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BIOL 200 - Molecular Biology > Lecture 21 - Chromatin, Epigenetics, and the Histone Code > Flashcards

Lecture 21 - Chromatin, Epigenetics, and the Histone Code Flashcards

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1
Q

What proteins wind DNA into nucleosomes?

A

Histones

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2
Q

What are the two types of chromatin?

A

Euchromatin and Heterochromatin

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3
Q

What type of chromatin is delicate and thread-like and tends to be associated with regions of chromatin that are being actively transcribed?

A

Euchromatin

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4
Q

In which kind of cells is euchromatin abundant?

A

It is abundant in actively transcribing cells.

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5
Q

What does euchromatin represent?

A

Euchromatin represents DNA that is unwound to provide a transcriptional template.

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6
Q

In what kind of chromatin are silenced genes found?

A

Heterochromatin

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7
Q

What kind of chromatin is most densely packed?

A

Heterochromatin

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8
Q

If you are looking at an electron micrograph, how would you distinguish heterochromatin from euchromatin?

A

Euchromatin is delicate and light while heterochromatin is not. Therefore, heterochromatin would show up as electron dense.

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9
Q

Why is some of the chromosome in heterochromatin form while some of it is in euchromatin form?

A

This is because the entire chromosome is not active at the same time. Some regions are silenced and maintained in heterochromatin form while other regions are being actively transcribed and maintained in euchromatin form.

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10
Q

What organism was used to better understand euchromatin and heterochromatin?

A

Yeast (Saccharomyces cerevisiae, or baker’s yeast to be specific)

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11
Q

What happens to a mother yeast when she buds off a daughter yeast cell?

A

The moment that a mother yeast buds, she’ll switch her mating type so that in case conditions are unfavourable, she could always mate with her progeny. The mother will be one mating type and the daughter will be the other.

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12
Q

What are the two mating types in yeast?

A

alpha and a

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13
Q

What controls the mating type of Saccharomyces cerevisiae?

A

There are 3 genetic loci on chromosome III that control the mating type of the yeast.

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14
Q

Where on the chromsome of Saccharomyces cerevisiae are the mating type genes situated?

A

They are situtated on two different extremities of the chromosome (chromosome III).

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15
Q

What happens when HMLalpha and HMRa are situated at distal extremitie of the chromosome? Why must this happen?

A

When they’re at distal extremities of the yeast chromosome, around telomeres, these 2 genes are never transcribed.

They must be silenced, otherwise the cell would be diploid alpha/a and not able to mate.

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16
Q

What must happen for a yeast to acquire a mating type? Why?

A

In order to acquire a mating type, the chromosome has to go through a non reciprocal recombination event, whereby you take out the mating type genes from their distal regions and bring them down to the middle of the chromosome.

Each mating type gene can only be expressed when they go to the center loci on chromosome III since every gene on the extremities are completely silence (it is impossible to access the DNA sequences there).

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17
Q

What does transcriptional repression depend on?

A

Transcriptional repression depends on silencer sequences.

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18
Q

What may block expression of tRNA genes (such as RNA pol III) or prevent methylation.

A

Silencer Sequences (around chromosomal extremities)

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19
Q

What does RAP1 do?

A

RAP1 binds to the DNA sequences of silencers and (by collaborating with other proteins) settles down on sequences around their extremities, near the telomeres. It then changes the chromatin (more precisely, the histones that make up the proteinaceous coat of the DNA) so that physically, it becomes more dense. RAP1 also binds to repetitive sequences in telomeres.

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20
Q

What allows the N-terminals of histone tails (in their normal state) to interact electrostatically with DNA phosphate groups? How does acetylation change this?

A

The N-terminals are positively charged while the phosphate groups are negatively charged.

Acetylation neutralizes the histone tails.

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21
Q

How are RAP1 and the SIR proteins recruited?

A

Hypoacetylated histone tails (H3 and H4) become a recruitment platform for more SIR proteins, so a positive reinforcement takes place. The first recruitment by RAP1 and SIR1 bring in SIR2, 3, and 4, and then the enzymatic activity will take place, hypoacetylating all the histone tails that continues to bring in more proteins.

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22
Q

Where are big aggregates of SIR proteins formed?

A

The SIR proteins form aggregates at the telomeres.

23
Q

What does RAP1 at the telomeres recruit?

A

Histone Deacetylation Complexes (HDACs)

24
Q

How does RAP1 indicude changes in the chromatin?

A

RAP1 recruits HDACs which induce changes in the histone tails, ultimately changing the configuration of the chromatin.

25
Q

Why does acetylating histone tails associated with opening up the chromatin?

A

Acetylating histone tails neutralizes them, which decreases the electrostatic interaction to a certain degree between the histone tails and the phosphate groups of the DNA.

26
Q

What happens when you deacetylate histone tails?

A

Deacetylation reverts histones back to positively charged entities that will interact with DNA to condense it. It results in the silencing of genes.

27
Q

What is the multiprotein complex (SIN3 bound to RPD3 and a bunch of other proteins) that interacts with a repressor domain within a transcription factor in yeast an example of?

A

Co-Repressor Complex

28
Q

What do the two proteins in a co-repressor complex do?

A

One protein binds to the desired gene while the other will deacetylate the histone.

29
Q

What do the two proteins in a co-activator do?

A

One binds to the gene and another acetylates the histone.

30
Q

What do co-activators work with to change a chromatin’s configuration in a gene-specific manner?

A

DNA-Binding Transcription Factors

31
Q

What do chromatin writers do?

A

Chromatin writers put down marks at specific sites within the histone that can change the way the histones interact with DNA and/or allow recognition by other proteins that will carry out specific activities on the regions.

32
Q

What are phosphorylations, acetylations, methylations, and ubiquitination all examples of?

A

Histone Marks

33
Q

What is the histone code?

A

The histone code is a hypothesis that the transcription of genetic information encoded in DNA is in part regulated by chemical modifications (marks) to histone proteins.

34
Q

What do histone marks allow for?

A

Histone marks are recognized by key effective proteins or protein complexes that ensure that the signal is transduced to somehow change the way that the chromatin will behave.

35
Q

What is the histone mark acetlyation almost always associated with?

A

Activation

36
Q

What can methylation histone marks result in?

A

Methylation marks can be read by proteins that are involved in silencing or they can be read by proteins that are involved in activating. The result is dependent on where the methylation occurs.

37
Q

What technique is used to determine where histone marks are?

A

Chromatin Immunoprecipitation (ChIP)

38
Q

When you use NGS to analyze the precipitate from ChIP in order to analyze histone marks, what genes will you see?

A

You will only see the genes that are in open histone form.

39
Q

What could be said about the dosage of sex chromosomes in men and women?

A

Men have the “recommended dose” (one X and one Y) while women have double the dose (which is usually not a good thing).

40
Q

What does it mean to say that women are mosaic? How does this happen?

A

Early during development, just before gastrulation, all cells randomly inactivate one of their two X chromosomes so that they only have one active one. As cells divide, the active and inactive chromosomes are maintained. As such, women have a mosaic of a different X cell being activated in different cluster of cells in their body.

41
Q

What is the inactivated X chromosome in women called?

A

Barr Body

42
Q

How many Barr bodies would a cell containing 3 X chromosomes have?

A

2

43
Q

What biological phenomenon is the reason for calico cats having two different fur colours?

A

Mosaicism

44
Q

How does chromosom inactivation occur in mammals?

A

Mammals express a long cis-acting RNA, encoded by the XIST locus, to coat the entire chromosome with non-coding RNA (XIST). By expressing XIST, gene expression is extinguished on the X chromosome that is going to be inactivated. Once XIST is expressed, the cells know that this chromosome has to remain inactive during cell division.

45
Q

What are epigenetic traits?

A

Epigenetic traits are changes in the phenotype that do not involve alterations in the DNA sequence.

46
Q

What are polycomb proteins an example of?

A

Developmental Restrictions (an example of Epigenetic Traits)

47
Q

What does gene expression very early in development depend on?

A

It depends on the parents and the imprints that come together.

48
Q

What is genomic imprinting? What causes it?

A

It is an epigenetic phenomenon that causes genes to be expressed in a parent-of-origin specific manner.

The process is dependent on DNA/histone methylation. These marks are imprinted into germline cells (sperm or egg) in the parents and maintained through mitotic division.

49
Q

What must be inherited in daughter cells following division to ensure proper function? Why? How?

A

Epigenetic Markers

This is so that daughter cells know which gene regions should be heterochromatin or euchromatin and therefore which regions shoulld be silenced.

During replication, all histones are thrown off of and reassemble on the DNA once it is formed. Some new histones will come in, but they’ll mix in with some of the old histones. The old histones retain a mark to signal to the cell whether they were active or repressed in the last cell. Readers read the old histones and mark the naive histones accordingly.

50
Q

What do readers do?

A

Readers are proteins that read and recognize marks on old histones so that they can accordingly mark new histones.

51
Q

What does HMT recognize to methylate neighbouring naive histones?

A

H3K9me3

52
Q

What two regions must be maintained in a silent state?

A

Telomeres and Centromeres

53
Q

What is required for centromere silencing? How does it silence the centromere?

A

Small Double-Stranded RNAs (dsRNA)

The dsRNA corresponds to the regions to be silenced and recruit complexes (histone methyltransferases) that condense the chromatin.

BIOL 200 - Molecular Biology (22 decks)

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