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GENE 404: Gene Regulation > Epigenetics > Flashcards

Epigenetics Flashcards

1
Q

What is chromatin?

A

Complex of DNA and proteins into which eukaryotic chromosomes are packaged

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2
Q

What is included in a nucleosome?

A

An octomeric histone core with 2 subunits of H2A, H2B, H3, and H4, with 147 base pairs of DNA

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3
Q

What are histones?

A

Positively charged DNA binding proteins with flexible tails

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4
Q

What is linker DNA?

A

DNA between histones

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5
Q

What do H1 histones do?

A

Linker histones that are involved in the assembly of nucleosomes into higher order structures

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6
Q

What are the two types of chromatin?

A

Euchromatin and heterochromatin

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7
Q

What is heterochromatin? Is it being transcribed?

A

Chromatin that is highly dense and compacted. It is not being transcribed

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8
Q

What is euchromatin? Is it being transcribed?

A

Chromatin that is more loosely packaged. Is being transcribed

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9
Q

Is chromatin always either euchromatin or heterochromatin?

A

No, it’s a lot more complicated and chromatin can quickly shift between the two

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10
Q

What are 3 common histone modifications?

A

Methylation, acetylation, and phosphorylation

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11
Q

What is histone acetylation?

A

Acetyl groups are added to lysine residues in the histone tails. They are rapidly reversible

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12
Q

What type of enzyme adds acetyl groups to histones?

A

Histone acetylases (HATs)

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13
Q

What type of enzyme removes acetyl groups from histones?

A

Histone deacetylases (HDACs)

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14
Q

Does histone acetylation typically activate or repress gene expression?

A

Activate

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15
Q

Does histone methylation typically activate or repress gene expression?

A

Can be either

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16
Q

What are 3 factors that determine whether histone methylation activates or represses gene expression?

A
  1. Which amino acids in the histone tail gets methylated
  2. Which gene
  3. Any other modifications
17
Q

Is H3K9 methylation associated with activated or repressed gene expression?

A

Repressed

18
Q

Is H4K4 methylation associated with activated or repressed gene expression?

A

Activated

19
Q

What are writer enzymes?

A

Enzymes that add histone modifications

20
Q

What are eraser enzymes?

A

Enzymes that remove histone modifications

21
Q

What are reader enzymes?

A

Enzymes that recognize histone modifications

22
Q

What are 3 mechanisms by which histone modifications change gene expression?

A
  1. Recruit nucleosome and chromatin remodelling proteins to change promoter accessibility
  2. Changing DNA accessibility
  3. Recruiting TFs
23
Q

Are nucleosomes randomly distributed through the genome?

A

Nope

24
Q

What is nucleosome positioning?

A

A measure of how often a nucleosome is in a particular spot at a particular time

25
Q

What are 3 ways to describe nucleosome positioning?

A

Perfect, partial, or no positioning

26
Q

What is perfect nucleosome positioning?

A

The nucleosome is always in the same spot in every cell of a certain type under certain conditions

27
Q

What is partial nucleosome positioning?

A

The nucleosome is often, but not always in the same spot in every cell of a certain type under certain conditions

28
Q

What is no nucleosome positioning?

A

Random

29
Q

What regions of the genome tend to be nucleosome poor?

A

Where things bind. Promoters, enhancers, terminators

30
Q

Where would perfect positioning be found?

A

Next to nucleosome poor regions

31
Q

What is nucleosome occupancy?

A

How frequently a locus tends to be occupied by nucleosomes, and how many

32
Q

How much genomic DNA is occupied by nucleosomes?

A

Most of it

33
Q

What sorts of regions have low nucleosome occupancy?

A

Functional regions

34
Q

What is a poised/closed enhancer?

A

The histones have a modification that allows for the enhancer to be accessible, but also another one that prevents that. The enhancer becomes available for binding once the repressing modification is removed

35
Q

What is a latent enhancer?

A

When the histones need a certain modification to become accessible, and do so once they receive that modification

36
Q

What do antirepressor transcription factors do?

A

Have the ability to overcome the repressive effects of chromatin and activate transcription, even when the chromatin is in a repressive state

37
Q

What are 5 factors that influence nucleosome positioning?

A
  1. DNA sequence. A and T rich sequences aren’t bound by nucleosomes as much
  2. Histone modifications
  3. Nucleosome remodelling enzymes
  4. RNAP II and GTFs
  5. TFs
38
Q

Why is competent chromatin structure necessary, but not sufficient for transcription to occur?

A

Still need RNAP II and the GTFs. But chromatin has to be competent for them to bind in the place

GENE 404: Gene Regulation (25 decks)

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