therese Flashcards
- What is the best definition of epigenetics?
A) Changes in DNA sequence that lead to gene expression changes
B) Heritable changes in gene function that do not involve changes in DNA sequence
C) The study of mutations in the genome
D) Random modifications in gene expression without a regulatory mechanism
Answer: B) Heritable changes in gene function that do not involve changes in DNA sequence
- Why do genetically identical cells (e.g., neurons and muscle cells) have different functions?
A) Because of epigenetic modifications that regulate gene expression
B) Due to differences in the number of chromosomes
C) Because they contain different sets of genes
D) Because their genomes mutate during differentiation
Answer: A) Because of epigenetic modifications that regulate gene expression
- What is the fundamental repeating unit of chromatin?
A) Nucleosome
B) Centromere
C) Exon
D) Polymerase complex
Answer: A) Nucleosome
- How does chromatin compaction affect gene transcription?
A) More compact chromatin (heterochromatin) is transcriptionally inactive
B) More compact chromatin allows more transcription factor binding
C) Euchromatin is more tightly packed than heterochromatin
D) Compaction levels do not influence gene expression
Answer: A) More compact chromatin (heterochromatin) is transcriptionally inactive
- What is the main role of DNA methylation in gene regulation?
A) It directly increases transcription levels
B) It represses gene expression by preventing transcription factor binding
C) It makes DNA more accessible to polymerases
D) It has no effect on gene regulation
Answer: B) It represses gene expression by preventing transcription factor binding
- Where does DNA methylation primarily occur in the genome?
A) At adenosine residues
B) At CpG dinucleotides
C) Only in coding regions of genes
D) In mitochondrial DNA
Answer: B) At CpG dinucleotides
- Which enzyme is responsible for maintaining DNA methylation patterns after DNA replication?
A) DNMT3A
B) DNMT3B
C) DNMT1
D) TET1
Answer: C) DNMT1
- What is the role of 5-hydroxymethylcytosine (5hmC) in epigenetic regulation?
A) It promotes gene expression and may be an intermediate in active demethylation
B) It permanently silences genes
C) It prevents histone modifications from occurring
D) It causes irreversible genetic mutations
Answer: A) It promotes gene expression and may be an intermediate in active demethylation
- In cancer, abnormal DNA methylation can lead to:
A) Global hypomethylation and promoter hypermethylation
B) Increased chromatin accessibility in all genes
C) Complete loss of histone modifications
D) Mutation of all methyltransferase enzymes
Answer: A) Global hypomethylation and promoter hypermethylation
- How can DNA demethylation occur?
A) By active removal through TET enzymes and base excision repair
B) By direct conversion of methylated cytosine into adenine
C) Only through passive loss during DNA replication
D) By random degradation of methyl groups
Answer: A) By active removal through TET enzymes and base excision repair
- Which histone modification is associated with active transcription?
A) H3K9me3 (Histone H3 lysine 9 trimethylation)
B) H3K27me3 (Histone H3 lysine 27 trimethylation)
C) H3K4me3 (Histone H3 lysine 4 trimethylation)
D) H3K9me3 and H3K27me3 together
Answer: C) H3K4me3 (Histone H3 lysine 4 trimethylation)
- What is the function of histone acetylation?
A) It compacts chromatin, making genes inaccessible for transcription
B) It relaxes chromatin, facilitating transcription factor binding
C) It permanently silences gene expression
D) It removes CpG methylation from promoters
Answer: B) It relaxes chromatin, facilitating transcription factor binding
- Which enzyme removes acetyl groups from histones, leading to chromatin compaction?
A) Histone acetyltransferase (HAT)
B) Histone deacetylase (HDAC)
C) DNA methyltransferase (DNMT)
D) TET demethylase
Answer: B) Histone deacetylase (HDAC)
- What is the “histone code” hypothesis?
A) Histone modifications occur in specific combinations that are read by proteins to regulate gene expression
B) Histone modifications are always associated with gene silencing
C) Only DNA methylation affects chromatin structure
D) Histone modifications only occur in embryonic development
Answer: A) Histone modifications occur in specific combinations that are read by proteins to regulate gene expression
- What role do long non-coding RNAs (lncRNAs) play in epigenetic regulation?
A) They directly modify DNA sequences
B) They recruit chromatin modifiers to specific genomic locations
C) They function as enzymes in DNA methylation
D) They are translated into regulatory proteins
Answer: B) They recruit chromatin modifiers to specific genomic locations
- Which of the following is a known function of microRNAs (miRNAs) in epigenetic regulation?
A) Direct histone acetylation
B) Post-transcriptional gene silencing by degrading target mRNAs
C) DNA methylation at CpG islands
D) Increasing histone methylation at gene promoters
Answer: B) Post-transcriptional gene silencing by degrading target mRNAs
- In a chromatin immunoprecipitation (ChIP) assay graph, what does a high peak in an active gene promoter region indicate?
A) Strong binding of transcriptional activators or acetylated histones
B) Lack of transcription factor binding
C) Inactive chromatin modifications
D) DNA mutation hotspots
Answer: A) Strong binding of transcriptional activators or acetylated histones
- In a DNA methylation heatmap, what does a region with low methylation intensity suggest?
A) Active transcription
B) Transcriptional silencing
C) Histone deacetylation
D) Irreversible genetic mutations
Answer: A) Active transcription
- If a genome-wide bisulfite sequencing study shows hypermethylation of tumor suppressor genes, what could be the biological consequence?
A) Reduced gene expression, contributing to cancer progression
B) Increased gene expression, preventing tumor formation
C) Enhanced histone acetylation
D) Activation of immune response genes
Answer: A) Reduced gene expression, contributing to cancer progression
- Which epigenetic therapy is used to reverse DNA methylation-related gene silencing?
A) DNA methyltransferase inhibitors (DNMTi)
B) Histone acetyltransferase inhibitors (HATi)
C) RNA polymerase activators
D) Transcription factor repressors
Answer: A) DNA methyltransferase inhibitors (DNMTi)
- Why are monozygotic (MZ) twins considered powerful tools in epigenetic epidemiology?
A) They have identical epigenomes from birth to adulthood
B) They share the same genetic background, allowing environmental influences to be studied independently
C) They always develop the same diseases
D) Their DNA sequences mutate more frequently than dizygotic twins
Answer: B) They share the same genetic background, allowing environmental influences to be studied independently
- What is the main difference between monozygotic (MZ) and dizygotic (DZ) twins?
A) MZ twins share 50% of their DNA, whereas DZ twins share 100%
B) MZ twins are genetically identical, while DZ twins share approximately 50% of their DNA
C) MZ twins are always of the same sex, while DZ twins are always of different sexes
D) DZ twins are genetically identical, while MZ twins have unique genomes
Answer: B) MZ twins are genetically identical, while DZ twins share approximately 50% of their DNA
In twin studies, what does the term “heritability” (h²) refer to?
A) The probability that a disease is inherited from parents
B) The proportion of phenotypic variance explained by genetic factors in a population
C) The absolute genetic contribution to disease in individuals
D) The environmental contribution to disease risk
Answer: B) The proportion of phenotypic variance explained by genetic factors in a population
- What is a key reason why identical twins can exhibit differences in disease susceptibility?
A) Random mutations accumulate at the same rate in both twins
B) Epigenetic modifications such as DNA methylation and histone modifications can be influenced by environmental factors
C) They have different genetic sequences from birth
D) They experience identical life exposures
Answer: B) Epigenetic modifications such as DNA methylation and histone modifications can be influenced by environmental factors
- Which environmental factors can lead to changes in the epigenome?
A) Diet, stress, toxins, and medication
B) DNA sequence variation only
C) Only factors encountered before birth
D) Epigenetic modifications are purely genetic and not affected by the environment
Answer: A) Diet, stress, toxins, and medication
- What role does DNA methylation play in schizophrenia risk in monozygotic twins?
A) Schizophrenia risk is determined entirely by DNA mutations, not methylation
B) MZ twins discordant for schizophrenia show differential DNA methylation patterns, suggesting epigenetic involvement
C) DNA methylation is identical in all MZ twin pairs
D) Schizophrenia is solely caused by common genetic variants
Answer: B) MZ twins discordant for schizophrenia show differential DNA methylation patterns, suggesting epigenetic involvement
In the twin-based Epigenome-Wide Association Study (EWAS) on schizophrenia, what was a key finding?
A) The HDAC4 gene showed significant DNA methylation differences between affected and unaffected twins
B) No DNA methylation differences were observed between discordant twins
C) Schizophrenia is only caused by mutations, not epigenetic modifications
D) DNA methylation differences were only found in non-coding regions
Answer: A) The HDAC4 gene showed significant DNA methylation differences between affected and unaffected twins
What is the function of the HDAC4 gene, which was identified in schizophrenia twin studies?
A) It is involved in synaptic plasticity and neurological processes
B) It is responsible for immune system regulation
C) It is a transcription factor that binds directly to schizophrenia-associated mutations
D) It plays no role in brain function
Answer: A) It is involved in synaptic plasticity and neurological processes
- What method is commonly used to measure DNA methylation in twin epigenetic studies?
A) Bisulfite conversion followed by microarray or sequencing
B) Direct visualization under a microscope
C) Western blot analysis
D) RNA-seq without modifications
Answer: A) Bisulfite conversion followed by microarray or sequencing
What is a Differentially Methylated Probe (DMP) in DNA methylation analysis?
A) A probe that detects mutations in DNA sequences
B) A site in the genome where DNA methylation differs between groups (e.g., discordant twins)
C) A probe that exclusively binds to histones
D) A DNA sequence that cannot be methylated
Answer: B) A site in the genome where DNA methylation differs between groups (e.g., discordant twins)
- In a DNA methylation heatmap comparing discordant twin pairs, what would a region with higher methylation in affected twins suggest?
A) Potential gene silencing associated with disease
B) Increased transcription of affected genes
C) Random sequencing errors
D) A deletion in that region
Answer: A) Potential gene silencing associated with disease
In a genome-wide association study (GWAS) of schizophrenia, how would a Manhattan plot indicate a significant association?
A) A peak above the genome-wide significance threshold
B) A completely flat distribution of points
C) All data points clustering around zero
D) No differences between affected and unaffected individuals
Answer: A) A peak above the genome-wide significance threshold
- What was the significance of the Agouti mouse experiment in epigenetics?
A) It demonstrated that maternal diet could alter offspring DNA methylation and phenotype
B) It proved that epigenetic changes cannot be inherited
C) It showed that DNA sequence is the sole determinant of phenotype
D) It was unrelated to epigenetics
Answer: A) It demonstrated that maternal diet could alter offspring DNA methylation and phenotype
- Which environmental factor was linked to altered DNA methylation in smoking-related twin studies?
A) Changes in DNA methylation at the AHRR gene
B) Increased mutational burden in the Y chromosome
C) Deletion of genes on chromosome 21
D) Formation of additional histone octamers
Answer: A) Changes in DNA methylation at the AHRR gene
. What is a major confounder in twin-based epigenetic studies?
A) Non-random X inactivation in female twins
B) Smoking history and medication use
C) Prenatal and birth order effects
D) All of the above
Answer: D) All of the above
How do monozygotic twins’ epigenomes change with age?
A) DNA methylation patterns diverge due to environmental influences
B) Their epigenomes remain identical throughout life
C) They acquire the exact same mutations in all tissues
D) Epigenetic marks are only inherited and do not change over time
Answer: A) DNA methylation patterns diverge due to environmental influences
- How does the epigenome interact with environmental exposures?
A) Environmental factors can directly alter DNA sequences
B) The epigenome is stable and unaffected by external stimuli
C) Environmental exposures such as diet, smoking, and stress can modify DNA methylation and histone modifications
D) Only genetic mutations influence the epigenome
Answer: C) Environmental exposures such as diet, smoking, and stress can modify DNA methylation and histone modifications
- Why is the perinatal period particularly sensitive to epigenetic changes?
A) DNA synthesis rates are high, and chromatin structures required for normal development are established
B) Cells are resistant to external environmental changes during this period
C) Epigenetic marks are completely erased and cannot be influenced by external factors
D) Epigenetic modifications only occur after birth
Answer: A) DNA synthesis rates are high, and chromatin structures required for normal development are established
. What was a key finding from the Dutch Hunger Winter study regarding epigenetics?
A) Individuals prenatally exposed to famine had decreased DNA methylation at the IGF2 gene six decades later
B) DNA methylation patterns were unchanged despite famine exposure
C) IGF2 methylation was only altered in individuals exposed after birth
D) Famine exposure led to permanent genetic mutations rather than epigenetic modifications
Answer: A) Individuals prenatally exposed to famine had decreased DNA methylation at the IGF2 gene six decades later
- What are some diseases influenced by epigenetic changes?
A) Cancer, autoimmune disorders, mental illness, and imprinting disorders
B) Only rare genetic disorders
C) Only diseases caused by single-gene mutations
D) None, as diseases are only influenced by genetic mutations
Answer: A) Cancer, autoimmune disorders, mental illness, and imprinting disorders
- How do epigenetic modifications contribute to cancer development?]
A) They silence tumor suppressor genes and activate oncogenes through DNA methylation and histone modifications
B) They permanently delete genes associated with cancer
C) They randomly modify the genome without specific targets
D) They prevent genetic mutations from occurring
Answer: A) They silence tumor suppressor genes and activate oncogenes through DNA methylation and histone modifications
. In the context of inflammatory bowel disease (IBD), what did EWAS reveal?
A) Significant DNA methylation changes in genes related to immune pathways, such as TRIM39-RPP21 and TRAF6
B) No epigenetic differences between Crohn’s disease (CD) and ulcerative colitis (UC)
C) IBD is caused solely by genetic mutations with no epigenetic influence
D) DNA methylation levels were identical between healthy and affected individuals
Answer: A) Significant DNA methylation changes in genes related to immune pathways, such as TRIM39-RPP21 and TRAF6
How has epigenetics contributed to understanding mental illness?
A) Epigenetic modifications regulate gene expression in neurodevelopment and brain function
B) All mental disorders are caused only by genetic mutations
C) There is no evidence linking epigenetics to psychiatric disorders
D) DNA methylation patterns remain identical between individuals with and without mental illness
Answer: A) Epigenetic modifications regulate gene expression in neurodevelopment and brain function
What was a major finding regarding DNA methylation and body mass index (BMI)?
A) Methylation of HIF3A is associated with BMI changes
B) Epigenetic modifications have no effect on BMI
C) DNA methylation only affects metabolism in childhood
D) There is no link between DNA methylation and obesity
Answer: A) Methylation of HIF3A is associated with BMI changes
- What is the main difference between EWAS and GWAS?
A) EWAS studies epigenetic changes, while GWAS studies genetic variants
B) GWAS identifies only environmental influences, while EWAS focuses on mutations
C) EWAS is used only for single-gene disorders
D) GWAS does not use statistical analysis, while EWAS doe
Answer: A) EWAS studies epigenetic changes, while GWAS studies genetic variants
- What are some challenges in interpreting EWAS results?
A) Tissue specificity, age, sex, environmental exposures, and cellular heterogeneity
B) EWAS results are always conclusive and do not require replication
C) Epigenetic changes are uniform across all tissues
D) EWAS can be conducted without considering confounders
Answer: A) Tissue specificity, age, sex, environmental exposures, and cellular heterogeneity
- What is transgenerational epigenetic inheritance?
A) The transmission of epigenetic marks (DNA methylation, histone modifications) across generations
B) A temporary environmental influence that does not persist beyond one generation
C) Only possible in plants, not mammals
D) The inheritance of genetic mutations rather than epigenetic modifications
Answer: A) The transmission of epigenetic marks (DNA methylation, histone modifications) across generations
. Why is transgenerational epigenetic inheritance debated in humans?
A) Epigenetic marks are largely reset during embryonic development
B) No epigenetic modifications persist after birth
C) DNA methylation changes cannot be inherited
D) There is no experimental evidence supporting transgenerational inheritance
Answer: A) Epigenetic marks are largely reset during embryonic development
- In an epigenome-wide association study (EWAS) graph, what does a higher signal at a CpG site suggest?
A) Increased DNA methylation at that site
B) A deletion in the genome
C) No difference in methylation between groups
D) A sequencing error
Answer: A) Increased DNA methylation at that site
. In a methylation heatmap comparing cancer and normal tissues, what does a region of hypermethylation in tumor samples indicate?
A) Potential silencing of tumor suppressor genes
B) Higher expression of oncogenes
C) No change in gene expression
D) Random mutations occurring in the DNA sequence
Answer: A) Potential silencing of tumor suppressor genes
. In a boxplot showing DNA methylation levels at a gene promoter in obese and lean individuals, what would a significant decrease in methylation in obese individuals suggest?
A) Increased expression of the gene associated with metabolism
B) Complete gene silencing
C) No effect on gene expression
D) A technical artifact in sequencing
Answer: A) Increased expression of the gene associated with metabolism
