Unequal Crossing-over Research Articles

2 α-Thalassaemia

alpha-Thalassaemias are genetic defects extremely frequent in some populations and are characterized by the decrease or complete suppression of alpha-globin polypeptide chains. The gene cluster, which codes for and controls the production of these polypeptides, maps near the telomere of the short arm of chromosome 16, within a G + C rich and early-replicating DNA region. The genes expressed during the embryonic (zeta) or fetal and adult stage (alpha 2 and alpha 1) can be modified by point mutations which affect either the processing-translation of mRNA or make the polypeptide chains extremely unstable. Much more frequent are the deletions of variable size (from approximately 3 to more than 100 kb) which remove one or both alpha genes in cis or even the whole gene cluster. Deletions of a single gene are the result of unequal pairing during meiosis, followed by reciprocal recombination. These unequal cross-overs, which produce also alpha gene triplications and quadruplications, are made possible by the high degree of homology of the two alpha genes and of their flanking sequences. Other deletions involving one or more genes are due to recombinations which have taken place within non-homologous regions (illegitimate recombinations) or in DNA segments whose homology is limited to very short sequences. Particularly interesting are the deletions which eliminate large DNA areas 5' of zeta or of both alpha genes. These deletions do not include the structural genes but, nevertheless, suppress completely their expression. Larger deletions involving the tip of the short arm of chromosome 16 by truncation, interstitial deletions or translocations result in the contiguous gene syndrome ATR-16. In this complex syndrome alpha-thalassaemia is accompanied by mental retardation and variable dismorphic features. The study of mutations of the 5' upstream flanking region has led to the discovery of a DNA sequence, localized 40 kb upstream of the zeta-globin gene, which controls the expression of the alpha genes (alpha major regulatory element or HS-40). In the acquired variant of haemoglobin H (HbH) disease found in rare individuals with myelodysplastic disorders and in the X-linked mental retardation associated with alpha-thalassaemia, a profound reduction or absence of alpha gene expression has been observed, which is not accompanied by structural alterations of the coding or controlling regions of the alpha gene complex. Most probably the acquired alpha-thalassaemia is due to the lack of soluble activators (or presence of repressors) which act in trans and affect the expression of the homologous clusters and are coded by genes not (closely) linked to the alpha genes. The ATR-X syndrome results from mutations of the XH2 gene, located on the X chromosome (Xq13.3) and coding for a transacting factor which regulates gene expression. The interaction of the different alpha-thalassaemia determinants results in three phenotypes: the alpha-thalassaemic trait, clinically silent and presenting only limited alterations of haematological parameters, HbH disease, characterized by the development of a haemolytic anaemia of variable degree, and the (lethal) Hb Bart's hydrops fetalis syndrome. The diagnosis of alpha-thalassaemia due to deletions is implemented by the electrophoretic analysis of genomic DNA digested with restriction enzymes and hybridized with specific molecular probes. Recently polymerase chain reaction (PCR) based strategies have replaced the Southern blotting methodology. The straightforward identification of point mutations is carried out by the specific amplification of the alpha 2 or alpha 1 gene by PCR followed by the localization and identification of the mutation with a variety of screening systems (denaturing gradient gel electrophoresis (DGGE), single strand conformation polymorphisms (SSCP)) and direct sequencing.

Evolution of repetitive proteins: spider silks from Nephila clavipes (Tetragnathidae) and Araneus bicentenarius (Araneidae)

Spider silks are highly repetitive proteins, characterized by regions of polyalanine and glycine-rich repeating units. We have obtained two variants of the Spidroin 1 (NCF-1) silk gene sequence from Nephila clavipes. One sequence (1726 bp) was from a cloned cDNA, and the other (1951 bp) was from PCR of genomic DNA. When these sequences are compared with each other and the previously published Spidroin 1 sequence, there are differences due to sequence rearrangements, as well as single base substitutions. These variations are similar to those that have been reported from other highly repetitive genes, and probably represent the results of unequal cross-overs. We have also obtained 708 bp of sequence from PCR of genomic DNA from Araneus bicentenarius. This sequence shows considerable similarity to a dragline sequence (ADF-3) from A. diadematus, as well as Spidroin 2 (NCF-2) from N. clavipes. Minor but consistent differences in the repeating unit sequence between A. bicentenarius and A. diadematus suggest that concerted evolution or gene conversion processes are acting to maintain similarity among repeat units within a single gene.

The mouse Mid1 gene: implications for the pathogenesis of Opitz syndrome and the evolution of the mammalian pseudoautosomal region.

We have recently reported isolation of the gene responsible for X-linked Opitz G/BBB syndrome, a defect of midline development. MID1 is located on the distal short arm of the human X chromosome (Xp22. 3) and encodes a novel member of the B box family of zinc finger proteins. We have now cloned the murine homolog of MID1 and performed preliminary expression studies during development. Mid1 expression in undifferentiated cells in the central nervous, gastrointestinal and urogenital systems suggests that abnormal cell proliferation may underlie the defect in midline development characteristic of Opitz syndrome. We have also found that Mid1 is located within the mouse pseudoautosomal region (PAR) in Mus musculus , while it seems to be X-specific in Mus spretus. Therefore, Mid1 is likely to be a recent acquisition of the M. musculus PAR. Genetic and FISH analyses also demonstrated a high frequency of unequal crossovers in the murine PAR, creating spontaneous deletion/duplication events involving Mid1. These data provide evidence for the first time that genetic instability of the PAR may affect functionally important genes. In addition, we show that MID1 is the first example of a gene subject to X-inactivation in man while escaping it in mouse. These data contribute to a better understanding of the molecular content and evolution of the rodent PAR.

Autosomal dominant Charcot-Marie-Tooth disease type 1A and hereditary neuropathy with liability to pressure palsies: detection of the recombination in Slovene patients and exclusion of the potentially recessive Thr118Met PMP22 point mutation.

Charcot-Marie-Tooth disease type 1 (CMT1) and hereditary neuropathy with liability to pressure palsies (HNPP) are the most frequent autosomal dominantly inherited disorders of the peripheral nervous system. The recessive inheritance is observed only exceptionally. Unequal crossing-over of misaligned flanking CMT1A-REP elements on chromosome 17p11.2 is the most frequent cause of the CMT1A duplication and of the reciprocal deletion in HNPP patients. Recently a recombination was noted. In our study 71 Slovene CMT1 patients from 36 families, 12 HNPP patients from 6 families and their 31 healthy relatives were analysed for the presence of these recombination mutations. In 29 of 36 unrelated CMT1 (81%) and in all 6 unrelated HNPP patients the duplication or the deletion, on chromosome 17p11.2-12 was detected. In 26 out of 29 duplication patients (CMT1A) (90%) a 3.2 kb EcoRI/SacI duplication junction fragment was observed. The analogous 7.8 kb EcoRI/EcoRI deletion junction fragment was found in 4 out of 6 unrelated HNPP deletion patients (67%). Overall we found a recombination mutation inside the in 86% of unrelated Slovene CMT1A and HNPP patients. One hundred and thirty-six DNA samples of the CMT1 and HNPP patients and of the healthy controls were negative for the potentially recessive Thr118Met PMP22 amino acid substitution. Dominantly inherited CMT1A duplications and HNPP deletions on chromosome 17p11.2 are thus, as in most other European countries, the most common mutations in Slovene CMT1 and HNPP patients. No signs of polymorphism or of potentially recessive mutation were found at the specific Thr118Met PMP22 site.

Fine mapping of de novo CMT1A and HNPP rearrangements within CMT1A-REPs evidences two distinct sex-dependent mechanisms and candidate sequences involved in recombination.

The molecular mechanism resulting in the duplication or deletion of a 1.5 Mb region of 17p11.2-p12, associated, respectively, with Charcot-Marie-Tooth type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP), has been proposed to be an unequal crossing-over during meiosis between the two chromosome 17 homologues generated by misalignment of the proximal and distal CMT1A-REP repeats, two homologous sequences flanking the 1.5 Mb CMT1A/HNPP monomer unit. In a recent study of a large series of de novo cases of CMT1A and HNPP, two distinct sex-dependent mechanisms were identified. Rearrangements of paternal origin, essentially duplications, were indeed generated by unequal meiotic crossing-over between the two chromosome 17 homologues, but duplications and deletions of maternal origin resulted from an intrachromosomal process, either unequal sister chromatid exchange or, in the case of deletion, excision of an intrachromatidal loop. In order to determine how these recombinations occur, 24 de novo crossover breakpoints were localized within the 1.7 kb rearrangement hot spot by comparing the sequences of the parental CMT1A-REPs with the chimeric copy in affected offspring. Nineteen out of 21 paternal crossovers were found in a 741 bp hot spot. All the breakpoints of maternal origin (n = 3), however, were located outside this interval, but in closely flanking sequences, supporting the hypothesis that two distinct sex-dependent mechanisms are involved. Several putative recombination promoting sequences in the hot spot, which are rare or absent in the surrounding 7.8 kb, were identified.

Intrachromosomal triplication of distal 7p.

A female infant who died at 2 years of age with growth and psychomotor retardation, wide anterior fontanelle, downward slanting palpebral fissures, large, simple ears, joint dislocation/contractures, recurrent infections, and...

Clustering of CMT1A duplication breakpoints in a 700 bp interval of the CMT1A‐REP repeat

The CMT1A-REP repeat is proposed to mediate unequal crossover leading to a 1.5 Mb duplication in chromosome 17p11.2-12 associated with Charcot-Marie-Tooth neuropathy type 1A (CMT1A). There is an apparent recombinational “hotspot” in the CMT1A-REP repeat since the majority of crossover breakpoints for CMT1A are located within a 1.7 kb interval. Further to characterize the crossover breakpoint region, we constructed PCR primers that specifically amplify the duplication breakpoint junctions in a series of Japanese and Caucasian CMT1A patients. We mapped the breakpoints in 89% of patients within a 700 bp interval of the CMT1A-REP repeat. This 700 bp region is 1.3 kb telomeric to a previously described mariner-like transposable element. Our observations further define the location of crossovers for CMT1A and provide additional evidence that this region is a recombinational “hotspot” within the CMT1A-REP repeat. Hum Mutat 11:109–113, 1998. © 1998 Wiley-Liss, Inc.

Expressed copies of the MN7 (D15F37) gene family map close to the common deletion breakpoints in the Prader-Willi/Angelman syndromes

Approximately 70% of patients with Prader-Willi syndrome or Angelman syndrome have a similar sized de novo deletion of 3–4 Mb in the proximal region of 15q. The distal breakpoints appear to cluster between the P gene (OCA2) and D15S24, whereas two deletion breakpoint clusters have been identified on the proximal side (one centromeric to D15S541 and one between D15S541 and D15S9). Based on the identification of a gene family in 15q11→q13 (MN7, D15F37), we have previously proposed that the presence of multiple copies of this sequence may be related to the instability of this region. Using fluorescence in situ hybridization and YAC mapping, we have found that at least one D15F37 locus is centromeric to D15S9 and at least two are between OCA2 and D15S24. As determined by cDNA cloning and sequence analysis, each of the individual loci is expressed. The close proximity of the D15F37 loci and the deletion breakpoints suggests that the common deletions arise by unequal crossover events at or near these loci.

Clustering of CMT1A duplication breakpoints in a 700 bp interval of the CMT1A-REP repeat.

The CMT1A-REP repeat is proposed to mediate unequal crossover leading to a 1.5 Mb duplication in chromosome 17p11.2-12 associated with Charcot-Marie-Tooth neuropathy type 1A (CMT1A). There is an apparent recombinational "hotspot" in the CMT1A-REP repeat since the majority of crossover breakpoints for CMT1A are located within a 1.7 kb interval. Further to characterize the crossover breakpoint region, we constructed PCR primers that specifically amplify the duplication breakpoint junctions in a series of Japanese and Caucasian CMT1A patients. We mapped the breakpoints in 89% of patients within a 700 bp interval of the CMT1A-REP repeat. This 700 bp region is 1.3 kb telomeric to a previously described mariner-like transposable element. Our observations further define the location of crossovers for CMT1A and provide additional evidence that this region is a recombinational "hotspot" within the CMT1A-REP repeat.

Epidemiology of hereditary neuropathy with liability to pressure palsies (HNPP) in south western Finland

An epidemiological study of hereditary neuropathy with liability to pressure palsies (HNPP) was carried out in south western Finland, with a population of 435 000. The diagnosis was established in 69 patients from 23 unrelated families through family and medical history, clinical neurological and neurophysiological examinations and with documentation of the deletion at gene locus 17p11.2 in at least one member of each family. This gave a prevalence of at least 16/100 000, which is remarkably high. However, due to the insidious nature of HNPP, most probably it is still an underestimation. This is the first population-based prevalence figure reported for HNPP. The prevalence is somewhat lower than that obtained for CMT in the same population, which agrees with the proposal that HNPP and CMT 1A are reciprocal products of the same unequal crossing-over. The clinical pictures of our patients were, in general, similar to those previously described in HNPP.

Identification of a 14 kb deletion involving the promoter region of BRCA1 in a breast cancer family.

BRCA1 is a breast and ovarian cancer susceptibility gene. An inferred germline regulatory mutation was previously reported in the BRCA1-linked kindred K2035, based on the absence of transcripts from the BRCA1 allele associated with the cancer susceptibility haplotype. In this study, the promoter region of BRCA1 was examined in individuals from K2035 for evidence of a mutation which could halt transcription. Evaluation of a polymorphism located within intron 2 of BRCA1 gave results consistent with the presence of a large deletion in K2035 mutation carriers. Southern blot analysis identified unique restriction fragments which occurred as a result of a 14 kb deletion that removed both of BRCA1's transcription start sites (exons 1a and 1b) as well as exon 2. Sequencing indicated that unequal crossover between Alu repeats was the likely cause of the deletion. Similar deletions may be responsible for other reported inferred regulatory mutations, as well as unidentified mutations in families linked to BRCA1.

Evolution of the rice Xa21 disease resistance gene family.

The rice disease resistance gene Xa21, encoding a receptor-like kinase, is a member of a multigene family. Sequence analysis of seven family members revealed two distinct classes of genes. One member from each class encodes a receptor kinase-like open reading frame. The other five members encode truncated open reading frames of the predicted receptor kinase. A highly conserved 233-bp sequence (HC) was also identified among the seven family members. Recombination at the HC region between family members apparently resulted in the precise swapping of promoter regions. Large sequence duplications were generated by a presumed unequal crossover event in intergenic regions. Insertions of transposon-like sequences truncated two of the predicted open reading frames. A model for amplification and diversification of the Xa21 gene family is presented.

Mineralocorticoid-induced hypertension

Several important advances have been made in the pathogenesis of mineralocorticoid induced hypertension. A hybrid gene was found to be responsible for glucocorticoid remediable hypertension. This extra gene contains fragments of 11-beta-hydroxylase and aldosterone synthase. The hybrid gene is the result of an unequal crossing-over of the two genes located in close proximity on chromosome 8, and leads to the production of aldosterone and the hybrid steroids 18-hydroxycortisol and 18-oxocortisol. These hybrid steroids are also detected in patients with aldosterone producing adenoma but not in patients with hyperaldosteronism due to bilateral adrenal hyperplasia. In Apparent "Mineralocorticoid Excess", inherited as an autosomal recessive disorder, an increased ratio of urinary cortisol metabolite to cortisone is diagnostic. The syndrome is due to a deficiency of the renal enzyme 11-beta-hydroxysteroid dehydrogenase type II, which protects the mineralocorticoid receptor against cortisol that binds to the mineralocorticoid receptor like aldosterone. Liddle's syndrome is a rare entity and due to a constitute activation of an aldosterone dependent protein which triggers the amiloride sensitive sodium channel in the kidney. This results in hypokalemic hypertension with suppressed aldosterone and renin levels.

Primary sequence of baboon CR1 demonstrates concerted evolution within the CR1 gene

Complement receptor type one (CR1) in primates has several remarkable structural features including a size polymorphism ( M r 190000, 220000, 250000 and 280000) in man, multiple size variants ( M r 55000–220000) among non-human primates, and a partial amino-terminal duplication (CR1-like gene) that appears to encode the short (55000–70000) forms expressed on primate erythrocytes. In general, these short CR1 forms, some of which are GPI anchored, are expressed on erythrocytes and the 220000 molecular weight CR1 form is expressed on PBMC, except in man, where only the 220000 molecular weight form has been detected. In addition, the M r 220000 human CR1 sequence carries several long internal repeats of up to 99% homology. It has been suggested that the highest homology is maintained by gene conversion and/or unequal crossover. To address further the evolutionary and biologic implications of these multiple forms, a 6 kb cDNA encoding baboon CR1 220 was identified by RTPCR using human CR1 primers. Its sequence contains the expected 30 complement control protein repeats (CCP) and demonstrates an overall homology to human CR1 of 95.4% at the nucleotide level and 93.2% at the amino acid level. As in human CR1, the first 28 CCP maintain the characteristic “seven CCP-long homologous repeats (LHR)” organization. Analysis of baboon CR1 220 indicates that horizontal or concerted evolution has maintained a high degree (>98%) of identity between corresponding CCP within the LHRs from CCP 4 to CCP 19, while this homology region extends from CCP 3 to CCP 18 in man. In contrast, substitutions occurring in other CCP are not propagated to the corresponding sites of other LHR. Sequence differences in CCP 1, 2 and 3 are likely to be related to the acquisition of enhanced C3b binding capability by this amino-terminal region of the protein. Thus, the sequence data strongly support the hypotheses that gene conversion and or unequal crossover events have driven the evolution of the protein in regions of high homology while selective forces, probably ligand binding requirements, have maintained the regions of divergence.

Higher-order organization of subrepeats and the evolution of cervid satellite I DNA.

Based on sequence analyses of 17 complete centromeric DNA monomers from ten different deer species, a model is proposed for the genesis, evolution, and genomic organization of cervid satellite I DNA. All cervid satellite I DNA arose from the initial amplification of a 31-bp DNA sequence. These 31-bp subrepeats were organized in a hierarchical fashion as 0.8-kb monomers in plesiometacarpalia deer and 1-kb monomers in telemetacarpalia deer. The higher-order repeat nature of cervid centromeric satellite DNA monomers accounts for their high intragenomic and intraspecific sequence conservation. Such high intraspecific sequence conservation validates the use of a single cervid satellite I DNA monomer from each deer species for interspecific sequence comparisons to elucidate phylogenetic relationships. Also, a specific 0.18-kb tandem duplication was observed in all 1-kb monomers, implying that 1-kb cervid satellite I DNA monomers arose from an unequal crossover event between two similar 0.8-kb ancestral DNA sequences.

Concerted evolution of the tandemly repeated genes encoding human U2 snRNA (the RNU2 locus) involves rapid intrachromosomal homogenization and rare interchromosomal gene conversion.

We have surveyed the tandemly repeated genes encoding U2 snRNA in a diverse panel of humans. We found only two polymorphisms within the U2 repeat unit: a SacI polymorphism (alleles SacI+ or SacI-) and a CT microsatellite polymorphism (alleles CT+ or CT-). Surprisingly, individual U2 tandem arrays are entirely SacI+ or SacI-, and entirely CT+ or CT-, although the SacI and CT alleles can occur in any combination. We also found that polymorphisms in the left and right junction regions flanking the tandem array fall into only two haplotypes (JL+ and JL-, JR+ and JR-). Most surprisingly, JL+ is always associated with JR+, and JL- with JR-. Thus individual U2 arrays do not exchange flanking markers, despite independent assortment and subsequent homogenization of the SacI and CT alleles within the U2 repeat units. We propose that the primary driving force for concerted evolution of the tandem U2 genes is intrachromosomal homogenization; interchromosomal genetic exchanges are much rarer, and reciprocal nonsister chromatid exchange apparently does not occur. Thus concerted evolution of the U2 tandem array occurs in situ along a chromosome lineage, and linkage disequilibrium between sequences flanking the U2 array may persist for long periods of time.

Facilitated diagnosis of CMT1A duplication in chromosome 17p11.2-12: analysis with a CMT1A-REP repeat probe and photostimulated luminescence imaging.

Charcot-Marie-Tooth disease type 1A (CMT1A) is a common autosomal dominant demyelinating peripheral neuropathy. Most patients with CMT1A have been found to have a 1.5 megabase tandem DNA duplication in chromosome 17p11.2-12. Meiotic unequal crossover mediated by the CMT1A-REP repeat is a proposed mechanism for generation of the duplication in CMT1A and a reciprocal deletion seen in hereditary neuropathy with liability to pressure palsies. Testing for the CMT1A duplication is frequently the first step in the molecular diagnosis of patients with suspected inherited demyelinating neuropathy. We used a 1.0 kb EcoRI-PstI DNA fragment (pHK1.0P) from the proximal CMT1A-REP repeat as a probe for Southern blot analysis and detected increased gene dosage in CMT1A by determining measuring radioactivity ratios with a photostimulated luminescence imaging plate. We found that this method is useful for rapid diagnosis of the DNA duplication associated with CMT1A.

Facilitated diagnosis of CMT1A duplication in chromosome 17p11.2‐12: Analysis with a CMT1A‐REP repeat probe and photostimulated luminescence imaging

Charcot-Marie-Tooth disease type 1A (CMT1A) is a common autosomal dominant demyelinating peripheral neuropathy. Most patients with CMT1A have been found to have a 1.5 megabase tandem DNA duplication in chromosome 17p11.2-12. Meiotic unequal crossover mediated by the CMT1A-REP repeat is a proposed mechanism for generation of the duplication in CMT1A and a reciprocal deletion seen in hereditary neuropathy with liability to pressure palsies. Testing for the CMT1A duplication is frequently the first step in the molecular diagnosis of patients with suspected inherited demyelinating neuropathy. We used a 1.0 kb EcoRI-PstI DNA fragment (pHK1.OP) from the proximal CMT1A-REP repeat as a probe for Southern blot analysis and detected increased gene dosage in CMT1A by determining measuring radioactivity ratios with a photostimulated luminescence imaging plate. We found that this method is useful for rapid diagnosis of the DNA duplication associated with CMT1A. Hum. Mutat. 9:563–566, 1997. © 1997 Wiley-Liss, Inc.

Unequal interchromosomal rearrangements may result in elastin gene deletions causing the Williams-Beuren syndrome.

Williams-Beuren syndrome (WBS) is generally the consequence of an interstitial microdeletion at 7q11.23, which includes the elastin gene, thus causing hemizygosity at the elastin gene locus. The origin of the deletion has been reported by many authors to be maternal in approximately 60% and paternal in 40% of cases. Segregation analysis of grandparental markers flanking the microdeletion region in WBS patients and their parents indicated that in the majority of cases a recombination between grandmaternal and grandpaternal chromosomes 7 at the site of the deletion had occurred during meiosis in the parent from whom the deleted chromosome stemmed. Thus, the majority of deletions were considered a consequence of unequal crossing-over between homologous chromosomes 7 (interchromosomal rearrangement) while in the remaining cases an intrachromosomal recombination (between the chromatids of one chromosome 7) may have occurred. These results suggest that the majority of interstitial deletions of the elastin gene region occur during meiosis, due to unbalanced recombination while a minority could occur before or during meiosis probably due to intrachromosomal rearrangements. The recurrence risk of the interchromosomal rearrangements for sibs of a proband with non-affected parents must be negligible, which fits well with the observation of sporadic occurrence of almost all cases of WBS.

Deletion of the PMP22 gene and hereditary neuropathy with liability to pressure palsies.

Deletion of the 1.5 Mb tract on chromosome 17p11.2-12 that is duplicated in Charcot-Marie-Tooth disease type 1A is commonly associated with hereditary neuropathy with liability to pressure palsies. The deletion, which originates from an unequal meiotic crossover involving two homologous repeats, causes underexpression of the peripheral myelin protein gene PMP22. PMP22 frameshift and non-sense mutations can be found in the rare nondeleted cases. Targeted disruption of the PMP22 gene in mice has provided an animal model for the disease. Current studies are aimed at characterising the genetics of this chromosomal rearrangement and the pathogenic role of altered PMP22 expression.