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. 2003 Jul;73(1):131-51.
doi: 10.1086/376565. Epub 2003 Jun 9.

Mutational mechanisms of Williams-Beuren syndrome deletions

Mònica Bayés  1 , Luis F Magano, Núria Rivera, Raquel Flores, Luis A Pérez Jurado
Affiliations

Mutational mechanisms of Williams-Beuren syndrome deletions

Mònica Bayés et al. Am J Hum Genet. 2003 Jul.

Abstract

Williams-Beuren syndrome (WBS) is a segmental aneusomy syndrome that results from a heterozygous deletion of contiguous genes at 7q11.23. Three large region-specific low-copy repeat elements (LCRs), composed of different blocks (A, B, and C), flank the WBS deletion interval and are thought to predispose to misalignment and unequal crossing-over, causing the deletions. In this study, we have determined the exact deletion size and LCR copy number in 74 patients with WBS, as well as precisely defined deletion breakpoints in 30 of them, using LCR-specific nucleotide differences. Most patients (95%) exhibit a 1.55-Mb deletion caused by recombination between centromeric and medial block B copies, which share approximately 99.6% sequence identity along 105-143 kb. In these cases, deletion breakpoints were mapped at several sites within the recombinant block B, with a cluster (>27%) occurring at a 12 kb region within the GTF2I/GTF2IP1 gene. Almost one-third (28%) of the transmitting progenitors were found to be heterozygous for an inversion between centromeric and telomeric LCRs. All deletion breakpoints in the patients with the inversion occurred in the distal 38-kb block B region only present in the telomeric and medial copies. Finally, only four patients (5%) displayed a larger deletion ( approximately 1.84 Mb) caused by recombination between centromeric and medial block A copies. We propose models for the specific pairing and precise aberrant recombination leading to each of the different germline rearrangements that occur in this region, including inversions and deletions associated with WBS. Chromosomal instability at 7q11.23 is directly related to the genomic structure of the region.

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Figures

Figure 1
Figure 1
Schematic representation of the 7q11.23 genomic region in normal chromosomes (N) and chromosomes with the WBS deletions. Blocks A, B, and C of centromeric (c), medial (m), and telomeric (t) LCRs are represented by black arrows that indicate their relative orientation. The single-copy regions between and outside the LCRs are depicted as gray lines. The limits of the common 1.55-Mb and the rarer 1.84-Mb deleted regions found in our patients with WBS are indicated by dotted lines. The few atypical nonrecurrent deletions that have been reported are not represented in this figure (reviewed by Korenberg et al. ; Pérez Jurado 2003). The locations of the relevant polymorphic markers used in this study are indicated.
Figure 2
Figure 2
Genotyping results of the multiple copy microsatellites BASTR1 (D7S489) and BBSTR1 in selected families (11: father, 01: patient and 12: mother). BASTR1 recognizes four loci, one within the commonly deleted region (D7S489B, allele range 168–180), one in block Am (D7S489A, allele range 136–144) and two different D7S489C loci (allele range 144–160) located in blocks Ac (D7S489Cc) and At (D7S489Ct). BBSTR1 recognizes three loci, one from each block B. Asterisks over each peak indicate the number of alleles, as predicted by dosage analysis. a, In family 28, the patient shows six alleles corresponding to loci D7S489A and D7S489C, but only one allele within the range of D7S489B (upper panel) and five alleles at BBSTR1 (lower panel). Therefore, this patient lacks one block B but none of the block A copies, indicating that he bears the typical 1.55-Mb deletion that arose as a result of crossing-over between blocks Bc and Bm. Both parents have a normal number of alleles at each locus. b, In family 34, the son affected with WBS displays only one allele at D7S489A and D7S489B (upper panel) and only four alleles at BBSTR1 (lower panel), whereas both parents have a normal number of alleles at each locus. Therefore, the patient has a larger deletion (1.84 Mb) that includes two blocks B (Bc and Bm) and one block A, most probably because of recombination between blocks Ac and Am.
Figure 3
Figure 3
Mapping the region of exchange in block B in 30 WBS unrelated patients with the common 1.55-Mb deletion. a, Detailed scheme representing the entire ∼143-kb length of block B. Note that the last 38 kb (dotted arrow) are absent in block Bc. Polymorphic microsatellite markers and genes are shown on the top. Exons are depicted as black boxes and numbers at the top indicate the first and last exons within the block. Locations and sequence differences of the 13 SSNs used in this study are indicated below the line. b and c, Each row represents the inferred recombinant block B in the deleted chromosome of each individual with WBS (Pt: patient; Ori: parental origin of the deletion, P: paternal, M: maternal). The predicted genotypes at each position are depicted as circles: white circles, Bc-type; black circles, Bm-type; gray circles, Bt-type; half-white/half-gray circles, either Bc-type or Bt-type; half-white/half-black circles, either Bc-type or Bm-type; half-gray/half-black circles, either Bm-type or Bt-type. A question mark is used when the number of Bc, Bm, or Bt copies cannot be determined because a polymorphism in this position is detected in at least one of the parents. Patients without the inversion (N) are grouped in b, whereas patients with predicted inversion (I) are displayed in c. For each patient, mapping of the region of exchange was narrowed between two SSNs as depicted by a thicker line. Note that in 7–12 of 19 patients without the inversion, the transition from Bc (half-white/half-gray circle, because Bt can not be ruled out) to Bm (black circle) occurs somewhere within the 12 kb between SSNs 1 and 2 (b). On the other hand, all patients with the inversion undergo the transition from Bt (gray circle) to Bm (black circle) somewhere between SSNs 11 and 13, at the end of the block (c).
Figure 4
Figure 4
Analysis of samples from patients with WBS and their progenitors with block B SSNs to map deletion breakpoints. Relative block dosages calculated from band intensities, as described in the “Methods” section, are depicted bellow each lane. a, Representative results of the SSN 4 assay, which amplifies exon 2 of the NCF1 gene and NCF1P1/NCF1P2 pseudogenes. Both pseudogenes in blocks Bc and Bt have a 2-bp deletion at the beginning of exon 2 (delGT) that is not present in the NCF1 gene in Bm. Patients 20.01 and 21.01 show one gene copy versus four pseudogenes, suggesting that the deletion breakpoint is telomeric to this point. Patients 3.01 and 61.01 display two gene copies versus three pseudogenes, indicating that the crossing-over occurred proximal to this position. Patients 17.01 and 35.01 have a 1 Bm:4 (Bc+Bt) ratio, most likely because of the presence of three block Bt copies (see fig. 3c). Progenitor 21.12 has three gene-type copies and three pseudogenes, most probably as a result of gene conversion. b, Results of the SSN 9 assay in a few patients. A nucleotide change in exon 14 of GTF2RD2/GTF2RD2P1/GTF2RD2P2 creates a restriction site for HaeIII in blocks Bm and Bt that is not present in Bc, as represented in the scheme. Patients 20.01 and 40.01 show three digested copies versus two nondigested copies, indicating that unequal crossing-over occurred distal to this position. On the contrary, patients 71.01 and 37.01 have three digested copies versus two nondigested copies, showing that the breakpoint is proximal to this nucleotide. Patients 17.01 and 35.01 display a 1 Bc:4 (Bc+Bt) ratio, most likely because of the presence of three block Bt copies (see panel c). c, SSN 11 assay allows detection of the inversion in patients with WBS. As represented in the scheme, a nucleotide change in block Bt destroys a Tru9I site that is present in blocks Bc and Bm. Patients 7.01, 71.01, and 42.01 show three digested copies (blocks Bc and Bm) versus two nondigested copies (block Bt), suggesting the existence of two block Bt copies, one in each chromosome. In patients 17.01 and 35.01, we observe a reduction of the intensity of bands 3 and 4 (Bc and Bm) and an increase of the intensity of band 1 (Bt). The patient/progenitor block B ratio is close to 3 in both cases, suggesting the existence of three block Bt copies (one in the normal chromosome and two in the WBS chromosome) but only two blocks Bc and Bm (both in the normal chromosome). The 3 Bt:2 (Bc+Bm) ratio suggests that the WBS chromosome arose in a progenitor heterozygous for the inversion. Dosage calculations in sample 23.11 indicate that he has only one Bt-like copy versus five Bc and Bm blocks, most probably as a result of gene conversion. His son, patient 23.01, inherited this polymorphism.
Figure 5
Figure 5
Amplification of a deletion-junction fragment in some patients. a, PCR strategy for amplifying a deletion-junction fragment containing the prohibitin (PHBP1) pseudogene and part of introns 19 and 20 of the GTF2I gene. Specific primers for blocks Bc and Bm/Bt allow the amplification of a recombinant Bc-Bm fragment of 3.4 kb. A nested primer that anneals to all three blocks and amplifies a 2.0-kb product from blocks Bm and Bt was used as an internal positive PCR control. b, The PCR assay detects a de novo 3.4-kb fragment in patients 37.01, 56.01, and 57.01 not present in their healthy parents. The same fragment is also found in patients 3.01 and 7.01 but also in one of their parents, probably because of the presence of a polymorphism.
Figure 6
Figure 6
Detection of the 7q11.23 inversion polymorphism in WBS transmitting progenitors by three-color interphase FISH. a, Order of the probes along a normal chromosome and a chromosome with the 7q11.23 inversion polymorphism. The probes, from centromere to telomere, correspond to RP11-421b22, RP11-622p13, and RP4-665p05. Centromeric, medial, and telomeric LCRs are depicted as black arrows. b, On interphase nuclei from two transmitting mothers showing a triple dosage of the Bt allele (60.12 and 35.12), two different chromosomes can be distinguished: one with the signals in the expected order (N) and another in which the yellow signal appears between the red and the green, indicating an inversion of the region (INV). A nucleus from a control individual with two normal chromosomes is also shown.
Figure 7
Figure 7
a, Mechanism for the origin of the inversion polymorphism. During chromosome pairing in cell division, the large inverted segmental duplications containing centromeric and telomeric blocks A, B, and C may favor the partial refolding of one chromosome, allowing intrachromatid or unequal sister chromatid synapsis. Nonallelic homologous recombination (black X) can occur in block C, A, or B, resulting in a paracentric inversion ranging in size from 2.34 to 1.79 Mb. b, Mechanism for the generation of the WBS deletion in parents heterozygous for the inversion polymorphism. Asynapsis at the inverted region promotes the folding of both chromosomes, to attempt pairing of homologous sequences. Note that the centromeric and telomeric segmental duplications are identical in length at blocks C and A, but block Bc is 38 kb shorter than block Bt, which is identical to Bm. In this model, all sequences of the region could undergo perfect matching with sequences from the homologous chromosome. The WBS chromosome is the result of unequal crossing-over (black X) either between block Bt from the inverted chromosome and Bm from the normal one (type 1) or between block Bm from the inverted allele and block Bt of the normal one (type 2). Recombination events at any other site within the loops would result in either acentric or dicentric chromosomes 7 (most likely nonviable). N: normal chromosome, I: inverted chromosome.
Figure 8
Figure 8
Haplotype analyses of 13 families with WBS, performed using polymorphic markers centromeric to (D7S653, D7S672, D7S1816, and BBSTR1cen), within (CR16T, ELN, and D7S1870), and telomeric to (WBStel1, BBSTR1tel, and D7S2518) the WBS deleted region. Absence or presence of recombination between centromeric and telomeric markers indicates that the deletion arose as a result of an intra- or interchromosomal recombination event, respectively. In the inverted chromosomes, absence or presence of recombination between centromeric markers and WBStel1 indicates that the deletion arose through a type 1 (patient 51.01) or type 2 (patients 16.01, 120.01, 35.01, 54.01, and 60.01) interchromosomal crossing-over event, respectively (fig. 7b). The brackets encompass the inverted interval with the arrows indicating the position of the WBStel1 marker in chromosomes with an inversion (.11: father, .01: patient, .02/.03: unaffected sibs, and .12: mother).
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References

Electronic-Database Information

    1. BLAST search engine, http://www.ncbi.nlm.nih.gov/BLAST/
    1. ClustalW, http://searchlauncher.bcm.tmc.edu/multi-align/multi-align.html
    1. DNAsp 3.51, http://www.ub.es/dnasp/
    1. GenBank, http://www.ncbi.nih.gov/GenBank/ (for BACs CTA-269p13 [accession number AC005080], RP11-396k3 [accession number AC006995], RP11-450o3 [accession number AC105418, RP11-483g21] [accession number AC00416], 239c10 [accession number AC004883], RP4-771p04 [accession number AC083884], RP11-813J7 [accession number AC005098], CTA-350l10 [accession number AC124781], RP11-729p19 [accession number AC027219], and RP11-219m8 [accession number AC124781]; prohibitin-related ESTs from fetal brain [accession number AA076811]; and stomach cancer [accession number AW814764])
    1. Genome Database, http://gdbwww.gdb.org/ for primer information on HSB055XE5 [ID number 609780], D7S489 [ID number 188049], D7S653 [ID number 199574], D7S672 [ID number 199800], D7S1816 [ID number 684408], D7S2518 [ID number 612411], and D7S1870 [ID number 377150])

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