Chromatin and the control of Transcription

Question 1

what is the basic function of chromatin

Answer 1

to compact DNA

Question 2

what are the small basic protein which primarly make up chromatin

Answer 2

histones

Question 3

what are the two basic types of histones

Answer 3

Core and linker

Question 4

what are the 4 types of histones

Answer 4

H2A,H2B,H3 and H4

Question 5

Core histones are highly conserved, describe the structure

Answer 5

• N terminal tails which are highly basic (rich in Lys & Arg)
• Globular domain which contain a-helices and loops

Question 6

how do histones interact

Answer 6

they fold and perform ‘handshake interaction’

Question 7

what are the repeating units called that core histones form

Answer 7

nucleosomes = 147 bp of DNA wrapped around an octamer

Question 8

What is the structure of a Octamer

Answer 8

Central H3-H4 tetramer + 2 flanking H2A-H2B dimers

Question 9

how are nucleosomes organised

Answer 9

• DNA passes directly from one nucleosome to the next and linker histones (H1) binds to the DNA between nucleosome
• forms 30nm fibre

Question 10

Chromatin inhibits transcription T/F ?

Answer 10

Yes, no transcription occurs when RNA pol II + transcription factors when added to a chromatin template

Question 11

describe the genetic studies of Saccharomyces cerevisiae linked to chromatin

Answer 11

a chromosamal copies of H4 gene was deleted and replaced by a plasmid which produce H4 under the control of a ‘regulatabled promoter’
- promoter = GAL4 promoter
- This is ON when there is GALACTOSE in the medium BUT OFF when GLUCOSE is present

Question 12

what evidence of S.cerevisiae study shows ghat chromatin inhibits transcription

Answer 12

Therefore when GLUCOSE was added to the medium the expression of H4 was rapidly shut off
This resulted in nucleosome depletion and the expression of many inducible genes

Question 13

chromatin structure is described as D_

Answer 13

Dynamic

Question 14

what are the 3 major mechansim for modulating chromatin structure

Answer 14

• histone variants
• Post-translational modification of histones
• ATP dependent chromatin remodelling

Question 15

what is the difference between convention histone and its variants

Answer 15

variants are encoded by genes that differ from the highly conserved major types, they are expressed at very low levels

Question 16

which conventional histone does not have variant

Answer 16

H4

Question 17

how do histone variants affect chromatin dynamics

Answer 17

confers novel structural and functional properties of the
nucleosome which affect the chromatin dynamics

Question 18

how do post translational modification of histones affect transcription

Answer 18

play a key role in controlling gene expression

Question 19

histones are subjected post translational modification such as

Answer 19

Acetylation, Methylation, Ubiquitylation, Phosphorylation

Question 20

what are the effects of histone modification

Answer 20

• Could directly alter chromatin folding/structure
• Could control the recruitment of non histone proteins to
  chromatin (which in turn influence the recruitment/function
  of the transcriptional machinery)

Question 21

what enzyme is responsible for acetylation

Answer 21

Histone acetyl transferase (HAT)

Question 22

what is the enzyme responsible for deacetylation

Answer 22

Histone Deacetylase (HDACs)

Question 23

Nuclear HATs are now know to function in large multisubunit complexes of two major types - Known as

Answer 23

GNAT and MYST

Question 24

How are HATs recruited

Answer 24

activators recruit HATs to specifc promoters, also some HATs are part of the gen transcription machinery

Question 25

How does acetylation mediate transcriptional activation

Answer 25

• Direct influence on chromatin structure
• Direct the recruitment of Bromodomain proteins

Question 26

Acetylation _ gene expression

Answer 26

enhances

Question 27

specific acetylated lysine residues are recognised by what

Answer 27

bromodomains

Question 28

bromodomain proteins often promote what

Answer 28

transcription

Question 29

Histone methylation can occur on _

Answer 29

Lysine and arginine residues (less understood)

Question 30

what enzyme is responsible for methylation

Answer 30

Histone lysine methyl transferase (HKMTs)

Question 31

what enzyme is responsible for removing the methyl group

Answer 31

lysine demethylases

Question 32

True/False - Methylation is readily reversible

Answer 32

False - but demethylases do exist

Question 33

HKMTs often contain _ domains

Answer 33

SET

Question 34

lysine may be _ by HKMTs

Answer 34

mono, di or tri methylated

Question 35

what effect does methylation have on chromatin structure

Answer 35

does not affect charge so probably has only minor if any influence on chromatin structure

Question 36

A variety of different domains have been shown to function as methyl-lysine binding modules

Answer 36

Chromo, Tudor, PWWP, MBT
PHD fingers, Ankyrin and WD repeats

Question 37

Specific methylated lysines are recognised by specific proteins, Depending upon the context methyl-lysine residues can function either _

Answer 37

activating’ or ‘repressing marks

Question 38

name example of both activating or repressing residuew

Answer 38

H3 Lys9 Repression
H3 Lys4 Activation