Chromatin structure and gene expression, including epigenetics

Question 1

Describe the different states of chromatin condensation”

Answer 1

• euchromatin
• heterochromatin

Question 2

Describe euchromatin

Answer 2

• “beads on a string”
• 11nm fiber - actively transcribed genes

Question 3

Describe heterochromatin

Answer 3

• 30nm chromatin fibre of packaged nucleosomes
• extended and condensed into a mitotic chromosome
• not transcribed

Question 4

Describe the function euchromatin

Answer 4

DNA accessible for transcription

Question 5

Describe the function heterochromatin

Answer 5

DNA inaccessible for transcription

Question 6

Describe the fundamental building block of chromatin

Answer 6

Nucleosomes

Question 7

Describe histones

Answer 7

• histone octamer forms a barrel from two of each of H2A, H2B, H3 and H4
• unstable in the absence of DNA
  147 bp of DNA to wrap twice around a nucleosome
• “tails” of each histone monomer extend out from the nucleosome

Question 8

Describe the two major factors regulating chromatin condensation

Answer 8

• histone H1
• post-translational modifications of “histone code”

Question 9

Describe histone H1

Answer 9

• “The linker histone”
• binds to histone octamer by linker DNA, with histone tails extended out
• stabilises chromatin, increasing condensation
• important for formation of 30nm fiber

Question 10

“histone code”

Answer 10

histone tails

Question 11

Describe histone tails

Answer 11

• lots of basic residues – K and R
• positive charge at neutral pH
• when histone tails interact with DNA, more condensed chromatin
• residues can be modified by acetylation or methylation

Question 12

K

Answer 12

lysine

Question 13

R

Answer 13

arginine

Question 14

acetylation

Answer 14

removes the basic charge of K or R residue

Question 15

Describe acetylation

Answer 15

removes the basic charge of K or R residue

Question 16

Describe methylation

Answer 16

does not affect charge of K or R residue

Question 17

Describe acetylated histone tails

Answer 17

• form weaker interaction with DNA
• chromatin loosened/decondensed
• associated with transcription

Question 18

Describe methylated histone tails

Answer 18

• interaction with DNA not directly disrupted
• changes histones affinity for different histone binding proteins
• different methylation states can either enhance or repress transcription

Question 19

How many possible combinations of acetylation/methylation are there

Answer 19

1013

Question 20

Different combinations of histone modifications are found in…

Answer 20

different regions of the genome

Question 21

How many nucleosomes are required to pack diploid human genome

Answer 21

3 x 10^7

Question 22

Give some regions of the genome

Answer 22

• telomeres
• centromeres
• retrotransposons
• microsatellites
• genes
• exons
• introns
• promoters

Question 23

Different combinations of histone marks result in

Answer 23

different condensation states of chromatin AND result in differential recruitment of other proteins

Question 24

Describe the function of histones in promotor regions

Answer 24

recruit histone acetylases and nucleosome remodellers e.g. SWI/SNF

Question 25

Describe epigenetics

Answer 25

daughter cells inherit the chromatin accessibility profile and therefore gene expression profile of their parent cell

Question 26

Describe inheritance

Answer 26

1) Histone code 2) RNA and protein made by parent cell 3) DNA methylation

Question 27

Describe over-expressed KMD1A during sperm formation in mice

Answer 27

- loss of H3K4 methylation at more than 2000 genes - methylation loss persisted for 3 generations even though they no longer had KDM1A gene expression - all 3 generations had abnormal development

Question 28

KMD1A

Answer 28

H3K4 demethylase

Question 29

Chromatin is made of ...

Answer 29

nucleosomes

Question 30

Nucleosomes made of

Answer 30

histones

Question 31

Histones have “tails” that can be modified to

Answer 31

influence DNA binding and recruitment of other proteins.

Question 32

The histone code

Answer 32

regulates chromatin condensation and transcription