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Homologous Nonallelic Recombinations Between the Iduronate-Sulfatase Gene and Pseudogene Cause Various Intragenic Deletions

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Homologous Nonallelic Recombinations Between the Iduronate-Sulfatase Gene and Pseudogene Cause Various Intragenic Deletions European Journal of Human Genetics (1998) 6, 492–500 t © 1998 Stockton Press All rights reserved 1018–4813/98 $12.00 http://www.stockton-press.co.uk/ejhg ORIGINAL PAPER Homologous nonallelic recombinations between the iduronate-sulfatase gene and pseudogene cause various intragenic deletions and inversions in patients with mucopolysaccharidosis type II Susanna Bunge1, Michaela Rathmann1, Cordula Steglich1, Marie-Louise Bondeson2, Anna Tylki-Szymanska3, Ewa Popowska4 and Andreas Gal1 1Institut f¨ur Humangenetik, Universit¨ats-Krankenhaus Eppendorf, Hamburg, Germany 2Beijer Laboratory, Department of Medical Genetics, Uppsala University, Uppsala, Sweden 3Departments of Metabolic Disease and 4Genetics, Child Health Centre, Warsaw, Poland About 20% of patients with mucopolysaccharidosis type II (MPS II) have gross structural rearrangements involving the iduronate-sulfatase (IDS) gene in Xq27.3–q28. A nearby IDS pseudogene (IDS-2) promotes nonallelic recombina- tion between highly homologous sequences. Here we describe major rear- rangements due to gene/pseudogene recombination. In two unrelated patients, partial IDS gene deletions were found joining introns 3 and 7 of the IDS gene together with gene to pseudogene conversion in the area of breakpoints. In a third patient, a junction between intron 3 of IDS-2 and intron 7 of IDS was seen that was due to a deletion and inversion of the 5' part of the gene. Characterisation of breakpoints in six patients with large inversions revealed that all recombinations of this type occurred in the same area of homology between IDS and IDS-2; they were molecularly balanced, and accompanied by gene conversions in most cases. Apart from diagnostic implications, such naturally occurring recombination ‘hot spots’ may allow some insight into general features of crossover events in mammals. Keywords: MPS II; Hunter syndrome; IDS-2; pseudogene; inversion; deletion; recombination; gene conversion Introduction dermatan and heparan sulfates patients present with hepatosplenomegaly, skeletal deformities, connective Mucopolysaccharidosis type II (MPS II, Hunter syn- tissue abnormalities, and mental retardation.1 Since drome) is an X-linked storage disorder caused by characterisation of the IDS cDNA and gene,2–4 disease- deficiency of the lysosomal enzyme iduronate-2-sulfa- causing mutations have been described for many tase (IDS). Due to accumulation of partially degraded unrelated patients.5,6 In more than 80% of patients with MPS II, impair- Correspondence: Dr Susanna Bunge, Institut fur ¨ Human- ment of enzyme function is caused by point mutations genetik, Universit¨ats-Krankenhaus Eppendorf, Butenfeld 42, or deletions/insertions of less than 20 base-pairs.5 22529 Hamburg, Germany. Tel: 49-40-4717-4597; Fax: About 20% of all patients have total or partial gene 49-40-4717-5138; Email: [email protected] Received 27 November 1997; revised 23 February 1998; deletions or other major gene rearrangements. Detec- accepted 6 March 1998 tion of an IDS pseudogene (IDS-2 or IDSψ)7,8 located Rearrangements due to recombination in MPS II S Bunge et al t 493 ™ in inverted orientation 20 kb telomeric to the functional Germany) on an ABI Prism sequencer. To obtain the gene9 offers a likely explanation of complex mutational complete sequence of the 2.8 and 1.3 kb fragments, internal sequencing primers were used. Sequences were compared to events by intrachromatid recombination between two the published IDS gene and pseudogene sequences. To highly homologous regions.10 A high frequency intra- analyse the second recombination breakpoint of patient 16, genic inversion has been reported in patients of the Universal Genome Walker Kit (Clontech, Heidelberg, different ethnic origin.11,12 In Southern analysis of Germany) was used. Briefly, genomic DNA of the patient was digested with different restriction enzymes and ligated to HindIII digested genomic DNA, all cases presented adaptor primers. Using a combination of adaptor-specific and with a characteristic and identical pattern consisting of IDS gene-specific primers in a nested PCR, it was possible to two junction fragments of about 3.2 and 12.9 kb. This characterise the sequence that follows gene intron 3 in patient finding was unexpected for MPS II, an X-linked 16’s genome. disorder genetically lethal for males, as such traits usually show an extreme allelic heterogeneity with most of the mutations being ‘private’. Results We describe here determination of breakpoints in six unrelated patients with inversions and in three patients Characterisation of Partial with partial deletions and show that, on the molecular Deletions/Complex Rearrangements level, the three latter rearrangements are different. A Table 1 summarises the genomic blot and PCR data on model is proposed of how gene/pseudogene inter- four patients with partial gene deletion. actions may lead to recurrent intragenic deletions. In patient 9 (P9), all exons except 5 and 6 were detected by PCR, and the sequences corresponding to exons 5 and 6 were also absent in the cDNA. Both the Materials and Methods StuI and HindIII restriction patterns of genomic DNA are consistent with deletion of exons 5 and 6. Attempts Patients with complex rearrangements investigated in this to amplify across the breakpoint with primers located study belong to a collective of more than 70 patients with upstream of exon 5 and downstream of exon 6 were MPS II from different European countries among whom we have performed IDS gene mutation screening. Table 1 lists the unsuccessful. The absence of the pseudogene-specific patients analysed and their countries of origin. All patients 6.5 kb HindIII band and presence of two novel (most presented with the classical severe form of MPS II. Prelimi- likely) junction fragments is difficult to explain at the nary data on some of the patients were presented in previous moment. The patient may carry two deletions. Inver- studies (see Table 1). DNA and RNA was extracted from whole blood samples or sion-specific PCRs did not result in any product, while cultured skin fibroblasts according to standard procedures. IDS and IDS-2 intron 7-fragments of normal size were Southern blots of HindIII and StuI digested genomic DNA 12 amplified from P9’s DNA. were hybridised with the IDS cDNA as described. Construc- Using genomic DNA of patients P1, JN, and P16, no tion of restriction maps and assignment of exons to Southern blot fragments was performed by using the published IDS amplification products were obtained for exons 4 to 7, gene and pseudogene sequences.9 RT-PCR amplification of whilst exons 1, 2, 3, 8, and 9 were detectable and IDS coding sequence from mRNA in four overlapping unaltered. Analysis of cDNA revealed transcripts with fragments was done as described.13 A schematic draw of 13 internal deletions of exons 4 to 7 in patients P1 and JN. RT-PCR fragments is given by Bunge et al. In addition, primers in the 5'- and 3'-regions of the cDNA were combined The StuI hybridisation pattern of P1 and JN was to analyse transcripts with internal deletions. Amplification of identical showing a junction fragment of about 2.7 kb, exons was done with intron-specific primers as described 6,14 while P16 had a junction fragment of 4.0 kb. Similarly previously. IDS exon 3-forward and exon 8-reverse primers HindIII-patterns of P1/JN and P16 were also different. were used to generate a 2.8 kb junction fragment that included both the proximal breakpoints of inversions and Unexpectedly, all three patients showed a HindIII internal deletion breakpoints. Primers IDS62 and IDS63 junction fragment migrating like the 3.2 kb junction (similar to 60033-F and 58740-B in ref. 15) were used to fragment of patients with inversions (see below). Also, amplify a 1.3 kb gene intron 7-fragment, IDS64 and IDS65 genomic PCR with exon 3-forward and exon 8-reverse (similar to 97690-F and 98855B in ref. 15) for a 1.3 kb IDS- 2-specific intron 7-fragment. Localisation of these primers is primers resulted in products similar in size to the distal given in Figures 1 and 3. Primer pairs IDS62/IDS65 and junction fragment of inversion patients. These frag- IDS64/IDS63 produced amplicons containing the distal and ments were sequenced for all three cases (Figure 1). It proximal inversion breakpoints, respectively. Amplification turned out that two different types of rearrangements products were purified with microcon 100 concentrators (Amicon, Witten, Germany) and sequenced with the Dye were present. In patients P1 and JN, there is a junction Terminator cycle sequencing kit (Perkin Elmer, Weiterstadt, between exons 3 and 8 of the IDS gene. The intron 494 t Table 1 Results of PCR and genomic Southern blot analyses of 10 patients with major rearrangements of the IDS gene in MPS II Rearrangements due to recombination PCR exons (amplified genomic Southern blot1 from genomic proximal distal Patient Origin DNA) cDNA2 junction junction StuI digest3 HindIII digest4 Reference P9 PL no amplification 1.1: + – – missing: missing: 4.5 (4,5) 6.5 (ps3), this study of exons 5 and 6 1.2; 2; 3:– 3.0 (6), 4.4 (4,5) 9.6 (6,7, part 8) 1.2F, 3R: del ex 5, 6 new: ~11.0, 14.0 P1 PL no amplification 1.1: + + – missing: 3.0 (6), 3.2 (7), missing: 2.5 (3), 4.5 (4,5), this study of exons 4–7 1.2;2;3:– 3.4 (part 1, 2, 3), 4.4 (4,5); 9.6 (6, 7, part 8) 1.2F, 3R: del ex 4–7 new: 2.75 new: 3.2 S Bunge JN DK see P1 see P1 + – see P1 see P1 12, patient 1; this study P16 PL see P1 1.1: + + – missing6: 3.0 (6), 3.2 (7), missing: 2.5 (3), 4.5 (4,5), 16, HP16; this study 1.2; 2; 3:– 3.4 (part
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