Podcast
Questions and Answers
Which of the following is the MOST accurate definition of an epigenetic trait?
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.
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?
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?
Which of the following BEST describes the focus of epigenetics?
What is the epigenome, and what role does it play in gene expression?
What is the epigenome, and what role does it play in gene expression?
Which of the following factors can influence gene expression, according to the information provided?
Which of the following factors can influence gene expression, according to the information provided?
What is the primary function of epigenetic events in eukaryotic organisms?
What is the primary function of epigenetic events in eukaryotic organisms?
Epigenetic traits play a crucial role in ______ stability by silencing centromeres, telomeres, and transposable elements.
Epigenetic traits play a crucial role in ______ stability by silencing centromeres, telomeres, and transposable elements.
What does the silencing of centromeres, telomeres, and transposable elements via genomic stability ensure?
What does the silencing of centromeres, telomeres, and transposable elements via genomic stability ensure?
Which of the following cellular components is directly acted upon by factors influenced by external stimuli, ultimately leading to changes in gene expression patterns?
Which of the following cellular components is directly acted upon by factors influenced by external stimuli, ultimately leading to changes in gene expression patterns?
Match the following lifestyle factors with their potential epigenetic effects:
Match the following lifestyle factors with their potential epigenetic effects:
What is the role of an epigenator in epigenetic regulation?
What is the role of an epigenator in epigenetic regulation?
What is the primary role of the epigenetic initiator?
What is the primary role of the epigenetic initiator?
What are the two main categories of epigenetic initiators described?
What are the two main categories of epigenetic initiators described?
Which of the following BEST describes how DNA-binding proteins recognize specific DNA sequences?
Which of the following BEST describes how DNA-binding proteins recognize specific DNA sequences?
Non-coding RNAs (ncRNAs) are translated into proteins.
Non-coding RNAs (ncRNAs) are translated into proteins.
What is the PRIMARY function of microRNAs (miRNAs) in epigenetic processes?
What is the PRIMARY function of microRNAs (miRNAs) in epigenetic processes?
What is the primary function of short interfering RNAs (siRNAs)?
What is the primary function of short interfering RNAs (siRNAs)?
What is the main function of piwi-interacting RNAs (piRNAs)?
What is the main function of piwi-interacting RNAs (piRNAs)?
What is the MAIN function of long non-coding RNAs (lncRNAs)?
What is the MAIN function of long non-coding RNAs (lncRNAs)?
How does DNA methylation typically affect gene expression?
How does DNA methylation typically affect gene expression?
Where does DNA methylation typically occur, and what base is methylated?
Where does DNA methylation typically occur, and what base is methylated?
What enzymes are responsible for catalyzing DNA methylation in mammalian cells?
What enzymes are responsible for catalyzing DNA methylation in mammalian cells?
Non-CpG cytosine methylation is MOST prevalent in ______ cells and may be critical in differentiation.
Non-CpG cytosine methylation is MOST prevalent in ______ cells and may be critical in differentiation.
How does an increased level of global methylation typically correlate with differentiation?
How does an increased level of global methylation typically correlate with differentiation?
Histone modification, defined as a covalent post-translational modification (PTM) to histone proteins, affects which of the following processes within a cell?
Histone modification, defined as a covalent post-translational modification (PTM) to histone proteins, affects which of the following processes within a cell?
Which of the following is NOT a type of histone modification?
Which of the following is NOT a type of histone modification?
On which part of histones do the majority of histone PTMs (post-translational modifications) occur?
On which part of histones do the majority of histone PTMs (post-translational modifications) occur?
How do epigenetic modifications, such as histone modifications, affect the accessibility of DNA to the transcriptional machinery?
How do epigenetic modifications, such as histone modifications, affect the accessibility of DNA to the transcriptional machinery?
What is the function of histone acetyltransferases (HATs)?
What is the function of histone acetyltransferases (HATs)?
How does the addition of an acetyl group affect the interaction between the histone tail and negatively charged DNA?
How does the addition of an acetyl group affect the interaction between the histone tail and negatively charged DNA?
What is the enzymatic function of histone methyltransferases (HMTs) and histone demethylases (HDMs)?
What is the enzymatic function of histone methyltransferases (HMTs) and histone demethylases (HDMs)?
How does histone phosphorylation typically affect transcriptional activity?
How does histone phosphorylation typically affect transcriptional activity?
What is the effect of H2A ubiquitination?
What is the effect of H2A ubiquitination?
What impact does the process of sumoylation have on transcriptional activity?
What impact does the process of sumoylation have on transcriptional activity?
Which of the following statements accurately describes the characteristics of histone variants?
Which of the following statements accurately describes the characteristics of histone variants?
What is the overall effect of nucleosome remodeling?
What is the overall effect of nucleosome remodeling?
In the example provided, which brain area is described as being implicated in the stress response?
In the example provided, which brain area is described as being implicated in the stress response?
The early life environment shapes the stress response later in life through:
The early life environment shapes the stress response later in life through:
What is the term for when the ratio of gene expression levels from two alleles in a diploid genome is not 1 to 1?
What is the term for when the ratio of gene expression levels from two alleles in a diploid genome is not 1 to 1?
Allelic imbalance affects all genes in the genome equally.
Allelic imbalance affects all genes in the genome equally.
What epigenetic phenomenon involves only one of the two copies of a gene being active while the other is silent?
What epigenetic phenomenon involves only one of the two copies of a gene being active while the other is silent?
Between 0.5% and 15% of ______ genes exhibit random monoallelic gene expression.
Between 0.5% and 15% of ______ genes exhibit random monoallelic gene expression.
Which of the following best describes somatic rearrangement as a type of monoallelic expression?
Which of the following best describes somatic rearrangement as a type of monoallelic expression?
Somatic rearrangement in immune cells contributes to antibody diversity.
Somatic rearrangement in immune cells contributes to antibody diversity.
In the context of somatic rearrangement, what is the mechanism that generates enormous antibody diversity?
In the context of somatic rearrangement, what is the mechanism that generates enormous antibody diversity?
Random allelic silencing or activation results in expression from only one gene copy due to different ______ changes.
Random allelic silencing or activation results in expression from only one gene copy due to different ______ changes.
Which cell type primarily utilizes random allelic silencing or activation in humans?
Which cell type primarily utilizes random allelic silencing or activation in humans?
Genomic imprinting affects the expression of genes based solely on environmental factors.
Genomic imprinting affects the expression of genes based solely on environmental factors.
In genomic imprinting, what is the term for the mechanism by which regions are marked epigenetically?
In genomic imprinting, what is the term for the mechanism by which regions are marked epigenetically?
Epigenetic silencing of a gene copy occurs in ______ regions.
Epigenetic silencing of a gene copy occurs in ______ regions.
What is the primary purpose of X chromosome inactivation in humans?
What is the primary purpose of X chromosome inactivation in humans?
In humans, the paternal X chromosome is always inactivated in females.
In humans, the paternal X chromosome is always inactivated in females.
What type of molecule does the XIST gene encode?
What type of molecule does the XIST gene encode?
X chromosome inactivation is accomplished by ______ of cytosine, H4 histone hypo-acetylation, and other histone modifications.
X chromosome inactivation is accomplished by ______ of cytosine, H4 histone hypo-acetylation, and other histone modifications.
Match the following epigenetic mechanisms with their characteristics:
Match the following epigenetic mechanisms with their characteristics:
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?
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?
The Dutch Hunger Winter study showed no correlation between prenatal famine exposure and later-life health outcomes.
The Dutch Hunger Winter study showed no correlation between prenatal famine exposure and later-life health outcomes.
What key factor, crucial for human growth and development, is maternally imprinted?
What key factor, crucial for human growth and development, is maternally imprinted?
Higher obesity rates are correlated with ______ methylation on the CpG island of an imprinted allele.
Higher obesity rates are correlated with ______ methylation on the CpG island of an imprinted allele.
What is a classic feature of cancer tissues concerning DNA methylation?
What is a classic feature of cancer tissues concerning DNA methylation?
Hypomethylation of oncogene promoters can lead to increased genome stability.
Hypomethylation of oncogene promoters can lead to increased genome stability.
What is generally observed for DNA methylation levels in cancer tissues?
What is generally observed for DNA methylation levels in cancer tissues?
DNA methylation changes may predispose to cancer by inducing a more ______ state.
DNA methylation changes may predispose to cancer by inducing a more ______ state.
What epigenetic modification is associated with Rett syndrome?
What epigenetic modification is associated with Rett syndrome?
The MeCP2 protein normally functions as a transcriptional activator.
The MeCP2 protein normally functions as a transcriptional activator.
What epigenetic modification is seen in individuals with addiction to drugs such as cocaine?
What epigenetic modification is seen in individuals with addiction to drugs such as cocaine?
In individuals with depression, ______ histone methylation results in the upregulation of repressive methyl marks on H3.
In individuals with depression, ______ histone methylation results in the upregulation of repressive methyl marks on H3.
What is one epigenetic change observed in the brains of individuals suffering from depression?
What is one epigenetic change observed in the brains of individuals suffering from depression?
The epigenome is solely determined by an individual's genetic code and is not influenced by environmental factors.
The epigenome is solely determined by an individual's genetic code and is not influenced by environmental factors.
What term describes the function of the epigenome as the key interface between environmental conditions and an individual's genetic makeup?
What term describes the function of the epigenome as the key interface between environmental conditions and an individual's genetic makeup?
The ______ is the connection between the environment and genome.
The ______ is the connection between the environment and genome.
What are the potential consequences of DNA hypomethylation in cancer tissues?
What are the potential consequences of DNA hypomethylation in cancer tissues?
The impact of environmental factors on the epigenome does not have long-lasting effects on human health.
The impact of environmental factors on the epigenome does not have long-lasting effects on human health.
How does the epigenetic landscape in cancer stem cells differ from that in differentiated cells?
How does the epigenetic landscape in cancer stem cells differ from that in differentiated cells?
When the repressive methyl marks on H3 are upregulated it leads to a down regulation of ______.
When the repressive methyl marks on H3 are upregulated it leads to a down regulation of ______.
What is the primary role of Xist RNA in X-chromosome inactivation?
What is the primary role of Xist RNA in X-chromosome inactivation?
The process of X-chromosome inactivation always results in the complete and irreversible silencing of all genes on the affected chromosome.
The process of X-chromosome inactivation always results in the complete and irreversible silencing of all genes on the affected chromosome.
Flashcards
Epigenetic trait
Epigenetic trait
A stably heritable phenotype resulting from changes in chromatin without alterations in the DNA sequence.
Epigenomics
Epigenomics
Epigenetic changes at the level of the whole genome.
Epigenetics
Epigenetics
Processes that regulate gene expression and genomic stability through chemical modifications.
Epigenome
Epigenome
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Epigenator
Epigenator
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Epigenetic Initiator
Epigenetic Initiator
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Non-coding RNA (ncRNA)
Non-coding RNA (ncRNA)
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MicroRNAs (miRNAs)
MicroRNAs (miRNAs)
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Short interfering RNAs (siRNAs)
Short interfering RNAs (siRNAs)
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Long ncRNAs
Long ncRNAs
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DNA methylation
DNA methylation
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DNA methyltransferases (DNMTs)
DNA methyltransferases (DNMTs)
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Histone modification
Histone modification
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Histone Methylation
Histone Methylation
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Histone Acetylation
Histone Acetylation
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Histone acetyltransferases (HATs)
Histone acetyltransferases (HATs)
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Histone Phosphorylation
Histone Phosphorylation
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Ubiquitylation
Ubiquitylation
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Sumoylation
Sumoylation
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Histone variants
Histone variants
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Nucleosome remodeling
Nucleosome remodeling
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Hippocampus
Hippocampus
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Glucocorticoids
Glucocorticoids
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Allelic imbalance
Allelic imbalance
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Monoallelic expression
Monoallelic expression
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Somatic rearrangement
Somatic rearrangement
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Genomic imprinting
Genomic imprinting
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X chromosome inactivation
X chromosome inactivation
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The epigenome
The epigenome
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Dutch Hunger Winter
Dutch Hunger Winter
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Cancer epigenomics
Cancer epigenomics
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Insulin-like growth factor II (IGF2)
Insulin-like growth factor II (IGF2)
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Rett syndrome
Rett syndrome
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X chromosome inactivation cause
X chromosome inactivation cause
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Cocaine addiction
Cocaine addiction
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HDAC2 and HDAC5
HDAC2 and HDAC5
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BDNF promoter region
BDNF promoter region
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Aberrant epigenome
Aberrant epigenome
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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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