Lecture 8 Flashcards
epigenome
The collection of epigenetic marks of a cell that regulate gene expression. ( set of on/off for your genes)
Epigenome-wide association studies (EWAS)
Which epigenetic marks in cells are associated with disease, trait or enviromental exposure?
Transcriptome
the collection of all RNA transcripts
where do we measure gene exression
In RNA we measure how much of the DNA is copied
The epigenetic landscape
Theory that explains how all different tissue types have the same genes but have different functionalities.
Cell expression
All cells have the same sequence but will only express the needed part.
Epigenetics
the study of molecular mechanisms that influence the activity of gene expression that are transmitted across cell division (mitosis)
What are the role of epigenetic mechanisms?
1- Tissue-specific gene expression
2-Development-specific gene expression
3- Adjusting to enviroment.
How many CPG sites does human genome contain?
30 million CpG sites
How to detect a gene promoter?
Many gene promoters contain lots of CPG. (Around CG areas in the nucleotide probably there are gene promoters)
Human epigenome research
creating extensive maps of different cell types in the human body at different stages of development.
1- Which genes are transcribed
2- which regions are methylated
3- Which regions are accessible
How does smoking cigarette impact DNA methylation?
1-In cigarette smokers 760 CpG have different methylation that causes cancer, inflammatory diseases and heart disease.
2-CACNA1D, GNG12 and G protein react with nicotinic acetylcholine receptor suggesting that methylation levels at this CpGs might be reactive to nicotine exposure.
3 main reasons of DNA methylation differing between people?
1-Enviromental (chemical exposure, diet)
2-SNPs that influence methylation
3-Stochastic (random)
Human epigenome research steps?
1-Collect DNA samples in large groups of individuals.
2-measure DNA methylation at thousands of sites in the genome.
3-For each genomic location test if DNA methylation differs between smokers and nonsmokers.
what is discordant monozygotic twin design
1-Compares DNA methylation patterns of phenotypically discordant monozygotic twins.
2- Rule out other possible explanations.
ex: Nasa twin study , smoking effects on twins
Transcriptome-wide asoociation
Which transcripts (RNA) are associated with a disease trait or environmental expression?
Issues in epigenetic research
1- Causality: Epigenetic differences between MZ twins can be a cause or a consequence of a disease.
2-Epigenetic marks are tissue-specific: How informative is DNA methylation in accessible tissues (blood issue etc.) for diseases to act in other tissues
(brain tissue)
- Methylation is partially correlated between tissues.
3-Exposures early development may leave epigenetic changes throughout the body.
4-Methylation in the blood may serve as a biomarker for disease, even if methylation in the blood is not the cause of disease.
