18.01.16 Origin of structural abnormalities Flashcards
What mechanisms can lead to genomic rearrangement? Give examples.
- Non-replicative non-homologous repair mechanisms e.g. NHEJ, MMEJ, Breakage-fusion-bridge cycle
- Replicative non-homologous repair mechanisms e.g. FoSTeS, MMBIR, chromothripsis
What are the potential underlying mechanisms of reciprocal translations?
Could be potentially formed via NHEJ, MMEJ, FoSTeS or MMBIR.
What is NHEJ?
Example of non-replicated non-homologous repair mechanism to repair double-strand breaks (DSB).
It requires no homology and often leads to small (1-4bp) deletions or insertions of free DNA at the breakpoints as a result of editing at breakpoints to make them compatible for ligation.
NHEJ is considered to be the major mechanism generating chromosomal translocations in cancer.
What is MMEJ?
This mechanism requires short regions of homology (5-25bp) at either side of a double strand break allowing repair to occur through annealing and ligation.
This mechanism often leads to deletion of sequences located between the regions of homology. This mechanism appears to be the one associated with chromosomal fusions formed between critically shortened telomeres
What is the breakage-fusion-bridge cycle?
Chromosome or sister-chromatid fusion due to telomere erosion can create dicentric chromosomes; during anaphase, these centromeres can be pulled to separate nuclei resulting in breakage of the chromosome.
The broken ends of this chromosome are then prone to further rounds of fusion and subsequent breakage.
This cycle will stop when the chromosome acquires a telomere.
This repeated cycle of breakage and fusion is believed to play an important role in the generation of chromosome instability in cancer.
Which mechanisms is thought to be a large contributor to translocations seen in leukaemia?
Incorrect repair by NHEJ and MMEJ in the presence of multiple double strand breaks is thought to be the major contributor to translocations seen in leukaemia.
Sequence motifs (e.g. TTTAAA) and repetitive sequences (such as LTRs, LINE, Alu) that promote secondary structure formation in DNA such as hairpin and cruciform are prone to DBSs and this may explain why such regions are often found in proximity of translocation breakpoints.
When do replicative non-homologous repair mechanisms act?
during DNA replication
What is FoSTeS?
During replication fork stalling, the 3’ end of the lagging DNA strand can disengage from the original template and anneal, by virtue of microhomology, to a single-stranded section of DNA in a nearby replication fork, where synthesis restarts. “Nearby” refers to spatial closeness and not necessarily adjacent in primary sequence.
How does FoSTeS lead to genomic rearrangements?
This mechanism could cause deletions, duplications, inversions or translocations depending on the relative position of the two replication forks.
Switching to a downstream fork would result in deletion, while switching to an upstream from would result in duplication. FoSTeS can occur multiple times in series leading to more complex rearrangements.
Like other mechanisms leading to rearrangements, FoSTeS is likely to be influenced by local genomic architecture (e.g. palindromes or cruciform), with fork stalling caused by secondary structure formation, lesions in the template strand or a shortage of dNTPs.
What is MMBIR?
This mechanism is often associated with restart of a collapsed replication fork, it is initiated by a single-single stranded region at a double-strand break, the 3’ end anneals to any single-stranded template with which it shares micro-homology and is present in close proximity. The break is repaired through DNA replication of this end, using the invaded region as a template.
How does MMBIR lead to genomic rearrangements?
Annealing of the invading end within a sister chromatid and depending upon the position and orientation of invasion can generate deletions, duplications and inversions, while annealing within a different chromosome can lead to translocation. Repeated MMBIR cycles can lead to complex chromosome rearrangements. MMBIR represents one model for the molecular mechanism of FoSTeS.
What is chromothripsis?
Chromothripsis: Joining, possibly via NHEJ, of chromosome portions that have been shattered into hundreds of pieces. This mechanism can explain highly complex derivative chromosomes seen in some cancers and in very few constitutional rearrangements. See review by Forment et al., (2012).
Give two examples of a recurrent translocation.
t(11;22)(q23.3;q11.2)
t(4;8)(p16;p23)
t(X;Y)(p22.3;p11)
Describe the formation of the recurrent t(11;22) translocation.
the most common recurrent translocation in humans is mediated by similar palindromic AT rich repeats (PATRR). A 450bp PATRR present on chr 11 and a 590bp PATRR on chr 22 (within LCR22) lead to intra-strand pairing and the formation of hairpin or cruciform structures. The centre of the palindrome is susceptible to DNA breakage that could lead to NHEJ between the two regions.
Describe the formation of the recurrent t(4;8) translocation.
t(4;8)(p16;p23): 8p23 contains two repeats of oldfactory receptor (OR) gene clusters, the distal (REPD) and the proximal (REPP)
4p16 also contains repeats of OR gene clusters with high degree of homology to the 8p23 repeats. It is thought that the similar REPs on chr 4 and 8 mediate the t(4;8)(p16;p23) translocation, however a specific mechanism does not seem to have been proposed.