L10 - Chromatin Structure and Gene Transcription

Question 1

Genetic alterations to DNA sequences

Answer 1

Permanently affect gene expression.

Question 2

Epigenetic changes to chromatin structure

Answer 2

Modulate gene expression. 
Do not alter DNA sequence
Are reversible 
Facilitate stable changes to gene expression which may persist for the life of a cell
Can be erased in the germ line

Question 3

What are nucleosomes?

Answer 3

Nucleosomes can be covalently modified.
N terminal lysine rich tails (8 of them) of core histones project radially from nucleosomal core.
Covalent modifications differ between condensed inactive and open active chromatin.

Question 4

Types of covalent modification to core histone N-terminal tails

Answer 4

• Acetylation of lysines
• Methylation of lysines and arginine’s
• Methylation/acetylation to termini lysine and serine side chains

Question 5

Histone acetyltransferases

Answer 5

Modify lysine residues
Histone code writers
Activates gene transcription

Question 6

Histone methyltransferases

Answer 6

Exhibit site specificities
Histone code writers
Represses gene transcription

Question 7

Histone deacetylases

Answer 7

Remove modification
Histone code erasers
Represses gene transcription

Question 8

Histone demethylases

Answer 8

Remove modification
Histone code erasers
Activates gene transcription

Question 9

Lysine and arginine methylation effects on gene expression?

Answer 9

• H3-K4 active
• H3-K9 inactive
• H3-K27 inactive
• H3-R17 active

Question 10

Lysine acetylation effects on gene expression

Answer 10

• H2A active
• H2B active
• H3 active
• H4 active

Question 11

What does acetylation of histones create binding sites for?

Answer 11

Transcription activators that contain a bromodomain

The bromodomain transcription activator is an epigenetic code reader

Question 12

Mapping of histone acetylation across genes

Answer 12

Histone acetylation is associated with transcriptionally active promoter sequences

Question 13

What does methylation of histones create binding sites for?

Answer 13

Transcriptional repressors that contain a chromodomain
Transcriptional activators that contain a PHD zinc finger domain
- Depends on the lysine amino acid residue modified

These are both epigenetic code readers

Question 14

What is the transcriptional regulatory code?

Answer 14

An epigenetic code that lies on top of the genetic code

Governs when and where genetic information is expressed

Question 15

How do transcription activator proteins work?

Answer 15

1. Nucleosome remodelling
2. Histone removal
3. Histone replacement
4. Histone modifications
   
   • Recruitment of code writers and readers

Question 16

Activator proteins

Answer 16

Typically induce combinations of these effects.

All the effects promote RNA polymerase II recruitment.

Question 17

How do transcription repressor proteins work?

Answer 17

1. Recruitment of chromatin remodelling complexes
2. Recruitment of histone deacetylases
3. Recruitment of histone methyltransferases
4. Competitive DNA binding
5. Masking activation surface
6. Direct interaction with general transcription factors

Question 18

What is the Polycomb Repressive Complexes?

Answer 18

Includes proteins that can generate or recognise repressive chromatin modification

• Histone code writing
  
  • H3-K27 methylation
  • Mediated by Enhancer of zeste (EZH2) component of PRC2
• Histone code reading
  
  • Recruitment of PRC1 via Polycomb chromodomain
  • Formation of silent, repressed heterochromatin

Question 19

Relationship between transcriptionally repressive histone methylation and DNA methylation

Answer 19

Transcriptionally inactive promoters are rich in methylated CpG dinucleotides
Addition of methyl groups to cytosine residues is mediated by DNA methyltransferases (DNMTs)
Histone methyltransferase (EZH2) interacts with DNMTs and mutually reinforce their effects

Question 20

Transcriptionally inactive promoters are rich in?

Answer 20

Methylated CpG dinucleotides

Question 21

Addition of methyl groups to cytosine residues is mediated by?

Answer 21

DNA methyltransferases (DNMTs)

Question 22

Mammalian X-chromosome inactivation

Answer 22

Equalises levels of X-chromosome derived gene products in males and females

• Males, XY - 1 dose of X-linked genes
• Females, XX - 2 doses of X-linked genes

Question 23

Silencing of one X chromosome of female embryo during development

Answer 23

Initial selection of the chromosome for silencing is random
Silenced by condensation
The silencing decision is propagated clonally
- All progeny of cells in which the silencing occurred inherit the same silenced X chromosome

Question 24

Calico cat is an example of?

Answer 24

X-chromosome inactivation

Question 25

Mechanism of X-inactivation

Answer 25

1. Xist RNA binds to the X chromosome in cis 2. Promotes chromatin condensation –spreads away from x-inactivation centre in both directions 3. Promotes formation of silent chromatin by recruiting histone modifying enzymes and other Polycomb group components 4. Leads to H3K27 and H3K9 methylation of core Histones 5. Leads to chromatin condensation and transcriptional repression  inactive X

Question 26

What is a Barr body?

Answer 26

A highly condensed inactive X chromosome at the periphery of the nucleus of female somatic cells

Question 27

Polycomb proteins role

Answer 27

Detect Xist transcripts on the X chromosome that is to be inactivated They cause its transcriptional silencing

Question 28

Agouti mouse is an example of?

Answer 28

How dietary components can affect DNA methylation patterns which regulate phenotypes

Question 29

Calico cat genes

Answer 29

``` Females: - XO XO : orange - Xo Xo: black - XO Xo: calico They are exclusively female They are heterozygous for 2 alleles of an X-linked coat pigment gene ```

Question 30

Agouti mouse genes?

Answer 30

Agoutivy - dominant mutant allele - Causes obesity and yellow fur - Due to constitutively high expression of the agouti protein - Contains an insertion of an IAP element - strongly activates the agouti gene

Question 31

IAP element in Agouti mouse

Answer 31

IAP element is sensitive to DNA methylation | - High levels of methyl donors in maternal diet represses Agoutivy transcription in progeny

Question 32

Increasing levels of methyl donor molecules in diet can?

Answer 32

Rescue the phenotypic effects of Agoutivy by increasing DNA methylation which represses transcription of the Agoutivy gene

Question 33

Methylation and acetylation of some lysines are?

Answer 33

Mutually exclusive

Question 34

Mechanism of X-inactivation

Answer 34

Involves synthesis of a non-coding RNA (Xist) from the X-inactivation centre (XIC) on the chromosome destined for inactivation