1. What is DNA Methylation? Describe its process and significance.
Answer:
Definition: DNA methylation is an epigenetic modification involving the addition of a methyl group to the cytosine base in DNA, typically at CpG dinucleotides.
Process:
- Enzyme Action: DNA methyltransferases (DNMTs) transfer a methyl group from S-adenosylmethionine (SAM) to the 5th carbon of cytosine.
- CpG Islands: Methylation commonly occurs in CpG islands located in gene promoter regions.
Significance:
- Regulates gene expression by silencing genes when promoters are methylated.
- Essential for processes like X-chromosome inactivation, genomic imprinting, and development.
- Aberrant methylation patterns are linked to diseases like cancer and neurological disorders.
2. Explain the role of DNA Methyltransferases (DNMTs) in DNA Methylation.
Answer:
Types of DNMTs:
- DNMT1: Maintains methylation during DNA replication by copying methylation patterns from the parent strand to the daughter strand.
- DNMT3A and DNMT3B: Responsible for de novo methylation, establishing methylation patterns during embryogenesis.
Role in Gene Silencing:
- DNMTs add methyl groups to CpG islands in gene promoters, recruiting methyl-binding proteins and histone-modifying enzymes, leading to chromatin condensation and transcriptional repression.
3. Discuss how DNA methylation contributes to gene silencing.
Answer:
- Mechanism:
- Methylation at CpG islands blocks transcription factor binding.
- Methyl-binding proteins (e.g., MECP2) recruit histone deacetylases (HDACs), leading to chromatin condensation.
- Outcome:
- Compact chromatin prevents RNA polymerase from accessing the DNA, effectively silencing gene transcription.
Biological Importance:
- Regulates developmental gene expression, prevents expression of transposable elements, and silences unwanted gene activity.
4. Describe the role of DNA Methylation in X-Chromosome Inactivation.
Answer:
Process:
- In female mammals, one X chromosome is inactivated to achieve dosage compensation.
- DNA methylation marks regions of the inactive X chromosome, ensuring long-term silencing.
Mechanism:
- CpG island methylation stabilizes the inactivation initiated by Xist RNA.
- Histone modifications like deacetylation and methylation support DNA methylation.
5. How does DNA Methylation affect tumor suppressor genes in cancer?
Answer:
- Hypermethylation:
- Promoter CpG islands of tumor suppressor genes are hypermethylated, leading to their silencing.
- Loss of tumor-suppressing activity promotes cancer progression.
- Hypomethylation:
- Global hypomethylation activates oncogenes and transposable elements, causing genomic instability.
Examples:
- Hypermethylation of genes like p16 and BRCA1 in various cancers.
6. What are CpG Islands, and why are they important in DNA methylation?
Answer:
Definition: CpG islands are regions with a high density of CpG dinucleotides, often located near gene promoters.
Importance:
- Methylation of CpG islands controls gene expression.
- Unmethylated CpG islands are associated with active transcription, while methylated ones are linked to gene silencing.
7. Explain the role of TET enzymes in DNA demethylation.
Answer:
Function:
- TET enzymes (TET1, TET2, TET3) oxidize methylated cytosines into hydroxymethylcytosines.
Pathway:
- Hydroxymethylcytosine is further processed into formylcytosine and carboxylcytosine.
- These intermediates are removed during base excision repair, leading to active or passive DNA demethylation.
Biological Role:
- Important for reprogramming DNA methylation during development and maintaining genomic flexibility.
8. How does DNA methylation influence genomic imprinting?
Answer:
Definition: Genomic imprinting is the parent-specific expression of alleles.
Mechanism:
- Differential DNA methylation at imprinting control regions (ICRs) silences one allele, ensuring monoallelic expression.
Examples: - H19 and IGF2 are regulated by methylation at their ICR.
9. Compare and contrast DNA methylation and histone modification.
Answer:
DNA Methylation:
- Involves the addition of methyl groups to cytosines.
- Leads to transcriptional repression.
Histone Modification:
- Includes acetylation, methylation, phosphorylation, etc.
- Modifications can activate or repress transcription.
Integration:
- DNA methylation and histone modifications work together to regulate chromatin structure and gene expression.
10. What is the role of DNA methylation in embryogenesis?
Answer:
- Establishes tissue-specific gene expression patterns.
- Silences pluripotency genes as cells differentiate.
- Prevents expression of transposable elements, ensuring genomic stability.
11. How does aberrant DNA methylation contribute to diseases?
Answer:
- Cancer: Hypermethylation silences tumor suppressor genes; hypomethylation activates oncogenes.
- Neurological Disorders: Altered methylation in genes like MECP2 leads to Rett Syndrome.
- Autoimmune Diseases: Hypomethylation of immune-related genes can cause overactivation.
12. Explain the process of active and passive DNA demethylation.
Answer:
- Active Demethylation: Involves enzymatic removal of methyl groups via TET enzymes.
- Passive Demethylation: Occurs during DNA replication when methylation is not maintained.
13. What is the role of DNA methylation in transposable element silencing?
Answer:
- Methylation at transposon regions prevents their activation.
- Ensures genomic stability by reducing recombination events.
14. How does environmental exposure affect DNA methylation?
Answer:
- Factors like diet, stress, and toxins influence DNA methylation patterns.
- Example: Folic acid deficiency affects SAM levels, altering methylation.
15. Discuss the methods used to study DNA methylation.
Answer:
- Bisulfite Sequencing: Differentiates between methylated and unmethylated cytosines.
- Methylation-Sensitive Restriction Enzymes: Analyze methylation at specific sites.
- MeDIP-Seq: Identifies methylated regions across the genome.
16. Describe the epigenetic relationship between DNA methylation and histones.
Answer:
- Methylated DNA recruits histone deacetylases, leading to chromatin compaction.
- Histone methylation reinforces DNA methylation patterns.
17. What is global DNA hypomethylation, and how does it affect cells?
Answer:
- Definition: A reduction in methylation across the genome.
- Effects:
- Activates transposable elements.
- Increases chromosomal instability, contributing to cancer.
18. How does DNA methylation affect transcription factors?
Answer:
- Methylated CpG sites block transcription factor binding, repressing gene expression.
19. Explain the significance of DNA methylation in aging.
Answer:
- Methylation changes lead to silencing of key genes and genomic instability, contributing to aging phenotypes.
20. How does DNA methylation regulate stress responses in plants?
Answer:
- Methylation patterns are altered under stress, modulating gene expression to enhance stress tolerance.
