chromatin and molecular mechanisms of transcription repression and activation

Question 1

describe “slicers”

Answer 1

positions within genomes where large heterochromatin blocks are built

Question 2

what happens to genes that are close to or within silencers?

Answer 2

strongly repressed

Question 3

list 2 examples of positional repression.

Answer 3

• mating type loci
• sub-telomeric genes

Question 4

explain the main points of mating type loci in yeast.

Answer 4

• HML and HMR are constantly repressed
• Rap1 binds next to the repressed loci and recruits Sir
  proteins
• Sir proteins spread over the repressed locus
• Sir2 is a histone deacetylase. (it deacetylates the histones
  at HML and HMR

Question 5

what do deacetylates histones form and prevent?

Answer 5

• form heterochromatin
• prevent the association of transcriptional activators to the promoters

Question 6

what is histone hypo-acetylation necessary for?

Answer 6

gene repression
- the fewer scuttle groups attached, the more gene repression

Question 7

steps of positional repression

Answer 7

• Rap1 and Sir proteins bind to the telomeres
• Sir proteins spread in the sub-telomeric regions of the chromosomes
• telomeres cluster at the periphery of the nucleus and are covered and condensed hypoacetylated

Question 8

describe the mutational analysis conducted on histones: Lysine -> Arginine

Answer 8

• Arg retains the positive charge, it cannot be acetylated to lose its positive charge.
• the DNA-histone interaction is strong, chromatin is compact
• gene repression cannot be reversed by acetylating the histones

Question 9

describe the mutational analysis conducted on histones: Lysine -> glutamine

Answer 9

• Glutamine has a neutral charge, resembles acetylated Lysine. it cannot be deacetylated to gain a positive charge.
• chromatin is decondensed, gene ca not be repressed

Question 10

does the lysine -> arginine mutation maintain or abolish gene repression at the telomeres?

Answer 10

maintain

Question 11

does the lysine -> glutamine mutation maintain or abolish gene repression at the telomeres?

Answer 11

abolish

Question 12

explain the process of telomeric gene repression

Answer 12

1. Rap1 (the repressor) binds to the telomere
2. Rap1 recruits co-repressors (Sir3/Sir4)
3. histone tail modification
4. further condensing of DNA because making histones more +ve attracts them

Question 13

what do transcriptional repressors often directly interact with?

Answer 13

HISTONE DEACTYLASE

Question 14

what is an example of a:
- transcription repressor
- co-repressor
- histone deactylase

Answer 14

• Ume6
• Sin3/Rpd3 complex
• Rpd3

Question 15

what do transcriptional activators often directly interact with?

Answer 15

histone acetyl-transferase

Question 16

what is an example of a transcription activator, co-activator, histone acetyl-transferase

Answer 16

• Gcn4
• SAGA complex
• Gcn5

Question 17

how can acetylated histones recruit more co-activators?

Answer 17

via bromo domains

Question 18

fill in the blanks with less or more
fewer acetylation = _____ repression = _____ expression

Answer 18

more, less

Question 19

fill in the blanks with less or more
more acetylation = _____ repression = _____ expression

Answer 19

less, more

Question 20

how do transcriptional activators de-condense chromatin?

Answer 20

via histone acetylation and chromatin remodling

Question 21

what yeast complex is chromatin remodelling complexes homologous to?

Answer 21

SWI/SNF complex

Question 22

explain histone acetylation and chromatin remodelling after the histones are acetylated.

Answer 22

nucleosomes-DNA interaction becomes loose
- chromatin-remodelling complexes then use ATP to push
nucleosomes along DNA to “open” promoters

Question 23

explain chromatin-remodelling factors. give an example

Answer 23

• example: SWI/SNF
• moves nucleosomes along the DNA by sliding or
  transferring them
• shifts the nucleosomes away from the promoter/enhancer sites and gives transcription factors access to the DNA

(COMPLEX BINDING, LOOSENING OF THE CHROMATIN STRUCTURE, REMODELLING)

Question 24

what do chromatin-remodelling factors use to move nucleosomes?

Answer 24

ATP