title: Microhomology-mediated mechanisms underlie non-recurrent disease-causing microdeletions of the FOXL2 gene or its regulatory domain.
abstract: Genomic disorders are often caused by recurrent copy number variations (CNVs), with nonallelic homologous recombination (NAHR) as the underlying mechanism. Recently, several microhomology-mediated repair mechanisms--such as microhomology-mediated end-joining (MMEJ), fork stalling and template switching (FoSTeS), microhomology-mediated break-induced replication (MMBIR), serial replication slippage (SRS), and break-induced SRS (BISRS)--were described in the etiology of non-recurrent CNVs in human disease. In addition, their formation may be stimulated by genomic architectural features. It is, however, largely unexplored to what extent these mechanisms contribute to rare, locus-specific pathogenic CNVs. Here, fine-mapping of 42 microdeletions of the FOXL2 locus, encompassing FOXL2 (32) or its regulatory domain (10), serves as a model for rare, locus-specific CNVs implicated in genetic disease. These deletions lead to blepharophimosis syndrome (BPES), a developmental condition affecting the eyelids and the ovary. For breakpoint mapping we used targeted array-based comparative genomic hybridization (aCGH), quantitative PCR (qPCR), long-range PCR, and Sanger sequencing of the junction products. Microhomology, ranging from 1 bp to 66 bp, was found in 91.7% of 24 characterized breakpoint junctions, being significantly enriched in comparison with a random control sample. Our results show that microhomology-mediated repair mechanisms underlie at least 50% of these microdeletions. Moreover, genomic architectural features, like sequence motifs, non-B DNA conformations, and repetitive elements, were found in all breakpoint regions. In conclusion, the majority of these microdeletions result from microhomology-mediated mechanisms like MMEJ, FoSTeS, MMBIR, SRS, or BISRS. Moreover, we hypothesize that the genomic architecture might drive their formation by increasing the susceptibility for DNA breakage or promote replication fork stalling. Finally, our locus-centered study, elucidating the etiology of a large set of rare microdeletions involved in a monogenic disorder, can serve as a model for other clustered, non-recurrent microdeletions in genetic disease.
authors.affiliation: Center for Medical Genetics, Ghent University, Ghent, Belgium.
authors.forename: Hannah
authors.initials: H
authors.lastname: Verdin
authors.forename: Barbara
authors.initials: B
authors.lastname: D'haene
authors.forename: Diane
authors.initials: D
authors.lastname: Beysen
authors.forename: Yana
authors.initials: Y
authors.lastname: Novikova
authors.forename: Björn
authors.initials: B
authors.lastname: Menten
authors.forename: Tom
authors.initials: T
authors.lastname: Sante
authors.forename: Pablo
authors.initials: P
authors.lastname: Lapunzina
authors.forename: Julian
authors.initials: J
authors.lastname: Nevado
authors.forename: Claudia M B
authors.initials: CM
authors.lastname: Carvalho
authors.forename: James R
authors.initials: JR
authors.lastname: Lupski
authors.forename: Elfride
authors.initials: E
authors.lastname: De Baere
mesh_terms: D000483:Alleles; D016569:Blepharophimosis / Q000209:etiology / Q000235:genetics; D002874:Chromosome Mapping; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations / Q000235:genetics; D059766:DNA End-Joining Repair / Q000235:genetics*; D004260:DNA Repair / Q000235:genetics*; D000074842:Forkhead Box Protein L2; D051858:Forkhead Transcription Factors / Q000235:genetics / Q000378:metabolism; D015894:Genome, Human; D059765:Homologous Recombination / Q000235:genetics*; D006801:Humans; D008594:Menopause, Premature / Q000235:genetics; D017434:Protein Structure, Tertiary; D017384:Sequence Deletion; D012868:Skin Abnormalities / Q000209:etiology / Q000235:genetics; D013698:Templates, Genetic
chemical_list: C421604:FOXL2 protein, human; D000074842:Forkhead Box Protein L2; D051858:Forkhead Transcription Factors