Epigenetics Flashcards
What is the nucleosome made of?
DNA (146)
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Histone Octamer:
H2A
H2B
H3
H4
Describe Heterochromatin
INACTIVE
Tightly packed
Highly Stained
Constitutive vs Facultative
Found in centromere and telomere
Describe Euchromatin
ACTIVE
Open Form
Beads on a String
Why are Histone Tails important?
They protrude from nucleosome with N-term out
They “Message Boards” - modified according to chromatin state (conveying identity)
What modifications constitute the “Histone Code”
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
What enzyme adds Acetyl groups (the “Writer”)?
HAT
Histone Acetyltransferases
What enzyme removes acetyl groups (The “Eraser”)?
HDAC
Histone DeACetlyase
What does Acetylation of H3 Lysines to do the chromatin?
OPENS it - TFs can interact
What does Methylation of H3 Lysine residues do?
It’s CONTEXT-SPECIFIC:
It can activate (H3K4me3) or silence (H3K9me3).
What occurs after Methylation of the H3K9 residue?
Recognised by HP1
Suvar 3-9 interacts with HP1
(*histone methyltransferase -
selectively methylates K9)
and with…
*another silencing factor, Suvar 3-7
Chromatin condenses.
How can we detect Histone Modification?
ChIP
Chromosome Immunoprecipitation
Outline the steps of ChIP
DNA Crosslinking (Freeze!)
Lyse and extract
Sonicate DNA
Add specific antibody (recog mark)
Purify DNA
Analyse with qPCR or GenSeq
What does methylation of the H3K4 residue mean?
A mark of activity
( ! ) What THREE kinds of chromatin changes cause altered gene activity?
- Histone Modification
2. Histone Re-Modelling
Nudgers moving nucleosomes
(Loose or Compact chromosome)
3. Variant Histone
What facilitates attachment of the Kinetochore?
CENP-A
a H3 variant protein - 60% similar
Differences at N-terminus
Present in centromeric chromatin
(SORT) Complete centromere structure between species generally
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)
What did Herman Muller (1930) conclude about epigenetics with the Variegated Eye experiment?
Epigenetic Silencing is HERITABLE from one cell to the next.
Silencing depends on LOCATION and PACKAGING
***
- The mutagenesis caused chromosomal inversion
- This caused relocation of the w+ gene to nearby a heterochromatin region
- This silenced the gene!
What was discovered with KO genetic screens (building off of Variegated Eye experiments)?
The SuVar gene
(Suppression of Variegation)
KO suppressed variegation (red eye)
Variegated eye = making heterochromatin as default
( ! ) BROADLY, where can methylation occur?
- The Arginines And Lysines of Histone Tails
2. Gs and Cs of DNA
What proportion of mammal CG sites are methylated?
70 - 80%
What kinds of DNA sequences are highly methylated?
Satellites
Repetitive elements
Intergenic DNA
Exons
What does DNA Methylation do?!
Repress a gene
A kind of protection for host
What kinds of DNA sequences are NOT methylated?
CpG islands
Describe CpG islands
1kb long
Mark 5’ regions and promoters
70% human genes have CGI promoters
What CpG islands are NEVER methylated?
Those around promoters -
Chromatin needs to be open for TFs!
(Intergenic CGIs can sometimes be)
What happens to methylated CpG islands?
They are bound by MeCP2
MeCP2 recruits repressive HDAC
Histone Deacetylase
What happens to unmethylated CpG islands?
They are recognised by Cfp1
These recruit Chromatin Activating Complexes
(H3K4 MTase - methyltransferase)
What is a Barr Body (1948)?
A condensed, inactivated X chromosome
What is the Lyon Hypothesis?
The inactivated X is random
and all clonal descendants inherit that inactivity
What is Constitutive and Facultative heterochromatin?
Constitutive -
pericentromeric and telomeric
Facultative -
In gene-silencing regions
(Activated under some conditions)
What is special for Xi (inactive X) GpG islands?
They are METHYLATED -
all along the chromosome EXCEPT at Xist
Xist methylation is what makes it active on the Xa (active X)
