VL 4 Epigenetics (I) Flashcards
What is epigenetics?
Epigenetics refers to any stable and heritable change in gene expression that occurs without a change in the DNA sequence. This can involve mechanisms like DNA methylation, histone modification, and RNA-associated silencing.
Practically, epigenetics describes phenomena in which genetically identical cells or organisms express their genomes differently, causing phenotypic differences.
What are some processes involving DNA methylation?
DNA methylation is involved in
* imprinting,
* X-chromosome inactivation,
* differentiation,
* gene expression regulation,
* aging,
* cancer,
* genome stability, and
* silencing transposons and viruses.
What is DNA methylation?
DNA methylation is the covalent addition of a methyl group to the 5th carbon of the cytosine ring, forming 5-methylcytosine.
- nomally a repressive mark, by reducing the bindng of protens to DNA, condensing chromatin structure n serving as bindngsite for methyl-binnding proteins (highest density at the repetitive elements around the centromere)
- Methylation patterns can be inherited, contributing to transgenerational epigenetic inheritance
- Occurs in Plants in CG, CHG, and CHH sequence contexts (where H represents A, C, or T).
- Animals only have CG methylation
What is the role of MET1 in Arabidopsis?
MET1 (METHYLTRANSFERASE 1) is responsible for maintaining CG methylation, silencing transposons, repetitive elements, and some imprinted genes in Arabidopsis.
5’-CG-3’ sites
What are the different types of DNA methyltransferases in Arabidopsis and their targets?
- MET1: Targets CG sites.
- CMT3 (CHROMOMETHYLASE 3): Targets CHG sites.
- DRM1 and DRM2 (DOMAINS REARRANGED METHYLTRANSFERASES): Target CHH sites and require siRNAs for targeting.
Describe the process of RNA-directed DNA methylation (RdDM)
RdDM involves small interfering RNAs (siRNAs) guiding DNA methylases to specific sites, leading to the methylation of these DNA regions.
This process is crucial for maintaining asymmetric methylation sites and transposon silencing.
How is DNA methylation related to transposon silencing?
DNA methylation is necessary to silence transposons.
In mutants with reduced DNA methylation (like met1 or ddm1), transposons become hypomethylated and active, leading to mutagenic activity.
What happens when DNA methylation is lost in Arabidopsis?
Loss of DNA methylation (e.g., in met1 or ddm1 mutants) leads to the activation and mobilization of transposons, resulting in increased mutagenic activity and developmental abnormalities over generations.
What is the significance of genomic imprinting in epigenetics?
Genomic imprinting is an epigenetic phenomenon where certain genes are expressed in a parent-of-origin-specific manner.
This regulation is often controlled by DNA methylation and histone modifications.
How is DNA methylation analyzed?
DNA methylation can be analyzed using methods such as:
* methylation-sensitive restriction enzyme digestion,
* bisulfite mutagenesis and sequencing, and
* whole-genome bisulfite sequencing.
Explain the role of siRNAs in maintaining DNA methylation.
siRNAs direct DNA methylases to specific DNA regions, maintaining methylation at asymmetric sites and ensuring stable silencing of transposons and repetitive elements.
How does the maintenance of DNA methylation differ between CG and non-CG sites?
CG and CHG methylation is maintained through the activity of MET1 and CMT3 during DNA replication. (Weil auf beiden Template strängen (beide von DS) methyliertes C)
Non-CG methylation (CHH) requires additional mechanisms such as histone modifications and siRNA-directed DNA methylation. (Weil nur an ein template strang die methylierung weitergegeben wird)
What are the cellular functions of DNA methylation in plants?
DNA methylation in plants contributes to
* transposon silencing,
* centromere function,
* genome stability,
* gene expression regulation, and
* protection against viruses and other foreign DNA elements.
What is the effect of DNA methylation on chromatin structure?
DNA methylation condenses chromatin structure, making it less accessible for transcription, and helps maintain a repressive state by binding methyl-binding proteins
Describe the relationship between DNA methylation and histone modifications.
DNA methylation and histone modifications often work together to regulate gene expression and maintain genome stability. For example, certain histone modifications can recruit DNA methyltransferases to specific genomic region.
