19.01.18 LCRs and genomic disorders Flashcards
What are low copy repeats?
- LCRs are sequence elements with high homology that are common in the human genome.
- 1-400kb in size with >90% homology
- They occur multiple times in the genome
- Thought to have arisen during evolution by duplication of genomic segments
- Can contain genes, pseudogenes, gene fragments, endogenous retroviral sequences etc
- Make up 5-10% of the genome
- Provide the substrate for NAHR
- Often located in pericentromeric (i.e. near centromere) and telomeric regions
What is a genomic disorder?
A condition that occurs due to rearrangement of the genome (and not a base pair change). Examples are:
- Mendelian disorder (NF1, CMT1A/HNPP)
- Contiguous gene syndrome (Williams, PWS/AS, DiGeorge)
- Chromosomal disorder (idic(15), translocations, markers)
Contiguous gene syndrome
- CGSs are caused by the loss or gain of multiple adjacent genes (some of which are dosage sensitive)
- Leads to a recognised clinical phenotype
LCRs - What mechanisms can lead to them causing disease?
- Normally get homologous recombination between allelic regions of DNA which is important to repair DNA damage, and to also introduce genetic variation during meiosis
- Recombination can take place between LCRs in different genomic positions due to Non-allelic homologous recombination (NAHR)
- Likelihood of NAHR occurring between LCRs depends on:
1) Repeat size
2) Degree of homology
3) Distance between LCRs
4) Orientation with respect to each other
5) MEPs (minimal effect processing segment) - NAHR can cause rearrangements, gains and losses
- Can led to recurrent changes, due to certain regions being rich in LCRs (i.e. recurrent del/dup syndromes with identical breakpoints)
- Can also get non-recurrent changes due to non-homologous end joining (NHEJ) and replication based mechanisms (RBMs)
NAHR
- Occurs between homologous regions what are in different genomic positions
- Mainly a recombination event during meiosis and mitosis
- Can get unequal crossovers during NAHR which cause genomic rearrangements
- Cause disease if get a change in copy number of dosage sensitive genes, gene disruption, creation of fusion genes, postion effects, unmasking of recessive traits or interruptions of transvection (communication between alleles)
- Recurrent genomic rearrangements are normally caused by NAHR between LCRs
- Can occur during meiosis or mitosis
- During meiosis - NAHR would cause constitutional rearrengements
- During mitosis - NAHR would cause somatic mosaicism or neoplasms
- Cohesin proteins usually hold sister chromatids together, and normally get recombination between them
- NAHR can be interchromosomal (between LCRs on two homologous chromosomes) or intrachromosomal (between LCRs on chromatids of the same chromosome) or intrachromatid (LCRs on the same chromatid)
NAHR hotspots
- Positions within LCRs where crossovers preferentially occur
- Hotspots normally occur where nucleotides are identical for 200 to 450bp in length
- Recurrent breakpoints occur in these regions
MEPS (Minimal efficient processing segment)
- This is the minimal stretch of identical sequence required to enable homologous recombination
- Length of MEPS can be different between meiosis (300-500bp) and mitosis (shorter region)
- Length of MEPS is also determined by how far the LCRs are from each other (the further away they are, the longer the MEPS)
What are paralogous genomic segments?
- Non-allelic genomic segments with identical DNA sequences
- Normally hundreds of kbs in size
- Flank breakpoint junctions for recurrent changes
- Can get del, dup, inversion, dicentric chr, ring
- Reciprocal dels and dups do not occur at same frequency
- During meiosis, dels more common than dups (but this could be due to dels having a more severe phenotype and therefore identified more often)
What are the 2 molecular mechanisms for NAHR?
1) Unequal crossing-over
- Recombination-based mechanism
- Can form dup and reciprocal del in the same event
2) BIR (Break-induced replication)
- Replication-based mechanism
- Occurs when a replication fork collapses or breaks and the broken molecular uses extopic homology to restart the replication fork
- BIR forms dups and dels in separate events
Name 2 other mechanisms that can form non-recurrent rearrangements?
1) NHEJ (non-homologous end joining)
2) FoSTes (Folk stalling and template switching)
LCRs do not mediate either of these mechanisms, but they are often found close to the breakpoints and therefore may stimulate the rearrangements.
NHEJ (non-homologous end joining) - list the stages of the process
- Mechanism for repair of double stranded DNA breaks
- Break is identified
- Broken DNA ends are bridged, modified and ligated
- Does not require LCRs
- Often the incorporation of additional bases leaves a ‘molecular scar’
FoSTes (Folk stalling and template switching)
- Plays an important role in the origin of genomic-disorder-associated non-recurrent rearrangements that have a complex structure
- DNA replication fork stalls and lagging strand disengages from the original template and anneals to another replication fork nearby
- Micro-homology-mediated break-induced replication (MMBIR) – depending on location of the new fork, a deletion or duplication will occur
- Shown to play a role in MECP2 dups, dels and dups of 17p13.3 etc
- Likely to be a major mechanism for generating structural variation, particularly non-recurrent CNVs
Example of LCR/NAHR disorders - Williams-Beuren Syndrome (WBS)
- 1.6Mb deletion at 7q11.23 (contains ELN gene)
- There are 3x300kb repeat structures (LCRs called cen, mid and tel)
- Common deletion results from NAHR between cen and mid LCRs
Example of LCR/NAHR disorders - PWS/AS
- Common 4Mb del and dup results from NAHR between complex >500kb LCRs at 15q11-q13
- 4 large clusters of complex repeats are called BP1 - BP4
- Distal breakpoints in 95% of cases is BP3
- Larger, less common, deletions use BP4
- Proximal breakpoints cluster with BP2 (60%) or BP1 (40%)
Example of LCR/NAHR disorders - CMT1A/HNPP
- 17p12 deletion of PMP22 = CMT1A
- 17p12 duplication of PMP22 = HNPP
- Recurrent breakpoints map to separate LCRs in region
