11 Epigenetics

Question 1

What makes all 10^13 cells in our body different despite the same DNA?

Answer 1

Gene expression regulation

Question 2

Other than cells being different to each other, why else do we need epigenetics?

Answer 2

To express different genes more or less in a time/situation dependent manner

Question 3

What is RNA polymerase a part of?

Answer 3

A multi-protein initiation complex

Question 4

What do the different parts of the multi-protein initiation complex do?

Answer 4

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

Question 5

What holds together the multi-protein initiation complex?

Answer 5

The mediator complex

Question 6

What do TFs recognise?

Answer 6

A short sequence motif

Question 7

Sequence motifs for TFs are usually at least a little what?

Answer 7

Variable

Question 8

Some TFs are generally always ______. Why?

Answer 8

Always present. Because of gene expression that is necessary in all cells.

Question 9

_____ binding to ______ is critical for gene expression

Answer 9

TFs binding to the promoter is critical for gene expression

Question 10

Each TF has a ________ interaction with the DNA

Answer 10

Each TF has a weak interaction with the DNA

Question 11

Why is the initiation complex so stable?

Answer 11

It is stabilised by many protein-protein interactions between various TFs and co-activators and co-repressors

Question 12

What’s the result of PAX6 gene having 3 alternative promoters which bind to different factors?

Answer 12

It gives 3 different isoforms of the protein in different tissues and at different times.

Question 13

On top of 3 alternative promoters for PAX6 there are also what?

Answer 13

6 enhancers that further control tissue specific expression by binding to tissue specific transcription factors and co-factors.

Question 14

What makes up a nucleosome?

Answer 14

2 of each type of 4 histone proteins, and a 5th type sticking out from the nucleosome, with DNA wrapped around it

Question 15

What protrudes out from histone proteins?

Answer 15

N terminal tails

Question 16

Only a small proportion of DNA is what?

Answer 16

Accessible to the initiation complex and not in nucleosomes

Question 17

The DNA that is accessible to the initiation complex and not in nucleosomes does what?

Answer 17

Differs between cell types

Question 18

How do you find the accessible DNA and not accessible DNA of a cell?

Answer 18

Digest the DNA carefully

Question 19

What are the 4 big things that decide accessibility of DNA?

Answer 19

Transcription factors.
DNA methylation.
Covalent modification of histone tails.
Chromatin remodelling complexes.

Question 20

What transcription factors are able to help change the accessibility of DNA and how?

Answer 20

Pioneer transcription factors are able to bind to inaccessible DNA and make it accessible

Question 21

What is cytosine methylation?

Answer 21

At CpG motifs, Cytosines are methylated by DNA methylation transferases to 5mC.

Question 22

Why do DNA methyl transferases methylate both Cs at CpG motifs?

Answer 22

So that methylation is heritable through mitosis. Helps keep daughter cell the same.

Question 23

What can studying CpG patterns tell you?

Answer 23

It helps define tissue specific gene expression patterns.

Question 24

How does the methylated cytosine turn off expression?

Answer 24

The methyl groups in the major groove of the DNA helix bind regulatory methyl DNA binding proteins like MECP2.

Question 25

How can lysines in histone tails be modified?

Answer 25

Acetylated, or mono-, di-, or tri-methylated

Question 26

How can amino acids in histone tails be modified?

Answer 26

Acetylated, methylated, phosphorylated, and ubiquitinylated

Question 27

Are histone modifications simple?

Answer 27

No, it's very messy and complex, interpretation is difficult.

Question 28

What are some of the most consistent histone modification trends?

Answer 28

At active promoters, >90% have H3Kme2, H3K27ac, and H3K9ac. Other positions are a lot less consistent.

Question 29

What does CTCF bind to in the DNA?

Answer 29

Insulator sequences

Question 30

What are insulator sequences?

Answer 30

Sequences that prevent enhancers from working across their boundaries by having CTCF bound. Cohesin also normally there at the boundary creating a loop

Question 31

What drives multiprotein Chromatin remodelling complexes?

Answer 31

ATP

Question 32

What do chromatin remodelling complexes do?

Answer 32

Take apart nucleosomes, move nucleosomes about, swap slightly different histones in and out. Help create accessible DNA

Question 33

What are some example chromatin remodelling complexes

Answer 33

NURD complex and BAF complex

Question 34

What helps chromatin remodelling complexes to bind to DNA?

Answer 34

Bromodomains to bind methylated histone tails, and chromodomains to bind to acetylated histone tails, and PHDs whatever they are

Question 35

Some DNA sequences are very distant in the sequence, but physically are close. How?

Answer 35

TADs! 500kd -1Mb loops in the DNA/ Well conserved across cell types and species.

Question 36

Enhancers only enhance genes in the same _______

Answer 36

TAD!

Question 37

What technique lets us study TADs?

Answer 37

Chromatin Conformation Capture - 3C, 4C, 5C, Hi-C

Question 38

What are 3 bigs ways epigenetics is used in normal human development?

Answer 38

Pluripotency and differentiation of cells. X chromosome inactivation. Imprinting

Question 39

What word describes a cell has the most potency?

Answer 39

totipotent

Question 40

Totipotent > ---- > ------ >-----

Answer 40

Totipotent > pluripotent > multipotent stem cells > terminally differentiated cells

Question 41

What does the epigenetic landscape describe?

Answer 41

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.

Question 42

How do we know that the cell 'counts' the number of X chromsomes in teh cell?

Answer 42

Because all but one is turned off when there are more than 2 X's present, and a single X is not turned off.

Question 43

What is the name for an inactivated X chromosome?

Answer 43

A barr body

Question 44

A cell with the paternal X inactivated will only create cells _____

Answer 44

that are a clonal population, so also have the paternal X inactivated

Question 45

How does Ectodermal Dysplasia get caused?

Answer 45

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.

Question 46

Roughly how many genes are imprinted?

Answer 46

100

Question 47

What does imprinting mean?

Answer 47

Cells that remember if they are paternally or maternally derived and have different expression levels based on that

Question 48

Is imprinting reversible?

Answer 48

Yes

Question 49

When is imprinting maintained and when is is erased?

Answer 49

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

Question 50

What cluster has a group of imprinted genes?

Answer 50

15q11-13

Question 51

At 15q11-13 what genes are only expressed from the paternal copy?

Answer 51

MAGEL2 and SNRPN

Question 52

At 15q11-13 what gene is only expressed from the maternal copy?

Answer 52

UBE3A

Question 53

What does a deletion from the paternal 15q11-13 lead to?

Answer 53

Prader Willi syndrome

Question 54

What are symptoms of Prader Willi syndrome?

Answer 54

Hypotonia, mild ID, uncontrollable eating leading to obesity

Question 55

What does the deletion from the maternal 15q11-13 lead to?

Answer 55

Angelman syndrome

Question 56

What are symptoms of angelman syndrome?

Answer 56

Stiff jerky movements, severe ID, little speech, excessive laughing

Question 57

Epigenetics can cause disease by having failures in what 4 types of things?

Answer 57

Writers that impose epigentic marks. Readers that react to epigenetic marks. Editors that remove epigenetic marks. Chromatin remodellers

Question 58

What are some diseases caused by variants in writers that impose epigenetic marks?

Answer 58

DNA methyl transferases -> ICF syndrome. Histone methyltransferases -> Sotos syndrome Histone acetyl transferases -> Rubinstein-Taybi syndrome Histone Kinases -> Coffin-Lowry syndrome

Question 59

What is a disease caused by variants in readers that react to epigenetic marks?

Answer 59

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.

Question 60

What are some editors that remove epigenetic marks and some of the diseases associated with them?

Answer 60

TET enzymes. Histone demethyltransferases - Kabuki 2 syndrome. Histone deacetylases - Cornelia de lange 5. Histone dephosphatases.

Question 61

What disease can be caused by variants in chromatin remodellers?

Answer 61

CHARGE syndrome