Week 2 - Genomic Instability

Question 1

Define Genomic instability

Answer 1

Unscheduled alterations, either of a temporary or permanent nature, within the genome.

Question 2

Name the types of Genomic Instability

Answer 2

Chromosomal Instability (CIN)
Nucleotide-Level Instability

Question 3

Name the types of CIN

Answer 3

Loss and Gain of Chromosomes (Aneuploidy)
Translocations
Deletions
Duplications
Inversions

Question 4

How to detect Nucleotide Level Changes

Answer 4

PCR

Sanger Sequencing

Question 5

What are the types of Translocations?

Answer 5

Balanced and Unbalanced exchange

Question 6

What are the outcomes of Genome Instability and Cancer? (4)

Answer 6

Point mutations - Affect gene product and control
Deletions - Loss of gene product and control
Duplications - Possible interferences in the balance of protein expression
Inversions/Translocations - Alteration in the gene products and control therefore can change transcription and expression

Question 7

How do you identify point mutations?

Answer 7

PCR/Sequencing

Question 8

What is an example of the effect of duplication? CLUE Protein Imbalance

Answer 8

Increase in protein concentration of Brachyury protein

Germ-line tandem duplication of the T (brachyury) gene causes familial chordoma

(Chordoma Foundation, 2017)

Question 9

Why is genomic instability good?

Answer 9

SNP’s - Natural Variation in population

Immune cells - Antibodies

Question 10

How can genomic instability not be bad?

Answer 10

Mutations in non-coding regions as well as point mutations within the 3rd base of a codon.

Question 11

Name the 4 processes which cause instability?

Answer 11

Loss of high-fidelity in DNA replication (in S phase)
Errors during chromosome segregation in mitosis
Un-coordinated cell cycle progression
Error prone repair of sporadic DNA damage

Question 12

Describe High-Fidelity?

Answer 12

The degree of exactness with which something is copied or reproduced.

Question 13

Name the 8 ways that maintenance of high-fidelity of DNA-Replication can be affected?

Answer 13

Polymerase accuracy
Mismatch repair
Origin licensing
Maturation of okasaki fragments
Restart stalled replication forks
Re-chromatinisation
Telomere maintenance
Preservation epigenetic signatures

Question 14

What type of mutations are implicated in polymerase accuracy?

Answer 14

Point mutations

Question 15

What type of mutations are implicated in mismatch repair (MMR)?

Answer 15

Point mutations

Question 16

What is Origin Licensing?

Answer 16

It is a process that occurs once per S phase and identifies regions of DNA replication (to begin).

Question 17

How can Origin Licensing be affected by mutations?

Answer 17

Causes DNA breakage and recombination. CIN most common.

Question 18

What are the results of mutations affecting Origin Licensing?

Answer 18

Over-replication gives potential amplification, DNA breakage and recombination.

Under replication gives potential loss of genome on cell division.

Question 19

Draw the process of over-initiation and name it.

Answer 19

Onion-Skinning model

See Sue Cotterill Lecture - Genomic Instability - Slide 18

Question 20

What are Okazaki Fragments?

Answer 20

Short, newly synthesized DNA fragments that are formed on the lagging template strand during DNA replication. They are complementary to the lagging template strand, together forming short double-stranded DNA sections.

Watch YouTube Video.

Question 21

How can maturation of Okazaki Fragments be affected in DNA maintenance?

Answer 21

Retention of RNA and generation of nicks and gaps causing DNA breakage and recombination.

Fragile.

Possible CIN.

Question 22

What are replication forks?

Answer 22

The first step in DNA replication is the separation of the two DNA strands that make up the helix that is to be copied. DNA Helicase untwists the helix at locations called replication origins. The replication origin forms a Y shape, and is called a replication fork.

Question 23

What is the outcome of restarting stalled replication forks?

Answer 23

Chance that the some of the genome is lost at cell division, therefore causing DNA breakage upon recombination.

Question 24

What is the outcome of not restarted stalled replication forks?

Answer 24

Under-initiation, meaning ends are un-replicated and can invade chromosomes.

See Onion Skinning.

Question 25

What are the effects of mutations on re-chromatinisation?

Answer 25

Potential to stall replication leading to potential loss of genome on cell division, DNA breakage and recombination.

Question 26

What are the implications of mutations on telomere maintenance?

Answer 26

Loss of sequences at chromosome ends, DNA breakage and recombination. High susceptibility for translocations.

Question 27

What are the effects of not preserving epigenetic signatures?

Answer 27

Lack of accurate transcriptional information. Preserving modifications such as methylation are key, otherwise you can change the gene expression, however this is temporary as you can add back to it.

Question 28

What are epigenetic signatures?

Answer 28

Epigenetic signatures are examples of DNA modifications that cause switching on and off of genes.

Epigenetics is the study of mechanisms that switch genes on or off.

Question 29

Name errors that occur during chromosome segregation in mitosis? (7)

Answer 29

Chromosome condensation
Sister chromatid cohesion
Kinetochore assembly and attachment
Centrosome duplication and attachment
Spindle formation
Chromatid segregation
Cytokinesis

Question 30

Problems with chromosome condensation?

Answer 30

If they do not condense they are hard to untangle.

Question 31

What is sister chromatid cohesion?

Answer 31

Chromatids join together and do not separate/or separate early.