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Characterization of the nonallelic homologous recombination hotspot PRS3 associated with type-3 F1 deletions

机译：与3型F1缺失相关的非等位基因同源重组热点PRS3的表征

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Nonallelic homologous recombination (NAHR) is the major mechanism underlying recurrent genomic rearrangements, including the large deletions at 17q11.2 that cause neurofibromatosis type 1 (NF1).Here, we identify a novel NAHR hotspot, responsible for type-3 NF1 deletions that span 1.0 Mb. Breakpoint clustering within this 1-kb hotspot, termed PRS3, was noted in 10 of 11 known type-3 NF1 deletions. PRS3 is located within the LRRC37B pseudogene of the NF1-REPb and NF1-REPc low-copy repeats. In contrast to other previously characterized NAHR hotspots, PRS3 has not developed on a preexisting allelic homologous recombination hotspot. Furthermore, the variation pattern of PRS3 and its flanking regions is unusual since only NF1-REPc (and not NF1-REPb) is characterized by a high single nucleotide polymorphism (SNP) frequency, suggestive of unidirectional sequence transfer via nonallelic homologous gene conversion (NAHGC). By contrast, the previously described intense NAHR hotspots within the CMT1AREPs, and the PRS1 and PRS2 hotspots underlying type-1 NF1 deletions, experience frequent bidirectional sequence transfer. PRS3 within NF1-REPc was also found to be involved in NAHGC with the LRRC37B gene, the progenitor locus of the LRRC37B-P duplicons, as indicated by the presence of shared SNPs between these loci. PRS3 therefore represents a weak (and probably evolutionarily rather young) NAHR hotspot with unique properties.
机译：非等位基因同源重组（NAHR）是潜在的基因组重排的主要机制，包括在17q11.2处导致1型神经纤维瘤病（NF1）的大缺失。在此，我们确定了一个新的NAHR热点，负责跨越3型NF1的缺失。 1.0 Mb。在11个已知的3型NF1缺失中，有10个出现在称为1个Pkb3的1kb热点内的断点聚类。 PRS3位于NF1-REPb和NF1-REPc低拷贝重复序列的LRRC37B假基因内。与其他先前表征的NAHR热点相反，PRS3尚未在预先存在的等位基因同源重组热点上发展。此外，PRS3及其侧翼区域的变异模式是不寻常的，因为只有NF1-REPc（而非NF1-REPb）的特征是高单核苷酸多态性（SNP）频率，这表明通过非等位基因同源基因转换（NAHGC）进行单向序列转移）。相比之下，先前描述的CMT1AREP中的强烈NAHR热点以及位于类型1 NF1缺失之下的PRS1和PRS2热点经历了频繁的双向序列转移。还发现NF1-REPc中的PRS3与LRRC37B基因（LRRC37B-P双链体的祖先基因座）LRNA37B基因一起参与了NAHGC，这两个基因座之间存在共享的SNP。因此，PRS3代表着具有独特属性的薄弱（可能在进化上还很年轻）的NAHR热点。

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