Gene Regulation and Transcription Quiz
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Questions and Answers

Which protein is associated with the poised state as mentioned in the content?

  • H3K9 acetylation (correct)
  • RNAPII
  • BMAL1
  • PER1

What does the presence of H3K9 acetylation indicate in the context of gene regulation?

  • Gene derepression (correct)
  • Stable chromatin structure
  • Delayed transcription initiation
  • Active repression of genes

Which protein is NOT listed among the components related to the poised state?

  • NPAS2
  • TP53 (correct)
  • PER2
  • CRY2

What role does RNAPII play in the gene expression process described in the content?

<p>It delays transcription (C)</p> Signup and view all the answers

Which of the following proteins is suggested to collaborate with CBP in this regulatory framework?

<p>BMAL1 (C)</p> Signup and view all the answers

Which percentage corresponds to the H3K9 acetylation peaks as indicated?

<p>20.1% (B)</p> Signup and view all the answers

In which physiological process are the components mentioned most likely involved?

<p>Circadian rhythms (A)</p> Signup and view all the answers

Which of the following pairs corresponds correctly to each protein's role in transcription regulation?

<p>CRY2 - Inhibition (A), NPAS2 - Activation (B)</p> Signup and view all the answers

What does the HNF6 ChIP-seq signal indicate when shown in gray?

<p>A baseline measurement across time points (B)</p> Signup and view all the answers

At what times were the HNF6 ChIP-seq signals measured in mouse livers?

<p>ZT08 and ZT20 (C)</p> Signup and view all the answers

What colors are used to represent CLOCK:BMAL1 and HNF6 consensus sequences in the genomic locations display?

<p>Blue for CLOCK:BMAL1 and black for HNF6 (A)</p> Signup and view all the answers

What was indicated by the disconnect between the amplitude of binding and rhythmicity according to the study?

<p>High amplitude binding does not guarantee rhythmicity (A)</p> Signup and view all the answers

What was the sample size for the HNF6 ChIP-seq analysis in mice?

<p>4 mice per time point (A)</p> Signup and view all the answers

What role does CLOCK:BMAL1 play in transcription?

<p>It serves as a pioneer transcription factor. (C)</p> Signup and view all the answers

How does CLOCK:BMAL1 contribute to rhythmic transcriptional output?

<p>Through its strong influence on nucleosome removal. (A)</p> Signup and view all the answers

What sequence of events is most likely affected by CLOCK:BMAL1 activity?

<p>The transition from transcriptional silencing to activation. (B)</p> Signup and view all the answers

Which interaction does CLOCK:BMAL1 facilitate that is essential for transcription?

<p>Nucleosome removal at binding sites. (C)</p> Signup and view all the answers

What experimental phase might demonstrate the influence of CLOCK:BMAL1 most strongly?

<p>In the rhythmic cycles between ZT02 and ZT14. (C)</p> Signup and view all the answers

Which property distinguishes CLOCK:BMAL1 from other transcription factors?

<p>Its role as a pioneer transcription factor. (C)</p> Signup and view all the answers

What is a characteristic feature of the binding sites for CLOCK:BMAL1?

<p>They exhibit rhythmic patterns of accessibility. (A)</p> Signup and view all the answers

What implication arises from CLOCK:BMAL1's role in transcription?

<p>It may impact gene expression related to metabolism. (B)</p> Signup and view all the answers

What role does CLOCK:BMAL1 play in relation to H2A.Z at transcription start sites (TSSs)?

<p>It facilitates a decrease in H2A.Z levels at TSSs. (B)</p> Signup and view all the answers

What happens to transcription in Bmal1 knockout mice compared to wild-type mice?

<p>Transcription levels are severely compromised. (C)</p> Signup and view all the answers

At what time point do H2A.Z levels reach a trough in wild-type mice?

<p>ZT22 (D)</p> Signup and view all the answers

Which of the following is true about transcription factors binding at control sites?

<p>Transcription factors do not bind at control sites. (D)</p> Signup and view all the answers

What is the correlation observed in H2A.Z signal and CLOCK:BMAL1 activity?

<p>A striking correlation exists with H2A.Z signal decreases. (D)</p> Signup and view all the answers

What is indicated about transcription factor binding at HNF6 sites?

<p>They occur without nearby CLOCK:BMAL1-binding sites. (D)</p> Signup and view all the answers

What happens to chromatin binding at rhythmic sites during the night?

<p>It decreases to a trough level. (D)</p> Signup and view all the answers

What is the significance of ZT22 in the context of H2A.Z levels?

<p>It indicates diminished H2A.Z levels. (B)</p> Signup and view all the answers

What role does the BMAL1-mediated rhythmic nucleosome removal play in relation to transcription factors?

<p>It promotes the rhythmic binding of transcription factors to DNA. (A)</p> Signup and view all the answers

Which protein associated with transcription factors is mentioned in the content?

<p>H2A.Z (C)</p> Signup and view all the answers

What is the focus of the analysis conducted on the mouse liver in the research referenced?

<p>Coassociation between transcription factors. (B)</p> Signup and view all the answers

What statistical method was used for analyzing the publicly available mouse liver ChIP-seq data?

<p>Genome Structure Correction statistic. (C)</p> Signup and view all the answers

What biological element is H2A.Z associated with in this context?

<p>Chromatin structure. (D)</p> Signup and view all the answers

In the research, what aspect of the genes was analyzed through the ChIP-seq data?

<p>Presence of clock genes. (B)</p> Signup and view all the answers

How many datasets were analyzed for transcription start sites (TSS) in the research?

<p>31 (D)</p> Signup and view all the answers

What factor is indicated to be necessary for establishing chromatin environment in the content?

<p>H2A.Z. (D)</p> Signup and view all the answers

What percentage overlap do the black rectangles, representing transcription factors, exhibit with core clock genes?

<p>Over 40% (A)</p> Signup and view all the answers

What does the nucleosome signal indicate at a CLOCK:BMAL1 DNA-binding site?

<p>High and low rhythmic activity (D)</p> Signup and view all the answers

At what times are the average high nucleosome signals observed according to the document?

<p>ZT6 and ZT10 (B)</p> Signup and view all the answers

Which transcription factor is shown to have a consensus sequence along with CLOCK:BMAL1?

<p>HNF6 (D)</p> Signup and view all the answers

What color represents the low average nucleosome signals?

<p>Red (B)</p> Signup and view all the answers

Which publication year is mentioned for the HNF6 ChIP-seq signal?

<p>2012 (C)</p> Signup and view all the answers

What is the visual representation of the transcription factors utilized in the data?

<p>Rectangles (D)</p> Signup and view all the answers

What does the gray signal in the nucleosome signal visualization denote?

<p>ChIP-seq signal for HNF6 (C)</p> Signup and view all the answers

Flashcards

Poised State

A state of readiness for gene expression.

H3K9 acetylation

A chemical modification of the histone protein H3, specifically at lysine 9, which can influence gene expression.

Gene Expression

The process by which information from a gene is used to create a functional product, like a protein.

PER1

A protein involved in the circadian rhythm.

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BMAL1

A protein involved in the circadian rhythm, related to PER1.

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NPAS2

A protein connected to the circadian rhythm, similar to BMAL1 and PER1.

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CRY2

A protein involved in regulating cells' circadian rhythm.

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RNAPII

RNA polymerase II, an enzyme that transcribes DNA into RNA, a key step in gene expression.

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CLOCK:BMAL1

A pioneer transcription factor that binds to DNA.

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Pioneer transcription factor

A protein that binds to DNA at specific locations in order to access the sites for transcription factors to follow

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DNA-binding sites

Specific sequences of DNA to which transcription factors attach in order to regulate gene expression

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transcription

The process of creating RNA from DNA.

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nucleosome removal

The process of removing nucleosomes from DNA, for example contributing to rhythmic CLOCK activity.

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rhythmic gene expression

Gene expression that occurs in cycles over time, like the day-night cycle.

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transcriptional output

The amount of RNA produced from a gene.

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H2A.Z nucleosome

A type of nucleosome involved in gene activity.

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What happens to H2A.Z levels during the night?

H2A.Z levels decrease throughout the night, reaching a low point at ZT22. This is important because it facilitates the binding of other transcription factors.

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How does BMAL1 affect H2A.Z levels?

BMAL1 is a transcription factor that helps regulate H2A.Z levels. In Bmal1 knockout mice, H2A.Z levels are significantly lower and don't exceed the trough levels seen in wild-type mice.

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What is the relationship between CLOCK:BMAL1 binding and H2A.Z signal?

There is a strong correlation between the decrease in CLOCK:BMAL1 binding and H2A.Z signal. Lower CLOCK:BMAL1 binding is associated with lower H2A.Z signal, suggesting a connection between them.

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What is the role of CLOCK:BMAL1 in gene regulation?

CLOCK:BMAL1 is a heterodimer that acts as a transcription factor. It binds to DNA at specific sites near genes, influencing their expression.

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What is a transcription factor?

A transcription factor is a protein that controls the rate of gene transcription. They bind to specific regions of DNA, influencing whether a gene is turned on or off.

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What is the significance of rhythmic binding of CLOCK:BMAL1?

Rhythmic binding of CLOCK:BMAL1 is crucial for regulating the circadian rhythm. It ensures that genes associated with this cycle are expressed at the right time during the day.

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Where does CLOCK:BMAL1 bind?

CLOCK:BMAL1 binds to specific DNA sequences called E-boxes. They are located close to the genes they regulate.

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What is REV-ERBa's role in the circadian rhythm?

REV-ERBa is a transcription factor that helps regulate the circadian rhythm by repressing the expression of certain genes, including BMAL1.

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HNF6

A protein that binds to specific DNA sequences and influences gene expression.

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ChIP-seq

A technique used to identify regions of DNA where specific proteins bind.

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Consensus sequences

Specific DNA sequences recognized and bound by proteins like HNF6.

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Nucleosome binding

The process by which proteins (like HNF6) attach to the DNA packaged in nucleosomes.

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Rhythmic Nucleosome Removal

The process of removing nucleosomes from DNA in a cyclical pattern, allowing for the rhythmic binding of transcription factors like CLOCK:BMAL1.

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Transcription Factor Binding

The attachment of transcription factors to specific DNA sequences, which can activate or repress gene expression.

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Genome Structure Correction

A statistical method used to analyze the overlap between DNA regions bound by different proteins, like transcription factors and H2A.Z nucleosomes.

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ChIP-seq Data

Experimental data that identifies regions of the genome bound by specific proteins, like transcription factors or histone modifications.

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Overlap Analysis

A method used to compare the regions of the genome bound by different proteins, like CLOCK:BMAL1 and H2A.Z.

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Mouse Liver

The organ used in this study was a mouse liver, and it is a good model for investigating circadian rhythms.

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Nucleosome signal

A measure of the presence of nucleosomes, which are DNA-packaging structures that can influence gene expression.

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Transcription factors

Proteins that bind to specific DNA sequences and regulate gene expression, acting as key controllers of cellular processes.

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Circadian rhythm

A natural, internal 24-hour cycle that regulates various biological processes, including sleep-wake cycles and hormone production.

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Study Notes

BSci 3230 Study Notes

  • File Use Policy: These files are for BSci 3230 student exam preparation only. Sharing or using them for other purposes is prohibited. Material may be copyrighted.

Gene Expression Outputs of the Mammalian Clock

  • TTFL Activation: The transcriptional-translational feedback loop (TTFL) leads to pervasive circadian transcription via CLOCK/BMAL1 activation.
  • Circadian Transcription Methods: DNA microarray, RNA-seq, and ChIP are used to understand circadian transcription.
  • Transcriptional Landscapes and Delay: The concept of "transcriptional landscapes" and the nature of the transcriptional delay are topics for further study.

Percentage of Genome Regulated by the Clock (Table 8.1)

  • Data Source Variation/Update: Data collected circa 2004 may not reflect current estimates which have been shown to be higher
  • Organism and Genome Percentage: Different organisms (cyanobacteria, fungi, insects, mammals, plants, marine algae) exhibit variable percentages of their genome undergoing clock-controlled regulation.

Mammalian TTFL: Transcriptional Outputs (CCGs)

  • Diagram Description: A diagram depicting the mammalian transcriptional-translational feedback loop (TTFL), emphasizing the process of clock-controlled gene (CCG) transcription, encompassing nuclear translocation and cellular processes.
  • Clock Output/Processes: The diagram highlights connections between the clock, its output processes, and rhythmic biological processes, illustrating feedback loops.
  • Process Diagram: A schematic of interactions including the regulation of genes, cellular signalling pathways, interactions, and various molecule functions.

Transcriptional Control of mRNAs (Slide 5)

  • Methods: DNA microarray technology using poly-A RNA and hybridization to DNA chips allows for the quantification of temporal patterns of gene expression.

Transcriptional Control of mRNAs: Mouse Tissue Studies (Slides 6-7)

  • Tissue Sampling: Mouse tissues (SCN and liver) were initially sampled for mRNA analysis.
  • Gene Assay Numbers: Approximately 7000 genes were screened, with 337 displaying rhythmic expression in the SCN and 335 in the liver.
  • Phase Specific Genes: Identified rhythmic genes exhibited "phase specificity", differing in peak expression times in different tissues.
  • Tissue Specific Rhythmic Genes: While many genes cycle rhythmically, a smaller subset (≈28) show rhythms in both tissues.

Transcriptional Control of RNAs Including Non-Coding RNAs (Slides 8-9)

  • RNA-Seq Technique: RNA sequencing (RNA-seq) methods and workflow for analysing transcriptomes in 12 mouse organs over time are detailed.
  • Organ-specific Manner: 43% of all protein-coding genes show circadian rhythms in some tissue.
  • Protein-Coding and Non-Coding RNA: Data on numbers and percentages of circadian-regulated protein-coding genes and various types of non-coding RNAs is presented, including novel, conserved, and non-conserved.

Relationships among Organs and Circadian Genese (Slide 10)

  • Organ-Specific Oscillations: Amplitude, phase, and rhythmic behavior of circadian genes are different across various tissues.
  • Histograms and Venn Diagrams: Graphs depicting the distribution of gene expression amplitudes and phases, plus comparisons/overlap of expression across tissues.

Transcriptional Control of Proteins (TFs?) Bound to DNA (Slides 11-15)

  • ChIP Technique: Chromatin Immunoprecipitation (ChIP) is employed to study changes in transcription factor binding.
  • DNA-Protein Crosslinking: Chromatin extraction from different phases, DNA crosslinking, fragmentation and sonication are part of the steps of the ChIP protocol.
  • Immunoprecipitation: Antibodies to specific transcription factors are used to isolate bound DNA.
  • De-Crosslinking and Sequencing: The bound DNA is extracted, sequenced and analysed.
  • Circadian Control of Protein Binding (Slides 12-15): Analysis of the binding of core circadian regulators (including BMAL1, CLOCK, NPAS2, PER1, PER2, CRY1, CRY2) within the DBP gene within the liver is shown via various graphs and plots.

Transcriptional Control of Proteins (TFs?): Supplementary details (16-18)

  • Intron-Exon-Specific mRNAs: Analysis of intron- and exon-specific mRNA cycling reveals that most intron and exons cycling is governed by changes in RNA production at the transcriptional level.
  • Phases of Transcription and Regulation: Discussion of circadian regulation of gene expression at both transcriptional and post-transcriptional levels.
  • Alternative Explanations for Delay: Alternative reasons for the observed delay between CLOCK/BMAL1 binding and transcription initiation are considered.

CLOCK-BMAL1 Pioneer Transcription Factor (Slides 19-21)

  • Pioneer Function: CLOCK-BMAL1's function as a pioneer transcription factor is explained, highlighting its role in facilitating the binding of other transcription factors.
  • Mechanism: The details of the CLOCK-BMAL1-DNA binding process, chromatin modifications, and accompanying histone and nucleosome changes are presented.
  • Binding of other TFs: Subsequent binding of other transcription factors is driven by CLK-BMAL1-induced chromatin remodeling allowing for transcriptional activation by these other TFs.

Gene Ontology: KEGG Metabolic Pathways (Slides 22-23)

  • Metabolic Pathway Map Visual representation of KEGG metabolic pathways, emphasizing connections.
  • BMAL1-regulated KEGG Metabolic Pathways: Specific pathways associated with BMAL1 regulation are shown within this visual representation.

Food for Thought (Slide 24)

  • Implications of Pervasive Regulation: Exploring the possible consequences of widespread clock regulation and the role of clock disruption in animal health.
  • Testing for Clock Control: Methods for evaluating the significance of clock control for particular transcriptional pathways are proposed.

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BSci 3230 Past Paper PDF

Description

Test your knowledge on the proteins and mechanisms involved in gene regulation, particularly focusing on the poised state and the significance of H3K9 acetylation. This quiz covers various aspects of transcription factors and their roles in gene expression as discussed in recent research.

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