II activity by binding to regulatory DNA regions.
RNA polymerase II is regulated by the mediator, which can be stimulated by activators or inhibited by repressors.
Proteins that influence DNA compaction can also control RNA polymerase II.

Insulators

Insulators prevent enhancers from influencing inappropriate promoters and can redirect them to different promoters.

Histone Modification

Histone proteins have amino (N) terminal tails subject to covalent modifications: acetylation, methylation, and phosphorylation.
The pattern of histone modifications, known as the histone code, affects chromatin compaction.
- Acetylation loosens DNA compaction, while deacetylation tightens it.
Histone acetyltransferases (HATs) add acetyl groups to histones, while histone deacetylases (HDACs) remove them.
- HATs loosen DNA-histone binding.
- HDACs tighten DNA-histone binding.

Chromatin Remodeling

ATP-dependent chromatin remodeling enzymes loosen DNA compaction.
These enzymes can:
- Change nucleosome position.
- Evict histones.
- Replace standard histones with variant histones.

DNA Methylation

DNA methylase adds methyl (-CH3) groups to cytosines.
Usually inhibits transcription.
Common in some eukaryotes, with 5% of mammalian DNA being methylated.
CpG islands are regions of DNA with frequent Cytosine-Guanine dinucleotides (connected by phosphodiester bonds) near promoters.
- Unmethylated CpG islands are associated with active genes.
- Methylated CpG islands are associated with repressed genes.

Inhibition of Transcription by Methylation

Methylation can block activators from binding to enhancers.
It converts chromatin from an open (euchromatin) to a closed (heterochromatin) conformation by recruiting proteins that condense chromatin..

MicroRNAs (miRNAs) and Small Interfering RNAs (siRNAs)

miRNAs and siRNAs are short RNA molecules that silence mRNA expression, preventing translation.
They play a crucial role in RNA interference (RNAi), a widely used mechanism of gene silencing in eukaryotes.

mRNA Silencing by miRNAs and siRNAs

miRNAs and siRNAs are synthesized as pre-miRNAs and pre-siRNAs, respectively.
Dicer, an RNA endonuclease, cleaves the double-stranded region of pre-miRNAs and pre-siRNAs, generating 22-bp RNA molecules.
The mature miRNA/siRNA associates with proteins to form the RNA-induced silencing complex (RISC).
One strand of the miRNA/siRNA in RISC is degraded, while the other guides RISC to target mRNAs.
RISC binds to target mRNAs based on sequence complementarity, leading to mRNA degradation or translational repression.

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Description

Explore the mechanisms of transcriptional regulation in eukaryotic cells, focusing on histone modifications such as acetylation and methylation. This quiz covers the roles of histone acetyltransferases, deacetylases, and the significance of DNA methylation in gene expression. Test your understanding of chromatin remodeling and its impact on transcription.