11 Epigenetics Flashcards
What makes all 10^13 cells in our body different despite the same DNA?
Gene expression regulation
Other than cells being different to each other, why else do we need epigenetics?
To express different genes more or less in a time/situation dependent manner
What is RNA polymerase a part of?
A multi-protein initiation complex
What do the different parts of the multi-protein initiation complex do?
RNA polymerase creates RNA, but some proteins detect the promoter, some detect maybe nerve specific promoters, and some detect enhancers up to 1 million base pairs away by having DNA looping thanks to cohesin
What holds together the multi-protein initiation complex?
The mediator complex
What do TFs recognise?
A short sequence motif
Sequence motifs for TFs are usually at least a little what?
Variable
Some TFs are generally always ______. Why?
Always present. Because of gene expression that is necessary in all cells.
_____ binding to ______ is critical for gene expression
TFs binding to the promoter is critical for gene expression
Each TF has a ________ interaction with the DNA
Each TF has a weak interaction with the DNA
Why is the initiation complex so stable?
It is stabilised by many protein-protein interactions between various TFs and co-activators and co-repressors
What’s the result of PAX6 gene having 3 alternative promoters which bind to different factors?
It gives 3 different isoforms of the protein in different tissues and at different times.
On top of 3 alternative promoters for PAX6 there are also what?
6 enhancers that further control tissue specific expression by binding to tissue specific transcription factors and co-factors.
What makes up a nucleosome?
2 of each type of 4 histone proteins, and a 5th type sticking out from the nucleosome, with DNA wrapped around it
What protrudes out from histone proteins?
N terminal tails
Only a small proportion of DNA is what?
Accessible to the initiation complex and not in nucleosomes
The DNA that is accessible to the initiation complex and not in nucleosomes does what?
Differs between cell types
How do you find the accessible DNA and not accessible DNA of a cell?
Digest the DNA carefully
What are the 4 big things that decide accessibility of DNA?
Transcription factors.
DNA methylation.
Covalent modification of histone tails.
Chromatin remodelling complexes.
What transcription factors are able to help change the accessibility of DNA and how?
Pioneer transcription factors are able to bind to inaccessible DNA and make it accessible
What is cytosine methylation?
At CpG motifs, Cytosines are methylated by DNA methylation transferases to 5mC.
Why do DNA methyl transferases methylate both Cs at CpG motifs?
So that methylation is heritable through mitosis. Helps keep daughter cell the same.
What can studying CpG patterns tell you?
It helps define tissue specific gene expression patterns.
How does the methylated cytosine turn off expression?
The methyl groups in the major groove of the DNA helix bind regulatory methyl DNA binding proteins like MECP2.
How can lysines in histone tails be modified?
Acetylated, or mono-, di-, or tri-methylated
How can amino acids in histone tails be modified?
Acetylated, methylated, phosphorylated, and ubiquitinylated
Are histone modifications simple?
No, it’s very messy and complex, interpretation is difficult.
What are some of the most consistent histone modification trends?
At active promoters, >90% have H3Kme2, H3K27ac, and H3K9ac.
Other positions are a lot less consistent.
What does CTCF bind to in the DNA?
Insulator sequences
What are insulator sequences?
Sequences that prevent enhancers from working across their boundaries by having CTCF bound. Cohesin also normally there at the boundary creating a loop
What drives multiprotein Chromatin remodelling complexes?
ATP
What do chromatin remodelling complexes do?
Take apart nucleosomes, move nucleosomes about, swap slightly different histones in and out. Help create accessible DNA
What are some example chromatin remodelling complexes
NURD complex and BAF complex
What helps chromatin remodelling complexes to bind to DNA?
Bromodomains to bind methylated histone tails, and chromodomains to bind to acetylated histone tails, and PHDs whatever they are
Some DNA sequences are very distant in the sequence, but physically are close. How?
TADs! 500kd -1Mb loops in the DNA/ Well conserved across cell types and species.
Enhancers only enhance genes in the same _______
TAD!
What technique lets us study TADs?
Chromatin Conformation Capture - 3C, 4C, 5C, Hi-C
What are 3 bigs ways epigenetics is used in normal human development?
Pluripotency and differentiation of cells. X chromosome inactivation.
Imprinting
What word describes a cell has the most potency?
totipotent
Totipotent > —- > —— >—–
Totipotent > pluripotent > multipotent stem cells > terminally differentiated cells
What does the epigenetic landscape describe?
That the potency of each cell gradually becomes restricted and its hard to revert. Hard to push up the hill or push into another valley.
How do we know that the cell ‘counts’ the number of X chromsomes in teh cell?
Because all but one is turned off when there are more than 2 X’s present, and a single X is not turned off.
What is the name for an inactivated X chromosome?
A barr body
A cell with the paternal X inactivated will only create cells _____
that are a clonal population, so also have the paternal X inactivated
How does Ectodermal Dysplasia get caused?
A variant in a gene leads to an inability to produce sweat glands. It’s on the X so this will be entirely in males, which is lethal. Or in patches in women based on which X is inactivated.
Roughly how many genes are imprinted?
100
What does imprinting mean?
Cells that remember if they are paternally or maternally derived and have different expression levels based on that
Is imprinting reversible?
Yes
When is imprinting maintained and when is is erased?
It’s maintained from a gamete to your somatic cells. But it’s wiped in germ cells. As the zygote develops, the egg and sperm obviously have different epigenetic patterns. When these are wiped, the imprinted genes escape erasure
What cluster has a group of imprinted genes?
15q11-13
At 15q11-13 what genes are only expressed from the paternal copy?
MAGEL2 and SNRPN
At 15q11-13 what gene is only expressed from the maternal copy?
UBE3A
What does a deletion from the paternal 15q11-13 lead to?
Prader Willi syndrome
What are symptoms of Prader Willi syndrome?
Hypotonia, mild ID, uncontrollable eating leading to obesity
What does the deletion from the maternal 15q11-13 lead to?
Angelman syndrome
What are symptoms of angelman syndrome?
Stiff jerky movements, severe ID, little speech, excessive laughing
Epigenetics can cause disease by having failures in what 4 types of things?
Writers that impose epigentic marks.
Readers that react to epigenetic marks.
Editors that remove epigenetic marks.
Chromatin remodellers
What are some diseases caused by variants in writers that impose epigenetic marks?
DNA methyl transferases -> ICF syndrome.
Histone methyltransferases -> Sotos syndrome
Histone acetyl transferases -> Rubinstein-Taybi syndrome
Histone Kinases -> Coffin-Lowry syndrome
What is a disease caused by variants in readers that react to epigenetic marks?
Many proteins do this. Rett syndrome is caused by variants in MECP2 that recognises methylated DNA. it affects girls, they start to lose abilities such as speech and movement.
What are some editors that remove epigenetic marks and some of the diseases associated with them?
TET enzymes.
Histone demethyltransferases - Kabuki 2 syndrome.
Histone deacetylases - Cornelia de lange 5.
Histone dephosphatases.
What disease can be caused by variants in chromatin remodellers?
CHARGE syndrome
