Epigenetics & Transcriptional gene regulation in eukaryotes Flashcards
What is epigenetics?
Epi=”on top of”-genetics.
Theoretically: The study of regulation of gene expression by modifications that make DNA accessible/inaccessible, rather than alteration of the genetic code itself.
Practically: epigenetics describes phenomena in which genetically identical cells or organisms express their genomes differently, causing phenotypic differences.
Basically, it’s genetic information not encoded by the DNA (but within the DNA structure). Not all epigenetic changes are inherited, but many are.
There are two main kinds of epigenetic modifications in eukaryotes, which are these?
Histone modifications (including histone variants) and DNA methylation.
On what level of the central dogma (DNA-RNA-Protein) does epigenetic modifications act?
Epigenetic modifications act on the DNA level, to regulate transcription (which is a better term than gene expression as everything in the genome is not genes).
Explain how DNA is packed in chromosomes in short.
DNA is wrapped around histones, which when bound is called nucleosomes. Nucleosomes are the basic structural subunit of chromatin, consisting of about 200 bp of DNA and an octamer of histone proteins. The nucleosomes are tightly packed in chromatin, which in turn is tightly packed in chromosomes.
There are two levels of packing/organisation of the chromatin in chromosomes. What are they called and how do they differ?
- Heterochromatin is densely packed, less available to transcription machinery –> silenced. Most often found on either side of the centromere and in the telomeres. In the nucleus, heterochromatin occupy the outer domain.
- Euchromatin is less densely packed, more available for the transcription machinery –> transcribed. Most often found in the arms of the chromosome. In the nucleus, euchromatin occupy the central domain.
How are epigenetic modifications inherited?
Epigenetic modifications are inherited during replication. If the template strand is methylated or have proteins bound to it during replication, both daughter strands will have the same modification as the template.
Although the modification dilute over time, there are some mechanisms to keep repression through cell divisions, like Pc-G proteins that remain bound even if silencing modifications disappear.
Explain what a nucleation event is and what consequences it can lead to.
A nucleation event is when heterochromatin starts to extend, out over regions that weren’t silenced before, until it gets to an insulation sequence/element which causes the heterochromatin to stop spreading. We are not entirely sure what causes these events, just that they happen.
The consequences of a nucleation event is that genes that should be active are instead included in the heterochromatin and gets silenced.
What is important to keep in mind about chromatin structure?
That it’s not two-dimensional but 3D, and that the 3D topography of chromatin has different functions. Nubs of looped chromatin usually silence transcription but on rare occasions they can be activating. The 3D topological structures can be changed systematically or random.
How does histone modifications work and what five modifications can be done?
Histones are octamers with several “tails” that stick out from the DNA coiled around it and are accessible to modifications (that can both repress/activate transcription).
The histone tails can be modified by:
– Acetylation (Ac)
– Ubiquitination (Ub)
– Methylation (Me)
– Phosphorylation (P)
– Sumoylation (SUMO (Small Ubiquitin-like Modifier))
What is meant by “the histone code”? How are modifications named?
The amino acid sequence of the tails.
Modifications are named with the tail name first, e.g. H3, and then the amino acid + it’s number in the order, e.g. K4 (lysine, which is commonly modified, as the fourth AA), and last the modification, eg me for mono-methylation. (me2/me3 for di- or tri-methylated). In this example the modification would be named “H3K4me”.
In the histone modification machinery, there are three groups of participating proteins. Which and what do they do?
The histone modification machinery consists of:
- Writers: Proteins that establish the posttranslational mark/modification on histones.
- Erasers: Proteins that remove the posttranslational
modification from the histone. - Readers: Proteins that recognize the DNA and histone residues with or without posttranslational
modification and recruit the writer proteins to
establish the mark.
For acetylation vs methylation (histone mods) which proteins are the writers and erasers?
The writers that perform acetylation of histones are histone acetyltransferases (HATs) and the erasers are Histone deacetylases (HDACs).
In methylation the writers are called Histone methyltransferases (HMTs) and the erasers are called Histone demethylases (HDMCs).
What can histone methylation lead to? Give two examples.
Histone methylation can both activate and repress transcription, depending on what residue is modified. For example:
- H3K4me (methylation of the fourth lysine on the H3 tail) is associated with actively transcribed genes and mRNA.
- H3K9me (methylation of the ninth lysine on the H3 tail) is associated with constitutive heterochromatin (basically permanent silencing) at transposons in the genome, which if active would be highly mutagenic.
What does histone acetylation usually lead to?
Histones are positively charged and therefore bind strongly to DNA. Acetylation of histones reduces the positive charge, which weakens their interaction with DNA and cause them to interact lessor disassociate from DNA, resulting in a more open configuration of DNA –> active transcription.
What protein plays a key role in the formation of mammalian heterochromatin?
HP1 is the key protein in forming mammalian heterochromatin. It acts by binding to methylated
histone H3 (methylation creates a binding site for HP1) and leads to the formation of heterochromatin (minimal transcription) through recruiting more methyltransferase when having bound, positive feedback loops that causes the spread of heterochromatin.
The histone modifications H3K27me1/3 have different functions in mammals. How do their function differ?
H3K27me3 represses genes in euchromatin in the arms of chromosomes while H3K27me1 maintains heterochromatin around the centromeric/pericentromeric regions of chromosomes.
Where does histone modifications that activate/repress genes generally take place in mammals?
- Modifications that silence genes are often acting on the promoters, and this results in the formation of facultative heterochromatin (temporary silencing). Modifications that silence transposons can be all over the gene body.
- Modifications that activate genes can happen in many places of the gene, like in the promoter, transcription start site or ORF.
Where does histone modifications that activate/repress genes generally take place in plants?
In plants, modifications that activate transcription are most common at the transcription start site (TSS), while mods that repress are more common downstream of the TSS. Modifications that silence transposons can be all over the gene body, as in mammals.
Histone variants can also influence transcription, how? Give an example.
Since histones are octamers, subunits can be switched out to change transcription.
- This could be to either maintain heterochromatin (silencing), which is applied in centromere by using the CENH3 variant there.
- Or it could be to activate genes, for example by switching to the H2A.Z variant.
Note: This is a very energy consuming process done by chromatin remodelers. They can also add/remove histones to make the chromatin more compact/loose. All in all, histone modifications is a very dynamic process.
