20.01.16 Origin of other structural abnormalities Flashcards
What produce double stranded breaks?
1) Clastogens (endogenous chromosome breaking agents)
2) exposure to exogenous agents (i.e. ionizing radiation)
- most get repaired, but if they don’t repair properly they can cause rearrangements
What causes most recurrent rearrangements?
- NAHR between LCRs
What causes non-recurrent rearrangements?
- Other DNA repair mechanisms (not NAHR)
1) Non-replicative non-homologous repair mechanisms - E.g. NHEJ, MMEJ, Breakage-fusion-bridge cycle
2) Replicative non-homologous repair mechanisms - E.g. FoSTeS, MMBIR, chromothripsis
Non-replicative non-homologous repair mechanisms
1) NHEJ (non-homologous end joining)
- Repairs DSBs
- Requires no homology
- Often leads to 1-4bp deletions or insertions at breakpoints (due to editing bp to make them compatible for ligation)
- Major method for generating translocations in cancer
- Steps of NHEJ:
1) heterodimer (containing Ku70 and Ku80) recognises broken site
2) form a scaffold to hole ends together
3) DNA-dependent protein kinase (artemis) is activated and trims the overhanging ends (exonuclease activity) and cleaves the hairpins together (endonuclease activity)
4) Polymerases will in single strand regions
5) DNA ligase end joins the double strands
Non-replicative non-homologous repair mechanisms
2) MMEJ (microhomology-mediated end joining or Alternative NHEJ)
- Mutagenic DSB repair mechanism
- causes deletions and insertions that flank break site
- requires short regions of homology (5-25bp) at either side of break
- Associated with HR defective tumours and chromosome fusions
- 3 steps to process:
1) Pre-annealing: ends are resected to expose regions of micro-homology by MRN/CtIP complex - introduces nicks to the BSD and degrades DNA by exonuclease
2) Annealing: Flanking regions of micro-homology then anneal
3) Post-annealing:XPF/ERCC1 nuclease complex then trims the non-homologous tails and DNA ligation occurs
Non-replicative non-homologous repair mechanisms
3) Breakage-fusion-bridge cycle
- Telomere erosion causes chromosomes or sister-chromatids to fuse - creating dicentric chromosomes
- During anaphase, centromeres can be puled to separate nuclei - breaking the chromosomes
- Broken ends can then go through further rounds of fusion and breakage
- Only stops when a new telomere is acquired
- Important process in MSI in cancer
Replicative non-homologous repair mechanisms
1) FoSTeS (fork stalling and template switching)
- If replication folk stalling occurs, 3’ end of lagging DNA strand disengages, and anneals to a isngle-stranded section of DNA in a physically nearby replication fork
- Synthesis then restarts
- Can cause dels, dups, invers, trans depending on position of two forks
- moving to downstream fork = deletion
- moving to upstream folk = duplication
- Can get inversions depending on whether the lagging or leading strand in the new fork was invaded and what orientation the second fork is in (compared to the first)
- Can occur multiple times causing complex rearrangements
Replicative non-homologous repair mechanisms
2) MMBIR (microhomology-mediated break-induced replication)
- Associated with restart of a collapsed replication fork
- Single-strand region in DSB initiates process
- 3’ end anneals to any single-stranded template with micro-homology and is physically close by
- Break is then repaired, using invaded region as a template
- can cause dels, dups and inversions if annealing occurs within a sister chromatid
- annealing with a different chromosome can cause translocation
- Repeated cycles can cause complex rearrangements
Replicative non-homologous repair mechanisms
3) Chromothripsis
- Normally cancer associated (?side effect of some treatments)
- massive rearrangements that occur in a short time
- Get lots of DSB in a micronucleus all at once, then repairing (maybe by NHEJ)
- Micronuclei are defective structures that only form during defective cell division (they trap mis-segregated and acentric chr fragments)
Other structural abnormalities - Reciprocal translocations
- can be formed by NHEJ, MMEJ, FoSTeS or MMBIR
- Can get recurrent ones in the population
1) t(11;22)(q23.3;q11.2) - most common human recurrent translocation
- caused by AT rich repeats (450bp PATRR on chr 11 and 590bp PATRR on chr 22)
- Causes formation of hairpin structures, and is susceptible to DNA breakage and NHEJ
- Balanced carriers at risk of offspring with Emanuel syndrome (due to 3:1 meiotic mal-segregation of the der(22)
2) t(X;Y)(p22.3;p11) - Inversion of Yp may predispose to this translocation causing XX males and XY females
Factors influencing partner choice in reciprocal translations
1) Spatial proximity
2) More likely at fragile sites (due to higher chance of having a DSB)
Other structural abnormalities - Robertsonian translocations
RTs can form via 5 methods:
1) centric fusion of two acrocentric chromosomes
2) break in one short arm and one long arm (whole arem translocation)
3) break in both short arms and formation of a dicentric chr
4) misdivision of the centromere
5) U-type exchange (break in both chromatids, they then loop around to join each other and form iso(chr) at next division)
- Type 1 is most common method for forming rob(13;14) and rob(14;21)
- Breakpoints are consistent - III seq on 14p, and I seq and rDNA seq on 13p and 21p respectively
- all other RT have variable breakpoints suggesting other mechanisms of formation
Other structural abnormalities - Terminal deletions
- Can be caused by DSBs that are repaired and stabilized
- 3 methods:
1) Telomere healing - synthesis of new telomere
2) Telomere capture - obtaining a new telomere sequence from another chromosome
3) Chromosome circularization - leading to ring formation
Other structural abnormalities - Ring chromosomes
- usually result from two terminal breaks in both chromosome arms, then get fusion of the broken ends = loss of material
- OR can get joining of one broken chromosome arm with telomeric region on other arm = loss of material
- OR can be formed by fusion of subtelomeric sequences or telomere-telomere fusion with no deletion = complete ring chromosome
Other structural abnormalities - 3 examples of Isodicentric chromosomes
1) idic(15q)
- Small ones use BP1 and BP2 of PWS/AS critical region
- Larger ones use BP3 and BP4 and other distal loci
- Majority occur via U-type exchange between LCRs on homologs
2) idic(22)(q11.2)
- Cat eye syndrome
- uses LCR22-A and LCR22-D
- Majority occur via U-type exchange between LCRs on homologs
3) idic(X)
- lots of palindromic segmental dups in proximal Xp region
- get NAHR between these regions which cause idic(X) with recurrent breakpoints
- Non-recurrent breakpoint forms most likely caused by FoSTeS or MMBIR
