Therese Flashcards by Isabelle Heffernan

What is the definition of epigenetics according to Riggs et al. (1996)?
A) The study of heritable changes in gene function that can be explained by DNA sequence changes
B) The study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by DNA sequence changes
C) The study of genetic mutations affecting chromatin structure
D) The study of protein modifications affecting DNA sequences

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Which of the following is the basic structural unit of chromatin?
A) Histone H1
B) Chromatin fiber
C) Nucleosome
D) Double-helix DNA

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Which histone protein is responsible for linking nucleosomes together?
A) H2A
B) H3
C) H4
D) H1

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What is the approximate length of DNA wrapped around a histone octamer in a nucleosome?
A) 100 bp
B) 147 bp
C) 200 bp
D) 300 bp

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Which statement about euchromatin and heterochromatin is correct?
A) Euchromatin is highly condensed and transcriptionally inactive
B) Heterochromatin is loosely packed and highly transcriptionally active
C) Euchromatin is less condensed and generally transcriptionally active
D) Heterochromatin is found only in bacterial cells

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What type of enzyme is responsible for removing epigenetic modifications?
A) Epigenetic writers
B) Epigenetic readers
C) Epigenetic erasers
D) DNA polymerases

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CpG islands are typically found in which regions of the genome?
A) Introns
B) Promoter regions
C) Telomeres
D) Centromeres

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Which enzyme is responsible for adding methyl groups to DNA?
A) Histone deacetylase (HDAC)
B) DNA methyltransferase (DNMT)
C) RNA polymerase
D) DNA ligase

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Which DNMT enzyme is primarily responsible for maintenance methylation?
A) DNMT1
B) DNMT2
C) DNMT3A
D) DNMT3B

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Which histone modification is generally associated with gene activation?
A) H3K9me3
B) H3K27me3
C) H3K4me3
D) H3K36me3

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Which modification can switch genes “on” or “off” by affecting transcription factor accessibility?
A) DNA phosphorylation
B) DNA methylation
C) DNA replication
D) DNA polymerization

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Which of the following histone modifications is linked to transcriptionally active chromatin?
A) H3K9me3
B) H3K27ac
C) H3K27me3
D) H4K20me3

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Which enzyme class is responsible for acetylation of histones?
A) Histone demethylases
B) Histone acetyltransferases
C) Histone deacetylases
D) DNA methyltransferases

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What is the main function of histone deacetylases (HDACs)?
A) Adding methyl groups to histones
B) Removing acetyl groups from histones
C) Unwinding DNA strands
D) Breaking down histone proteins

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Which of the following statements about DNA demethylation is correct?
A) It only occurs through passive mechanisms
B) It involves the removal of methyl groups by DNMT3A
C) Active demethylation is facilitated by TET enzymes
D) It is irreversible in mammalian cells

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Which molecule serves as the methyl donor in DNA methylation reactions?
A) ATP
B) S-adenosylmethionine (SAM)
C) Acetyl-CoA
D) NADH

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Which epigenetic modification is most commonly associated with gene repression?
A) DNA acetylation
B) Histone phosphorylation
C) DNA methylation
D) Histone deacetylation

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Which region of the nucleosome is most frequently modified by post-translational modifications?
A) Histone core
B) Histone tails
C) DNA backbone
D) Nucleosome linker DNA

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Which of the following statements best describes the function of histone modifications?
A) They irreversibly change the DNA sequence
B) They alter chromatin structure and gene expression
C) They only function in embryonic development
D) They occur randomly without any functional consequences

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Which term describes proteins that “read” histone modifications to regulate chromatin structure and function?
A) Epigenetic writers
B) Epigenetic erasers
C) Epigenetic readers
D) Transcription factors

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Which of the following statements best describes the relationship between epigenetics and disease?
A) Epigenetic changes are static and do not contribute to disease development.
B) Epigenetic mechanisms explain differences in disease susceptibility even in individuals with identical genotypes.
C) All diseases are caused solely by genetic mutations, with no influence from epigenetic factors.
D) DNA methylation and histone modifications only affect non-coding regions of the genome.

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Monozygotic (MZ) twins carrying the same genetic mutation can exhibit different clinical phenotypes. This is likely due to:
A) Differences in DNA sequence variation.
B) Differences in inherited chromosomal abnormalities.
C) Epigenetic variations influenced by environmental exposures.
D) Random segregation of alleles during meiosis.

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Which of the following is NOT a characteristic of complex disease epigenetics?
A) It involves epigenetic modifications influencing gene expression without altering DNA sequence.
B) It affects diseases such as cancer, auto-immune disorders, and mental illnesses.
C) It only occurs in somatic cells and is not inherited across generations.
D) Environmental factors can contribute to epigenetic changes leading to disease.

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Which environmental factor has been shown to cause epigenetic changes associated with increased disease risk?
A) Exposure to famine during early development.
B) High-altitude oxygen levels.
C) Increased daily water consumption.
D) Presence of non-coding RNA in the genome.

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n the Dutch Hunger Winter study, individuals prenatally exposed to famine showed: A) Increased DNA methylation of the IGF2 gene. B) Decreased DNA methylation of the IGF2 gene. C) No detectable epigenetic changes. D) Increased histone acetylation leading to overexpression of IGF2.

Which of the following statements about genomic imprinting is correct? A) It is a reversible epigenetic mechanism. B) It results in differential gene expression depending on the parental origin of alleles. C) It only occurs in somatic cells. D) It is not involved in any known human diseases.

Which disorder is caused by a deletion or imprinting defect in the maternal chromosome 15q11-q13 region? A) Prader-Willi Syndrome B) Angelman Syndrome C) Silver-Russell Syndrome D) Beckwith-Wiedemann Syndrome

Epigenome-wide association studies (EWAS) have identified DNA methylation differences associated with which common health phenotype? A) Bone density B) Blood pressure C) Body Mass Index (BMI) D) Eye color

Which gene was identified in an EWAS study as being associated with BMI? A) TP53 B) FTO C) HIF3A D) IGF2

The role of epigenetics in auto-immune diseases includes: A) Regulation of immune-related gene expression via DNA methylation. B) Direct mutation of immune system genes. C) Increasing the mutation rate of T-cell receptor genes. D) Blocking antigen recognition by immune cells.

What is the primary epigenetic alteration observed in cancer cells? A) Increased acetylation at heterochromatin regions. B) Genome-wide hypomethylation with promoter hypermethylation of tumor suppressor genes. C) Genome-wide histone methylation at active enhancers. D) Increased phosphorylation of DNA repair proteins.

Which of the following explains the role of epigenetics in schizophrenia? A) DNA sequence mutations exclusively cause schizophrenia. B) Epigenetic modifications, such as DNA methylation at neurotransmission genes, have been observed in patients. C) Schizophrenia has no genetic or epigenetic basis. D) Histone acetylation has been shown to prevent schizophrenia entirely.

Which neurodegenerative disease has been linked to age-related epigenetic changes? A) Huntington’s Disease B) Alzheimer’s Disease C) Duchenne Muscular Dystrophy D) Sickle Cell Anemia

Which of the following is a key challenge in conducting EWAS? A) Identifying single nucleotide polymorphisms (SNPs) affecting epigenetic markers. B) Distinguishing between causal and correlated epigenetic changes. C) Measuring protein expression levels from RNA sequencing data. D) Isolating mitochondria from epigenetically modified cells.

Why is DNA methylation considered a stable epigenetic modification? A) It cannot be removed once established. B) It persists through cell divisions and can be inherited. C) It occurs only in differentiated cells. D) It is resistant to environmental influences.

What is the primary function of DNA methylation in gene regulation? A) Enhancing gene transcription B) Silencing gene expression by preventing transcription factor binding C) Increasing mutation rates D) Preventing histone modifications

Which epigenetic process contributes to the silencing of one X chromosome in female mammals? A) Histone phosphorylation B) X-inactivation via DNA methylation and histone modifications C) RNA interference by microRNAs D) Genetic mutation of the X chromosome

Which term describes the phenomenon where epigenetic changes are inherited across generations without direct DNA sequence alterations? A) Transgenerational epigenetic inheritance B) Somatic mutation theory C) Horizontal gene transfer D) DNA recombination

Which factor is NOT commonly considered a confounder in EWAS studies? A) Age B) Cell composition C) Number of chromosomes D) Smoking status

What is one reason epigenetic research is still considered an emerging field? A) Lack of technological advancements in detecting epigenetic changes. B) The complexity of interactions between genetics, epigenetics, and the environment. C) Epigenetics is not relevant to most diseases. D) Limited understanding of the human genome.

What was a key finding from epigenetic studies on Body Mass Index (BMI)? A) BMI is only influenced by genetic factors. B) DNA methylation at CpG sites in HIF3A correlates with BMI changes. C) Epigenetic changes do not influence obesity risk. D) Histone phosphorylation was the primary factor in BMI variation.

Which tissue is commonly used in EWAS studies due to its accessibility? A) Brain tissue B) Peripheral blood C) Liver cells D) Pancreatic tissue

Which of the following is a primary focus of epigenetics in disease research? A) Understanding how genetic mutations alter protein function B) Investigating how environmental factors influence gene expression without altering DNA sequence C) Identifying structural chromosomal abnormalities D) Studying mitochondrial DNA inheritance

What is a key characteristic of the epigenome that distinguishes it from the genome? A) It is immutable and does not change over an individual's lifetime B) It can be dynamically modified by environmental and developmental signals C) It only affects protein-coding genes D) It is identical in all tissues of the body

Which of the following factors is NOT considered a major environmental influence on the epigenome? A) Diet B) Exercise C) Lunar cycles D) Psychological stress

Why is the perinatal period considered a critical window for epigenetic regulation? A) DNA synthesis and cell division rates are high, allowing for the establishment of epigenetic marks B) The genome is more prone to mutations during this time C) Chromosomes are still being formed and are susceptible to rearrangement D) The immune system begins to recognize self and non-self antigens

The Dutch Hunger Winter study provided evidence for which key concept in epigenetics? A) That famine exposure in early life does not affect later generations B) That periconceptional exposure to environmental stressors can lead to persistent epigenetic changes C) That genetic mutations are responsible for metabolic changes in famine-exposed individuals D) That DNA methylation cannot be inherited

Which term describes the ability of epigenetic changes to be passed on from one generation to the next through gametes? A) Horizontal gene transfer B) Transgenerational epigenetic inheritance C) Genetic drift D) Reverse transcription

In the Dutch Hunger Winter study, what epigenetic modification was observed in individuals exposed to famine in utero? A) Increased methylation of the IGF2 gene B) Decreased methylation of the IGF2 gene C) Loss of all histone modifications D) Increased acetylation of H3K27

What is a major challenge in proving transgenerational epigenetic inheritance in humans? A) The inability to track genetic changes over multiple generations B) The difficulty in distinguishing between direct environmental effects and true epigenetic inheritance C) The lack of reliable sequencing technologies D) The inability of DNA methylation patterns to change over time

Which of the following best describes epigenome-wide association studies (EWAS)? A) They identify genetic mutations associated with disease B) They analyze epigenetic variations across the genome to identify associations with traits or diseases C) They measure only histone modifications in cancer cells D) They focus solely on promoter regions of genes

Which of the following diseases has been linked to epigenetic modifications in EWAS studies? A) Huntington’s Disease B) Alzheimer’s Disease C) Down Syndrome D) Sickle Cell Anemia

What distinguishes EWAS from genome-wide association studies (GWAS)? A) EWAS focuses on DNA mutations, while GWAS focuses on epigenetic modifications B) EWAS examines dynamic environmental influences on gene expression, whereas GWAS focuses on fixed genetic variants C) EWAS is used only for rare diseases, while GWAS is used for common diseases D) EWAS does not use high-throughput sequencing technologies

Which epigenetic mark has been most extensively studied in relation to body mass index (BMI)? A) DNA methylation B) RNA splicing C) Histone phosphorylation D) Chromosomal translocations

What was a significant finding regarding DNA methylation and BMI in EWAS studies? A) Methylation levels in the HIF3A gene correlated with BMI variation B) Methylation changes in FTO were responsible for all cases of obesity C) DNA methylation had no association with BMI D) Methylation changes were only present in brain tissue and not in adipose tissue

Which factor is a major confounder in EWAS studies and must be carefully controlled for? A) Hair color B) Cellular heterogeneity in tissue samples C) Number of mitochondria per cell D) Blood pH levels

What is a primary difference between genetic and epigenetic studies in disease research? A) Genetic studies only examine rare diseases, while epigenetic studies focus on common diseases B) Genetic studies identify fixed sequence variations, whereas epigenetic studies examine reversible modifications C) Epigenetic studies cannot be conducted in humans D) Genetic studies do not require high-throughput sequencing technologies

Which of the following statements about epigenetics in mental illness is correct? A) Epigenetic modifications have been identified in schizophrenia and depression B) Epigenetic changes play no role in psychiatric disorders C) DNA methylation only affects cognitive function in early childhood D) Histone modifications are irrelevant to neuronal plasticity

Which of the following is an example of an epigenetic mechanism contributing to cancer? A) Mutation of tumor suppressor genes B) Hypermethylation of tumor suppressor gene promoters leading to gene silencing C) Frameshift mutations in oncogenes D) Deletion of regulatory enhancer regions

What makes epigenetic modifications attractive targets for therapeutic intervention? A) They are irreversible, preventing disease recurrence B) They can be dynamically altered by drugs, unlike genetic mutations C) They only occur in stem cells and are easily modified D) They function independently of environmental influences

What is the significance of X-inactivation in epigenetics? A) It demonstrates how epigenetic mechanisms regulate gene dosage compensation in females B) It is caused by genetic mutations on the Y chromosome C) It leads to chromosomal deletions D) It is a random process with no biological consequences

Which of the following best describes the concept of “epigenetic drift”? A) The accumulation of random epigenetic changes over time, contributing to aging and disease B) The process of epigenetic modifications being inherited without genetic mutations C) A type of genetic recombination occurring in germline cells D) The inability of epigenetic marks to be erased

What is one major limitation of EWAS studies? A) Inability to distinguish cause from effect in disease associations B) Limited ability to detect DNA sequence mutations C) Lack of available tissue samples D) Low-throughput sequencing technology

Which technology is commonly used in EWAS to assess DNA methylation? A) Whole-genome bisulfite sequencing B) RNA-Seq C) Polymerase chain reaction (PCR) D) Sanger sequencing

What type of epigenetic modification is most commonly analyzed in EWAS? A) RNA methylation B) DNA methylation C) Histone phosphorylation D) Protein ubiquitination

Which of the following is a primary goal of an Epigenome-Wide Association Study (EWAS)? A) Identifying genetic mutations associated with disease B) Detecting epigenetic modifications correlated with disease phenotypes C) Measuring protein expression levels D) Studying RNA splicing variations

Which of the following best describes a challenge in EWAS compared to genome-wide association studies (GWAS)? A) The need to control for environmental factors that influence epigenetic modifications B) The inability to analyze DNA sequences C) The exclusion of genetic variation from the analysis D) The limited availability of sequencing technology

Which chemical treatment is used to differentiate between methylated and unmethylated cytosines in DNA? A) Formaldehyde B) Sodium bisulfite C) Ethanol D) Hydrogen peroxide

What is the main effect of sodium bisulfite conversion on DNA? A) It replaces adenine with guanine B) It deaminates unmethylated cytosines to uracil, but leaves methylated cytosines unchanged C) It increases the length of DNA strands D) It removes histones from the nucleosomes

What is a key advantage of using reduced representation bisulfite sequencing (RRBS) in EWAS studies? A) It sequences the entire genome with high accuracy B) It provides targeted analysis of CpG-rich regions at a lower cost than whole-genome bisulfite sequencing C) It does not require any chemical treatment of DNA D) It is the only method capable of detecting histone modifications

Which technology is widely used for high-throughput DNA methylation analysis in EWAS? A) RNA-Seq B) Illumina Infinium Methylation Arrays C) CRISPR-Cas9 gene editing D) Western blotting

What is the primary function of the minfi package in R? A) Normalizing and analyzing DNA methylation array data B) Identifying single nucleotide polymorphisms (SNPs) C) Measuring protein levels in cells D) Editing DNA sequences in real-time

Which of the following describes the importance of controlling for cell composition in EWAS studies? A) Different tissues and cell types have distinct DNA methylation profiles, which can confound results B) Cell composition has no effect on DNA methylation levels C) It ensures that only genetic variations are analyzed D) It is used to adjust for mRNA splicing errors

What is the significance of normalizing methylation data in an EWAS? A) It corrects for batch effects and technical variation in data collection B) It ensures that all methylation values are identical across samples C) It eliminates all genetic influences on DNA methylation D) It converts CpG islands into non-coding regions

Which of the following is a common method for quality control in EWAS? A) Checking for gender mismatches using methylation-based sex prediction B) Sequencing only the coding regions of the genome C) Filtering out all CpG sites from analysis D) Discarding all samples with any variation in DNA sequence

Which factor is NOT commonly considered a confounder in EWAS studies? A) Age B) Blood cell composition C) Smoking status D) Hair color

Why is multiple testing correction important in EWAS? A) It ensures that only genes with known functions are analyzed B) It controls for the increased likelihood of false positives due to testing thousands of CpG sites C) It removes all non-significant methylation sites from the genome D) It guarantees that all detected methylation differences are biologically relevan

Which statistical approach is commonly used in EWAS to correct for multiple testing? A) T-test B) Benjamini-Hochberg false discovery rate (FDR) correction C) Chi-square test D) Simple linear regression without adjustment

What is a key difference between whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS)? A) WGBS provides comprehensive genome-wide methylation coverage, while RRBS focuses on CpG-rich regions B) RRBS sequences the entire genome, while WGBS targets specific promoter regions C) WGBS is more cost-effective than RRBS D) RRBS requires additional CRISPR-based analysis for validation

Which of the following techniques does NOT require bisulfite conversion for analyzing DNA methylation? A) Whole-genome bisulfite sequencing (WGBS) B) Methylated DNA immunoprecipitation sequencing (MeDIP-seq) C) Reduced representation bisulfite sequencing (RRBS) D) Pyrosequencing

What is the primary purpose of using methylated DNA immunoprecipitation sequencing (MeDIP-seq) in epigenetics research? A) To directly measure RNA modifications B) To selectively enrich and sequence methylated DNA fragments C) To detect protein-protein interactions D) To measure chromatin accessibility

What is a major limitation of EWAS compared to GWAS? A) EWAS studies require larger sample sizes than GWAS B) Epigenetic modifications can change over time, making it difficult to establish causality C) EWAS can only be conducted in humans D) EWAS does not use statistical correction methods

What is one advantage of targeted bisulfite pyrosequencing in DNA methylation analysis? A) It provides single-base resolution for specific genomic regions of interest B) It allows for whole-genome methylation analysis at low cost C) It can detect all types of histone modifications D) It is used exclusively for RNA sequencing

Which factor is critical when interpreting the results of an EWAS? A) Ensuring that findings are replicated in independent cohorts B) Assuming all observed methylation changes are causal C) Ignoring environmental influences on DNA methylation D) Using only one tissue type for all analyses

Which method is used to estimate cell composition in whole blood samples for EWAS? A) Horvath’s epigenetic clock B) The estimateCellCounts function in the minfi package C) Southern blotting D) Fluorescence microscopy

What is the significance of Horvath’s epigenetic clock in EWAS research? A) It estimates biological age based on DNA methylation patterns B) It predicts genetic mutations based on chromosomal structure C) It determines protein expression levels in different tissues D) It measures histone acetylation changes