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Question 1

1. 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 1

Answer: B) Heritable changes in gene function that do not involve changes in DNA sequence

Question 2

2. 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 2

Answer: A) Because of epigenetic modifications that regulate gene expression

Question 3

3. What is the fundamental repeating unit of chromatin?

A) Nucleosome

B) Centromere

C) Exon

D) Polymerase complex

Answer 3

Answer: A) Nucleosome

Question 4

4. 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 4

Answer: A) More compact chromatin (heterochromatin) is transcriptionally inactive

Question 5

5. 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 5

Answer: B) It represses gene expression by preventing transcription factor binding

Question 6

6. 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 6

Answer: B) At CpG dinucleotides

Question 7

7. Which enzyme is responsible for maintaining DNA methylation patterns after DNA replication?

A) DNMT3A

B) DNMT3B

C) DNMT1

D) TET1

Answer 7

Answer: C) DNMT1

Question 8

10. 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 8

Answer: A) It promotes gene expression and may be an intermediate in active demethylation

Question 8

8. 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 8

Answer: A) Global hypomethylation and promoter hypermethylation

Question 9

9. 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 9

Answer: A) By active removal through TET enzymes and base excision repair

Question 10

11. 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 10

Answer: C) H3K4me3 (Histone H3 lysine 4 trimethylation)

Question 11

12. 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 11

Answer: B) It relaxes chromatin, facilitating transcription factor binding

Question 12

13. 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 12

Answer: B) Histone deacetylase (HDAC)

Question 13

4. 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 13

Answer: A) Histone modifications occur in specific combinations that are read by proteins to regulate gene expression

Question 14

15. 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 14

Answer: B) They recruit chromatin modifiers to specific genomic locations

Question 15

16. 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 15

Answer: B) Post-transcriptional gene silencing by degrading target mRNAs

Question 16

17. 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 16

Answer: A) Strong binding of transcriptional activators or acetylated histones

Question 17

18. 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 17

Answer: A) Active transcription

Question 18

19. 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 18

Answer: A) Reduced gene expression, contributing to cancer progression

Question 19

20. 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 19

Answer: A) DNA methyltransferase inhibitors (DNMTi)

Question 20

1. 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 20

Answer: B) They share the same genetic background, allowing environmental influences to be studied independently

Question 21

2. 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 21

Answer: B) MZ twins are genetically identical, while DZ twins share approximately 50% of their DNA

Question 22

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 22

Answer: B) The proportion of phenotypic variance explained by genetic factors in a population

Question 23

4. 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 23

Answer: B) Epigenetic modifications such as DNA methylation and histone modifications can be influenced by environmental factors

Question 24

5. 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 24

Answer: A) Diet, stress, toxins, and medication

Question 25

6. 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 25

Answer: B) MZ twins discordant for schizophrenia show differential DNA methylation patterns, suggesting epigenetic involvement

Question 26

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 26

Answer: A) The HDAC4 gene showed significant DNA methylation differences between affected and unaffected twins

Question 27

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 27

Answer: A) It is involved in synaptic plasticity and neurological processes

Question 28

9. 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 28

Answer: A) Bisulfite conversion followed by microarray or sequencing

Question 29

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 29

Answer: B) A site in the genome where DNA methylation differs between groups (e.g., discordant twins)

Question 30

11. 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 30

Answer: A) Potential gene silencing associated with disease

Question 31

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 31

Answer: A) A peak above the genome-wide significance threshold

Question 32

3. 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 32

Answer: A) It demonstrated that maternal diet could alter offspring DNA methylation and phenotype

Question 33

4. 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 33

Answer: A) Changes in DNA methylation at the AHRR gene

Question 34

. 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 34

Answer: D) All of the above

Question 35

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 35

Answer: A) DNA methylation patterns diverge due to environmental influences

Question 36

1. 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 36

Answer: C) Environmental exposures such as diet, smoking, and stress can modify DNA methylation and histone modifications

Question 37

2. 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 37

Answer: A) DNA synthesis rates are high, and chromatin structures required for normal development are established

Question 38

. 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 38

Answer: A) Individuals prenatally exposed to famine had decreased DNA methylation at the IGF2 gene six decades later

Question 39

4. 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 39

Answer: A) Cancer, autoimmune disorders, mental illness, and imprinting disorders

Question 40

5. 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 40

Answer: A) They silence tumor suppressor genes and activate oncogenes through DNA methylation and histone modifications

Question 41

. 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 41

Answer: A) Significant DNA methylation changes in genes related to immune pathways, such as TRIM39-RPP21 and TRAF6

Question 42

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 42

Answer: A) Epigenetic modifications regulate gene expression in neurodevelopment and brain function

Question 43

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 43

Answer: A) Methylation of HIF3A is associated with BMI changes

Question 44

9. 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 44

Answer: A) EWAS studies epigenetic changes, while GWAS studies genetic variants

Question 45

10. 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 45

Answer: A) Tissue specificity, age, sex, environmental exposures, and cellular heterogeneity

Question 46

1. 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 46

Answer: A) The transmission of epigenetic marks (DNA methylation, histone modifications) across generations

Question 47

. 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 47

Answer: A) Epigenetic marks are largely reset during embryonic development

Question 48

3. 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 48

Answer: A) Increased DNA methylation at that site

Question 49

. 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 49

Answer: A) Potential silencing of tumor suppressor genes

Question 50

. 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 50

Answer: A) Increased expression of the gene associated with metabolism