Lecture 17a

Question 1

___ ___________ is a feature that is shared by all repressive chromatin in mammals.

Answer 1

DNA methylation

Question 2

T/F: DNA in euchromatin or yeast is methylated.

Answer 2

False! Only heterochromatin has DNA methylation. DNA is never methylated in euchromatin or yeast.

Question 3

Where does heterochromatin tend to form?

Answer 3

Over repetitive sequences.

Question 4

What does this symbol mean?

Answer 4

DNA methylation or methylated CpG

Question 5

What does this symbol mean?

Answer 5

Unmethylated DNA or unmethylated CpG

Question 6

Where is DNA methylation in heterochromatin found on?

Answer 6

It is only found on cytosines that are followed by guanines residue.

Question 7

T/F: The DNA methylation that occurs in heterochromatin is asymmetric.

Answer 7

False! It is symmetric.

Question 8

What two things are needed to add a methyl group to DNA?

Answer 8

DNA methyltransferase 1 adds the methyl group. Folate pathway indirectly provides the methyl.

Question 9

On what carbon is the methyl group added to the cytosine?

Answer 9

The 5th carbon gets the methyl group.

Question 10

Generally, explain what happens with DNA methyltransferases during the replication of DNA thats in heterochromatin.

Answer 10

DNA methyltransferase 1 chases after the DNA polymerase and adds methyl groups where the newly synthesized strand does not have it.

Question 11

Define fully methylated.

Answer 11

Both strands are methylated.

Question 12

Define hemi-methylated.

Answer 12

Only one strand is methylated and the newly synthesized strand is unmethylated.

Question 13

Hemi-methylated ——> Fully methylated.

What performs this?

Answer 13

DNA methyltransferase 1 + folate

Question 14

Relative to chemical modifications, what do histones have?

Answer 14

Histones also have chemical modifications that are specific to heterochromatin or euchromatin.

Question 15

Where do histone modifications often take place? Where is this on the nucleosome?

Answer 15

Mostly on the N-terminal “tails” of all 4 histones (H2A, H2B, H3, H4). These tails are sticking out of the nucleosomes.

Question 16

What is the N-terminal end of the nucleosome?

Answer 16

This is the first part of each histone molecule where H2A, H2B, H3, and H4 are present.

Question 17

Each _____ has, on average, ~__% of the amino acids of the histone.

Answer 17

tail, 25%

Question 18

Generally, what effect do histone tail chemical modifications have?

Answer 18

They control chromatin structure

Question 19

What does chromatin remodeling do?

Answer 19

It opens (loosens) or closes (tightens) chromatin structure, which regulates the ability of transcription factors to access genes.

Question 20

How are amino acids in each histone labeled?

Answer 20

Numbered starting at the tip of the N-terminal tail.

Question 21

T/F: In heterochromatin, all 4 histones have all of their Lysines acetylated in the N-terminal tails.

Answer 21

False! It is actually euchromatin that has all 4 of their histones with Lysines that are acetylated in the N-terminal tails.

Question 22

The __-terminal tails of the histones are modified by over __ different enzymes.

Answer 22

N, 50

Question 23

What are 3 examples of covalent changes that can be made to modify N-terminal tails of histones?

Answer 23

Acetylation, methylation, phosphorylation.

Question 24

What is acetylation ONLY added to? Is acetylation giving a positive or negative charge?

Answer 24

Lysines and Arginines. It provides a negative charge.

Question 25

What do the three alternate tri-methylation sites on the Histone H3 tail represent?

Answer 25

These are three alternative repressive chromatin (heterochromatin) structures, which are all mutually exclusive.

Question 26

If I wanted to convert euchromatin to heterochromatin, what needs to leave?

Answer 26

Acetyl groups

Question 27

Name the 3 types of repressive chromatin.

Answer 27

H3K9me3 H3K27me3 H3K36me3

Question 28

What does 3 methyl groups on Lysine 9 of H3 (H3K9me3) cause?

Answer 28

The nucleosome will be bound by a protein called Heterochromatin Protein 1 (HP1).

Question 29

What does 3 methyl groups on Lysine 27 of H3 (H3K27me3) cause?

Answer 29

The nucleosome will be bound by a complex of Polycomb (heterochromatin) proteins called PRC1.

Question 30

What does 3 methyl groups on Lysine 36 (H3K36me3) cause?

Answer 30

We actually do not know. We just know that there are proteins that bind nucleosomes with this histone modification, but we have not yet identified them.

Question 31

Is there potentially a 4th type of heterochromatin? Where may we find it?

Answer 31

Yes, likely in the regions where there are no genes but there are LINE elements.

Question 32

How many genes do standard histones have? Why?

Answer 32

Each have 10-17 genes. We need HELLA of these proteins.

Question 33

T/F: There is no such thing as non-standard proteins.

Answer 33

False! There are also non-standard proteins in addition to standard proteins (H2A, H2B, H3, and H4).

Question 34

What is the variant of H2A called? What does it do?

Answer 34

MacroH2A, which is a much larger histone than H2A. This is present in a subset of heterochromatin nucleosomes and plays a role in chromatin compaction.

Question 35

What does the H2A.X variant do?

Answer 35

Accumulates at the site of damage on chromosomes (double-strand breaks) and recruits repair proteins.

Question 36

Where do we find the cenH3 variant?

Answer 36

This is in the nucleosomes of the kinetochores of centromeres.

Question 37

What do repetitive sequences promote?

Answer 37

The formation of heterochromatin.

Question 38

Where do constitutive heterochromatins?

Answer 38

Forms over repetitive sequences and can spread beyond the repetitive sequences.

Question 39

What are 3 examples of repetitive sequences?

Answer 39

LINE-1, ERV, and Alu elements.

Question 40

What do clusters of repetitive sequences form?

Answer 40

Heterochromatin domains, which can spread past repetitive sequences into adjacent euchromatin.

Question 41

Where are large and strong heterochromatin domains found?

Answer 41

Wherever there are lots of repetitive sequences, such as telomeres and centromeres.

Question 42

T/F: Many copies of a repetitive sequence go against each other in the formation of heterochromatin.

Answer 42

False! Many copies of a repetitive sequence reinforce each other in the formation of heterochromatin.

Question 43

T/F: Strong heterochromatin does not spread.

Answer 43

False! Strong heterochromatin spreads variable distances beyond the repeats. The boundary moves.

Question 44

What can happen to a gene near the heterochromatin-euchromatin boundary?

Answer 44

The gene will alternate between being silent and being expressed depending on the boundary.

Question 45

In the fruit fly, what does the expression of the gene produce? What does the silencing of the gene produce?

Answer 45

Expression is red eye color. Silence is white eye color.

Question 46

T/F: The spread of heterochromatin is dependent in each cell of the Drosophila compound eye.

Answer 46

False! The spread of heterochromatin is independent of each cell. This means that we can have an eye that is both partially red and white.

Question 47

What did mutations in the heterochromatin genes of the Drosophila cause?

Answer 47

It weakened the heterochromatin causing it to be compressed and making more cells of the eye red.

Question 48

What did two of the mutations in the heterochromatin genes of the Drosophila turn out to be?

Answer 48

It turned out to be the enzyme that adds 3 methyl groups to H3K9 to obtain H3K9me3. The other was for HP1. The heterochromatin produced by these repeats was therefore H3K9me3 and this was how it was discovered.

Question 49

T/F: Both the H3K9me3 and HP1 gene copies can be mutated.

Answer 49

False! Only one of the two copies of these genes can be mutated because they are essential.

Question 50

When one of the two copies of the H3K9me3 and HP1 gene copies were mutated, what happened to the heterochromatin?

Answer 50

It contracted rather than expanded, so more gene was expressed than silenced.

Question 51

What do mutations in euchromatin-promoting genes cause in the Drosophila?

Answer 51

Silencing of the gene causing the eye to be white. The euchromatin was weakened.

Question 52

How were most heterochromatin and euchromatin promoting genes originally discovered?

Answer 52

By using mutational screens to identify mutations that alter the heterochromatin-euchromatin balance.

Question 53

Heterochromatin and euchromatin can be said to "______________" for the genome.

Answer 53

compete. Whichever is stronger will help to either express or silence the gene nearby.

Question 54

T/F: Some repetitive elements drift back and forth between heterochromatin and euchromatic states.

Answer 54

True!

Question 55

What is an example of repetitive elements drifting back and forth between heterochromatin and euchromatic states

Answer 55

Inbred mouse strain with an ERV element (repetitive) near Agouti gene.

Question 56

What did heterochromatin of the ERV element near the Agouti gene do?

Answer 56

Create brown fur which was normal

Question 57

What did euchromatin of the ERV element near the Agouti gene do?

Answer 57

Overexpressed creating yellow fur as well as more prone to obesity and unhealthy.

Question 58

What is pseudoagouti?

Answer 58

Coat looks agouti in mice but there are some yellow hairs in fur.

Question 59

What is epistasis?

Answer 59

When you have a mutation that causes 2 or more different phenotypes.