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Molecular Genetics > Epigenetics > Flashcards

Epigenetics Flashcards

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1
Q

What is the nucleosome made of?

A

DNA (146)

+

Histone Octamer:

H2A
H2B
H3
H4

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2
Q

Describe Heterochromatin

A

INACTIVE

Tightly packed

Highly Stained

Constitutive vs Facultative

Found in centromere and telomere

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3
Q

Describe Euchromatin

A

ACTIVE

Open Form

Beads on a String

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4
Q

Why are Histone Tails important?

A

They protrude from nucleosome with N-term out

They “Message Boards” - modified according to chromatin state (conveying identity)

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5
Q

What modifications constitute the “Histone Code”

A

Acetlyation (most common)

Arginine Methylation (H3 + H4)

Rep Lysine Methylation (H3 + H4)

Active Lysine Methylation (H3)

Some Lysines get EITHER Rep Lysine Methylation OR Acetylation

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6
Q

What enzyme adds Acetyl groups (the “Writer”)?

A

HAT

Histone Acetyltransferases

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7
Q

What enzyme removes acetyl groups (The “Eraser”)?

A

HDAC

Histone DeACetlyase

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8
Q

What does Acetylation of H3 Lysines to do the chromatin?

A

OPENS it - TFs can interact

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9
Q

What does Methylation of H3 Lysine residues do?

A

It’s CONTEXT-SPECIFIC:

It can activate (H3K4me3) or silence (H3K9me3).

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10
Q

What occurs after Methylation of the H3K9 residue?

A

Recognised by HP1

Suvar 3-9 interacts with HP1
(*histone methyltransferase -
selectively methylates K9)
and with…

*another silencing factor, Suvar 3-7

Chromatin condenses.

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11
Q

How can we detect Histone Modification?

A

ChIP

Chromosome Immunoprecipitation

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12
Q

Outline the steps of ChIP

A

DNA Crosslinking (Freeze!)

Lyse and extract

Sonicate DNA

Add specific antibody (recog mark)

Purify DNA

Analyse with qPCR or GenSeq

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13
Q

What does methylation of the H3K4 residue mean?

A

A mark of activity

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14
Q

( ! ) What THREE kinds of chromatin changes cause altered gene activity?

A
  1. Histone Modification

2. Histone Re-Modelling
Nudgers moving nucleosomes
(Loose or Compact chromosome)
3. Variant Histone

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15
Q

What facilitates attachment of the Kinetochore?

A

CENP-A

a H3 variant protein - 60% similar

Differences at N-terminus

Present in centromeric chromatin

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16
Q

(SORT) Complete centromere structure between species generally

A

DNA sequences are DIVERSE between species

Chromatin structure is SHARED by most eukaryotes

CENP-A is ALWAYS flanked
by pericentromeric heterochromatin (H3K9)

(Core centromere is surrounded by hetero)

17
Q

What did Herman Muller (1930) conclude about epigenetics with the Variegated Eye experiment?

A

Epigenetic Silencing is HERITABLE from one cell to the next.

Silencing depends on LOCATION and PACKAGING
***

  1. The mutagenesis caused chromosomal inversion
  2. This caused relocation of the w+ gene to nearby a heterochromatin region
  3. This silenced the gene!
18
Q

What was discovered with KO genetic screens (building off of Variegated Eye experiments)?

A

The SuVar gene
(Suppression of Variegation)

KO suppressed variegation (red eye)

Variegated eye = making heterochromatin as default

19
Q

( ! ) BROADLY, where can methylation occur?

A
  1. The Arginines And Lysines of Histone Tails

2. Gs and Cs of DNA

20
Q

What proportion of mammal CG sites are methylated?

A

70 - 80%

21
Q

What kinds of DNA sequences are highly methylated?

A

Satellites

Repetitive elements

Intergenic DNA

Exons

22
Q

What does DNA Methylation do?!

A

Repress a gene

A kind of protection for host

23
Q

What kinds of DNA sequences are NOT methylated?

A

CpG islands

24
Q

Describe CpG islands

A

1kb long

Mark 5’ regions and promoters

70% human genes have CGI promoters

25
Q

What CpG islands are NEVER methylated?

A

Those around promoters -

Chromatin needs to be open for TFs!

(Intergenic CGIs can sometimes be)

26
Q

What happens to methylated CpG islands?

A

They are bound by MeCP2

MeCP2 recruits repressive HDAC
Histone Deacetylase

27
Q

What happens to unmethylated CpG islands?

A

They are recognised by Cfp1

These recruit Chromatin Activating Complexes

(H3K4 MTase - methyltransferase)

28
Q

What is a Barr Body (1948)?

A

A condensed, inactivated X chromosome

29
Q

What is the Lyon Hypothesis?

A

The inactivated X is random

and all clonal descendants inherit that inactivity

30
Q

What is Constitutive and Facultative heterochromatin?

A

Constitutive -
pericentromeric and telomeric

Facultative -
In gene-silencing regions
(Activated under some conditions)

31
Q

What is special for Xi (inactive X) GpG islands?

A

They are METHYLATED -

all along the chromosome EXCEPT at Xist

Xist methylation is what makes it active on the Xa (active X)

Molecular Genetics (5 decks)

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