Lecture 17a Flashcards
___ ___________ is a feature that is shared by all repressive chromatin in mammals.
DNA methylation
T/F: DNA in euchromatin or yeast is methylated.
False! Only heterochromatin has DNA methylation. DNA is never methylated in euchromatin or yeast.
Where does heterochromatin tend to form?
Over repetitive sequences.
What does this symbol mean?
DNA methylation or methylated CpG
What does this symbol mean?
Unmethylated DNA or unmethylated CpG
Where is DNA methylation in heterochromatin found on?
It is only found on cytosines that are followed by guanines residue.
T/F: The DNA methylation that occurs in heterochromatin is asymmetric.
False! It is symmetric.
What two things are needed to add a methyl group to DNA?
DNA methyltransferase 1 adds the methyl group. Folate pathway indirectly provides the methyl.
On what carbon is the methyl group added to the cytosine?
The 5th carbon gets the methyl group.
Generally, explain what happens with DNA methyltransferases during the replication of DNA thats in heterochromatin.
DNA methyltransferase 1 chases after the DNA polymerase and adds methyl groups where the newly synthesized strand does not have it.
Define fully methylated.
Both strands are methylated.
Define hemi-methylated.
Only one strand is methylated and the newly synthesized strand is unmethylated.
Hemi-methylated ——> Fully methylated.
What performs this?
DNA methyltransferase 1 + folate
Relative to chemical modifications, what do histones have?
Histones also have chemical modifications that are specific to heterochromatin or euchromatin.
Where do histone modifications often take place? Where is this on the nucleosome?
Mostly on the N-terminal “tails” of all 4 histones (H2A, H2B, H3, H4). These tails are sticking out of the nucleosomes.
What is the N-terminal end of the nucleosome?
This is the first part of each histone molecule where H2A, H2B, H3, and H4 are present.
Each _____ has, on average, ~__% of the amino acids of the histone.
tail, 25%
Generally, what effect do histone tail chemical modifications have?
They control chromatin structure
What does chromatin remodeling do?
It opens (loosens) or closes (tightens) chromatin structure, which regulates the ability of transcription factors to access genes.
How are amino acids in each histone labeled?
Numbered starting at the tip of the N-terminal tail.
T/F: In heterochromatin, all 4 histones have all of their Lysines acetylated in the N-terminal tails.
False! It is actually euchromatin that has all 4 of their histones with Lysines that are acetylated in the N-terminal tails.
The __-terminal tails of the histones are modified by over __ different enzymes.
N, 50
What are 3 examples of covalent changes that can be made to modify N-terminal tails of histones?
Acetylation, methylation, phosphorylation.
What is acetylation ONLY added to? Is acetylation giving a positive or negative charge?
Lysines and Arginines. It provides a negative charge.
What do the three alternate tri-methylation sites on the Histone H3 tail represent?
These are three alternative repressive chromatin (heterochromatin) structures, which are all mutually exclusive.
If I wanted to convert euchromatin to heterochromatin, what needs to leave?
Acetyl groups
Name the 3 types of repressive chromatin.
H3K9me3
H3K27me3
H3K36me3
What does 3 methyl groups on Lysine 9 of H3 (H3K9me3) cause?
The nucleosome will be bound by a protein called Heterochromatin Protein 1 (HP1).
What does 3 methyl groups on Lysine 27 of H3 (H3K27me3) cause?
The nucleosome will be bound by a complex of Polycomb (heterochromatin) proteins called PRC1.
What does 3 methyl groups on Lysine 36 (H3K36me3) cause?
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.
Is there potentially a 4th type of heterochromatin? Where may we find it?
Yes, likely in the regions where there are no genes but there are LINE elements.
How many genes do standard histones have? Why?
Each have 10-17 genes. We need HELLA of these proteins.
T/F: There is no such thing as non-standard proteins.
False! There are also non-standard proteins in addition to standard proteins (H2A, H2B, H3, and H4).
What is the variant of H2A called? What does it do?
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.
What does the H2A.X variant do?
Accumulates at the site of damage on chromosomes (double-strand breaks) and recruits repair proteins.
Where do we find the cenH3 variant?
This is in the nucleosomes of the kinetochores of centromeres.
What do repetitive sequences promote?
The formation of heterochromatin.
Where do constitutive heterochromatins?
Forms over repetitive sequences and can spread beyond the repetitive sequences.
What are 3 examples of repetitive sequences?
LINE-1, ERV, and Alu elements.
What do clusters of repetitive sequences form?
Heterochromatin domains, which can spread past repetitive sequences into adjacent euchromatin.
Where are large and strong heterochromatin domains found?
Wherever there are lots of repetitive sequences, such as telomeres and centromeres.
T/F: Many copies of a repetitive sequence go against each other in the formation of heterochromatin.
False! Many copies of a repetitive sequence reinforce each other in the formation of heterochromatin.
T/F: Strong heterochromatin does not spread.
False! Strong heterochromatin spreads variable distances beyond the repeats. The boundary moves.
What can happen to a gene near the heterochromatin-euchromatin boundary?
The gene will alternate between being silent and being expressed depending on the boundary.
In the fruit fly, what does the expression of the gene produce? What does the silencing of the gene produce?
Expression is red eye color.
Silence is white eye color.
T/F: The spread of heterochromatin is dependent in each cell of the Drosophila compound eye.
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.
What did mutations in the heterochromatin genes of the Drosophila cause?
It weakened the heterochromatin causing it to be compressed and making more cells of the eye red.
What did two of the mutations in the heterochromatin genes of the Drosophila turn out to be?
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.
T/F: Both the H3K9me3 and HP1 gene copies can be mutated.
False! Only one of the two copies of these genes can be mutated because they are essential.
When one of the two copies of the H3K9me3 and HP1 gene copies were mutated, what happened to the heterochromatin?
It contracted rather than expanded, so more gene was expressed than silenced.
What do mutations in euchromatin-promoting genes cause in the Drosophila?
Silencing of the gene causing the eye to be white. The euchromatin was weakened.
How were most heterochromatin and euchromatin promoting genes originally discovered?
By using mutational screens to identify mutations that alter the heterochromatin-euchromatin balance.
Heterochromatin and euchromatin can be said to “______________” for the genome.
compete.
Whichever is stronger will help to either express or silence the gene nearby.
T/F: Some repetitive elements drift back and forth between heterochromatin and euchromatic states.
True!
What is an example of repetitive elements drifting back and forth between heterochromatin and euchromatic states
Inbred mouse strain with an ERV element (repetitive) near Agouti gene.
What did heterochromatin of the ERV element near the Agouti gene do?
Create brown fur which was normal
What did euchromatin of the ERV element near the Agouti gene do?
Overexpressed creating yellow fur as well as more prone to obesity and unhealthy.
What is pseudoagouti?
Coat looks agouti in mice but there are some yellow hairs in fur.
What is epistasis?
When you have a mutation that causes 2 or more different phenotypes.
