Epigenetics

Question 1

What is epigenetics?

Answer 1

The phenomenon where genetically identical cells can express their genome differently, because of either cytosine methylation of DNA or histone modifications. This can cause phenotypic differences.

Question 2

What are the two main ways of epigenetic modifications in eukaryotes?

Answer 2

Histone modifications

Cytosine methylation of DNA

Question 3

What is heterochromatin?

Answer 3

Densely packed chromatin, less accessible.

Question 4

What is euchromatin?

Answer 4

Less densely packed chromatin, more accessible.

Question 5

What is the purpose of Polycomb proteins (Pc-G)?

Answer 5

The function of the polycomb group proteins is mainly to maintain epigenetic gene silencing across cell divisions. They don’t initiate repression, but they can maintain it.

Question 6

What is position-effect variegation?

Answer 6

When gene regions that are normally in euchromatin are packed into heterochromatin and silenced - this can occur in a stochastic pattern, and the silencing may vary from cell to cell.

Question 7

How does histone modification work?

Answer 7

The histone proteins consist of octamer protein complexes that the DNA is wrapped around. The amino terminus tails of the histone can be modified in different ways, for example by methylation or acetylation. The histone code determines however the modifications affect the accessibility of the DNA.

Question 8

What is a commonly modified amino acid at the amino tails of the histone proteins?

Answer 8

K - Lysine

Question 9

In the histone machinery: what are writers, erasers and readers?

Answer 9

Writers: proteins that establish the mark on the histones.

Erasers: proteins that remove the marks on the histones.

Question 10

What are writers and erasers that add and remove acetyl groups from histones called, respectively?

Answer 10

Writers: histone acetyltransferases (HATs)

Erasers: histone deacetylases (HDACs)

Question 11

What are writers and erasers that add and remove methyl groups from histones called, respectively?

Answer 11

Writers: histone methyltransferases (HMTs)

Erasers: histone demethylaces (HDMs)

Question 12

What happens when lysine residues are acetylated?

Answer 12

The positive charge of histones are reduced, therefore weakening their interaction with the negatively charged phosphate DNA backbone. Opens the configuration.

Question 13

What happens when residues are methylated?

Answer 13

Methylation adds neutral charge and increases histone interaction

Question 14

Give some examples of heterochromatin histone codes.

Answer 14

H3K9me2, H3K9me3, H3K27me1-3

Question 15

What is HP1 and what is its function?

Answer 15

HP1 is a protein that binds to methylated histones in mammals and self-aggregates, creating a higher order chromatin structures.

Question 16

What is H3K4me associated with?

Answer 16

Actively transcribed genes.

Question 17

What is H3K9me associated with?

Answer 17

Less transcribed genes.

Question 18

What is CENH3?

Answer 18

A variant of histone H3 that accumulates at the centromere and is necessary for centromere maintenance.

Question 19

What are chromatin remodelers?

Answer 19

Proteins that use ATP to remove histones from the chromatin and incorporate other variants in its place. This is another layer of regulation.

Question 20

What is DNA methylation?

Answer 20

Methylation of cytosine residues in DNA and works as a type of transcriptional repressor. It is reversible and is performed by methyltransferases.

Question 21

What are CpG islands?

Answer 21

In mammals, methylation occurs at cytosine residues located adjacent to guanine residues. CpG islands are regions of the genome have a high abundance of CpG. CpG islands are often found in transposons, repetitive regions and promoters - places where DNA may need to be inaccessible.

Question 22

About how many active genes have CpG islands on their promoters?

Answer 22

60-70%

Question 23

What is the purpose of the Dmt1 enzyme?

Answer 23

Sites in the genome that are fully methylated (methylated on both strands) will be hemimethylated after replicated. Dnmt1 recognizes these sites and recruits methyltransferases to fully methylate the daughter strands.

Question 24

How is bisulfite treatment of DNA used to determine sites of cytosine methylation?

Answer 24

The DNA is sequenced and saved as a reference. Treating the DNA with bisulfite will convert all unmethylated cytosines to uracil, which means they will be read as thymines by the replication fork and Adenine is incorporated into the complementary strand. Methylated Cs are resistant to the treatment. When the DNA is sequenced again, it will be possible to pinpoint the unmethylated sites by comparing it to the reference.

Question 25

What is genomic imprinting?

Answer 25

An epigenetic phenomenon that determines the expression of genes depending on they are maternally or paternally inherited.

Question 26

How is X-chromosome inactivation connected to epigenetics and explain what Barr bodies are related to this?

Answer 26

X-chromosome inactivation occurs in organisms (usually females) with two X-chromosomes, where one X per somatic cell is inactivated by histone methylation. This produces a Barr body - i.e one Barr body per somatic cell. Also called X-chromatin. This is a form of dosage compensation.

Question 27

How does the dosage compensation (inactivation of one X) mechanism work?

Answer 27

A gene called Xic is located around the centromere. From this, large amounts of a ncRNA called Xist is transcribed, and Xist coats the whole chromosome, inhibiting transcription. Xist also attracts histone modifications, resulting in heterochromatin formation and inactivation of the X.

Question 28

What are some key biological processes that DNA methylation plays an important role in?

Answer 28

Silencing of transposons
Regulating the silencing and accessibility of promoters
Genomic imprinting
X-chromosome inactivation
Suppression of repetitive element transcription