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Molecular Genetics > Lecture 3 - Chromosome Epigenetics > Flashcards

Lecture 3 - Chromosome Epigenetics Flashcards

1
Q

What is epigenetics?

A

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

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2
Q

Is differentiation a epigenetic process or a genetic one?

A

epigenetics

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3
Q

What is epigenetic memory?

A

Ensures all cell types are locked into their specific cell type

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4
Q

Where is epigenetic information found?

A

The epigenome

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5
Q

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

A

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

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6
Q

What is the basic package of chromatic?

A

Nucleosome

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7
Q

What is chromatin?

A

An assembly of proteins and dna

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8
Q

What happens if chromatin is closed and inaccessible?

A

The gene is silenced

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9
Q

What happens if chromatin is open and accessible?

A

The gene can be translated

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10
Q

What is the Histone code hypothesis?

A

That gene regulation is partly dependent on Histone modifications

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11
Q

What is constitutive heterochromatin?

A

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

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12
Q

What is euchromatin?

A

Accessible chromatin which means dna can be activated

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13
Q

What is facilitate heterochromatin?

A

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

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14
Q

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

A

Cohesins

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15
Q

How does dna form Nucleosome (which makes chromatin)

A

Wrapped around the Histone octamer

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16
Q

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

A

Nanodomians

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17
Q

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

A

Active chromatin

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18
Q

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

A

Heterochromatin

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19
Q

What is the chromatosome?

A

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

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20
Q

What does adding the linker Histone do?

A

Make it less accessible

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21
Q

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

A

The n- and c- terminal

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22
Q

What does post translational modifying histones do to the DNA?

A

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

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23
Q

What modifications can happen to the histones tail?

A

Acetylation, methylation, phosphorylation or ubiquitination

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24
Q

Where do most post translational modifications occur on the tails?

A

N-terminal

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25
Q

What are Histone writers, readers and erasers?

A

Proteins or enzymes which add a modification to a Histone

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26
Q

What is an example of a Histone writer?

A

Histone acetaltransferase which adds an acetyl

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27
Q

What do Histone readers specifically do?

A

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

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28
Q

What do Histone erasers do?

A

Erase any Histone modifications

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29
Q

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

A

No they are recruited by transcription factors at enhancers or promotors

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30
Q

What does Histone acwtylation indicate?

A

Gene activations

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31
Q

What is Histone acetylation regulated by?

A

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

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32
Q

What does Histone acetylation do to lysine?

A

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

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33
Q

What does Histone methylation do?

A

Histone methylation - writer
Histone demethylase - eraser

Activates or deactivates genes drowning in context

34
Q

What does H3K4me3 do?

A

Activation

35
Q

What is H3K9?

A

Heterochromatin marker

36
Q

How does ChIP work?

A

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

37
Q

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

A

Gene activation

38
Q

Where does the kinetochore attach the chromosomes to?

A

Spindle fibres

39
Q

What do centromeres contain?

A

CENP-A histone and pericentromeric heterochromatin

40
Q

What is CENP-A the variant histone of?

A

H3

41
Q

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

A

Yes

42
Q

Is centromere CENP-A conserved across species?

A

Yes

43
Q

What are point centromeres?

A

Centromeres with only CENP-A and nothing else

44
Q

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

A

The gene is turned off

45
Q

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

A

Yes

46
Q

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

A

red

47
Q

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

A

Less heterochromatin can form

48
Q

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

A

Cause lots of heterochromatin formation

49
Q

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

A

It has spread lots

50
Q

What does Suvar bind to to stop heterochromatin spread?

A

H3K9

51
Q

What is the second component of the epigenetic code?

A

DNA methylation

52
Q

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

A

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

53
Q

Where are CpG islands located?

A

Around transcriptional start sites

54
Q

What are regions of high CpG density?

A

Hypermethylated = open chromatin

55
Q

What is H3K4me3 in terms of open or shut chromatin?

A

Open

56
Q

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

A

Highly methylated

57
Q

Is a region of high methylation got heterochromatin?

A

Yes

58
Q

what would reducing DNA methylation do to repressed genes?

A

They would be expressed

59
Q

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

A

DNA methylation

60
Q

What does Methyl-CpG recognise on proteins?

A

Methyl DNA binding domains

61
Q

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

A

Chromatin repressor complexes

62
Q

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

A

Yes and these recruit chromatin activating complexes

63
Q

How does methyl-CpG condense chromatin?

A

Recruits structures such as a HDAC

64
Q

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

A

cfp1

65
Q

What controls gene dosage?

A

DNA methylation

66
Q

Why does x inactivation happen?

A

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

67
Q

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

A

We package one of the X chromosomes into facilitate heterochromatin

68
Q

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

A

The Barr body

69
Q

What is created for dosage compensation?

A

The Barr body

70
Q

Is the inactive X chromosome chosen at random?

A

Yes

71
Q

what maintains the Barr body?

A

All clonal descendent cells.

72
Q

What is necessary and sufficient for x-inactivation?

A

The x-inactivation centre (XIC)

73
Q

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

A

XIST - (inactive x-specific transcripts)

74
Q

What is the product of the XIST gene?

A

Non-coding RNA

75
Q

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

A

The inactive X chromosome in the female interphase nuclei

76
Q

What genes lie within the xic?

A

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

77
Q

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

A

No they are methylated

78
Q

Is XIST active?

A

No

79
Q

When silencing whole chromosomes what type of methylation is needed?

A

You need to methylate it all

80
Q

Is xist methylate in the methylated x-inactivated chromosome?

A

Yes

81
Q

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

A

Yes as this needs to be turned off

82
Q

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

A

DNA methylation and recruits chromatin modifications

Molecular Genetics (20 decks)

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