Landsberger: Lecture XIII Flashcards
Role of Epigenetics in the Regulation of Gene Expression and in our Health
What is epigenetics?
how cells interpret what is written on DNA
it is the information that is deposited on top of a nucleotide in order to regulate gene expression and other processes
Epigenetics is…
information that affects our phenotype (physiological or pathological conditions), which is given both by genetic (our genotype) and epigenome
What mechanisms are involved in epigenetics?
DNA methylation
histone composition
Why are the 2 mechanisms involved in epigenetics important?
they amplify the information contained in our genome and inform the cell about when, where and how a gene has been transcribed
Even though we have the same number of genes as Drosophila, what makes us more complicated?
we use more gene regulation
What allows us to have so many different types of cells?
when different cells express the same protein at different levels
What is Adrian Bird’s theory?
cells evolved from prokaryotes to eukaryotes and started to generate multicellular organisms
this along with an increase in genome size and genome complexity allowed for genes to code for protein and ncRNA
if a cell or organism has to increase its complexity, it is very good in controlling its gene expression
the cells learn how to use the genes in a proper way, and it can only achieve this by telling a gene to be expressed or repressed
What are the mechanisms that have been put into place to better control gene expression?
presence of nucleus (debatable “check-point”): if a gene must be translated, its mRNA will pass through the nuclear pore and go to the cytoplasm to be translated; if it does not need to be translated, it will be degraded in the nucleus (it is not certain if this is how it works)
chromatin: nucleosomes inhibit gene expression because when the DNA is wrapped around the nucleosomes, it cannot be read by TF → this means that in eukaryotic nuclei, DNA is repressed by default because it is assembled into chromatin
Describe transcription in prokaryotic cells:
transcription is a basal transcription: the DNA is almost naked and therefore transcription depends only on RNA Polymerase and on the sequence of the promoter (only sometimes by activators and repressors)
Describe transcription in Eukaryotic cells:
the promoter (TATA box and the core promoter) is assembled into nucleosomes, so TBP is unable to bind the TATA box so there is no transcription going on and DNA is repressed so the cell only activates what it needs
What is unique about our cell?
we have layers of epigenetics: post-translational modification of histones, DNA methylation, RNA-editing…
Why does epigenetics exist?
it allows us to fine tune our gene expression and it introduces the repressing mechanism to not express what is not needed
the different layers of repression have to be removed only when a gene must be expressed
How do our genes become so complex even though we only have 1 genome?
we have many epigenomes that permit our cells to differentiate subsets of the same cell type
How is epigenetics different from genomic code?
it is flexible and dynamic: it is affected by the environment
During the experiment with mice in regards to how epigenetics is affected by the environment, what 2 mothers were used?
High LG: good mothers
Low LG
What were the results of the experiment with the mice and how epigenetics is affected by the environment?
good mother → puppies are less sensitive to stress and have less chance to develop cardiovascular pathologies (they become good mothers)
bad mother → puppies were more sensitive to stress and have a greater chance of developing cardiovascular pathologies (they become bad mothers)
Why does the mother’s behavior affect cardiovascular pathology? How was this analyzed?
gene expression of specific genes that respond to stress (hippocampus) was analyzed and it was found that:
high LG → promoter of these genes was not methylated
low LG → promoter sequence was methylated
*this occurs in the first 6 days of life in these animals, which translates to 3 human years
Recap the mouse experiment that involves environmental factors:
environment in first days of life affects methylation level of genes → phenotypic outcome of kid is affected →capacity to be resilient affects health
Did they translate this to humans?
yes and it makes sense because children who suffer abuse usually suffer from depression and the same methylation pattern was found in humans
Why was the monozygotic twins experiment carried out?
to understand how the environment affects epigenetics
What were the results of the monozygotic twin experiment?
twins are born with similar epigenetic patterns, but the pattern can change over the years, which can lead to sensitivity of diseases → if 2 monozygotic twins are seperated, they have a different epigenetic pattern compared to monozygotic twins that have not been seperated
What was the found in the NASA twin epigenetic experiment?
gene expression is different
epigenetic change based on the 2 situations (one in space the other in America)
when the one that went to space came back to Earth, most of the epigenetics and gene expression quickly came back to the normal level (5 months)
*this suggests the environment affects and our epigenetics are dynamic
What is a fun fact about a discovery from the NASA twins?
telomeres get longer in space but shorten upon returning to Earth
Describe how epigenetics is different in bees:
Queen bee has the same epigenetics as the workers, but she eats a lot of royal jelly which contains donors for methylation
Review the chromatin structure:
What are the 4 core histones?
H2A
H2B
H3
H4
What does the N-shape domain contain?
long alpha helix in the middle and 2 sides
it is a protein-protein interaction domain that stabilizes the interaction between histones
the histone tails are directed toward the outside of the domain
How can you prove that nucleosomes are inhibitory for binding TF?
you can use Electrophoretic Mobility Shift Assay (EMSA) to prove proteins are bound to DNA or a piece of DNA
List a specific example of an experiment where TF could not bind to nucleosomal DNA:
Pu1 TF
Pu1 is the central TF for hematopoietic differentiation
40% of Pu1 is not bound despite have many sites all over the genome
Why? BECAUSE THEY ARE ASSEMBLED INTO NUCLEOSOMES
Pu1 binding is limited and controlled by nucleosomes, and steric hinderance causes nucleosomes to avoid the binding of TF they are supposed to bind to!!
What is PHO4?
TF that has to bind to activate transcription
regulated by phosphate
not phosphorylated = binds
phosphorylated = not bound
In the absence of phosphate, ____
Pho4 is active, protein is bound that recruits chromatin remodeling complexes so that chromatin eventually opens up
