Lecture 7: Epigenetics Flashcards
What are the two types of chromatin?
The two types of chromatin are heterochromatin and euchromatin.
• Euchromatin is associated with active genes.
• Heterochromatin is associated with inactive DNA. Examples are centromeres, inactive mammalian X-chromosomes and telomeres.
What are the two types of heterochromatin? How does heterochromatin work?
The two types of constitutive and facultative (inducible). Both types form repressive structures and are associated with gene silencing. It can be used to silence genes in a certain cell type or tissue, which is important for development.
• Constitutive chromatin is highly condensed. It is not usually transcribed, and it has a reduced sensitivity to nucleases. DNA is heavily methylated. It is likely to have H3K9me3 and HP1 as modifiers or no modifications at all. It is associated with repetitive genetic elements like centromeres and telomeres. It is thought to act as a genome stabiliser and prevent gene rearrangements between similar genetic sequences.
• Facultative heterochromatin is often associated with genes. It can be present at a single nucleosome or nucleosomes spread over many kb of DNA. This is likely to have H3K27me3 and polycomb or H3K9me3 and HP1.It is often localised at promoters and is established in response to development or environmental triggers.
What is position effect variegation?
Position effect variegation is a phenomenon when genes are silenced in some cells through abnormal juxtaposition with heterochromatin.
• This can be caused by rearrangement or transposition.
• If a gene is that is not normally next to heterochromatin is moved to a centromere/telomere, its expression becomes variegated.
• The classic examples are variegated eye colour in Drosophila and changes in expression near yeast telomeres.
How does PEV work in the eyes of Drosophila?
In Drosophila eye colour can become variegated in mutants.
• In the wild type, the white gene causes the red phenotype.
• PEV is caused by a gene inversion which puts white gene next to heterochromatin.
• Some of the genes will be repressed but some won’t.
• Su(var) genes are suppressors of variegation which can be found by screening for genes which suppress PEV. This led to isolation of genes involved in the formation of heterochromatin.
• The molecular basis of PEV was found to be enzymes that methylate H3K9 and the reader proteins HP1.
How can we use fission yeast to look for genes involved in heterochromatin?
- We add a marker gene (ura4+) into the pericentromeric heterochromatin composed of repetitive sequences.
- The normal ura4+ gene is deleted. The yeast will therefore be unable to grow on medium lacking uracil.
- Mutagenize and look for cells which express the ura4+ gene and grow.
- Examine the genes.
What is X chromosome inactivation?
- Females of most animals have 2 X chromosomes in each cell.
- One has to be inactivated so cells can receive the correct dosage of proteins.
- Mammals randomly inactivate one of them in each cell just after the blastocyst stage (around the time of implantation).
- Xa is organised into TADs.
- Xi is organised into two megadomains, separated by the Dxz4 locus. These two domains are made up two non-overlapping types of heterochromatin.
- One domain has macroH2A, H3K27me3 and Xist. The other type has H3K9me3 and HP1.
- Within Xi and Xa there are two types of nuclear component: ANC and INC. Transcription occurs in the active nuclear compartment (ANC), which is composed of the perichromatic region (PR) and the interchromatin channel (IC). Genes are silent in the inactive nuclear component (INC). It contains compacted chromatin domain clusters (CDCs).
- Not all genes on Xi are silent. Active genes can be expressed. These genes are known as escapees.
How does X-chromosome inactivation work?
Inactivation occurs through the X chromosome inactivation centre (XIC). This produces a non-coding RNA transcript only from the inactive X-chromosome.
• The transcript is called Xist and it made from a gene in the XIC.
• The transcript coats the chromosome and prevents transcription.
• Control of Xist expression appears to be due to DNA methylation. The gene control region is unmethylated in Xi but methylated in Xa.
• The inactive X chromosome is maintained in the inactive state through histone deacetylation and DNA methylation. Macro H2A is exclusively found in Xi nucleosomes.
• Most of the control regions of genes along Xi are DNA methylated. This locks them in an inactive state and prevents transcription.
• The methylation pattern is erased in germ cells and begins anew during the development of each organism.
• The XIC contains multiple non-coding RNAs which are involved in inactivation.
• Jpx is a long non-coding RNA which upregulates Xist expression. Jpx evicts CTCF at the Xist promoter as a method of activating Xist.
• The mechanism isn’t fully understood. It is though that Jpx acts as a chromosome numerator and ensures that genes are expressed on only one chromosome.
