1
Define the term "epigenetics."
: Epigenetics is the study of changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence.
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2
What is an epigenetic trait? Is it heritable?
: An epigenetic trait is a stable, heritable phenotype resulting from changes in gene expression without altering the DNA sequence. It can be heritable across cell divisions and sometimes generations.
3
What is the difference between genome and epigenome?
: The genome refers to the complete set of DNA, including all genes, while the epigenome consists of chemical modifications to DNA and histones that regulate gene expression.
4
What are the three ways epigenetic alteration of the genome can take place?
:
1. DNA methylation
2. Histone modification
3. RNA-mediated mechanisms
4. acetylation
5
What are readers, writers, and erasers?
• Readers: Proteins that recognize and interpret epigenetic marks (e.g., bromodomains).
• Writers: Enzymes that add epigenetic marks (e.g., DNA methyltransferases).
• Erasers: Enzymes that remove epigenetic marks (e.g., histone deacetylases).
6
Which base in the DNA is methylated? Name the enzyme that methylates the DNA.
: Cytosine in CpG dinucleotides is methylated. The enzyme is DNA methyltransferase (DNMT).
De novo (complete new methyl)
Maintenance methylases — Methyl on the complementary Strand
7
What are CpG islands? Where are they located in a gene? What is the net effect of DNA methylation on gene expression?
: CpG islands are regions of DNA with a high frequency of CpG sites, typically located near gene promoters. DNA methylation of CpG islands generally represses gene expression.
CG sequencen only are stable if evolutionary really needed
8
What chemical modifications are found in histones? Which region of histone is modified? What are HAT and HDAC? What do they do? What effects on transcription are seen as a result of HAT activity and HDAC activity?
• Chemical Modifications: Acetylation, methylation, phosphorylation, ubiquitination, sumoylation
• Region Modified: Histone tails.
• HAT (Histone Acetyltransferase): Adds acetyl groups, increasing transcription.
• HDAC (Histone Deacetylase): Removes acetyl groups, repressing transcription.
9
What are siRNAs? How do they affect gene expression?
: Small interfering RNAs (siRNAs) are short RNA molecules that guide the degradation of specific mRNA, leading to gene silencing.
Ähnlich microRNA (they are from own genome )
10
Explain genomic imprinting. How does imprinting affect gene expression? When does it take place? Is imprinting permanent?
Genomic imprinting is the selective expression of genes based on parental origin. It affects gene expression by silencing one allele. Imprinting occurs during gamete formation and is not always permanent; it can reset in the next generation.
DNA methylation
11
Explain the regulation of Igf2 and H19 in relation to Beckwith-Wiedemann syndrome (BWS).
In the fetus, Igf2 on the maternal chromosome is silenced due to methylation, while H19 on the paternal chromosome is silenced. Imprinting control regions and methylation patterns regulate this expression. Disruptions can lead to BWS.
—> to much IgF2 the embryos will be too large
How does This regulation happen: insulator element And igf2 And H19 are on same chromosome in same Region the insulator element (CTCF) is in the middle of them in parental insulator reg element is methylated thats why IgF2 is transcribed And in maternal Not methylated only H19 is transcribed
12
What is Tet dioxygenase?
Tet dioxygenase enzymes catalyze the oxidation of 5-methylcytosine in DNA, contributing to DNA demethylation. —> to hydroxymethylcytosin
13
How does epigenetics alter Mendelian Genetics?
Epigenetics introduces heritable changes in gene expression that do not involve changes to the DNA sequence, adding complexity to Mendelian inheritance patterns.
14
What are examples of epigenetic changes caused by RNA molecules?
• siRNAs mediate mRNA degradation.
• piRNAs silence transposons.
• Long non-coding RNAs (lncRNAs) modify chromatin structure.
X inactivation (when embryo in few hundret cell state) calico cats
Barr body, condensed chromatin
Silenced X still initiates the XX non coding RNA thats condenses the chromatin
15
What is an essential source of methyl groups for a healthy epigenome during gestation?
Folic acid is a critical source of methyl groups for proper DNA methylation during gestation.
Gefahr für spina bifica sinkt stark
16
How can environmental factors acting on a pregnant female affect the long-term fitness of offspring, even into the next generations?
Environmental factors, such as diet, stress, or toxins, can alter the epigenome of the fetus, leading to heritable changes in gene expression and potential health effects.
Hungersnot kinder 2. weltkrieg
Verhalten Stress mause die ihre Kinder vernachlässigt
17
How is DNA methylation detected?
DNA methylation can be detected using bisulfite sequencing, methylation-specific PCR, or microarrays.
DNA control and the other half we do bisulfite and then sequencing and compare where there is no b-sulfite it was protected by methylation
The emerging trends of ‘‘big data’’ analysis of embryonic development (integrating transcriptomics, proteomics, and epigenetics), the continuous development of new and ever more sensitive (epi)genomic techniques (ATAC sequencing [Buenrostro et al., 2013], ChIP/tagmentation [Schmidl et al., 2015], and single-cell techniques [Buenrostro et al., 2015; Jin et al., 2015]), and the combination of these approaches with powerful and fast genetic modifications (CRISPR/Cas9) should allow increasingly more powerful analyses of chromatin state, regulatory networks, and developmental plasticity in cellular and whole embryo model systems alike.
18
How are histone modifications detected?
Histone modifications are detected using techniques such as chromatin immunoprecipitation (ChIP), mass spectrometry, and western blotting.
Good antibodys against many modifications
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