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Evidence for non-homologous end joining and non-allelic homologous recombination in atypical NF1 microdeletions

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Abstract

NF1 microdeletion syndrome is caused by haploinsufficiency of the NF1 gene and of gene(s) located in adjacent flanking regions. Most of the NF1 deletions originate by non-allelic homologous recombination between repeated sequences (REP-P and -M) mapped to 17q11.2, while the remaining deletions show unusual breakpoints. We performed high-resolution FISH analysis of 18 NF1 microdeleted patients with the aims of mapping non-recurrent deletion breakpoints and verifying the presence of additional recombination-prone architectural motifs. This approach allowed us to obtain the sequence of the first junction fragment of an atypical deletion. By conventional FISH, we identified 16 patients with REP-mediated common deletions, and two patients carrying atypical deletions of 1.3 Mb and 3 Mb. Following fibre-FISH, we identified breakpoint regions of 100 kb, which led to the generation of several locus-specific probes restricting the atypical deletion endpoint intervals to a few kilobases. Sequence analysis provided evidence of small blocks of REPs, clustered around the 1.3-Mb deletion breakpoints, probably involved in intrachromatid non-allelic homologous recombination (NAHR), while isolation and sequencing of the 3-Mb deletion junction fragment indicated that a non-homologous end joining (NHEJ) mechanism is implicated.

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Acknowledgements

The authors thank Dr. C. Sala (YAC Screening Center HSR-DIBIT, Milan) for providing BAC and PAC clones, Dr. F. Natacci for valuable clinical evaluation of NF1 patients, Dr. D. Jenne for providing DJ2290 and DJ2314 primers and useful suggestions for REP-PCR assay. This work was supported by FIRST (P.R.) and Italian Ministry of Health on Neurofibromatosis 1 (1999–2000).

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Authors and Affiliations

  1. Department of Biology and Genetics, Medical Faculty , University of Milan, via Viotti 3/5, 20133, Milan, Italy

    Marco Venturin, Cristina Gervasini, Francesca Orzan, Angela Bentivegna, Lucia Corrado, Patrizia Colapietro, Lidia Larizza & Paola Riva

  2. Clinical Genetics and Epidemiology Unit, Department of Pediatrics, University of Padua, Padua, Italy

    Alessandra Friso & Romano Tenconi

  3. Institute of Medical Genetics, University of Wales College of Medicine, Cardiff

    Meena Upadhyaya

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  1. Marco Venturin
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  2. Cristina Gervasini
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  3. Francesca Orzan
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  4. Angela Bentivegna
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  5. Lucia Corrado
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  6. Patrizia Colapietro
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  9. Meena Upadhyaya
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  10. Lidia Larizza
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  11. Paola Riva
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Correspondence to Paola Riva.

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M. Venturin and C. Gervasini contributed equally to the study

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Venturin, M., Gervasini, C., Orzan, F. et al. Evidence for non-homologous end joining and non-allelic homologous recombination in atypical NF1 microdeletions. Hum Genet 115, 69–80 (2004). https://doi.org/10.1007/s00439-004-1101-2

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