A novel mechanism generating short deletion/insertions following slippage is suggested by a mutation in the human [alpha]2-globin gene
A novel mechanism generating short deletion/insertions following slippage is suggested by a mutation in the human [alpha] 2 -globin geneVarda Oron-Karni, Dvora Filon, Deborah Rund and Ariella Oppenheim*
Department of Hematology, Hebrew University-Hadassah Medical School and Hadassah University Hospital, Jerusalem 91120, Israel
Received January 31, 1997;Revised and Accepted March 12, 1997
A novel mechanism generating short deletion/insertions is described based on a mutation in the human [alpha]2-globin gene. A deletion of 9 bp (codons 39-41) is replaced by an eight nucleotide insertion, duplicating the adjacent downstream sequence. We propose that the mutation arose by slipped strand mispairing (SSM), creating a single-stranded loop, followed by DNA elongation, strand breathing and the formation of a mismatch bubble. An extensive literature search has revealed six additional deletion/insertion mutations in humans in which the inserted nucleotides come from the same DNA strand. Our model explains all six mutations, suggesting that rearrangement of a mismatch loop or bubble during DNA replication may be not uncommon.
Human mutations provide a rich source of information for the study of mechanisms of genomic instability. Over 15 years ago it was first suggested by Efstratiadis et al. (1 ) that slipped strand mispairing (SSM) is enhanced by short (2 -8 ) direct repeats, which may induce short deletions in mammalian DNA. SSM has since been suggested to play an important role in the expansion of trinucleotide repeats, causing a number of neurodegenerative disorders (Fragile X, spinocerebellar ataxia, Huntington's disease and others) (2 ,3 ). In addition, the size variation of microsatellite repeats, seen as polymorphic markers, is also thought to result from SSM. SSM probably also leads to the variability in microsatellite repeats seen in tumor cells, reflecting the high degree of genomic instability in those tissues (4 ,5 ). Thus SSM appears to occur both in germline and in somatic cells.
Slippage of the replication fork is not in itself sufficient to explain the more complex mutations in which small deletions are combined with insertions. Here we describe a deletion/ duplication mutation in the human [alpha]2-globin gene which allowed us to formulate a novel mechanism accounting for the generation of this mutation, as well as a number of other additional human mutations.
The human [alpha]-globin cluster is composed of two functional genes ([alpha]2 and [alpha]1) which are located in a duplicated region of 4 kb. Unequal crossing over is presumed to be the cause of the common genetic lesions (single gene deletions and triplications), with point mutations being less frequent (6 ,7 ). Such molecular lesions lead to [alpha]-thalassemia by impairing production of the [alpha]-globin chains of the hemoglobin tetramer. The various molecular lesions in heterozygotes lead to a wide range of phenotypes, which may be diagnosed by hematological criteria. In general, the red blood cells are found to have microcytosis (low mean corpuscular volume, MCV) and hypochromia (low mean corpuscular hemoglobin, MCH), and mild anemia may be noted (6 ,7 ). The severe forms of [alpha]-thalassemia are HbH disease, with three non-functional [alpha]-globin genes, causing moderate congenital anemia, and hydrops fetalis, with no functional [alpha]-globin genes, causing intrauterine death.
Analysis of the DNA of patient 1 for gross rearrangements in the [alpha]-globin gene by Southern analysis demonstrated heterozygosity for a common single [alpha]-globin gene deletion (genotype -[alpha]3.7/[alpha][alpha]). A normal [alpha]-globin gene configuration ([alpha][alpha]/[alpha][alpha]) was found for patient 2 (data not shown). These results are consistent with the milder phenotype of patient 2. However, they do not fully account for the low MCV and MCH values of the patients, suggesting the presence of point mutation(s). Screening for point mutations known in our population was unrevealing.
Sequencing of both strands of the [alpha]2-globin gene revealed a novel deletion/duplication mutation in both patients (Fig. 1 ). A deletion of 9 bp (codons 39-41, exon 2) is replaced by an insertion of eight nucleotides, which represents a duplication of the adjacent downstream sequence. The mutation changes the reading frame, resulting in a termination signal, TGA, 10 codons downstream.+
Two unrelated individuals of Yemenite-Jewish origin were referred for evaluation of unexplained mild microcytic anemia. Their hematological data was compatible with an [alpha]-thalassemia trait. Patient 1 is 20 years old. Her hematological data is compatible with an [alpha]-thalassemia trait (Hb 11.1 g/dl, MCV 66.8 fl, MCH 19.8 pg). Patient 2 is 13 years old. Her hematological data is also compatible with an [alpha]-thalassemia trait, with a milder phenotype (Hb 12.6 g/dl, MCV 74.5 fl, MCH 23.6 pg). In both, iron deficiency and a [beta]-thalassemia trait were excluded.
Complete blood counts were performed on a Coulter S Plus IV analyzer.
DNA was isolated from peripheral blood leukocytes according to standard procedures (15 ,16 ). Southern analysis was performed using BglII digestion, with a [zeta]-globin-specific probe (17 ).
PCR of the complete [alpha]2-globin gene was performed with Taq DNA polymerase (Appligene), using the conditions recommended by the manufacturer, with ~1 [mu]g of genomic DNA. The amplification cycle consisted of 1 min at 94oC, 1.5 min at 62oC and 1.5 min at 72oC. Thirty five cycles of PCR were usually sufficient. Primers were P56: 5'-CCCCAAGCATAAACCCTGGC and P52: 5'-CCTCCATTGTTGGCACATTCC, yielding a product of 922 bp. The PCR product was isolated following electrophoresis on a 1% low-melting agarose gel. The band was removed and kept frozen. Prior to sequencing, the agarose was melted at 68oC and 14 [mu]l was used for each reaction. Direct sequencing was performed using the internal primers P57: 5'-ACAGGCCACCCTCAACCGTC (sequencing the `sense' strand) and P66: 5'-CTTCTTGCCGTGGCCCTTAAC (for the `antisense' strand), with Sequenase Version 2 (USB).
A literature search was performed using Medline Subset Query Form with the following key words (including search of Mesh headings): `insertion deletion' and `human' and `base sequence' but not `polymorphism'. Out of 419 titles retrieved, we found 13 which were relevant.
We thank Dr Amos B. Oppenheim for fruitful discussions.This work was supported by grant 91-00055 from the United States-Israel Binational Science Foundation (BSF), Jerusalem; and by grants 2310 and 3172 from the Ministry of Health, Israel.
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*To whom correspondence should be addressed. Tel: +972 2 677 6753; Fax: +972 2 642 3067; Email: ariella@cc.huji.ac.il
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