L20 Chromatin Gene Regulation

Question 1

DNA is part of a complex in chromatin

Answer 1

see onenote

Nucleosomes need to be displaced for transcription

Question 2

Nucleosome distribution

Answer 2

see onenote

• not randomly distributed along DNA (chromatin architecture)
  1. more or less random
  2. phased, occupy identical positions on DNA throughout population
  3. 100-300bp that bear no nucleosomes (nucleosome free regions, NFR)
  4. 10-20bp segments, hyper-sensitive sites
  4. nucleosomes containing histone variants

Question 3

Nucleosome position

Answer 3

see onenote

Must have access to DNA to start transcription i.e. nfr after regulatory region so that RNA pol2 can access it

Question 4

Nucleosome position can be directed

Answer 4

see onenote

protein to form nfr

protein to form nucleosome

Question 5

NFR region

Answer 5

• binding sites for regulatory proteins, assembly site for transcriptional apparatus

If you can detect H2A.Z variant (e.g. via antibodies), can tell where on a chromosome there is possibly an active gene as there are variant histones

Question 6

Nucleosome position can be mapped by micrococcal nuclease digestion

Answer 6

see onenote

cuts accessible DNA between nucleosomes

Question 7

Chromatin remodelling

Answer 7

see onenote slides

Nucleosomes can be moved along DNA

• Catalyses sliding of DNA around histone optimer or removal depending on the context
• Energy driven

Histones can be exchanges in nucleosomes
- E.g. exchange of H2A with H2A.Z

Question 8

Histone remodelling complexes

Answer 8

see onenote

Question 9

Histone modification - modifying histone tails

Answer 9

see onenote slides

Amino terminal end can be modified, can signal that different things are going on for that particular gene near that nucleosome

• phosphorylation
• methylation
• acetylation

Lysine acetylation and methylation are competing reactions

Depending on which is acetylated or phosphorylated, signals that different things are happening

Each histone sub unit has its own set of modifications

Each modification generally tells us something about that gene BUT it is not absolute. More often than not tells us the same thing for each kind of modification.

Question 10

Lysine - average consequences

Answer 10

see onenote

Question 11

Histone tail modification consequences

Answer 11

see onenote

Question 12

Dosage compensation

Answer 12

see onenote

MSL2 complex

• active in males only
• recruited to X chromsome
• leads to histone H4 K16 acetylation => activates gene expression

Question 13

Histone modification - H3K9me, H2S10P

Answer 13

see onenote

H3K9me - promotes binding of heterochromatin protein (HP1) => establishment of heterochromatin

H2S10p => reverses binding by HP1

Question 14

Epigenetics

Answer 14

stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence

usually in somatic cells

• transmitted from parent to daughter cells
• epigenetic phenotypes stable through mitosis

transmitted through meiosis
- imprinting

Question 15

Epigenetic inheritance - somatic

Answer 15

see onenote

Question 16

Epigenetic inheritance - imprinting

Answer 16

see onenote

epigenetic inheritance between generations

Question 17

Epigenetic inheritance - stable regulatory loop

Answer 17

see onenote slides

Question 18

Epigenetic inheritance - stable chromatin pattern

Answer 18

see onenote

random x chromosome inactivation in mammals

Question 19

Epigenetic inheritance - stable DNA methylation pattern

Answer 19

see onenote

Question 20

Epigenetic inheritance - stable protein conformation

Answer 20

see onenote slides

prion, misfolded protein
protein aggregation state