Week 2 - Genomic Instability Flashcards
Define Genomic instability
Unscheduled alterations, either of a temporary or permanent nature, within the genome.
Name the types of Genomic Instability
Chromosomal Instability (CIN) Nucleotide-Level Instability
Name the types of CIN
Loss and Gain of Chromosomes (Aneuploidy) Translocations Deletions Duplications Inversions
How to detect Nucleotide Level Changes
PCR
Sanger Sequencing
What are the types of Translocations?
Balanced and Unbalanced exchange
What are the outcomes of Genome Instability and Cancer? (4)
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
How do you identify point mutations?
PCR/Sequencing
What is an example of the effect of duplication? CLUE Protein Imbalance
Increase in protein concentration of Brachyury protein
Germ-line tandem duplication of the T (brachyury) gene causes familial chordoma
(Chordoma Foundation, 2017)
Why is genomic instability good?
SNP’s - Natural Variation in population
Immune cells - Antibodies
How can genomic instability not be bad?
Mutations in non-coding regions as well as point mutations within the 3rd base of a codon.
Name the 4 processes which cause instability?
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
Describe High-Fidelity?
The degree of exactness with which something is copied or reproduced.
Name the 8 ways that maintenance of high-fidelity of DNA-Replication can be affected?
Polymerase accuracy Mismatch repair Origin licensing Maturation of okasaki fragments Restart stalled replication forks Re-chromatinisation Telomere maintenance Preservation epigenetic signatures
What type of mutations are implicated in polymerase accuracy?
Point mutations
What type of mutations are implicated in mismatch repair (MMR)?
Point mutations
What is Origin Licensing?
It is a process that occurs once per S phase and identifies regions of DNA replication (to begin).
How can Origin Licensing be affected by mutations?
Causes DNA breakage and recombination. CIN most common.
What are the results of mutations affecting Origin Licensing?
Over-replication gives potential amplification, DNA breakage and recombination.
Under replication gives potential loss of genome on cell division.
Draw the process of over-initiation and name it.
Onion-Skinning model
See Sue Cotterill Lecture - Genomic Instability - Slide 18
What are Okazaki Fragments?
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.
How can maturation of Okazaki Fragments be affected in DNA maintenance?
Retention of RNA and generation of nicks and gaps causing DNA breakage and recombination.
Fragile.
Possible CIN.
What are replication forks?
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.
What is the outcome of restarting stalled replication forks?
Chance that the some of the genome is lost at cell division, therefore causing DNA breakage upon recombination.
What is the outcome of not restarted stalled replication forks?
Under-initiation, meaning ends are un-replicated and can invade chromosomes.
See Onion Skinning.
What are the effects of mutations on re-chromatinisation?
Potential to stall replication leading to potential loss of genome on cell division, DNA breakage and recombination.
What are the implications of mutations on telomere maintenance?
Loss of sequences at chromosome ends, DNA breakage and recombination. High susceptibility for translocations.
What are the effects of not preserving epigenetic signatures?
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.
What are epigenetic signatures?
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.
Name errors that occur during chromosome segregation in mitosis? (7)
Chromosome condensation Sister chromatid cohesion Kinetochore assembly and attachment Centrosome duplication and attachment Spindle formation Chromatid segregation Cytokinesis
Problems with chromosome condensation?
If they do not condense they are hard to untangle.
What is sister chromatid cohesion?
Chromatids join together and do not separate/or separate early.
