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Hum Mol Genet. 2009 June 15; 18(12): 2188–2203.
Published online 2009 March 26. doi:  10.1093/hmg/ddp151
PMCID: PMC2685756

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

Abstract

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 ~250 kb 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.

INTRODUCTION

Loss-of-function mutations of the gene enconding X-linked methyl-CpG-binding protein 2 (MECP2) at Xq28 are associated with Rett syndrome [RTT (MIM 312750)], a neurodevelopmental disorder that affects 1:10 000 girls. In boys, similar mutations are associated with syndromic and non-syndromic forms of developmental delay (DD), mental retardation (MR) and fatal infantile encephalopathy. Recent reports suggest that increased MECP2 gene copy number also conveys a clinical phenotype, resulting in a DD/MR plus seizures syndrome in males (14). It is increasingly apparent that many neurological disease traits do not result from coding region mutations, but instead manifest due to subtle alterations in gene copy number caused by submicroscopic genomic duplications or deletions (e.g. Charcot–Marie–Tooth disease type 1A, Pelizaeus-Merzbacher disease, Parkinson disease, Alzheimer disease, Williams-Beuren syndrome and the reciprocal dup(7)(q11.23q11.23), 17q21.31 deletion syndrome etc.) (5,6).

Lubs et al. (7) described the first linkage study of a family in which five males manifested X-linked mental retardation (XLMR); the causal locus was narrowed to a 5 cM interval in Xq28, including MECP2 [MRXSL (MIM 300260)]. Ariani et al. (8) reported the first duplication of the MECP2 gene in a girl diagnosed as having the preserved-speech variant of Rett syndrome. However, they could not assess whether the duplication involved the entire gene or only the interrogated MECP2 exon due to methodology constraints. Subsequently, duplications of the MECP2 gene were reported in males with DD/MR and several other associated clinical signs. In contrast to the patient reported by Ariani et al. (8), MECP2 duplication female carriers are generally asymptomatic mothers of affected males and display a skewed X-chromosome inactivation pattern (14).

The predominant clinical features of males carrying MECP2 gene duplications are DD/MR (100%), infantile hypotonia (100%), absent speech (84%) and a history of recurrent infections (80%); other clinical signs such as genital or digital abnormalities, seizures, or lack of ambulation, sometimes followed by other sporadic signs, may be present in 40–60% of the patients (3). The reason for such phenotypic variability is not fully understood. However, duplication disorders such as Charcot–Marie–Tooth disease type 1A due to the CMT1A duplication have long been known to have variable phenotypes that can even be discordant in identical twins (9). Recently, our group observed that autism is a defining feature of boys with the MECP2 duplication syndrome, and female carriers also manifest neuropsychiatric phenotypes despite the nearly 100% favorable skewing of X-inactivation in peripheral blood (10).

The molecular mechanism(s) associated with MECP2 copy-number alteration is still not well defined. Characteristically, such rearrangements are non-recurrent and show a broad size variation among patients. Non-recurrent rearrangements such as these do not usually originate by non-allelic homologous recombination (NAHR), responsible for the generation of a number of recurrent rearrangements associated with genomic disorders (11). Instead, non-homologous end joining (NHEJ) and break-induced replication (BIR) have been suggested as possible mechanisms producing the MECP2 rearrangements (3,12). An alternate possibility is the recently described replication-based mechanism, Fork Stalling and Template Switching (FoSTeS) (13). FoSTeS was proposed as the mechanism responsible for non-recurrent PLP1 duplications at Xq22, associated with the genomic disorder Pelizaeus-Merzbacher disease [PMD (MIM 312080)]. FoSTeS is a replication-based mechanism that produces non-recurrent rearrangements potentially facilitated by the presence of low-copy repeats (LCRs) with unusual symmetry (e.g. inverted repeats). These rearrangements may be complex, for example, duplicated regions containing stretches of non-duplicated sequences, inverted regions, or triplications. Some of these complexities can be resolved only at the DNA sequence level as revealed by breakpoint junction sequencing (13). The FoSTeS model has been generalized and specific molecular details provided by the microhomology-mediated BIR (MMBIR) model that appears to be operative in all domains of life (14).

Based on the finding of a MECP2 duplication containing a triplicated region (3), we hypothesized that FoSTeS could be a mechanism underlying the genomic duplication rearrangements including MECP2. To test this hypothesis, we ascertained 30 patients with MECP2 duplications by chromosomal microarray analysis (CMA) and designed and applied a custom array for high-resolution genome analysis. This high-resolution analysis of the MECP2 rearrangements revealed complex genomic alterations observed at the array level of resolution in eight patients (27%). Statistical and bioinformatic analyses of the genomic architecture surrounding the breakpoint regions revealed a non-random grouping of most of the distal breakpoints into two LCR clusters, both telomeric to the MECP2 gene. Sequencing of five breakpoint junctions from four duplications revealed microhomologies at most of the junctions. One of the duplications had a complex breakpoint junction, including a gap and an inversion of the same region, consistent with the FoSTeS mechanism. FoSTeS thus appears to be a prevalent mechanism responsible for MECP2 gene duplications, possibly triggered by genomic instability due to the presence of complex LCRs (LCRs consisting of a cluster of different repeat subunits lying in either direction) (11) that facilitate the formation of single-stranded DNA sequences.

RESULTS

Duplicated and complex rearrangements detected using custom oligonucleotide array CGH

Diagnostic testing in our Medical Genetics Laboratories and other collaborating laboratories identified 30 males with increased MECP2 gene copy number using quantitative DNA methods and BAC or oligonucleotide-based CMA (15,16). FISH analyses confirmed duplication including MECP2 (data not shown). To determine the size, extent, genomic content and fine map position of the breakpoints for each duplication, we designed a tiling path oligonucleotide microarray spanning 4 Mb surrounding the MECP2 region at Xq28. Each duplication had a different size, ranging from 250 kb to 2.6 Mb (Fig. 1A, Table 1), and, therefore, varied in gene content (Fig. 1A). The smallest region of overlap (SRO) was 149 kb and included the MECP2 and IRAK1 genes.

Figure 1.
(A) Genomic region harboring duplications in our cohort of 30 patients analyzed by oligonucleotide array CGH. Solid red bars represent oligonucleotide probes for which the mean normalized log2 (Cy5/Cy3) ratio of the CGH signal, amid a 5 kb window, reached ...
Table 1:
Summary of results for the MECP2 duplication observed in 30 male patients.

The oligoarray resolution enabled us to detect the presence of complex rearrangements within the MECP2 region in eight out of 30 patients (27%) (Fig. 1A and B). In two patients (BAB2622, BAB2624), the duplication had interspersed stretches of non-duplicated sequences. In six patients (BAB2681, BAB2727, BAB2772, BAB2796, BAB2797, BAB2801), the duplication contained a triplicated region (Fig. 1A and B). The triplications varied in size: 33 kb (BAB2681), 41 kb (BAB2772), 90 kb (BAB2727), 174 kb (BAB2796), 359 kb (BAB2801) and 537 kb (BAB2797), and, in most cases did not involve the MECP2 gene, except in patients BAB2797 and BAB2801. Oligonucleotide array CGH revealed that all complexities were inherited from the mother in all cases tested (5 out of 8: BAB2622, BAB2727, BAB2772, BAB2797, BAB2801, Fig. 1B, Table 1). The MECP2 triplication present in patients BAB2797 and BAB2801 were inherited from the mother as shown by oligonucleotide CGH and/or FISH (Fig. 1C).

Features of a rearrangement prone region distal to MECP2

Bioinformatic analysis of the MECP2 genomic region was performed to investigate for the presence and characterize the structure of LCRs mapping within the interval. We found two LCR groups, in direct and inverted orientations, 47 kb and 201 kb telomeric to the MECP2 gene, respectively. del Gaudio et al. (3) designated these LCRs J and K. LCR J spans 114 kb and is formed by two genes that constitute the Opsin array, OPN1LW and OPN1MW, arranged in a head-to-tail tandem array and interrupted by copies of a gene with unknown function, TEX28 (Fig. 2). Each OPN1 plus TEX28 array set has a size range of 37–38 kb and they are termed JA, JB and JC. The OPN1LW and OPN1MW genes encode the visual red and green pigments, respectively. The nearby K1 and K2 LCRs are positioned in inverted orientation, have 99% sequence identity and are 11.3 kb long. In total, the LCR-containing region spans 215 kb.

Figure 2.
Breakpoints/join points group near or at the SDs around the MECP2 gene. (A) Solid red bars represent duplicated regions and blue bars represent triplicated regions. LCR J spans 114 kb and is formed by three genes that constitute the Opsin array, OPN1LW ...

Remarkably, we mapped 77% (23/30) of the distal duplication breakpoints in one of the LCRs within the ~215 kb region (Fig. 2). This region represents <10% of the 2.6 Mb genomic interval in which breakpoints were mapped. The K1 and K2 inverted LCRs seem especially associated with the complex rearrangements since at least one of their breakpoints mapped at these repeats. The distal breakpoints of all six triplications were mapped to the proximal K LCR (Fig. 2).

As one way to model the expected distribution of the distal endpoints for these segmental copy number changes, we used the locations of the proximal endpoints as an internal control. Assuming a completely random model for breakpoint occurrence, we observed 30 proximal endpoints over an ~1.8 Mb region. Using the Poisson distribution and Poisson process assumptions, these observations suggest a rate of breakpoint occurrence of approximately one breakpoint every 60 kb in our patient cohort. We can use this distribution of proximal endpoints to model a completely random-based case for the distribution of distal breakpoints. Under this Poisson model, a 215 kb region would have approximately 3.58 (about 3 or 4) breakpoint events in a cohort of 30 patients. However, 23/30 MECP2 duplication distal breakpoints group within this 215 kb LCR containing region giving us an excess of 19.42 or 6-fold more than expected (P < 2.2 × 10−16). It is important to note that the breakpoints of the complex rearrangements (e.g. the triplications) were not considered in the calculations, thus, even though we used a conservative sum, this simple Poisson model suggests an extremely unusual concentration of distal breakpoints.

To further refine our analysis of breakpoint positioning in the genome, we performed 10 000 replicate Monte Carlo simulations to better evaluate the non-random distribution of breakpoints considering a random allocation of segments and requiring them to overlap the MECP2 gene. To summarize these Monte Carlo outcomes, we determined two summary statistics for each of the simulation runs: the variance of the segment locations and the mean segment distal breakpoint. We find that our segments have far less variable locations (as measured by average breakpoint location) than would be expected for randomly simulated segments as only 415 of 10 000 or 0.0415 of the simulations segments had locations as variable or less variable than what we observed. We also found our observed segments to be very highly shifted relative to what would be expected. Only 165 of 10 000 or 0.0165 of the simulation runs had an average distal breakpoint that mapped as centromeric as what we observed (Fig. 2A). These results are represented in the graphic seen in Figure 2B. Moreover, the average distal breakpoint of our data maps at 153.0888 Mb, included within the 215 kb laden-LCR region, while the simulation results have an average breakpoint of 153.1899 Mb, which is outside of the LCR region (Fig. 2A and B). Taken together, these Monte Carlo results demonstrate not only that our segments are highly non-randomly distributed across this genomic region but also they are grouping around the shifted average breakpoint (153.0888 Mb), even accounting for the bias introduced by the fact that the segments overlap MECP2.

Additionally, five out of seven distal breakpoints that do not map to the 215 kb LCR region map in proximity to another pair of LCRs located >400 kb telomeric to the MECP2 gene. This LCR pair is constituted by 99% identical subunits (L1 and L2), lying in inverted orientation to each other (3) (Fig. 2A).

Breakpoint junction analysis reveals both simple and complex rearrangements

The breakpoint junctions were amplified using outward facing primers positioned at both ends of the duplication, as determined by aCGH, under the assumption that the repeated copies were arranged in tandem. Difficulties amplifying unique junctions and resolving them at the nucleotide level were anticipated, because the genomic interval surrounding MECP2 is laden with LCRs (3) thus often hampering the ability to uniquely position the exact breakpoint in the genome. Several other breakpoints were not obtained under the above assumptions despite multiple attempts, consistent with potential further unanticipated complexity at the breakpoints. Five breakpoint junctions from four duplications were obtained by long-range PCR and directly sequenced (Fig. 3A–D). Three out of four rearrangements were simple, resulting in tandem duplications (BAB2629, BAB2688 and BAB2770). The fourth one (BAB2727) was complex, and included an inversion.

Figure 3.Figure 3.
(AC) Breakpoints/Join points of the duplications in patients BAB2629, BAB2688, BAB2770, respectively. Reference and rearranged genomic structures are shown. The duplicated region is boxed with a black rectangle. Primers used to obtain breakpoint ...

The breakpoint junction from the duplication in BAB2629 was amplified using forward and reverse primers facing outwards, designed at the very end of the duplication breakpoints as determined by aCGH. The PCR product was sequenced and the breakpoint junction showed no microhomology between the distal and proximal reference sequences (Fig. 3A). The distal breakpoint occurred within an AluJo element, whereas the proximal breakpoint occurred within one of the introns of the GABRA3 gene. No SINEs/LINEs were detected within the surrounding 175 nt genomic interval (Fig. 3A).

The breakpoint junctions from the duplication in patients BAB2688 and BAB2770 were obtained as described for BAB2629. The distal breakpoint of BAB2688 duplication occurred in one of the FLNA introns and the proximal occurred in one of the L1CAM introns, very close to the next exon boundary. No SINEs/LINEs were detected within a 175 nt window around either proximal or distal breakpoint reference sequences. A TCC microhomology was observed at the junction point (Fig. 3B). In patient BAB2770, a microhomology of 4 nt (GCCT) was detected. The distal breakpoint was located in an AluSx element, whereas the proximal one was located in one of the exons of the PDZK4 gene (Fig. 3C).

Patient BAB2727 has a complex rearrangement observed at oligonucleotide array resolution: a triplication spanning ~90 kb encompassing the Opsin array and the proximal LCR K (Fig. 2A and and3D).3D). The non-functional copy of the Opsin array plus the functional gene, TKL1, are involved in the triplication. We designed forward and reverse primers for the duplicated and triplicated segment ends based on the oligoarray results. Long-range PCR reactions were performed using all possible primer combinations in both direct and inverted orientation. One of the breakpoint junctions was obtained using the proximal duplicated reverse primer plus the proximal triplicated reverse primer (Fig. 3D; the complete alignment of 175 nt flanking the breakpoints can be seen in Supplementary Material, Fig. S1). The sequence data revealed that the triplicated segment was inserted in an inverted orientation with respect to the reference genome. The breakpoint junction alignment plus the oligoarray probes involved in the triplication revealed that the first template switch probably occurred at the second TEX28 gene, located within the Opsin array (here termed as TEX28B). A second template switch, with the same strand orientation, occurred again and produced a gap of 74 bp at the junction. The new alignment region (an AluSx element) showed a 2 bp microhomology (GG) between proximal and distal reference sequences. An additional ACA triplet was inserted at the third breakpoint junction. Interestingly, the end of the second breakpoint junction was a short CACA repeat, suggesting that the polymerase enzyme may have ‘stuttered’ at this point and inserted the ACA by mistake. It may be generated by slipped-strand mispairing during DNA replication as there is a CA repeat before the junction (Fig. 3D). The third breakpoint occurred within the AluSx element, 15 bp from the second junction. This new junction aligned to the proximal duplicated region, extending into one of the introns of the ARHGAP4 gene. There was a 2 bp nucleotide microhomology (CA) between the breakpoint junction and the reverse strand within the intron of the ARHGAP4 gene; thus the ACA insertion due to the polymerase ‘stuttering’ preceded a switch of strand orientation. Analysis of this flanking region revealed a LINE element (L1 family) starting 5 bp from this junction point. Figure 3D summarizes our findings. We repeated the complete assay for this patient starting from the genomic DNA and confirmed the above findings. This complex rearrangement can be explained by a FoSTeS × 3 event (Fig. 3E). A summary of these results is presented in Table 1.

Presence of repetitive elements and high incidence of CTG/CAG motifs at the breakpoint junctions

Repetitive elements such as SINEs and LINEs were present at some, but not all, breakpoints in our cohort. Alu families were observed in four breakpoints in different patients and a LINE element was observed just once, 5 nt away from the junction (BAB2727). An AluJo family member was detected at the distal breakpoint of the BAB2629 duplication and an AluSx was observed at the distal breakpoint in BAB2770 duplication. In neither BAB2629 nor BAB2770 duplication did the proximal breakpoint have repetitive elements within a window of 175 nt. Interestingly, BAB2727 had two break events at the same AluSx element, only 15 bp apart from each other (Fig. 3D). In both events, the similarity between the exchanging strands was restricted to microhomologies at their join points, as the Alu elements are present in just one of the strands. BAB2688 duplication presented no repetitive sequences either at or within a window of 175 nt around the breakpoint junctions.

We analyzed the DNA sequence around the join points of the three MECP2 duplications potentially generated by FoSTeS (BAB2688, BAB2727 and BAB2770) for the presence of the trinucleotide sequence 5′-CTG-3′ and its complementary 5′-CAG-3′ sequence. Slack et al. (41) found a high incidence of the 5′-CTG-3′motif at the junctions produced by gene amplification apparently induced under stress in Escherichia coli. For our analysis, we defined a 175 nt window containing the breakpoint junctions at both distal and proximal reference genomic sequences. The CG median value for those genomic intervals was calculated (52%) in order to estimate the expected number of the CTG/CAG sequences. The expected number of CTG/CAG sequences was 45, whereas the observed number was 78, a statistically significant difference (Fisher exact test, P < 0.003).

We analyzed the breakpoint junction data reported for patients with PLP1 duplications in order to examine whether the frequency of that trinucleotide motif is increased in other regions shown to have complexities at the breakpoint junctions [data provided from Lee et al. (13)]. Considering a window of 175 nt and a GC median value of 41.7%, we also found an increased frequency of CTG/CAG motifs at the PLP1 duplication breakpoint junctions; the expected number of CTG/CAG sequences was 44, whereas the observed was 79 (Fisher exact test, P < 0.0017). Interestingly, Kornreich et al. (17) reported a high incidence of the 5′-CCTG-3′motif, which contains the trinucleotide CTG, at the junctions of non-homologous recombination sites causing deletions and duplications (including one complex rearrangement) in the human GLA gene.

DISCUSSION

High-resolution oligonucleotide array CGH confirms a broad size variation of duplications involving MECP2

MECP2 duplications are among the most frequently identified subtelomeric rearrangements in a cohort of 5380 cases referred for clinical array CGH (18). Duplications involving the MECP2 gene are characteristically non-recurrent, that is, each rearrangement has a different size and distinct breakpoints. In our cohort of 30 patients, they vary from~250 kb to~2.6 Mb in size. Syndrome-associated non-recurrent rearrangements usually share a common genomic region-of-overlap, the smallest region of overlap or SRO, encompassing the locus associated with the conveyed genomic disorder. The analysis of 30 patients with MECP2 rearrangements using high-density arrays enabled us to narrow the SRO to 149 kb. This region contains two genes, IRAK1 and MECP2, and the increased dosage of either one or both may cause the clinical phenotypes; although the current data in the aggregate suggest over-expression of the MECP2 gene as the main culprit. Supporting evidence comes from animal models as MECP2 duplication syndrome was predicted by the observation that mice engineered to over-express MECP2 develop a progressive neurological disorder, stereotypic and repetitive movements, epilepsy, spasticity, hypoactivity and early death (19). Furthermore, a patient with a complex rearrangement including MECP2 triplication, had the most severe phenotype consistent with an MECP2 dosage role in the development of the salient clinical endophenotypes (3).

The reason for the observed phenotypic variability among patients with MECP2 duplication is not fully understood. Each patient has a different duplication size, as observed in this present work and by others (3,12), consequently, different genes are involved. Some are well-known genes implicated in human diseases when deleted or harboring pathological point mutations, for example, ABCD1, can cause adrenoleukodystrophy [ALD (MIM 300100)], L1CAM, can cause hydrocephalus due to congenital stenosis of the aqueduct of Sylvius [HSAS (MIM 307000)], rearrangements and point mutations of the OPN1 array can cause colorblindness, deutan series [CBD (MIM 303800)] or protan series [CBP (MIM 303900)], FLNA can cause X-linked periventricular heterotopia [MIM 300049] and EMD can cause Emery–Dreifuss muscular dystrophy [EDMD (MIM 310300)]. Their roles, if any, when in functional disomy are not established. Reported data (2,4,20) suggest that duplication size is not correlated to severity or specificity of any neuropsychiatric phenotype and our data confirmed this contention (10). It is possible that genetic background plays a role in such variability, including SNP variation within the rearranged genomic segment on the non-duplicated allele (21), but further studies are required to clarify this hypothesis. Variable expressivity is a hallmark of duplication disorders; it occurs in patients carrying dup(7)(q11.23q11.23) (2225), dup(17)(p11.2p11.2) (26), dup(17)(q12q12) (27), dup(22)(q11.2q11.2) (28), etc. Such a characteristic was remarkably shown by discordant phenotypes in identical twins with the CMT1A duplication (9).

A genomic interval prone to polymorphic and disease-causing rearrangements

A first glimpse of MECP2 duplications at the array level reveals proximal and distal breakpoints scattered along the MECP2 flanking regions. The size of each duplication is unique, and the breakpoints are different, thus revealing the prominent feature of such rearrangements, their non-recurrent nature. However, careful analysis of the distal breakpoints reveals a remarkable grouping pattern: 77% or 23/30 of the breakpoints mapped within a 215 kb region 47 kb distal from the MECP2 gene. This 215 kb region is formed by the J LCR group (JA, JB, JC) and the K LCR group (K1 and K2) sharing 99% sequence identity within each LCR (3,29). Using a Monte Carlo algorithm and considering the bias introduced by the fact that all duplications must overlap the MECP2 gene, we showed that not only the distal breakpoints are non-randomly distributed across the genomic region but also they present an unexpected average location within the LCR-laden region. This result confirmed a Poisson analysis, which revealed that this breakpoint grouping is highly significant (P < 2.2 × 10−16). Despite not considered in calculations, we can also clearly observe that the distal breakpoints of all six triplications detected in our cohort are grouped at the proximal K LCR.

LCR J is formed by two genes that constitute the Opsin array, OPN1LW and OPN1MW, plus three copies of the TEX28 gene. The OPN1LW and OPN1MW genes provide one of the earliest examples of tandem repeats and NAHR associated with a common human trait, color blindness (30). Usually, more than one OPN1MW gene is present, but only the proximal is functional. Approximately 25% of Caucasians have one copy, 50% two copies and 25% three or more copies of the gene (reviewed in 31). The Opsin genes share 99% sequence identity and undergo frequent rearrangements, probably by unequal crossing-over between the highly similar units, and gene conversions producing common variation in color vision and red–green color vision defects.

The region between the LCRs K is inverted in 33% of females of European descent and represents a common polymorphism within this population (32). Non-recurrent deletions involving one of the K LCRs and the EMD gene have been reported to cause EDMD (32,33). Remarkably, another LCR inverted pair (L1 and L2, >400 kb telomeric to the MECP2 gene) is associated with the two most distal breakpoint duplications. Each L subunit displays one copy of the NEMO gene (L1 has a functional copy and L2 has a non-functional copy), in which intragenic deletions produce most of the de novo cases of Incontinentia Pigmenti [IP (MIM 308300)] (34). Rearrangements and gene conversion involving L1 and L2 have been reported (35). In total, 83% (25/30) of the distal duplication breakpoints map within an LCR region, suggesting an association between the local genomic structure (presence of LCRs) and the occurrence of rearrangements therein.

In aggregate, these findings suggest that the genomic interval telomeric to MECP2 is a highly unstable region that undergoes frequent rearrangements leading to either human population polymorphism or disease. The genomic architecture neighboring the MECP2 gene, in this case the presence of the LCRs J and K, seems to have an important role in the origin of such events. LCRs mediating recurrent rearrangements through NAHR can cause deletions and duplications in many genomic disorders (5,11). For non-recurrent rearrangements there is evidence for an alternative role by which LCRs lead to genomic instability and consequently stimulate such events rather than mediate them (13,29,3638). Bacolla et al. (39) showed an association of genomic rearrangement breakpoints with alternative DNA conformations, represented by non-B DNA (i.e. slipped, cruciform structures, etc.) that can potentially trigger genomic rearrangements in humans because they are expected to increase the rate of single-strand lesions at these sequences. Such alternative conformations can be formed by regions presenting, for instance, direct, mirror or inverted repeats. Thus, by inference LCRs may be appropriate substrates in which alternative conformations can form. We propose that J and K LCRs form non-B DNA structures, potentially cruciforms, and cause DNA single-strand lesions and rearrangements involving the MECP2 gene. Single strand lesions can lead to collapsed replication forks and the formation of one-ended, double-stranded DNA (dsDNA) ends that stimulate FoSTeS/MMBIR (13,14). A similar ‘grouping’ of breakpoints on one side near complex genome architecture was also observed with PLP1 duplications (13).

Complex rearrangements associated with MECP2 duplications implicate FoSTeS

The use of high-resolution tiling-path oligonucleotide arrays to investigate rearrangements involving the MECP2 gene enabled us to detect complexities at the array level. Such complexities were observed either as triplications of varying sizes interrupting the duplicated regions or duplicated regions interrupted by long stretches of normal copy number. At the sequencing level, we also detected a complex rearrangement in the breakpoint junction of patient BAB2727, involving at least three DNA strand discontinuities (FoSTeS × 3), including a triplication and an inversion of one of the DNA stretches (Fig. 3D). These complex alterations as described are not readily explained by either NAHR or NHEJ, the usual recombination-based mechanisms proposed to explain human genomic rearrangement events. NAHR is mostly mediated by LCRs with recombination hotspots, gene conversion and apparent minimal processing fragments (MEPS), usually producing recurrent rearrangements and clustering of breakpoints (reviewed in 36). Here, we demonstrate an absence of such characteristics in MECP2 duplication samples.

NHEJ and homologous recombination (HR) are the repair pathways responsible for double-strand break (DSB) repair in cells. Following detection of DSBs, NHEJ re-joins the broken DNA ends without homology requirements; this process requires the preparation of damaged ends using base removal and insertions of new bases, without ensuring sequence restoration around the break. Woodward et al. (40) and Lee et al. (29) used a two-step model of HR and NHEJ DSB repair to explain the origin of duplications involving the proteolipid protein 1 (PLP1) gene in patients with PMD.

However, Lee et al. (13), using high-resolution oligoarray CGH and breakpoint junction sequencing, detected complex rearrangements not observed before with PLP1 duplications, likely reflecting technology limitations. The presence of complex rearrangements therein, similar to those observed in MECP2 duplication patients described herein, led Lee et al. (13) to propose a new replication-based mechanism, FoSTeS to explain them. This is a modified mechanism based on long-distance template switching during DNA replication, proposed by Slack et al. (41) as a model to explain gene amplification induced under stress in Escherichia coli. According to Slack et al. (41), events are initiated by collapsed forks that are repaired by recombination, initiating replication. If this replication stalls, 3′-ends are released, and these might resume DNA synthesis on a different template, possibly on a second nearby replication fork. Microhomologies at the junctions or ‘join point’ reflect priming on the switched template strand, possibly later stalling, disengaging and switching template again. Serial replication fork and lagging strand invasion could occur several times (e.g. FoSTeS × 2, FoSTeS × 3, etc.) before resumption of replication on the original template by the tethered strand (13,36). Such long-distance template switches driven by microhomologies can explain the origin of duplications and triplications (if the switches occur to a fork that is replicating the region before the stalling point), inversions (switching to a template in the reverse orientation), as well as the occurrence of gaps and duplications interspersed by normal copy number (14). Slack et al. (41) showed that the proposed template switching events can involve a switch of a nascent lagging strand to a lagging strand template, but they also reported switching between leading and lagging strands producing DNA inversions.

Hastings et al. (14) proposed a novel MMBIR pathway. This model hypothesizes that chromosomal structural changes result from aberrant repair of collapsed (broken) replication forks. In certain cell environments, the normal repair of collapsed forks by BIR is unavailable because of down-regulation of Rad51, the protein that allows 3′-ends at collapsed forks to re-invade the sister molecule. Under these circumstances, after the processing of the single dsDNA end generated from the collapsed fork, the single-strand 3′-tails will anneal with microhomology to any single-stranded DNA nearby, prime low processivity polymerization with multiple template switches and eventual re-establishment of processive replication. Hastings et al. (14) proposed MMBIR as a mechanistically specific general model applicable to all life forms that encompasses the FoSTeS model for human genomic rearrangements. Recent work in yeast shows that broken forks are the precursor lesions directly processed into segmental duplications (SDs) (42). Importantly, a functional Pol32, one of the subunits from the major replicative DNA polymerase in S. cerevisae, is a crucial requirement for the formation of SD in yeast, therefore, suggesting that genomic duplications can arise from DNA synthesis rather than unequal crossing-over (42).

Similar to what is observed with MECP2, duplications involving the PLP1 gene are non-recurrent. Most PLP1 duplication distal breakpoints group in the vicinity of complex LCRs, intervals to which complex rearrangements also map (13,29,43). Furthermore, the complex LCRs, wherein the PLP1 duplication breakpoints group, are highly polymorphic in the population, a similar observation to that described here for MECP2 rearrangements and summarized in Figure 4.

Figure 4.
Alignment of the join points to the genomic locations of each FoSTeS in the context of regional LCRs. Positions are given relative to NCBI Build 35 for the X chromosome. Rearrangements reported previously in the literature are represented in different ...

Distinguishing features at the MECP2 duplication breakpoint junctions/join points

We were able to sequence five breakpoints/join points in four patients. One of them (BAB2629) had an apparent simple duplication by aCGH and showed no microhomology at the breakpoint junction suggesting NHEJ as the mechanism for formation. Two of them (BAB2688 and BAB2770 with apparent simple duplication by aCGH) had microhomologies of 3–4 nt, suggesting either the NHEJ mechanism or, alternatively, FoSTeS × 1. Remarkably, though, the occurrence of complex rearrangements in 27% of patients is strongly suggestive of the FoSTeS mechanism and that mechanism alone is sufficient to explain the observed junction complexity at the sequencing level. Under the FoSTeS hypothesis, breakpoint junctions might be better referred to as ‘join points’ because junctions arise by the juxtaposition of genomic sequences and microhomology reflecting the priming of DNA replication. The join point of patient BAB2727 (Fig. 3D and E), who has a complex duplication–triplication–duplication by aCGH, is consistent with the occurrence of FoSTeS a total of three times, including two switches of the template strand direction resulting in an inversion (FoSTeS × 3). The second breakpoint junction, deleted for 74 nt, can also be explained by the serial replication slippage model (SRS) (44). SRS assumes that the 3′-end of the nascent strand dissociates from the original template and invades other templates based on microhomology. SRS and FoSTeS share some general features. SRS can promote rearrangements between sequences at the same replication fork, and requires nascent strand disassociation presumably by a helicase. FoSTeS allows switching of replication forks, thus, the rearrangements can occur over longer distances, and initiates from a collapsed fork that generates a single dsDNA end with an available 3′ end for priming DNA synthesis on the switched template (36,45). Noteworthy, there is a region of perfect complementary match GCCA/CGGT just posterior or anterior to each GG direct repeats. The presence of this tract may approximate both direct repeats in the same strand and stimulate either FoSTeS or SRS to occur.

We examined for the occurrence of particular sequences flanking the breakpoint regions in both MECP2 and PLP1 duplication join points; such consistent presence might provide clues to the mechanism/enzymes involved on the rearrangements. In this regard, we found an increased frequency of the sequences 5′-CTG-3′/5′-CAG-3′ flanking the breakpoint junctions of the rearrangements. In prokaryotes, the 5′-CTG-3′ trinucleotide represents a minimal primase recognition site (the so-called G-site) (46,47). It signals the start of the synthesis of primer RNAs that initiate DNA replication leading and lagging-strand synthesis. In Escherichia coli, the high incidence of the 5′-CTG-3′ trinucleotide in or near the junctions produced by gene amplification induced under stress has been suggested as evidence for a relationship between such junction occurrences and the ends of the Okazaki fragments (41). The participation of the lagging strand and the involvement of the ends of the Okazaki fragments are features seen with the Long Distance Template Switching model proposed by Slack et al. (41). The observation of increased incidence of 5′-CTG-3′ trinucleotides near the junction of both MECP2 and PLP1 duplications raises the intriguing question as to whether such a motif might represent a cis acting sequence that may be a recognition site for proteins involved in priming DNA replication in eukaryotes.

The presence of repetitive sequences, especially Alu families, is a remarkable characteristic of the MECP2 duplication breakpoints, despite the fact that they do not seem fundamental to the formation of the breakpoint junctions. Bauters et al. (12) reported a 2.5-fold enrichment of Alu elements at the breakpoint of MECP2 duplications. In our cohort, we found Alu elements in 40% of the proximal/distal reference sequences involved at the breakpoints/join points (4 in 10) but none has an Alu present on both sides, a requirement for substrates participating in NAHR. Repetitive elements may have an important role in homologous recombination. Shaw and Lupski (48) showed that Alu elements could be used as substrates for NAHR in non-recurrent 17p11.2 chromosomal deletions causing Smith–Magenis Syndrome. The role of such sequences in other mechanisms, such as NHEJ and FoSTeS, is not well understood, but they are more frequent than expected if the breakpoints occurred randomly throughout the genome (48). Woodward et al. (40) found a high incidence of interspersed repetitive elements (69%) at the breakpoint junctions of patients with PLP1 duplications. Toffolatti et al. (49) also found a high incidence of such elements at the breakpoints of deletions within the dystrophin gene. Importantly, Alu repeats have been postulated to play a role in the spread of SDs in humans. Bailey et al. (50) analyzed 9464 SD junctions and found a statistically significant enrichment of Alu elements near or within the junctions; and similar to our results, most of them showed Alu repeat sequences in only one side of the alignment. A similar result was obtained by Babcock et al. (51) when they analyzed the genomic sequence of known LCR22 genes and their duplicated derivatives. Thus, an association between Alu elements and rearrangements throughout the genome is consistently observed; however, its biological significance remains elusive.

The occurrence of similar characteristics at the breakpoint junctions of non-recurrent rearrangements in different genomic locations such as duplications involving MECP2, PLP1 and dystrophin gene, with or without complexities, raises the intriguing hypothesis that the underlying mechanisms may be the same. Since neither NAHR nor NHEJ are sufficient to explain the more complex rearrangements, we propose that the mechanism is FoSTeS/MMBIR (13,14).

Bauters et al. (12) reported sequencing of three MECP2 duplicated breakpoint junctions in three patients, all of them with 2–5 bp microhomologies at the juxtaposition region. Remarkably, two out of three patients have duplicated DNA stretches of the Xq28 distal region inserted amid the MECP2 duplications. Bauters et al. (12) proposed BIR as the mechanism by which such complexities have arisen. Indeed, BIR and its extended version, Template Switching BIR (52), have been suggested as mechanisms underlying SDs and other structural changes in yeast and human. This mechanism is strongly RecA/Rad51-dependent and homology-dependent, and because of that it is usually an accurate process involving long lengths of homology between DNA sequences (reviewed by 14). This, however, does not fit with the microhomology junctions (usually between 2 and 6 nt) found at the breakpoint junctions of the rearrangements generated by MMBIR/FoSTeS (13). Therefore, we propose that the presence of short microhomologies, such as those reported by Bauters et al. (11), is rather consistent with a FoSTeS/MMBIR mechanism.

In conclusion, the presence of complex rearrangements, characteristically observed in rearrangements generated by FoSTeS/MMBIR, imply that this mechanism underlies many MECP2 rearrangements. Recently, Bi et al. (53) identified patients carrying submicroscopic duplication in 17p13.3 involving the PAFAH1B1 (LIS1) and/or the YWHAE (14-3-3ϵ) genes; three out of seven patients with complex rearrangements are also suggestive of FoSTeS as a mechanism for formation. Likewise, the FoSTeS mechanism can potentially explain some of the complex LCR-associated rearrangements observed in the literature, such as a patient with aplasia of Mullerian ducts carrying a complex rearrangement at the 22q11.21 region (54), and the patients carrying duplication/triplication/inversion involving the olfactory receptors/defensin repeats at 8p23.1 (55). The LCRs associated with these rearrangements, even though not mediating FoSTeS directly, might be able to bring the replication forks together and facilitate the replication fork-switching event (36). Alternatively, the presence of LCRs in the MECP2 vicinity can generate an unstable DNA structure, which can induce DNA strand lesions and collapsed forks that facilitate FoSTeS/MMBIR during the replication process. Additionally, the local presence of SINEs, LINEs or the enrichment of specific sequences, such as the 5′-CTG-3′/5′-CAG-3′, may influence the occurrence of FoSTeS at a given location, reinforcing the importance of genomic architecture for this mechanism.

MATERIALS AND METHODS

Samples

Peripheral blood samples from patients were submitted for clinical testing to the Baylor Medical Genetics Laboratories for either MECP2 deletion/duplication analysis or CMA. The methodology used to screen the samples (quantitative DNA methods and BAC-based chromosomal microarray analysis) has been described (3). All the duplications were confirmed by either aCGH platform [such as a commercial aCGH for patient BAB2797 or aCGH X-chromosome tiling-path (56) for patient BAB2688] or by another methodology such as FISH or MLPA as described (3): BAB2616, BAB2617, BAB2618, BAB2619, BAB2620, BAB2622, BAB2623, BAB2624, BAB2625, BAB2626, BAB2627, BAB2628, BAB2629, BAB2769, BAB2770, BAB2771, BAB2796, BAB2798, BAB2799, BAB2800, BAB2801, BAB2802; FISH and/or MLPA as described (20): BAB2681, BAB2682 and BAB2683; Agilent 244K Oligonucleotide array CGH: BAB2727. Microduplications in patients BAB2666 and BAB2772 were identified by Signature Genomics Laboratories and confirmed by FISH or MLPA. We identified 21 males with increased MECP2 gene copy number. Three laboratories (one from the Department of Pediatrics at Baylor College of Medicine, Houston, TX, USA, and two from genetics institutes in Poland and Brazil) identified nine additional patients based on clinical characteristics associated with MECP2 duplication and further MECP2 screening analysis. Genomic DNA was extracted from blood leukocytes using the Puregene DNA isolation kit (Gentra Systems, Minneapolis, MN), and DNA concentration was measured using the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Rockland, DE). The screening protocol was approved by Baylor College of Medicine Institutional Review Board.

Parental analysis was done by FISH or MLPA, when DNA was available. Most of the patients (21 out of 30) inherited the duplication from their mother. Two duplications were de novo (BAB2618 and BAB2620). In patient BAB2620 the duplication inserted into the Y-chromosome, but the father is not a carrier. In seven cases parental DNA was not available (BAB2616, BAB2619, BAB2624, BAB2625, BAB2626, BAB2628, BAB2799). Five mothers of patients carrying complexities were analyzed by oligonucleotide array CGH. The complexities were inherited from the mother for all patients, including the complex junction found in BAB2727, as confirmed by DNA sequencing.

Probes design

We designed a tiling-path oligonucleotide microarray spanning 4 Mb around the MECP2 region at Xq28. The custom 4X44K Agilent Technologies microarray (#G4426A) was designed using the Agilent website (http://earray.chem.agilent.com/earray/). We selected 8323 probes covering the ChrX: 150 400 000–154 400 000 (NCBI build 35), including the MECP2 gene, which represents an average resolution of one probe per 500 bp. Probe labeling and hybridization were performed following the manufacturer’s protocol (Agilent Oligonucleotide Array based CGH for Genomic DNA analysis, version 4.0 plus the 4X44K complementary protocol with modifications unique to the four-pack format). Briefly, 1.5 µg of genomic male/female reference and patient DNA were digested with AluI (5 U) and RsaI (5 U) (Promega) for 2 h at 37°C. Digestions were verified by agarose gel electrophoresis. Labeling reactions with Cy5-dUTP for patient DNA and Cy3-dUTP for male/female reference DNA were performed according to the manufacturer’s instructions (Agilent Genomic DNA Labeling Kit Plus, #5188–5309). Individual dye-labeled reference and patient samples were purified using Microcon Ym-30 filters (Millipore Corporation). DNA yield was determined using a NanoDrop ND-1000 UV-VIS spectrophotometer. Each dye-labeled patient and gender-matched reference DNA was combined with 5 µg human Cot-1 DNA (Invitrogen Corporation), Agilent Blocking Agent, and Agilent hybridization buffer (#5188–5220). These mixtures were denatured at 95°C for 3 min, pre-incubated at 37°C for 30 min, and hybridized to the array in a hybridization chamber (Agilent Technologies) for 40 h at 65°C in a rotating oven (Agilent Technologies). Array slides were washed using Agilent Wash solutions 1 and 2 (#5188–5226), Acetonitrile (Sigma-Aldrich), and Stabilization and Drying Solution (#5185–5979), according to the manufacturer’s instructions.

Slides were scanned on a GenePix 4000B Microarray Scanner (Axon Instruments). Images were analyzed and data were extracted, background subtracted, and normalized using Agilent Feature Extraction Software A.7.5.1. These data were subsequently imported into array CGH Analytics software v3.1.28 (Agilent Technologies). The genomic copy number was defined by the analysis of the normalized log2 (Cy5/Cy3) ratio average of the CGH signal, amid a 5 kb window. Regions that reached a threshold of 0.6 were considered as duplication, whereas thresholds of 1.2 were considered as triplication.

Based on the high-resolution data, sets of primers were designed at the apparent boundaries of each duplicated segment(s) (as determined by a transition from normal copy number to gain in copy number) for all patients but BAB2796 and BAB2797, and used for long-range PCR amplification as described below (primers facing outward, inward and in the same direction).

Long-range PCR amplification using outward-facing primers

Assuming tandem duplications, and using outward-facing primers (with respect to the reference sequence), long-range PCR was performed using TaKaRa LA Taq (TAKARA Bio) or Phusion high-fidelity polymerase with HF buffer (Finnzymes Oy). A 50 µl PCR analysis was performed using 2.5 U TaKaRa with 1× PCR buffer, 0.4 mm dNTP, 10 pmol of each primer, 1 µl DMSO and 200 ng DNA template. The PCR conditions were as follows: 98°C for 30 s, 32 cycles at 94°C for 1 min, 65°C for 20 s and 68°C for 20 min, followed by 68°C for 10 min. The Phusion polymerase reaction conditions were as follows: 98°C for 30 s, followed by 12 cycles of 98°C for 10 s, 67°C for 30 s (−1°C/cycle) and 72°C for 30 s per kb (initial attempt: 15 kb or 7 min and 30 s), followed by 30 cycles of 98°C for 10 s, 55°C for 30 s and 72°C for 30 s per kb finalizing with 72°C for 10 min. Amplification products were electrophoresed on 0.8–1% agarose gels, PCR products from any unique bands were purified, using a gel extraction kit, and were analyzed by DNA sequencing.

To investigate the possibility of small inversions at breakpoint junctions, PCR amplification was attempted using forward and reverse primers at the apparent boundaries of each duplicated segment(s) using both pairs of primers facing in only one direction and pairs of primers facing inward.

Bioinformatic and sequence analysis

The human reference genome sequence for the MECP2 gene and flanking regions covering 4 Mb of repeat-masked DNA sequence was analyzed using NCBI build 35 at the Genome Browser Gateway at the University of California Santa Cruz (http://genome.ucsc.edu/cgi-bin/hgGateway) and Blast 2 browser with default parameters (http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi). We aimed to define the genomic architecture in the Xq28 region that potentially facilitates the MECP2 duplication events. Specifically, this analysis was performed by dividing the entire analyzed region into ~1 Mb segments; the sequence for each ~1 Mb segment was then compared with itself and with each of the other segments by BLAST 2 to identify LCR sequence and genomic architecture within the analyzed region. CG content was calculated using the web-based software MCLAB (http://www.mclab.com/toolbox/oligo_calculator2.jsp). DNA motifs were determined using The Sequence Manipulation suite (http://www.bioinformatics.org/sms2/).

Statistical analysis

We performed 10 000 replicate Monte Carlo simulations to evaluate the non-random distribution of breakpoints considering a random allocation of segments and requiring them to overlap the MECP2 gene. To perform the simulation, we first determined each segment’s size. We then simulated locations of segments in our cohort as follows: we randomly chose a start position for each segment by drawing uniformly from the values from the interval (MECP2-start-S, MECP2-stop), where S= segment size–1. This procedure was repeated for each segment adjusting the maximal start and stop position accordingly. Each simulation run determined a randomly distributed set of segment locations with the same distribution of segment sizes as for our observed data and with the restriction that each segment would overlap MECP2. To summarize these Monte Carlo outcomes, we determined two summary statistics for each of the simulation runs: the variance of the segment locations and the mean segment distal breakpoint.

FUNDING

This work was supported by the Thrasher Research Fund (NR-0017 to C.M.B.C.); the National Institute of Child Health and Human Development (NICHD) and Mental Retardation and Developmental Disabilities Research Center (HD024064); Texas Children’s Hospital GCRC grant (M01RR00188). Additional support was obtained from Conselho Conselho Nacional de Desenvolvimento Científico e Tecnológico of Brazil (CNPq) (to C.M.B.C.); National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) (T32 NS43124 and 1K08NS062711-01 to M.B.R); Polish Ministry of Education and Science grant PBZ KBN-122/PO5/2004/01-9. The content is solely the responsibility of the authors and does not necessarily represent the official views of NICHD, NINDS, or NIH.

Supplementary Material

[Supplementary Data]

ACKNOWLEDGEMENTS

The authors are grateful to Philip J. Hastings for his valuable critical reviews. We thank Marjorie A. Withers for her outstanding technical support.

Conflict of Interest statement. None declared.

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