Complex rearrangements in patients with duplications of MECP2 can occur by fork stalling and template switching

Duplication at the Xq28 band including the MECP2 gene is one of the most common genomic rearrangements identified in neurodevelopmentally delayed males. Such duplications are non-recurrent and can be generated by a non-homologous end joining (NHEJ) mechanism. We investigated the potential mechanisms for MECP2 duplication and examined whether genomic architectural features may play a role in their origin using a custom designed 4-Mb tiling-path oligonucleotide array CGH assay. Each of the 30 patients analyzed showed a unique duplication varying in size from similar to 250 kb to similar to 2.6 Mb. Interestingly, in 77% of these non-recurrent duplications, the distal breakpoints grouped within a 215 kb genomic interval, located 47 kb telomeric to the MECP2 gene. The genomic architecture of this region contains both direct and inverted low-copy repeat (LCR) sequences; this same region undergoes polymorphic structural variation in the general population. Array CGH revealed complex rearrangements in eight patients; in six patients the duplication contained an embedded triplicated segment, and in the other two, stretches of non-duplicated sequences occurred within the duplicated region. Breakpoint junction sequencing was achieved in four duplications and identified an inversion in one patient, demonstrating further complexity. We propose that the presence of LCRs in the vicinity of the MECP2 gene may generate an unstable DNA structure that can induce DNA strand lesions, such as a collapsed fork, and facilitate a Fork Stalling and Template Switching event producing the complex rearrangements involving MECP2.

Thrasher Research Fund[NR-0017]

Thrasher Research Fund

U.S. National Institutes of Health (NIH)

National Institute of Child Health and Human Development (NICHD/NIH)

Mental Retardation and Developmental Disabilities Research Center[HD024064]

Mental Retardation and Developmental Disabilities Research Center

Texas Children`s Hospital GCRC

Texas Children`s Hospital GCRC[M01RR00188]

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Conselho Conselho Nacional de Desenvolvimento Cientifico e Tecnologico of Brazil (CNPq)

U.S. National Institutes of Health (NIH)

National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)[T32 NS43124]

National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)[1K08NS062711-01]

U.S. National Institutes of Health (NIH)

Polish Ministry of Education and Science[PBZ KBN-122/PO5/2004/01-9]

Polish Ministry of Education and Science