Intrachromosomal mitotic nonallelic homologous recombination is the major molecular mechanism underlying type-2 NF1 deletions

Abstract

Nonallelic homologous recombination (NAHR) is responsible for the recurrent rearrangements that give rise to genomic disorders. Although meiotic NAHR has been investigated in multiple contexts, much less is known about mitotic NAHR despite its importance for tumorigenesis. Because type-2 NF1 microdeletions frequently result from mitotic NAHR, they represent a good model in which to investigate the features of mitotic NAHR. We have used microsatellite analysis and SNP arrays to distinguish between the various alternative recombinational possibilities, thereby ascertaining that 17 of 18 type-2 NF1 deletions, with breakpoints in the SUZ12 gene and its highly homologous pseudogene, originated via intrachromosomal recombination. This high proportion of intrachromosomal NAHR causing somatic type-2 NF1 deletions contrasts with the interchromosomal origin of germline type-1 NF1 microdeletions, whose breakpoints are located within the NF1-REPs (low-copy repeats located adjacent to the SUZ12 sequences). Further, meiotic NAHR causing type-1 NF1 deletions occurs within recombination hotspots characterized by high GC-content and DNA duplex stability, whereas the type-2 breakpoints associated with the mitotic NAHR events investigated here do not cluster within hotspots and are located within regions of significantly lower GC-content and DNA stability. Our findings therefore point to fundamental mechanistic differences between the determinants of mitotic and meiotic NAHR.

Tissue-specific differences in the proportion of mosaic large NF1 deletions are suggestive of a selective growth advantage of hematopoietic del(+/−) stem cells

“…By contrast, type-2 deletions frequently arise during postzygotic cell division giving rise to somatic mosaicism with normal cells coexisting alongside those harboring the deletion Petek et al, 2003;Roehl et al, 2010;Steinmann et al, 2007]. At least 44% of all patients with type-2 NF1 deletions exhibit somatic mosaicism [Messiaen et al, 2011].…”

“…Table S4. Additionally, we investigated the intrinsic error rate of the FISH analysis using EBV-transformed lymphoblastoid cell lines from a patient with a non-mosaic (germline) type-2 NF1 deletion (patient 2429), previously characterized by Roehl et al [2010], and two patients with type-1 NF1 deletions (patients 1746 and 2490.1). Both these patients had type-1 deletions with breakpoints located within the paralogous recombination site 2 (PRS2) hotspot as determined by breakpoint-spanning PCR .…”

“…Type-2 NF1 deletions are also smaller, spanning 1.2 Mb and including only 13 genes. The breakpoints of type-2 deletions are located within SUZ12 and its pseudogene SUZ12P [KehrerSawatzki et al, 2004;Petek et al, 2003;Roehl et al, 2010;Steinmann et al, 2007]. A third type of recurrent NF1 deletion (type-3) has been reported recently [Bengesser et al, 2010;Pasmant et al, 2010;Zickler et al, 2011].…”

Alu elements mediate large SPG11 gene rearrangements: further spatacsin mutations

“…39 Moreover, this motif was present in breakpoint regions of disease-causing nonallelic homologous recombination hotspots 40 and could, in theory, also be involved in SPG11 deletions. Through bioinformatic analysis, we found 13 degenerate sequences that occur 23 times over the gene's length, although none of them is located near any of the deletions identified in SPG11 patients.…”

NF1 microduplications: identification of seven nonrelated individuals provides further characterization of the phenotype

“…8 Type 2 microdeletions have predominantly been seen as a result of mitotic NAHR and are 1.2 Mb in size with breakpoints within SUZ12 and its pseudogene SUZ12P adjacent to NF1-REP C and NF1-REP A, respectively (Figure 1). [12][13][14] The 1.0-Mb type 3 NF1 microdeletions are the smallest of the three, mediated by LCRs NF1-REP B and NF1-REP C (Figure 1). 6,11 NAHR between LCRs, such as NF1-REPs A, B, and C, lead to both deletion and duplication of the intervening sequence.…”