RR6

Question 1

What is DNA tightly wound with?

Answer 1

DNA is tightly would with histones and nucleosomes.

Question 2

What is the function of a nucleosome?

Answer 2

Nucleosomes are necessary to package genomic DNA into the nucleus in the form of chromosomes.

Question 3

What is heterochromatin?

Answer 3

Transcriptionally inactive region of gene that stains heavily and is very dense. It localized at the nuclear envelope, often near nuclear pores.

Question 4

What is Euchromatin?

Answer 4

An actively transcribing region of gene. It is delicate and stains lightly. It may represent unwound DNA.

Question 5

What state are transcriptionally inactive regions in?

Answer 5

“heterochromatinized” state

Question 6

What study was done to understand the “heterochromatinized” state?

Answer 6

There was a study of mating types. This was done in Saccharomyces Cerevisiae (yeast). The mating type is controlled by 3 genetic loci on chromosomes III. There are two mating types, HMLalpha and HMRa, loci must first be silence other cells will be diploid and they cannot mate.

Question 7

What does transcriptional repression depend on?

Answer 7

It depends on silencer sequences and can even block RNA Pol III.

Question 8

Histones effect repression, what other regions behave similarly?

Answer 8

The regions around telomeres behave similarly.

Question 9

Why must silent mating types be repressed?

Answer 9

They must be repressed so they do not become a diploid and they can still mate.

Question 10

What are the three factors that are required for the repression of silent mating type loci?

Answer 10

1) RAPI
2) SIRI
3) SIR2,3, and 4

Question 11

What is the function of RAPI?

Answer 11

RAPI is a factor that is required for the repression of silent mating type loci. It binds to DNA in the region of the silencer and it also binds to repetitive sequence in telomere.

Question 12

What is the function of SIRI?

Answer 12

SIRI is a factor that is required for the repression of silent mating type loci. It stands for “Silent Information Regulator”. It cooperates with RAPI and is important for binding the silencer region in silent mating type loci.

Question 13

What is the function of SIR2, 3, and 4?

Answer 13

SIR 2, 3, and 4 are factors that are required for the repression of silent mating type loci. They bind to histone tails and recruits SIR2. They form large complexes with telomeric DNA.

Question 14

What is it believed that SIR2 plays a role in?

Answer 14

It is believed that it plays a role in aging.

Question 15

Describe the structure of Histones.

Answer 15

Histones have positively charged inner region and disordered internal tails.

Question 16

How can histone tails sometimes be modified?

Answer 16

They can sometimes be modified post-translation. H3K4 is methylated to activation and H3K9 is methylated to inactivation.

Question 17

What is a key function of histone proteins?

Answer 17

They can suggest codes because key proteins can recognize residues and modify them.

Question 18

When would a histone act as a epigenetic reader and writer?

Answer 18

Histone methyltransferase (HMT) recognizes H3K9me3 to methylate neighbouring naive histones. HMT ensures daughter cell has some marks after cell division.

Question 19

What is an example of a function of an epigenetic reader?

Answer 19

Epigenetic readers recognize marks and effect methylation of neighbouring histones to they can have the same mark. It ensures consistency of daught cells.

Question 20

How can antibodies against histone tails be used in chIP?

Answer 20

Through reversible cross-linking agents, proteins bound to chromatin can be isolated using antibodies and the sequence can be determined. 1) you must use a known primer if you want to know whether a specific gene is affected. 2) Entire genome can be analyzed using NGS (next generation sequencing). Because it is an entire genome chIP is performed with antibodies against transcription factors to find enhancer positions and other key elements) Now - if you compare NGS and chIPs you can identify regions that are bound by transcription factors)

Question 21

What are histone acetyl transferases? What are there functions?

Answer 21

They are enzymes that induce acetylation of histone tails that allow some transcriptional activators to overcome being repressed. The (+) charge of N-terminal histone tail interacts with DNA phosphate group. It is neutralized by acetylation and this permits formation of a complex.

Question 22

How are chromatins modified? Give an example.

Answer 22

You can use enzymes to change the way that gene expression will take place. For example, if you acetylate histone tails, you neutralize charge, allowing for chromatin to decondense. GCN4 is necessary - has TF GCN5. RpD3P is a histone deacetylase. Specific targeting requires UMeGp and finally Sin3p. If you have an activator, you also need a repressor. The repressor will interact with large multi protein complex and change the chromatin configuration by getting rid of acetylases which block activation.

Question 23

How can activation domains trigger chromatin decondensation?

Answer 23

Activation Domains shift around nucleosomes in ATP dependent manner. SWI/SNF delocalize nucleosomes so specific regions are open to transcription factors. When LACi is stained, it interacts with condensed portion of the nucleus.

Question 24

What are/the function of pioneer transcription factors?

Answer 24

They are DNA binding transcriptional activators that interact with DNA exposed on the outside of DNA. They recruit enzymes that alter configuration of neighbouring histone tails, this opens chromatin and allows for general transcription factors.

Question 25

What is an essential part of transcriptional activation?

Answer 25

It is the ability to recruit a mediator with transcription factors to the transcriptional initiation site.

Question 26

What are epigenetic marks?

Answer 26

They are DNA marks that are read by specific proteins and then used to modify histones in proximity through mSin3 recruitment.

Question 27

What are epigenetic writers?

Answer 27

Histone marks can nucleate histone methyltransferase to repress gene activity across genetic regions, and are often heritable marks.