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Questions and Answers
What is epigenetics primarily concerned with?
What is epigenetics primarily concerned with?
Epigenetic changes cannot occur in response to physiological stimuli.
Epigenetic changes cannot occur in response to physiological stimuli.
False
Name one factor influencing epigenetic changes in obesity.
Name one factor influencing epigenetic changes in obesity.
Maternal nutrition, diet and lifestyle, physical activity, chronic stress
Epigenetics can influence how genes involved in ________ and ________ are expressed.
Epigenetics can influence how genes involved in ________ and ________ are expressed.
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Match the following factors with their effects on epigenetics in obesity:
Match the following factors with their effects on epigenetics in obesity:
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Which of the following is NOT a mechanism through which epigenetics affects gene expression?
Which of the following is NOT a mechanism through which epigenetics affects gene expression?
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Stress has no effect on gene expression related to metabolism.
Stress has no effect on gene expression related to metabolism.
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The exposure to a high-glucose environment in utero can alter the baby’s epigenome, affecting ________ sensitivity.
The exposure to a high-glucose environment in utero can alter the baby’s epigenome, affecting ________ sensitivity.
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What is the primary function of DNA methylation?
What is the primary function of DNA methylation?
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All CpG islands are methylated in the genome.
All CpG islands are methylated in the genome.
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What process restores gene expression by removing methyl groups from DNA?
What process restores gene expression by removing methyl groups from DNA?
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The majority of gene promoters, roughly 70%, reside within __________.
The majority of gene promoters, roughly 70%, reside within __________.
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Match the following techniques with their respective applications:
Match the following techniques with their respective applications:
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Which statement is true regarding genomic imprinting?
Which statement is true regarding genomic imprinting?
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High-throughput technologies are used to study DNA methylation.
High-throughput technologies are used to study DNA methylation.
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What characteristic do transcription factor binding sites typically have in relation to CpG islands?
What characteristic do transcription factor binding sites typically have in relation to CpG islands?
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Study Notes
Genomics 2024-2025, T7
- Topic: Genomics overview
- Date: 11-11-2024
- Lecturer: Ana Karina Mendes
Epigenetics and Gene Regulation
- Epigenetics describes heritable changes in gene expression not encoded in DNA.
- Epigenetic modifications occur in response to physiological stimuli, disease states, and specific cell types.
- Epigenetic modifications alter gene activity by modifying chromatin structure (closed/on, open/off).
- Epigenetic mechanisms affect where and whether genes are activated or deactivated
Epigenetic Mechanisms of Genome Regulation
- DNA Methylation: A reversible process that can silence genes (adding methyl groups) or activate them (removing methyl groups).
- Histone Modifications: Adding or removing chemical tags to histones changes chromatin structure and gene expression. (Acetylation, Methylation, Phosphorylation, Ubiquitination)
- Non-coding RNAs (miRNAs): Small RNA molecules that regulate gene expression by targeting mRNA for degradation or translational repression.
Epigenetics and Obesity
- Epigenetic modifications (DNA methylation, histone modifications and non-coding RNAs) affect genes related to metabolism, appetite, fat storage and energy balance.
- These changes can potentially contribute to obesity development.
- Environmental factors (diet, physical activity, chemicals, and stress) influence epigenetic changes and the development of obesity.
- Prenatal and early-life factors such as maternal nutrition and gestational diabetes can also affect epigenetic changes and development of obesity.
DNA Methylation
- Reversible process: Methylation can be added (de novo) by Dnmt3 enzymes (DNA methyltransferases) or maintained during replication (Dnmt1) and removed (demethylation) by other enzymes (TET enzymes, among them).
- Replication-coupled passive loss: DNA methylation patterns are partially erased during DNA replication, resulting in reduced methylation levels.
- Active demethylation—Removal of methyl group during replication.
CpG Islands
- Stretches of DNA with a high density of CpG sites (cytosine-guanine dinucleotides).
- Often not methylated.
- Location of many gene promoters (70% of gene promoters).
- Enhance accessibility of DNA and promote transcription factor binding.
Normal and Cancer Genomes
- Normal and cancer genomes differ in DNA methylation profiles.
- Cancer cells often have aberrant gene silencing (turning off tumor suppressor genes) and/or aberrant gene reactivation/activation (turning on oncogenes).
- Hypo-methylation is reduced methylation compared to normal cells.
- Hyper-methylation is increased methylation compared to normal cells.
Genomic Imprinting and X-chromosome Inactivation
- Genomic imprinting is when expression of a gene depends on its parental origin.
- X-chromosome inactivation is when one X chromosome is randomly inactivated to avoid gene dosage issues.
High-throughput Technologies to Study DNA Methylation
- Techniques for genome-wide DNA methylation analysis (includes microarray, next-generation sequencing techniques and others).
- Various methods like antibody or bisulfite methods.
Bisulfite Conversion
- Converts unmethylated cytosines to uracil without altering 5-methylcytosine.
- Used in various whole-genome DNA methylation assays to study methylation patterns.
Whole Genome Bisulfite Sequencing (WGBS)
- High-throughput sequencing technology that identifies DNA methylation across entire genome.
- Provides detailed information about methylation patterns.
EpiTYPER MassARRAY
- Method uses mass spectrometry for detecting, characterizing, and quantifying DNA methylation patterns.
RNA Sequencing
- Method to determine whether and how much of a particular RNA molecule (transcript) is present.
- Can identify differences in RNA levels in different conditions.
- Helps to understand gene activity levels and expression patterns.
Combined Analysis
- Combines analyses of DNA methylation and RNA expression to identify gene methylation differences correlated with gene expression.
- Aims to find new predictive markers for diseases.
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Description
Test your knowledge on the intricate relationship between epigenetics and obesity in this quiz. Explore how environmental factors influence gene expression and the role of epigenetic mechanisms such as DNA methylation. Perfect for students and enthusiasts looking to deepen their understanding of this fascinating field.
