Gene Regulation and Chromatin Structure Quiz

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Questions and Answers

What is the primary function of histone acetyltransferases (HATs)?

To condense chromatin, inhibiting transcription.

To add acetyl groups to histones, decreasing positive charge. (correct)

To remove acetyl groups from histones, increasing positive charge.

To bind to methylated histones, promoting gene silencing.

Which of the following describes euchromatin?

An open and accessible form of chromatin, promoting gene transcription. (correct)

A region rich in methylated histones, leading to gene silencing.

A condensed form of chromatin that inhibits gene transcription.

A tightly packed nucleosome structure, blocking transcription factors.

What is the role of bromodomains in gene regulation?

They facilitate the removal of acetyl groups from histones, repressing transcription.

They directly recruit RNA polymerase II to the promoter of a gene.

They bind to methylated DNA, leading to gene silencing.

They bind to acetylated histones, attracting chromatin remodeling complexes. (correct)

How can transcription repressors on silencer elements inhibit gene transcription?

By inducing chromatin condensation and preventing RNA Pol II recruitment. Signup and view all the answers

What is a direct consequence of nucleosomes preventing transcription?

Inhibition of transcription complex access to the gene promoter. Signup and view all the answers

What is the main type of electrostatic interaction between DNA and histones?

The interaction between positively charged histones and negatively charged DNA. Signup and view all the answers

In the context of chromatin remodeling, what do ATP-dependent enzymes primarily facilitate?

Nucleosome displacement. Signup and view all the answers

What is the primary reason for regulating gene expression?

To make sure different cells express only the correct needed genes. Signup and view all the answers

Which histone modification is typically associated with gene silencing?

Histone deacetylation. Signup and view all the answers

During which phase can the regulation of gene expression occur?

At epigenetic/chromatin remodelling, transcriptional, post-transcriptional, and translational levels. Signup and view all the answers

What is the role of the N-terminal tail in histone proteins?

To provide sites for covalent modifications. Signup and view all the answers

Which of the following is NOT a typical function of corepressors?

Recruiting RNA Pol II. Signup and view all the answers

Which example is considered a short-term regulation of gene expression?

Changes in gene expression in response to a growth factor. Signup and view all the answers

What is the role of transcription factors in gene expression?

To bind to regulatory DNA sequences and control gene transcription. Signup and view all the answers

What is the effect of histone acetylation in the context of gene expression?

It loosens chromatin, which promotes gene transcription. Signup and view all the answers

What is the purpose of tissue-specific gene regulation?

To allow each cell type to produce only the proteins needed for its specific function. Signup and view all the answers

How does the information in DNA become a protein?

DNA is first transcribed into mRNA, which is then translated into protein. Signup and view all the answers

What happens after a protein is made?

Protein activity and function give rise to the observable traits of a cell or organism Signup and view all the answers

What is the primary function of basic transcription factors?

To recruit RNA polymerase II to the gene promoter. Signup and view all the answers

Specific transcription factors are best described by which of the following traits?

They exhibit tissue-specificity and regulate gene transcription. Signup and view all the answers

Where is the core promoter located relative to the gene it regulates?

Upstream of the gene, at a fixed position close to the start site. Signup and view all the answers

Which of the following best describes enhancer and silencer elements?

They contain motifs for specific transcription factor binding and regulate core promoter activity from a distance. Signup and view all the answers

What is the main function of cohesins and condensins in gene regulation?

Forming chromatin loops to bring enhancer/silencer sequences near the promoter. Signup and view all the answers

Which of these is NOT a characteristic of a core promoter?

Binding site for specific transcription factors. Signup and view all the answers

How do enhancers and silencers influence gene transcription?

By recruiting specific transcription factors, and through chromatin looping, they come within proximity of the core promoter to modulate its activity. Signup and view all the answers

What is the role of co-activators?

They increase gene transcription by associating with the promoter after being recruited by transcription activators. Signup and view all the answers

Given the provided information, which statement about the location of enhancer/silencer elements is most accurate?

They can be located upstream or downstream and at a variable distance from the gene promoter (100bp to Mbp). Signup and view all the answers

What is the transcription start site?

The region of the core promoter where RNA synthesis begins, and it's denoted as +1. Signup and view all the answers

What is the primary role of transcription factors in the process of transcription?

To guide RNA polymerase to the core promoter and regulate its activity. Signup and view all the answers

Which event signals the release of RNA Polymerase II from the promoter and the start of transcription elongation?

The phosphorylation of RNA Polymerase II at RBP1. Signup and view all the answers

Which of the following best describes the function of co-activators in gene transcription?

They increase gene transcription by interacting with transcription factors. Signup and view all the answers

What is the function of the DNA-binding domain found in all transcription factors?

To recognize specific short DNA sequences near the target gene. Signup and view all the answers

What determines the specificity of a transcription factor for a particular DNA sequence?

The amino acid sequence of its DNA-binding domain. Signup and view all the answers

How do transcription factors that act as repressors inhibit gene transcription?

By recruiting co-repressors to the target gene. Signup and view all the answers

A transcription factor binds to a DNA sequence with the motif 'TATAAAA'. Which similar sequence is it also likely to bind to?

TATATAT Signup and view all the answers

What is the termination signal for transcription in the newly formed mRNA?

An AAUAAA hexamer. Signup and view all the answers

What is the role of the trans-activation/trans-repression domain found in transcription factors?

To bind with co-activators or co-repressors. Signup and view all the answers

What is the effect of ligand binding to a transcription factor, when a ligand-binding domain is present?

It is required for transcription factor activation in some cases. Signup and view all the answers

What is the primary effect of histone acetylation on chromatin structure?

Unraveling of chromatin and increased accessibility. Signup and view all the answers

Which protein domain is typically found in transcription factors and chromatin remodeling proteins that recognizes acetylated histones?

Bromodomain Signup and view all the answers

How do histone deacetylases (HDACs) contribute to gene regulation?

By removing acetyl groups from histones, leading to chromatin condensation and gene repression. Signup and view all the answers

What is the primary role of histone acetyltransferases (HATs) during gene regulation?

Adding acetyl groups to histones, promoting gene activation. Signup and view all the answers

What is a consequence of recruiting histone deacetylases to a gene promoter region?

Repression of gene activity due to chromatin condensation. Signup and view all the answers

Which of the following is a mechanism used by transcription factors to activate gene expression?

Recruiting histone acetyltransferases and chromatin remodeling complexes. Signup and view all the answers

How does the position of acetyl groups on histones influence gene expression?

The exact position of acetyl groups determines whether the gene is transcribed or repressed. Signup and view all the answers

How is tissue-specific gene regulation achieved given that all cells contain the same DNA?

Different genes are turned 'on' and 'off' in different tissues and cell types. Signup and view all the answers

What is the primary role of tissue- and cell type-specific transcription factors?

To regulate gene expression specific to certain tissues and cell types Signup and view all the answers

Which of the following best describes the activity of enhancers?

Their activity can be different in different tissues and cell types. Signup and view all the answers

What is the role of histone modifications, such as acetylation, in the context of enhancer activity?

Histone modifications can either activate or inactivate enhancers in different tissues and cells. Signup and view all the answers

In the context of lung fibroblasts and hepatocytes, what is the key difference in histone modification and enhancer activity?

Lung fibroblasts exhibit low histone acetylation and inactive enhancers, while hepatocytes show high histone acetylation and active enhancers. Signup and view all the answers

What role does the silencer play in the expression of gene X in the example?

Silencers repress the expression of gene X in certain tissues. Signup and view all the answers

Considering the presented information on tissue-specific gene regulation, how would the activity of an enhancer differ between the two tissues?

The enhancer would be active in one tissue and inactive in another. Signup and view all the answers

What is a possible consequence of having different sets of transcription factors in different types of lung epithelial cells?

It is critical in differentiating specific types of cells and functions of lung epithelium. Signup and view all the answers

In the cases of the fibroblasts and the hepatocytes, how does condensed/open chromatin influence the enhancer activity?

Condensed chromatin correlates with inactive enhancers, and open chromatin correlates with active enhancers. Signup and view all the answers

Study Notes

Gene Expression & Regulation

Gene expression is controlled in time and space. Every cell has the same DNA, but different genes need to be "on" and "off" in different cell types. This regulation is essential for cell diversity.

Lecture Objectives

Understanding the fundamental structures and types of transcription factors and their roles in transcriptional regulation.
Understanding the pivotal role of regulatory DNA sequences in regulating gene transcription.
Grasping the significance of histone acetylation and chromatin remodeling in the regulation of gene transcription.
Familiarizing with the core concepts of tissue-specific regulation of gene transcription.

Gene Regulation

Gene expression is regulated at various levels, including short-term (e.g., responding to external signals like growth factors or hormones) and long-term (e.g., tissue-specific identity maintained through cell division).
Epigenetic modifications (e.g., chromatin remodeling), transcriptional, post-transcriptional, and translational mechanisms all play a role in regulating gene expression.

Gene Expression During Development

Gene expression is dynamic across the life cycle. Different genes need to be "on" or "off" at various stages.

Gene Regulation During Transcription

DNA is transcribed into mRNA.
mRNA is translated into proteins.
Protein activity leads to a phenotype.

Transcription Initiation

RNA Pol II binds to a non-coding DNA region (core promoter).
Transcription factors (TFs) guide RNA Pol II to the core promoter.
RNA Pol II and TFs form a pre-initiation complex.
RNA Pol II phosphorylation initiates transcription.

Transcription Elongation

RNA Pol II unwinds the DNA ("transcription bubble").
RNA Pol II uses one strand as a template to synthesize a complementary RNA sequence.
RNA Pol II adds nucleotides to the 3' end of the growing RNA molecule.

Transcription Termination

RNA Pol II encounters a termination signal (e.g., AAUAAA hexamer).
Transcription stops.
RNA Pol II and mRNA are released.
A new transcription cycle begins.

Transcription Factors

Transcription factors are proteins that bind specific DNA sequences and control gene transcription (activating or inhibiting).
Most transcription factors work with other proteins (co-activators/co-repressors) to regulate transcription.
Transcription factors can either activate or repress transcription. Activators recruit co-activators, and repressors recruit co-repressors.

Transcription Factor Domains

Transcription factors have specific structural domains for interaction with DNA or other proteins.
DNA-binding domains recognize specific short DNA sequences (transcription factor binding motifs).
Trans-activation/trans-repression domains interact with co-activators or co-repressors.
Some factors have ligand-binding domains (e.g., hormone receptors)
Some have dimerization domains (to bind to DNA in pairs).

Regulatory DNA Sequences

Core promoter: Immediately upstream of the gene
Contains the transcription start site (+1)
Binding sites for basal transcription factors
Needed for gene transcription
Enhancers/Silencers: Can be upstream or downstream of a gene, and affect the activity of the core promoter (increasing or decreasing).
Enhancers/silencers can be far from the target gene, but transcription factors bring them close through chromatin looping.

Co-activators and Co-repressors

Co-activators increase gene transcription by opening chromatin.
Co-activators recruit RNA Pol II and basal transcription factors to the promoter.
Co-repressors decrease gene transcription by inducing chromatin condensation.
Co-repressors prevent RNA Pol II recruitment to the promoter.

Histone Modifications and Chromatin Remodeling

Nucleosomes (DNA wrapped around histone proteins) can block access for transcription factors.
Chromatin remodeling enzymes (e.g. ATP-dependent chromatin remodeling enzymes) reposition or remove nucleosomes.
Histone modifications (e.g., acetylation) affect chromatin structure.

Histone Acetylation

Histone acetyltransferases (HATs) add acetyl groups to lysines on histones.
Histone deacetylases (HDACs) remove acetyl groups.
Bromodomains are special protein modules found in transcription factors, as well as chromatin remodeling complexes, which recognise acetylated lysine residues on histones.

Tissue-Specific Regulation

Every cell has the same genes, but different genes are expressed in different tissues and cells.
Tissue-specific transcription factors regulate gene transcription.
Enhancers/silencers have tissue-specific activity, determined by histone modifications.

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Description

Test your understanding of gene regulation mechanisms and chromatin structure with this quiz. Questions cover histone acetylation, the role of transcription factors, and the functions of various chromatin remodeling components. Perfect for students studying molecular biology and genetics.