Mol bio L5

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Questions and Answers

Which of the following is the MOST accurate definition of an epigenetic trait?

  • A stably heritable phenotype resulting from changes in chromatin without alterations in the DNA sequence. (correct)
  • A phenotype that is only observable in certain cell types.
  • A phenotype resulting from alterations in the DNA sequence.
  • A temporary change in gene expression due to environmental factors.

Epigenetic changes are always irreversible modifications to gene expression.

False (B)

During which of the following stages are crucial epigenetic reprogramming events MOST likely to occur in mammals?

  • Somatic cell differentiation
  • During the cell cycle
  • Germ cell development and early embryogenesis (correct)
  • Adulthood and aging

Which of the following BEST describes the focus of epigenetics?

<p>The study of chemical modifications that regulate gene expression and genomic stability. (B)</p> Signup and view all the answers

What is the epigenome, and what role does it play in gene expression?

<p>The epigenome is a multitude of chemical compounds that can instruct the genome what to do, influencing gene expression.</p> Signup and view all the answers

Which of the following factors can influence gene expression, according to the information provided?

<p>All of the above (E)</p> Signup and view all the answers

What is the primary function of epigenetic events in eukaryotic organisms?

<p>To provide a more precise and stable control of gene expression and genomic regulation across multiple generations. (D)</p> Signup and view all the answers

Epigenetic traits play a crucial role in ______ stability by silencing centromeres, telomeres, and transposable elements.

<p>genomic</p> Signup and view all the answers

What does the silencing of centromeres, telomeres, and transposable elements via genomic stability ensure?

<p>The correct attachment of microtubules to centromeres. (D)</p> Signup and view all the answers

Which of the following cellular components is directly acted upon by factors influenced by external stimuli, ultimately leading to changes in gene expression patterns?

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

Match the following lifestyle factors with their potential epigenetic effects:

<p>Diet = Influences DNA methylation and histone modification patterns. Exercise = Modulates inflammation and impacts DNA methylation. Psychological stress = Alters histone modifications and DNA methylation. Social interactions = Influences gene expression related to behavior and immunity.</p> Signup and view all the answers

What is the role of an epigenator in epigenetic regulation?

<p>Triggering epigenetic changes in the cell in response to environmental changes. (D)</p> Signup and view all the answers

What is the primary role of the epigenetic initiator?

<p>To translate the Epigenator signal and identify specific locations on a chromosome for epigenetic modification. (D)</p> Signup and view all the answers

What are the two main categories of epigenetic initiators described?

<p>DNA binding proteins and noncoding RNAs (C)</p> Signup and view all the answers

Which of the following BEST describes how DNA-binding proteins recognize specific DNA sequences?

<p>Through noncovalent interactions between an alpha-helix in the protein domain and atoms within the DNA major groove. (A)</p> Signup and view all the answers

Non-coding RNAs (ncRNAs) are translated into proteins.

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

What is the PRIMARY function of microRNAs (miRNAs) in epigenetic processes?

<p>To bind to a specific target mRNA with a complementary sequence to induce cleavage, degradation, or block translation. (B)</p> Signup and view all the answers

What is the primary function of short interfering RNAs (siRNAs)?

<p>To mediate post-transcriptional gene silencing, leading to mRNA degradation. (B)</p> Signup and view all the answers

What is the main function of piwi-interacting RNAs (piRNAs)?

<p>To regulate chromatin structure and suppress transposon activity in germline and somatic cells. (C)</p> Signup and view all the answers

What is the MAIN function of long non-coding RNAs (lncRNAs)?

<p>To serve as adaptors, forming complexes with chromatin-modifying proteins and directing their activity to specific sites in the genome. (A)</p> Signup and view all the answers

How does DNA methylation typically affect gene expression?

<p>It represses gene expression, typically by blocking the binding of transcription factors or recruiting proteins that condense chromatin. (A)</p> Signup and view all the answers

Where does DNA methylation typically occur, and what base is methylated?

<p>In CpG islands; cytosine is methylated. (C)</p> Signup and view all the answers

What enzymes are responsible for catalyzing DNA methylation in mammalian cells?

<p>DNA methyltransferases (DNMTs). (D)</p> Signup and view all the answers

Non-CpG cytosine methylation is MOST prevalent in ______ cells and may be critical in differentiation.

<p>stem</p> Signup and view all the answers

How does an increased level of global methylation typically correlate with differentiation?

<p>Inversely proportional; the level of global methylation and the degree of non-CpG methylation is lower in differentiated cells than in stem cells. (D)</p> Signup and view all the answers

Histone modification, defined as a covalent post-translational modification (PTM) to histone proteins, affects which of the following processes within a cell?

<p>Gene expression, DNA repair, and chromosome condensation. (D)</p> Signup and view all the answers

Which of the following is NOT a type of histone modification?

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

On which part of histones do the majority of histone PTMs (post-translational modifications) occur?

<p>The N-terminal tail (C)</p> Signup and view all the answers

How do epigenetic modifications, such as histone modifications, affect the accessibility of DNA to the transcriptional machinery?

<p>They alter the condensation of the chromatin, thereby influencing the accessibility of DNA. (B)</p> Signup and view all the answers

What is the function of histone acetyltransferases (HATs)?

<p>Add acetyl groups to histone tails, typically leading to increased gene expression. (D)</p> Signup and view all the answers

How does the addition of an acetyl group affect the interaction between the histone tail and negatively charged DNA?

<p>It neutralizes the positive charge of the amino group of lysine, leading to decreased affinity between the histone tail and the negatively charged DNA. (B)</p> Signup and view all the answers

What is the enzymatic function of histone methyltransferases (HMTs) and histone demethylases (HDMs)?

<p>HMTs add methyl groups to histone proteins, while HDMs remove methyl groups from histone proteins. (C)</p> Signup and view all the answers

How does histone phosphorylation typically affect transcriptional activity?

<p>It is most commonly associated with transcriptional activation. (B)</p> Signup and view all the answers

What is the effect of H2A ubiquitination?

<p>H2A ubiquitination is considered repressive (C)</p> Signup and view all the answers

What impact does the process of sumoylation have on transcriptional activity?

<p>Sumoylation is related to transcriptional repression.</p> Signup and view all the answers

Which of the following statements accurately describes the characteristics of histone variants?

<p>They exhibit differences in amino acid sequence, leading to specific expression, localization, and distribution patterns. (A)</p> Signup and view all the answers

What is the overall effect of nucleosome remodeling?

<p>It changes the structure of chromatin, influencing DNA accessibility and gene expression. (A)</p> Signup and view all the answers

In the example provided, which brain area is described as being implicated in the stress response?

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

The early life environment shapes the stress response later in life through:

<p>Epigenetic changes. (B)</p> Signup and view all the answers

What is the term for when the ratio of gene expression levels from two alleles in a diploid genome is not 1 to 1?

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

Allelic imbalance affects all genes in the genome equally.

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

What epigenetic phenomenon involves only one of the two copies of a gene being active while the other is silent?

<p>Monoallelic expression</p> Signup and view all the answers

Between 0.5% and 15% of ______ genes exhibit random monoallelic gene expression.

<p>autosomal</p> Signup and view all the answers

Which of the following best describes somatic rearrangement as a type of monoallelic expression?

<p>A change in DNA organization to produce a functional gene at only one gene copy. (A)</p> Signup and view all the answers

Somatic rearrangement in immune cells contributes to antibody diversity.

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

In the context of somatic rearrangement, what is the mechanism that generates enormous antibody diversity?

<p>Cutting and pasting of DNA sequences</p> Signup and view all the answers

Random allelic silencing or activation results in expression from only one gene copy due to different ______ changes.

<p>epigenetic</p> Signup and view all the answers

Which cell type primarily utilizes random allelic silencing or activation in humans?

<p>Sensory neurons (A)</p> Signup and view all the answers

Genomic imprinting affects the expression of genes based solely on environmental factors.

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

In genomic imprinting, what is the term for the mechanism by which regions are marked epigenetically?

<p>Parent-of-origin mechanism</p> Signup and view all the answers

Epigenetic silencing of a gene copy occurs in ______ regions.

<p>imprinted</p> Signup and view all the answers

What is the primary purpose of X chromosome inactivation in humans?

<p>To equalize the dosage of X chromosome genes between males and females (B)</p> Signup and view all the answers

In humans, the paternal X chromosome is always inactivated in females.

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

What type of molecule does the XIST gene encode?

<p>ncRNA</p> Signup and view all the answers

X chromosome inactivation is accomplished by ______ of cytosine, H4 histone hypo-acetylation, and other histone modifications.

<p>methylation</p> Signup and view all the answers

Match the following epigenetic mechanisms with their characteristics:

<p>Allelic Imbalance = Unequal expression of two alleles in a diploid genome. Monoallelic Expression = Only one of the two copies of a gene is active. Genomic Imprinting = Epigenetic silencing of a gene copy based on parental origin. X Chromosome Inactivation = Silencing of genes on one female X chromosome.</p> Signup and view all the answers

Which of the following best describes the outcome for babies born during the Dutch Hunger Winter whose mothers suffered famine during the last few months of pregnancy?

<p>They had small birth weights. (D)</p> Signup and view all the answers

The Dutch Hunger Winter study showed no correlation between prenatal famine exposure and later-life health outcomes.

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

What key factor, crucial for human growth and development, is maternally imprinted?

<p>Insulin-like growth factor II (IGF2)</p> Signup and view all the answers

Higher obesity rates are correlated with ______ methylation on the CpG island of an imprinted allele.

<p>less</p> Signup and view all the answers

What is a classic feature of cancer tissues concerning DNA methylation?

<p>DNA methylation is reduced globally. (A)</p> Signup and view all the answers

Hypomethylation of oncogene promoters can lead to increased genome stability.

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

What is generally observed for DNA methylation levels in cancer tissues?

<p>Reduced globally</p> Signup and view all the answers

DNA methylation changes may predispose to cancer by inducing a more ______ state.

<p>stem-cell-like</p> Signup and view all the answers

What epigenetic modification is associated with Rett syndrome?

<p>Changes in the MeCP2 gene (A)</p> Signup and view all the answers

The MeCP2 protein normally functions as a transcriptional activator.

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

What epigenetic modification is seen in individuals with addiction to drugs such as cocaine?

<p>Histone acetylation, histone methylation and DNA methylation</p> Signup and view all the answers

In individuals with depression, ______ histone methylation results in the upregulation of repressive methyl marks on H3.

<p>increased</p> Signup and view all the answers

What is one epigenetic change observed in the brains of individuals suffering from depression?

<p>Downregulation of HDAC2 and HDAC5 upon chronic social defeat stress. (B)</p> Signup and view all the answers

The epigenome is solely determined by an individual's genetic code and is not influenced by environmental factors.

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

What term describes the function of the epigenome as the key interface between environmental conditions and an individual's genetic makeup?

<p>Key Interface</p> Signup and view all the answers

The ______ is the connection between the environment and genome.

<p>epigenome</p> Signup and view all the answers

What are the potential consequences of DNA hypomethylation in cancer tissues?

<p>Reduced defense against repetitive sequences. (B)</p> Signup and view all the answers

The impact of environmental factors on the epigenome does not have long-lasting effects on human health.

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

How does the epigenetic landscape in cancer stem cells differ from that in differentiated cells?

<p>Reduced H3K9me2/3, reduced DNA methylation and increased gene activity</p> Signup and view all the answers

When the repressive methyl marks on H3 are upregulated it leads to a down regulation of ______.

<p>BDNF</p> Signup and view all the answers

What is the primary role of Xist RNA in X-chromosome inactivation?

<p>To induce epigenetic changes for silencing the inactive X chromosome. (B)</p> Signup and view all the answers

The process of X-chromosome inactivation always results in the complete and irreversible silencing of all genes on the affected chromosome.

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

Flashcards

Epigenetic trait

A stably heritable phenotype resulting from changes in chromatin without alterations in the DNA sequence.

Epigenomics

Epigenetic changes at the level of the whole genome.

Epigenetics

Processes that regulate gene expression and genomic stability through chemical modifications.

Epigenome

A multitude of chemical compounds that can influence the genome's behavior.

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Epigenator

Changes in the environment trigger epigenetic changes of the cell; considered the environmental signal.

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Epigenetic Initiator

Translates the Epigenator signal to specific locations on the chromosome.

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Non-coding RNA (ncRNA)

Functional RNA that is transcribed from DNA but not translated into proteins; regulates gene expression.

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MicroRNAs (miRNAs)

Binds to a specific target mRNA to induce cleavage, degradation or block translation

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Short interfering RNAs (siRNAs)

mediate post-transcriptional gene silencing which results in mRNA degradation.

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Long ncRNAs

Forms complex with chromatin-modifying proteins and recruit their catalytic activity to specific sites in the genome resulting in modification of chromatin state and gene expression.

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DNA methylation

Addition of a methyl group to the 5-carbon of cytosine in CpG islands, typically repressing gene expression.

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DNA methyltransferases (DNMTs)

Enzymes that methylate CpG sites in DNA

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Histone modification

A covalent post-translational modification (PTM) to histone proteins, affecting chromatin structure.

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Histone Methylation

Histone enzyme addition of a methyl group (CH3) to a molecule.

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Histone Acetylation

Histone enzyme addition of a acetyl group (CH3CO) to a molecule.

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Histone acetyltransferases (HATs)

Enzymes regulating histone acetylation

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Histone Phosphorylation

Histone enzyme addition of a phosphate group (PO4) to a molecule.

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Ubiquitylation

Histone modification that is the attachment of ubiquitin protein to a substrate protein.

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Sumoylation

Histone modification that is addition of Small Ubiquitin-like Modifier protein to a substrate protein.

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Histone variants

Representing one or a few amino acid differences in the histone tails or in the globular central domains and have specific expression, localization and distribution patterns.

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Nucleosome remodeling

Change in the structure of chromatin; requires ATP energy.

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Hippocampus

A brain area implicated in the stress response.

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Glucocorticoids

Primary stress hormones necessary for life, regulate numerous physiological processes to maintain homeostasis.

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Allelic imbalance

When the ratio of gene expression levels from two alleles in a diploid genome is not 1:1.

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Monoallelic expression

Only one of the two gene copies is active; the other is silent.

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Somatic rearrangement

Changes in DNA to produce a functional gene at only one gene copy.

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Genomic imprinting

Epigenetic silencing of a gene copy in imprinted regions.

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X chromosome inactivation

Epigenetic approach to equalize gene dosage between sexes.

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The epigenome

The key interface between environment and genome.

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Dutch Hunger Winter

A famine that influenced birth weights in children.

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Cancer epigenomics

Reduction in DNA methylation that occurs globally in cancer tissues.

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Insulin-like growth factor II (IGF2)

A key factor in human growth, maternally imprinted.

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Rett syndrome

Changes in MeCP2 sequence leads to reduced function and aberrant epigenetic regulation.

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X chromosome inactivation cause

Methylation of cytosine, H4 histone hypo-acetylation and other histone modifications

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Cocaine addiction

Acute and chronic exposure to this substance induces differential Histone acetylation.

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HDAC2 and HDAC5

Is down regulated in depression upon stress.

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BDNF promoter region

Repressive methyl marks on H3 are upregulated here due to chronic social defeat stress.

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Aberrant epigenome

Methylation changes predispose cell to cancerous stem-cell-like state.

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Study Notes

  • Associate professor Zanda Daneberga gave a lecture on Epigenomics.

Allelic Imbalance

  • Allelic imbalance occurs when the ratio of gene expression levels from two alleles in a diploid genome is not 1 to 1.
  • Affects 5% to 20% of autosomal genes.
  • Caused by variants in gene regulatory sequences or epigenetic marks which leads to different expression levels at two gene copies.
  • Usually observed in early embryogenesis.

Monoallelic Expression

  • Monoallelic expression involves only one of the two gene copies being active, while the other is silent.
  • Between 0.5% and 15% of autosomal genes display random monoallelic gene expression.
  • Different cells express only one allele independently of the underlying genomic sequence, in a cell type-specific manner.
  • During differentiation from Embryonic Stem Cells (ESC) to Neural Progenitor Cells (NPC), there is a 5.6 fold increase in monoallelic expression (67 genes to 376 genes).

Types of Monoallelic Expression

  • Somatic rearrangement
  • Random allelic silencing or activation
  • Genomic imprinting
  • X chromosome inactivation

Somatic Rearrangement

  • Changes in DNA organization produce a functional gene at one gene copy, but not at the other.
  • Random choice of one gene copy
  • Example: Immunoglobulin genes, T-cell receptor genes.
  • Occurs in B- and T-cell lineage.
  • Bacteria and viruses are recognized by the B and T cells of the immune system via antigen receptors, producing antibodies.
  • Mechanism involves cutting and pasting of DNA sequences to rearrange genes in somatic cells, generating antibody diversity.

Random Allelic Silencing or Activation

  • Expression from only one gene copy due to different epigenetic changes.
  • Random choice of one gene copy takes place in specific cell types.
  • Observed in olfactory receptor genes in sensory neurons.
  • Observed in other chemosensory or immune system genes; up to 10% of all genes in other cell types.

Genomic Imprinting

  • Epigenetic silencing of a gene copy in imprinted regions.
  • More than 100 genes are known to have developmental functions.
  • The imprinted region is marked epigenetically according to its parental origin using a parent-of-origin mechanism.
  • Parental gametogenesis

Sex Chromosome Inactivation

  • Epigenetic gene dosage compensation mechanisms of genes located on the sex chromosomes vary with species.
  • Can range from transcriptional modulation to the entire silencing of one sex chromosome.
  • In humans, X-chromosome gene dosage between the sexes is equalized by inactivating one X chromosome in females and happens randomly (paternal or maternal).
  • Epigenetic silencing of X chromosome-linked genes on one female chromosome.
  • Most X-linked genes are affected in females.
  • The choice of which X chromosome gets inactivated is random
  • Occurs in early embryogenesis.
  • XX female pluripotent progenitor cells have two active X chromosomes and express the products of escape genes at equal levels from both.
  • Upon differentiation, the 2x dose of the escape gene products robustly induces the XIST gene (X-inactive specific transcript).
  • XIST encodes ncRNA (epigenetic initiator) to ensure epigenetic changes in the silenced X chromosome.
  • Inactivation takes place around day 3-7 of embryonal development.
  • Once XIST is induced, gene silencing on the inactive X chromosome begins.
  • X chromosome is inactivated by methylation of cytosine and H4 histone hypo-acetylation, along with other histone modifications.
  • In XY males, there is a lower dose of the escape gene product, therefore it is insufficient to induce XIST and silence X-linked genes.

Environmental Influence on the Epigenome

  • Dutch Hunger Winter in 1944–1945.
  • Investigated the effect of famine on birth weights.
  • Infants born to mothers who suffered famine only during the last few months of pregnancy had small birth weights.
  • Infants born to mothers who suffered famine only during the first three months of pregnancy were abnormally-sized.
  • Babies who were small at birth stayed small throughout their lives.
  • Children who suffered early in pregnancy were observed to have higher obesity rates than normal.
  • Insulin-like growth factor II (IGF2) is a key factor in human growth and development and is maternally imprinted.
  • The methylation of five CpG dinucleotides within the IGF2 differentially methylated region (DMR) was measured 6 decades later.
  • Higher obesity rates were linked to less methylation on the CpG island of imprinted allele.
  • Small body mass in adulthood had no epigenetic changes.

Cancer Epigenomics

  • In cancer tissues DNA methylation is classically reduced globally.
  • Hypomethylating oncogene promoters reduces defense against repetitive sequences leading to genome instability and chromosome structural changes.
  • Decreased gene methylation has subsequent effects on transcription.

Aberration of the Epigenome

  • Intra-individual changes in global DNA hypomethylation are observed over time.
  • DNA methylation changes may predispose to cancer by inducing a more stem-cell-like state.

Pathological Epigenetic Regulation

  • Rett Syndrome: Changes in the MeCP2 gene (methyl-CpG-binding protein-2) sequence lead to reduced function. Normally recognizes methylated CpG islands and acts as a transcriptional repressor. Also linked to aberrant changes in epigenetic regulation (DNA methylation, Histone methylation, Histone acetylation)
  • Psychiatric disorders:
    • Addiction to cocaine. Acute and chronic cocaine exposure induce differential H3 and H4 acetylation. Chronic cocaine exposure reduces H3K9 di-methylation, mediated by the HMT G9a, while it concurrently increases MeCP2 and MBD1 expression.
    • Depression: there is downregulated HDAC2 and HDAC5 upon chronic social defeat stress, and an upregulation in the repressive methyl marks on H3 are upregulated in the promoter region of BDNF, as in DNA methylation levels at GABA receptorcoding gene.

Summary

  • The epigenome is the key interface between environment and genome.

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