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FLS > Histones and packaging > Flashcards

Histones and packaging Flashcards

1
Q

What is the problem of packaging DNA?

A

One complete turn on double helical DNA has 10 bases and is 3.4nm long.
Human haploid genome is 3x10^9 bases.
In each diploid cell there is 2m of DNA.

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2
Q

How is DNA packaged?

A

It is stored in chromatin.
Nucleosome is the fundamental unit of chromatin, and is made from histones.

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3
Q

What are histones?

A

The most common nuclear proteins, almost half.
1:1 ratio of histones to DNA.

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4
Q

What are NHC?

A

Non-histone chromatin proteins is important for high level packing of DNA.

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5
Q

What are the types of histones?

A

H2A
H2B
H3
H4 - these are core
There is one linker histone - H1

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6
Q

What are the properties of histones?

A

Most abundant in the nucleus.
Small and highly positively charged.
Very highly conserved - significant.

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7
Q

How is DNA stored?

A

DNA is packaged at all times, unless it acts as a linker between nucleosomes.
It protects the genome during the mitotic phase by being highly packaged.

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8
Q

What is the structure of the nucleosome?

A

There are 2 molecules of each of the 4 core histones.
These forms a central octameric core.
Around this are 146 base pairs of DNA that wraps in a left handed superhelix around the nucleosome.
The DNA path is 1.8 superhelical turns.

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9
Q

How much DNA is in the nucleosome?

A

2x each amount of DNA of each core histone = a total of 108Kda of protein.
The histone octamer has 146 base pairs of DNA which wraps around the core.
Each nucleosome must attach to the next, so linker DNA joins it to the next, adding to a total of 200 base pairs.

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10
Q

What is heterodimerization?

A

H3 and H4 have a histone fold, and join together in a histone handhake motif.
There’s 2 molecules of each so 2 handshakes and join together in the centre of the core in a horseshoe shape.

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11
Q

How do H2s join?

A

H2A and H2B have histone folds and heterodimerize, and form a histone handshake.
They bind above and below the tetramer to protect H3 and H4 in the centre.

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12
Q

What is the canonical nucleosome?

A

The normal joining together of H3 and H4 in a tetramer, and H2A and H2B binding above and below.

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13
Q

What happens at the dyad access?

A

H1 binds at the dyad access and holds the DNA in place around the octameric core.

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14
Q

What are N-terminal tails?

A

At the centre of the octamer are the N-terminal tails which can reach out and signal transcription factors or remodellers, or replication machinery.

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15
Q

What happens if you change the canonical histone?

A

The interaction of H3 and H4 is altered, which alters the interaction of H2a and H2b, which alters the path of the DNA around the nucleosome.

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16
Q

What are H2 variants?

A

H2A.X
H2A.Z
macro H2A
H2A.Bbd

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17
Q

What is H2A.Z?

A

H2A.Z:
Alters the interaction stability between H2A and H2B.
Alters the interactionof the H2A-H2B dimer, with its H3-H4 tetramer.
Alters the canonical nucleosome.
Contains nucleosomes often associated with transcriptionally active chromatin.

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18
Q

What is macroH2A?

A

Enriched on the inactive X chromosome - inactivation is random but after will remain inactivated.
Is made different, in order to remain inactivated, by pushing away the normal H2A and filling with macroH2A.

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19
Q

What is H2A.X?

A

When there is a break in DNA, because it is packaged in nucleosomes, a break is signified by the expulsion of normal H2A and is replaced by H2A.X.

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20
Q

What are the histone variants of H3?

A

H3.1
H3.2
H3.3
CenpA
H3.lt

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21
Q

What is interesting about the H3 variants?

A

There is hardly any difference in amino acid sequence.
But the changes are enough to change the structure of the tetramer in the octamer, and has a big impact on the nucleosome.

22
Q

What is CenpA?

A

It is enriched in the centromeres and the telomers.

23
Q

What is H3.3?

A

It is an important variant when trying to change the transcriptional process outside of replication.
Displaces canonical H3 so genes can be turned on.

24
Q

What happens during replication with the nucleosomes?

A

Nucleosomes need moving out the way so DNA polymerase acts smoothly.
Histones hold the DNA by the tails, splits the nucleosome open.
After the polymerase has gone the nucleosome reforms, but a transcription factor can gain access before it reforms and changes transcription.

25
Q

How does H2A.Z affect the nucleosome?

A

The tetramer is looser, so the octameric core is bigger.
This alters the DNA wrapped around the nucleosome - more DNA is wrapped around.
Transcriptionally active genes have H2A.Z so that transciption can happen (DNA is open to machinery).

26
Q

Why is the accessibility of nucleases restricted?

A

DNA does not follow a smooth path around the nucleosome due to it being a double helix.
This also means that only the things on the outside are accessible.

27
Q

What is the 10nm fibre?

A

The lowest level of packaging in the nucleus.
Each nucleosome holding on to the next.
The double helix is present in the linker DNA, but connected to another nucleosome.

28
Q

What is the order of packaging?

A

Nucleosome
10nm fibre
30nm solenoid
300nm solenoid
700nm fibre
Metaphase chromosome

29
Q

What is the 30nm solenoid?

A

10nm fibre coils to form 30nm fibre.
6 nucleosomes need to be in a coil and H1 be in the centre, so the solenoid can form.

30
Q

What is the packing ratio of 10nm fibre?

A

6-7

31
Q

What is the packing ratio of the 30nm solenoid?

A

40

32
Q

What is the 300nm solenoid?

A

The 30nm solenoid further coils employing a protein scaffold to condense the DNA further.
Each loop contains 60-100kb of DNA tethered by nonhistone scaffold proteins.

33
Q

What is the packing ratio of the 300nm solenoid?

A

680

34
Q

What is the 700nm fibre?

A

The coiled coil - requires the loops of chromatin to coil again to form a condensed fibre.

35
Q

What is the packing ratio of the 700nm fibre?

A

10^4

36
Q

What is the metaphase chromosome?

A

The chromosome is packaged with a p-arm (short) and q-arm (long).The centromere is in the centre and the telomeres at the ends.

37
Q

Where does transcription occur within the levels of chromosome?

A

The 10nm fibre as it is the most open structure.
Transcription can be initiated at the 30nm fibre provided that the promoter is accessible, to allow the chromatin remodellers in and bring the 30nm fibre back to the 10nm fibre so transcription can happen.
Past this point transcription cannot happen.

38
Q

Why is the packaging important?

A

It regulates the gene expression that happens at each cell lineage.
Different parts of the genome will be packaged in different ways - in each lineage there are some genes that are required so are at a lower level of packaging. There are other genes that are never needed so are tightly packed away.

39
Q

What are the different types of chromatin?

A

Euchromatin
Heterochromatin

40
Q

What is euchromatin?

A

In p-arm and q-arm.
Contains the genes.

41
Q

What is heterochromatin?

A

Found at the centromere and telomeres.
Contains no genes.

42
Q

How do the types of chromatin appear?

A

Euchromatin is lightly stained
Heterochromatin is dark as it is very highly packed.

43
Q

What are the types of heterochromatin?

A

Constitutive
Facultative
They are both very highly condensend.
In general they are transcriptionally inactive.

44
Q

Where are the genes?

A

In most cells, 90% of the genome is inactive but only 10% is in the highly conserved form in the heterochromatin.
Most genes, even if not on, are just packaged more highly than 10nm and carry different epigenetic markers to keep them silent.

45
Q

What DNA is in the constitutive heterochromatin?

A

All cells of a given species will package the same regions of DNA here - centromeres and telomeres.
Regions are always very highly condensed.
If a gene is in the constitutive region it will be poorly expressed.

46
Q

What is the Y chromosome?

A

Very small and few genes - only ones that make men men.
Mostly made from constitutive heterochromatin - on the q-arm and highly packaged.
Most of the expressed genes are on the p-arm.

47
Q

What is the facultative heterochromatin?

A

DNA packaged here will not be consistent within cell types of a species.

48
Q

What is the X chromosome?

A

Early on in the development process one of the X chromosomes - either maternal or paternal - are randomly inactivated, and cannot be reactivated.
The inactive chromosome is condensed so it takes on the form of facultative heterochromosome.

49
Q

How is facultative heterochromatin different to constitutive?

A

A sequence in one cell that is packaged in facultative heterochromatin may be packaged in euchromatin in another cell.
Whereas in constitutive all DNA regions are packaged there.

50
Q

What are the characteristics of heterochromatin?

A

Replicated late in S phase - as the chromatin needs unravelling down to the 10nm fibre.
DNA replication takes a long time due to this.

51
Q

What are characteristics of euchromatin?

A

In a more open conformation.
Replicated early in S phase - when actively being transcribed it will be in the 10nm fibre.
Afterwards will go into the 30nm fibre, ready to be moved back to 10nm when needed.

FLS (14 decks)

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