Chromatin & Epigenetics Flashcards
What is epigentic inheritence?
The ability of a daughter cell to retain memory of the gene expression patterns that were present in the parent cell.
E.g - female cats can have patchy coloured fur, what is this a result of?
Random X-inactivation. Two alleles, one is suppressed whilst the other is expressed.
What did Mary Frances Lyon hypothesise?
She said that X-inactivation is to prevent XX female cells from expressing twice as many X-linked gene products as XY male cells.
X- chromosome inactivation - early development - random inactivation - heritable in somatic cells
What is dosage compensation?
Transcriptional X-inactivation in female somatic cells
How does X-inactivation arise and what does it lead to?
The cells in the early embryo have a condensation of RANDOMLY SELECTED X chromosome during embryonic development - silenced. The future cells memorise which X chromosome is silenced. This leads to mosaicism.
What does Xist stand for and what is it?
X-inactive specific transcript and is a lncRNA
How does Xist lead to inactivation of an X chromosome?
Both X chromosomes during ES Cell development express Xist but one will express it more than the other. Xist RNA will ‘coat’ the Xi (inactive X). Xist RNA coating enables the complementarity with transcriptional repression complexes and chromatin modifiers leading to heterochromatinisation.
What is the Xi now known as?
Barr body
Where is Xist located on the X chromosome?
X-chromosome Inactivation Center (XIC)
Where does the Barr body reside within the nucleus?
Localised close to the nuclear periphery 65%-80% of interphase cells.
What is a nucleosome?
It is an octamer of histones. 147 base pairs wrapped around 8 histones.
What are the histones?
Two copies of each H2A, H2B, H3, and H4
Histone tails extend beyond the DNA
What do the units of TADs (spatial organisation of chromatin in 3D space within the nucleus) represent?
Segregation of chromatin into active and inactive domains
What are some covalent modifications the N-terminal tail can undergo?
Methylation, ubiquitylation, phosphorylation, biotinylation, acetylation, and more.
Are these modifications reversible?
Yes
Each particular histone modification is created by a specific enzyme. E.g - histone acetyl transferases (HATs) and histone deacetylase complexes (HDACs).
Two forms of chromatin
Euchromatin & Heterochromatin. Either being transcriptionally active/inactive.
What recognises the specific marks found on the histones?
Transcription factors
What causes androgenetic lethality?
Two paternal chromosomes leads to failure of embryonic development
What causes gynogenetic lethality?
Two maternal chromosomes leads to failure of extraembryonic development
What do these show?
Chromosomes can carry parent-specific memories (imprints)
What is the timeline of imprinting?
- 1st generation imprints in maternal and paternal parents before fertilisation
- Imprinting erasure precedes sex determination in gonads of developing embryo
- 2nd generation imprints acquired in oocytes/sperm
When should imprinting be stable and not erased?
Once established, the imprint must remain on the same chromosome after fertilisation and be resistant to post-fertilisation reprogramming.
When should imprinting be erasable?
During the reprogramming of germline cells
What donates a methyl group to a DNMT for it to be donated to a cytosine?
S-adenosyl-L-methionine (SAM)
Where are the predominant sites of methylation?
CpG dinucleotides (C in front of the G)
Which enzymes are responsible for de novo methylation?
DNA methyltransferases - DNMT3A & DNMT3B
Which enzyme is responsible for maintenance methylation?
DNMT1
What are usually unmethylated and why?
CpG islands because they contain promoters
Transposable elements are usually methylated to remain inactive
Demethylation occurs after fertilisation for most genes, which genes do not get methylated during the first wave of demethylation?
Imprinted genes are not demethylated.
When do they undergo demethylation and why?
During the production of PGCs so that new sex-specific imprints can be established depending on whether the embryo is male or female.
Which enzymes remove methyl groups from the cytosine and what is the pathway after this? (active demethylation)
Tet enzymes oxidise the 5mC
- 5mC (5 methyl cytosine)
- 5hmC (5 hydroxymethyl cytosine)
- 5caC (5 carboxyl cytosine)
- 5fC (5 formyl cytosine)
What are two mechanisms of passive demethylation?
- DNMT1 fails to recognise 5hmC
- DNMT1 is absent or inhibited
What are four processes associated with DNA methylation in mammals?
- Genomic imprinting
- X-chromosome inactivation
- Repression of TEs
- Ageing
Most imprinted genes appear in clusters, what are they controlled by?
Imprint Control Element (ICE)
