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Gene regulation in eukaryotes II: Epigenetics - Heterochromatin: function, structure, formation, and maintenance

44 important questions on Gene regulation in eukaryotes II: Epigenetics - Heterochromatin: function, structure, formation, and maintenance

In which two general forms does chromatin occur?

In euchromatin and heterochromatin.

What are the differences between euchromatin and heterochromatin?

- Euchromatin is not stained during interphase, and heterochromatin remains stained throughout the entire cell cycle;
- Heterochromatin is more compact;
- Heterochromatin has an inhibitory effect on gene expression.

What are the three different functional roles of heterochromatin?

- Gene silencing;
- Prevention of transposable element movement;
- Prevention of viral proliferation.

How does heterochromatin silence genes?

It can limit the access to the DNA, so that activators and other proteins are not able to bind.

What are transposable elements?

Mobile segments of DNA that can insert themselves into multiple sites within a genome.

How does heterochromatin inhibit TE movement?

TEs are located in sites which are converted to heterochromatin, which silences genes that are needed for the transposition process.

How does heterochromatin prevent viral proliferation?

Viruses integrate their DNA into the host genome. When those regions are converted into heterochromatin, the expression of viral genes is inhibited.

Which two types of heterochromatin are there?

- Facultative heterochromatin;
- Constitutive heterochromatin.

What is the difference between facultative and constitutive heterochromatin?

The locations of constitutive heterochromatin is the same in all cell types, and the locations of facultative differ among cell types.

Where is constitutive often located within a chromsome?

Close to the centromere (pericentric region), and at telomeres.

What kind of sequences within the constitutive heterochromatin may have an important role in the formation of the compact structure?

Repeat sequences called satellite sequences.

How is constitutive chromatin remodeled in some species?

It is highly methylated on cytosines in some species-

What is a hallmark characteristic of constitutive chromatin in yeast and animal cells?

The trimethylation of a lysine at the ninth position in histone H3 (H3K9me3).

What is the modification H3K9me3 an example of?

Of a posttranslational modification (PTM).

How do specific proteins bind to particular PTMs in nucleosomes?

Via protein domains known as reader domains.

What domains on the same protein as the reader domains modify chromatin?

Writer domains.

What kind of domains remove PTMs?

Eraser domains.

How can reader domains contribute to the formation of heterochromatin?

They can bind to chromatin-modifying enzymes or chromatin-remodeling complexes and recruit them to the nucleosome, which causes PTMs and chromatin remodeling that contribute to teh formation of heterochromatin.

What kind of histone PTM can cause transcription to be inhibited?

Hypoacetylation, which means that constitutive chromatin is not acetylated. This cause histones to bind more tightly, which inhibits transcription.

What is a difference in the stability of facultative and constitutive chromatin?

Constitutive chromatin is very stable, and facultative chromatin is reversible.

On what depends the heterochromatic state of facultative heterochromatin?

The stage of development of the cell type.

Where is facultative heterochromatin located within the chromosome?

It occurs at multiple sites that are located between the centromere and telomeres.

What kind of repeat sequences does the DNA of facultative heterochromatin contain?

LINE-type repeated sequences, which initiates the propagation of a condensed chromatin structure.

To what extent is facultative heterochromatin methylated?

To a lower extent than constitutive heterochromatin, it often occurs in CpG island in regulatory regions of genes, which plays a role in gene silencing.

What kind of PTMs are found in facultative chromatin?

The H3K9me3 modification, but also the H3K27me3 modification.

What happens to the constitutive and facultative heterochromatin in the daughter cell after cell division?

The daughter cell has the same pattern of constitutive and facultative heterochromatin.

What is higher-order structure?

The assemblage of nucleosomes that assumes a reproducible conformation in three-dimensional space.

Which 5 molecular events does heterochromatin formation involve?

- Posttranslational modifications of histones;
- Binding of proteins to nucleosomes;
- Chromatin remodeling;
- DNA methylation;
- Binding of non-coding RNAs-

What are two consequences of those 2 molecular events?

- Some of them silence gene expression;
- Higher-order structures, in which heterochromatin has the following characteristics:

Closer, more stable contacts of nucleosomes with each other;
Formation of loop domains;
Binding of heterochromatin to the nuclear lamina.

Reader domains in which kind of proteins recognize the H3K9me3 modification?

Heterochromatin protein 1 (HP1).

How does HP1 contribute to a closer and more stable contact between nucleosomes?

HP1 forms a dimer and bridges two nucleosomes by binding to the H3K9me3 modifications in each of them.

What kind of proteins play a role in promoting the formation of loop domains, and how do they do that?

SMC proteins, such as
- condensin, which promotes chromosome compaction via loop domain formation;
- cohesin, which facilitates the formation of loop domains during interphase;
- CTCFs, which bind to sites containing three copie of a CCCTC sequence and then bind to each other. This promotes loop formation.

What are the nuclear lamina (NL)?

Layers of proteins that line the inner nuclear membrane.

How are the chromosomal regions that are in contact with the NL called?

The lamina-associated domains (LADs).

What are the 2 important roles of LADs?

- NL-anchoring via LADs may help to organize interphase chromosomes into chromosome territories;
- The genes in LADs are expressed at low levels, which suggests a role for LADs in gene repression.

What are the three phases of heterochromatin formation?

- Nucleation;
- Spreading;
- Barriers.

How does heterochromatin formation spread?

Chromatin-modifying enzymes are recruited to a nucleation site, which could lead to binding of HP1, which recruits methyltransferases to adjacent sites.

How is the spreading phase stopped, so that a euchromatic region is protected from heterochromatin?

- The barrier is a nucleosome-free region, in which the PTMs of histones needed for heterochromatin formation can not occur;
- The barrier contains antisilencing protiens that counteract the effects of proteins required for heterochromatin formation (for example, enzymes that catalyze acetylation of histones).

What happens with epigenetic changes after cell division?

It is maintained, epigenetic changes can be passed from cell to cell during cell divison.

What kind of chromatin is established in embryonic development?

Constitutive and facultative heterochromatin.

How are PTMs on histones transmitted from cell to cell during cell division (steps)?

- The original histones with PTMs are randomly incorporated into both daughter chromatids, so that approximately half of the histones of a daughter chromatid has the PTM;
- The original histones recruit chromatin-modifying and chromatin-remodeling complexes, which lead to changes in chromatin structure.

How does DNA polymerase contribute to the maintenance of heterochromatin structure in the daughter cells of cell division?

Components of DNA polymerase recruit chromatin-modifying enzymes that help to reestablish heterochromatin structure.

How do higher-order structures of chromatin play a role in maintaining heterochromatin structure after cell division?

The higher-order structure may favor the formation of heterochromatin by facilitating an environment that is favorable to spreading.

Name 2 diseases that are due to abnormalities in heterochromatin formation, and tell what the problem in this disease is.

- ICF syndrome: a loss-of-function mutation in a gene that encodes a DNA methyltransferase. This causes hypomethylation in regions with constitutive chromatin.
- Roberts syndrome: a loss-of-function mutation in a gene that encodes an acetyltransferase.

The question on the page originate from the summary of the following study material:

Genetics: Analysis & Principles II

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