Lecture 3 - Chromosome Epigenetics

Question 1

What is epigenetics?

Answer 1

The difference of trains whether that be due to external or internal ques

Question 2

Is differentiation a epigenetic process or a genetic one?

Answer 2

epigenetics

Question 3

What is epigenetic memory?

Answer 3

Ensures all cell types are locked into their specific cell type

Question 4

Where is epigenetic information found?

Answer 4

The epigenome

Question 5

What are DNA modifications specific to and what does this allow them to do?

Answer 5

Each cell type and they do this by turning on some genes and not the other

Question 6

What is the basic package of chromatic?

Answer 6

Nucleosome

Question 7

What is chromatin?

Answer 7

An assembly of proteins and dna

Question 8

What happens if chromatin is closed and inaccessible?

Answer 8

The gene is silenced

Question 9

What happens if chromatin is open and accessible?

Answer 9

The gene can be translated

Question 10

What is the Histone code hypothesis?

Answer 10

That gene regulation is partly dependent on Histone modifications

Question 11

What is constitutive heterochromatin?

Answer 11

Closed chromatin which is gene poor and gene indicative.
It replicates in late s phase

Question 12

What is euchromatin?

Answer 12

Accessible chromatin which means dna can be activated

Question 13

What is facilitate heterochromatin?

Answer 13

This is where genes are silenced not inactivated this means that in different cell types and epigenomes these can be turned on

Question 14

What protein holds topical associating domains and nano domains which are both found in chromatin together?

Answer 14

Cohesins

Question 15

How does dna form Nucleosome (which makes chromatin)

Answer 15

Wrapped around the Histone octamer

Question 16

After Nucleosome are made they come together in clutches or what?

Answer 16

Nanodomians

Question 17

Tads come together to make compartments a and b. What does compatment a contain?

Answer 17

Active chromatin

Question 18

Tads come together to make compartments A and B what does compartment B contain?

Answer 18

Heterochromatin

Question 19

What is the chromatosome?

Answer 19

A linker Histone has bound to the Nucleosome centre and wraps the DNA more

Question 20

What does adding the linker Histone do?

Answer 20

Make it less accessible

Question 21

What part of the core histones are targets for post translational modifications?

Answer 21

The n- and c- terminal

Question 22

What does post translational modifying histones do to the DNA?

Answer 22

Can drive the opening and closing of chromatin and therefore turning genes on or off

Question 23

What modifications can happen to the histones tail?

Answer 23

Acetylation, methylation, phosphorylation or ubiquitination

Question 24

Where do most post translational modifications occur on the tails?

Answer 24

N-terminal

Question 25

What are Histone writers, readers and erasers?

Answer 25

Proteins or enzymes which add a modification to a Histone

Question 26

What is an example of a Histone writer?

Answer 26

Histone acetaltransferase which adds an acetyl

Question 27

What do Histone readers specifically do?

Answer 27

Read the Histone code and so bind to modified parts of it

Question 28

What do Histone erasers do?

Answer 28

Erase any Histone modifications

Question 29

Do Histone writers, erasers and readers bind to Dna directly?

Answer 29

No they are recruited by transcription factors at enhancers or promotors

Question 30

What does Histone acwtylation indicate?

Answer 30

Gene activations

Question 31

What is Histone acetylation regulated by?

Answer 31

Histone acetyltransferase (HATS - writers) and Histone deacetylases (HDACs - erasers)

Question 32

What does Histone acetylation do to lysine?

Answer 32

Neutralises it’s positive charge leaving a weak interaction with the phosphate backbone and therefore looser chromatin triggering transcription

Question 33

What does Histone methylation do?

Answer 33

Histone methylation - writer Histone demethylase - eraser Activates or deactivates genes drowning in context

Question 34

What does H3K4me3 do?

Answer 34

Activation

Question 35

What is H3K9?

Answer 35

Heterochromatin marker

Question 36

How does ChIP work?

Answer 36

Fraction chromatin by signification into Nucleosome and put a specific antibody against it. This attaches to bead and is pulled down by centrifugation Purify DNA and identify DNA based in Histone modification

Question 37

What does lysine acetylation of H3 and H4 tails correlate with?

Answer 37

Gene activation

Question 38

Where does the kinetochore attach the chromosomes to?

Answer 38

Spindle fibres

Question 39

What do centromeres contain?

Answer 39

CENP-A histone and pericentromeric heterochromatin

Question 40

What is CENP-A the variant histone of?

Answer 40

H3

Question 41

Does CENP-A and H3 have different N-terminals?

Answer 41

Yes

Question 42

Is centromere CENP-A conserved across species?

Answer 42

Yes

Question 43

What are point centromeres?

Answer 43

Centromeres with only CENP-A and nothing else

Question 44

Position effect Variegation in drosophila - what happens if chromosomal inversion causes the gene to be close to the heterochromatin?

Answer 44

The gene is turned off

Question 45

Can epigenetic silencing due to position of the gene near heterochromatin be inherited?

Answer 45

Yes

Question 46

what colour of eyes do drosophila have if they have the W+ gene?

Answer 46

red

Question 47

What does the one Su(var) gene do to heterochromatin?

Answer 47

Less heterochromatin can form

Question 48

What does three copies of the Su(var) gene do to heterochromatin?

Answer 48

Cause lots of heterochromatin formation

Question 49

If drosophila have white eyes what has happened to the heterochromatin?

Answer 49

It has spread lots

Question 50

What does Suvar bind to to stop heterochromatin spread?

Answer 50

H3K9

Question 51

What is the second component of the epigenetic code?

Answer 51

DNA methylation

Question 52

How does DNA methylation work? And what is it known as?

Answer 52

Methyl group is added to a cytosine before a guanine in a 5’ to 3’ section - this is known as CpG dinucleotides

Question 53

Where are CpG islands located?

Answer 53

Around transcriptional start sites

Question 54

What are regions of high CpG density?

Answer 54

Hypermethylated = open chromatin

Question 55

What is H3K4me3 in terms of open or shut chromatin?

Answer 55

Open

Question 56

What type of methylation is in areas of low CpG density?

Answer 56

Highly methylated

Question 57

Is a region of high methylation got heterochromatin?

Answer 57

Yes

Question 58

what would reducing DNA methylation do to repressed genes?

Answer 58

They would be expressed

Question 59

The status of what maintains active or inactive states via chromatin modification?

Answer 59

DNA methylation

Question 60

What does Methyl-CpG recognise on proteins?

Answer 60

Methyl DNA binding domains

Question 61

what does the methyl DNA Binding domain recruit after methyl-CpG is bound?

Answer 61

Chromatin repressor complexes

Question 62

Is unmethylated CpG recognised by different proteins? What do they recruit?

Answer 62

Yes and these recruit chromatin activating complexes

Question 63

How does methyl-CpG condense chromatin?

Answer 63

Recruits structures such as a HDAC

Question 64

What specifically is a reader which binds to the unmethylated CpG island to act as transcriptional factors to recruit chromatin activating complexes?

Answer 64

cfp1

Question 65

What controls gene dosage?

Answer 65

DNA methylation

Question 66

Why does x inactivation happen?

Answer 66

The X chromosome is so large compared to the y so when passed on it would cause genetic inequality

Question 67

In early development we inactive an X chromosome. How do we do this?

Answer 67

We package one of the X chromosomes into facilitate heterochromatin

Question 68

what is the name of the bundled X chromosome and the facultative heterochromatin?

Answer 68

The Barr body

Question 69

What is created for dosage compensation?

Answer 69

The Barr body

Question 70

Is the inactive X chromosome chosen at random?

Answer 70

Yes

Question 71

what maintains the Barr body?

Answer 71

All clonal descendent cells.

Question 72

What is necessary and sufficient for x-inactivation?

Answer 72

The x-inactivation centre (XIC)

Question 73

What gene is transcribed from the inactive x but not the active x gene?

Answer 73

XIST - (inactive x-specific transcripts)

Question 74

What is the product of the XIST gene?

Answer 74

Non-coding RNA

Question 75

Where does the non-coding XIST gene remain associated with?

Answer 75

The inactive X chromosome in the female interphase nuclei

Question 76

What genes lie within the xic?

Answer 76

Brx - Brian x-linked Tsx -testis x-linked Cdx4 - caudal-4

Question 77

CpG islands are usually unmethylated. Is this true in CpG islands in the x-chromosomes?

Answer 77

No they are methylated

Question 78

Is XIST active?

Answer 78

No

Question 79

When silencing whole chromosomes what type of methylation is needed?

Answer 79

You need to methylate it all

Question 80

Is xist methylate in the methylated x-inactivated chromosome?

Answer 80

Yes

Question 81

Is the xist gene methylated in the unmethylated active CpG on the active x-chromosomes?

Answer 81

Yes as this needs to be turned off

Question 82

Xist is spread over the x-inactivated chromosomes which causes what?

Answer 82

DNA methylation and recruits chromatin modifications