Localization of the beta-globin gene by chromosomal in situ hybridization

A 3.7-kilobase (kb) genomic clone of the human beta-globin gene, including 1.5-kb upstream and approximately 0.5-kb downstream, was utilized in chromosomal in situ hybridization for precise mapping of the beta-globin locus on peripheral blood lymphocyte-derived metaphases from a normal male, and for further evaluation of a clonal t(7;11) (q22;p15) translocation on bone marrow-derived metaphases from a 46-year-old male with erythroleukemia. Analyses of 205 midmetaphases from a normal male hybridized with the tritium-labeled beta-globin probe and stained with quinacrine mustard dihydrochloride revealed approximately 12% of spreads to have silver-grain deposition over the p15 band of chromosome 11. Of the 365 silver grains observed to be located on or beside chromosomes, 25 (approximately 7%) grains were localized in band p15. Karyotype analysis of a bone marrow specimen from the patient with erythroleukemia revealed hypodiploidy with various unidentified marker chromosomes as well as a presumably balanced translocation between 7q and 11p . Chromosomal in situ hybridization showed localization of silver grains at the junction between chromosomes 7 and 11 as well as to the normal chromosome 11, indicating that the beta-globin locus had not been translocated in the chromosomal rearrangement. This case demonstrates the value of chromosomal in situ hybridization in the definition of chromosome rearrangements and provides further evidence for the localization of the beta-globin gene to 11p15 .

Restriction site polymorphism in the phosphoglycerate kinase gene on the X chromosome

Using a human phosphoglycerate kinase (PGK) cDNA probe, we have identified a common Pst I restriction site polymorphism on the human X chromosome in all ethnic groups studied. The polymorphic Pst I site was absent in 40.4% of 94 X chromosomes of unrelated subjects. Heterozygous females can only be detected by the combined use of a Pst I digest and a Xba I + Pst I digest due to the presence of autosomal and X-linked bands of the same size in simple Pst I digests. Since 48% of females are heterozygotes for the Pst I polymorphism, this site can serve as a useful genetic marker on the long arm of X chromosome in man.

Molecular characterization of seven beta-thalassemia mutations in Asian Indians

To characterize systematically the mutations which produce beta-thalassemia in Asian Indians, we first determined the DNA polymorphism haplotype in the beta-globin gene cluster of 44 beta-thalassemia chromosomes in the ethnic group. Nine different haplotypes were observed. Upon molecular cloning and partial DNA sequencing of one beta-gene from each of eight haplotypes and two from the ninth, seven different mutations were found. None of these have been identified in Mediterranean patients, even among the five haplotypes which appeared identical in the two groups. Asian Indian mutations included one nonsense and three frameshift mutations, one deletion affecting an acceptor splice site, and two mutations affecting a donor splice site. The correlation of a specific mutation with a specific haplotype was high but not invariant. Two mutations were associated with more than one haplotype but, in each instance, the mutation spread to a new haplotype could be explained most simply by recombination 5' to the beta-globin gene. In addition, four mutations, one reported here and three others previously reported, have been observed on two chromosome backgrounds that are identical except for the status of a polymorphic HinfI site 5' to the beta gene. This HinfI site does not show significant linkage disequilibrium with markers both 5' and 3' to it, suggesting that it lies within a region of relative sequence randomization.

Boundaries of gene conversion within the duplicated human alpha-globin genes. Concerted evolution by segmental recombination

The human adult alpha-globin genes, alpha 1 and alpha 2, are embedded in homologous duplication units, each of which spans approximately 4 kilobase pairs of chromosomal DNA. Previous studies established that the 3'-ends of the duplication units are located adjacent to the polyadenylation sites of the two genes. We have now determined the 5'-boundary of the homology which includes both the structural genes and their upstream sequences. The 5'-flanking regions of alpha 1 and alpha 2 are perfectly homologous for 868 base pairs, with the exception of two single nucleotide differences. This is in contrast to the considerable divergence of the 3'-ends of these loci. Since the alpha-genes undergo concerted evolution by homologous unequal crossing over and/or gene conversion, the presence of adjacent regions with different degrees of homology indicates that this process is segmental. Furthermore, we have determined that an alpha-thal-2 gene, a variant alpha-globin allele resulting from unequal crossing over between normal alpha 1 and alpha 2 genes, has a mosaic arrangement of parental sequences. This patchwork structure may have arisen from a single recombination event which was limited in both the 5' and 3' directions by flanking non-homologies and in which mismatch repair occurred in a heteroduplex intermediate. Unequal crossing over and gene conversion of this type may effect the segmental concerted evolution of the human alpha-globin locus. Restriction mapping of additional alpha-thal-2 genes and of the reciprocal triplicated alpha-gene complex was consistent with this hypothesis.

Molecular cloning of human adenosine deaminase gene sequences

Using a mixture of synthetic 17-mer oligonucleotides encoding the 64 possible sequences for a peptide of adenosine deaminase as probe, we have isolated a clone for adenosine deaminase mRNA sequences from a collection of T-cell cDNA recombinants. This cDNA clone, phADA-1, contains an insert of 0.8 kilobase. In addition to the peptide chosen for synthesis of the oligonucleotide probe, the complete DNA sequence predicts 16 other experimentally determined peptides. Mapping of total cellular human DNAs with several restriction enzymes revealed relatively simple patterns of hybridization with phADA-1 as probe, including a polymorphism for PvuII cleavage. In agreement with previous studies, the adenosine deaminase gene was localized by blot hybridization to chromosome 20 in a hybrid cell mapping panel. Using the cDNA as probe, an 18-kilobase EcoRI fragment of human cellular DNA was also cloned in bacteriophage Charon 4A. These adenosine deaminase clones will prove valuable in the full characterization of the cellular gene, molecular analysis of inherited enzyme deficiency associated with immunodeficiency, and regional mapping of human chromosome 20.

beta-Thalassemia due to a deletion of the nucleotide which is substituted in the beta S-globin gene

Sickle-cell anemia results from an A leads to T transversion in the second nucleotide of codon 6 of the beta-globin gene. We now report an uncommon beta-thalassemia gene that contains a deletion of this nucleotide. Thus, one mutation (GAG leads to GTG) produces sickle-cell anemia, while the other (GAG leads to GG) eliminates beta-globin production. These data establish that different alterations affecting one specific nucleotide can produce either an abnormal hemoglobin or beta-thalassemia. Moreover, the nucleotide sequence comprising codons 6-8 of the beta-globin gene appears to be particularly susceptible to mutations affecting nucleotide number.

Early pre-B cells from normal and X-linked agammaglobulinaemia produce C mu without an attached VH region

Differentiation of B lymphocytes follows an ordered pathway marked by somatic rearrangements of immunoglobulin heavy- and light-chain genes in conjunction with cellular transitions. Although low level constitutive transcription of the mu heavy-chain constant region (C mu) genes may occur in early precursor cells, activation of synthesis and translation of complete mu RNA is thought to accompany somatic rearrangements of DNA. Cytoplasmic mu-chain protein serves as a marker for pre-B cells, the earliest cells committed to differentiation into B lymphocytes, mu-chain gene expression in pre-B cells pre-cedes rearrangement and expression of light-chain genes. We now report that early human pre-B cells, Epstein--Barr virus transformed pre-B cells, and pre-B cell hybrid analogues, produce C mu without the normally associated heavy-chain variable (VH) region. Approximately 5% of normal pre-B cells from adult human bone marrow produce these incomplete mu-chains. Pre-B cells from three patients with X-linked agammaglobulinaemia are exclusively of this immature form, producing C mu without associated VH. This immune deficiency disease represents a block in differentiation secondary to failure to express VH genes.

ATA box transcription mutation in beta-thalassemia

DNA sequence analysis of a cloned beta-globin gene from a Chinese patient with beta-thalassemia revealed a single nucleotide substitution (A leads to G) within the ATA box homology and 28 base pairs upstream from the cap site. The patient was homozygous for this particular allele based on restriction mapping at nine different polymorphic sites in the beta-globin gene cluster. Upon transient expression in HeLa cells this gene directed the production of 3-5-fold less beta-globin mRNA than the normal beta-gene. In RNA isolated from the patient's erythroid cells beta-RNA was 10-fold less abundant relative to alpha-RNA than normal, indicating close approximation of the heterologous cell expression results and the in vivo state. These findings support the validity of such transient expression assays for analysis of phenotypes associated with naturally occurring mutant genes and establish the functional significance of nucleotide substitutions at position -28 for human beta-globin gene transcription.

Isolation of a cDNA clone for human antithrombin III

Antithrombin III (ATIII) is an important plasma protease inhibitor with a central role in the coagulation system. On the basis of its protein sequence, ATIII is one member of a "super family" of protease inhibitors that includes alpha 1-antitrypsin and chicken ovalbumin. An increased risk of thromboembolism is associated with inherited ATIII deficiency. To study the structure and expression of the human ATIII gene, we have isolated complementary (cDNA) clones for ATIII from human liver mRNA. ATIII cDNA clones were identified by hybridization to a mixture of synthetic oligodeoxynucleotides encoding amino acids 251-256 of the ATIII protein sequence. The largest cDNA clone (1.4 kilobases) included the coding region of ATIII mRNA from codon 10 through a 3'-untranslated region. Comparison of ATIII cDNA clones from two different sources revealed a sequence polymorphism at an internal PstI restriction site. Analysis of both total genomic DNAs and an ATIII gene cloned in a bacteriophage Charon 4A showed that the ATIII gene is present once per haploid genome and is distributed over 10-16 kilobases of DNA. Computer-assisted comparison of the cDNA sequence with those for baboon alpha 1-antitrypsin and chicken ovalbumin revealed homologies consistent with their inclusion in the protease inhibitor superfamily.

Molecular heterogeneity of inherited antithrombin III deficiency

Inherited antithrombin III deficiency is associated with an increased risk of thromboembolism. Using recombinant-DNA techniques, we isolated a molecular probe for the antithrombin III structural gene and identified a common DNA polymorphism within the gene. We found that there is genetic heterogeneity in this disorder. In one family, the antithrombin III gene was deleted in affected members, whereas in another no deletion occurred. Use of the DNA polymorphism should allow identification and further characterization of abnormal antithrombin III genes.

Inactivation of an acceptor RNA splice site by a short deletion in beta-thalassemia

The cloned beta-globin gene of an Indian patient with beta-thalassemia revealed a 25-nucleotide deletion at the 3'-end of the first intervening sequence, including the acceptor RNA splicing site. RNA transcripts of this mutant gene produced following transfection into HeLa cells remained unspliced at both the first intervening sequence donor and acceptor sites. This beta-thalassemic gene is the first in which critical sequences of an acceptor splice junction are mutated and associated with abnormal RNA processing.

The molecular basis for the clinical diversity of beta thalassaemia in Cypriots

Much of the clinical variability in the course of homozygous beta thalassaemia in the Cypriot population can be accounted for by the interaction of alpha thalassaemia and by the existence of different molecular forms of beta thalassaemia. Most severe forms of the disorder result from the homozygous state for the common Mediterranean type of beta thalassaemia. One particularly mild form of beta thalassaemia, which also occurs in other Mediterranean populations, results from a single base change at position 6 in the first intervening sequence of the beta-globin gene. These observations provide a basis for the development of a programme for first-trimester antenatal diagnosis using oligonucleotide probes.

The entire beta-globin gene cluster is deleted in a form of gamma delta beta-thalassemia

We have used restriction endonuclease mapping to study a deletion involving the beta-globin gene cluster in a Mexican-American family with gamma delta beta-thalassemia. Analysis of DNA polymorphisms demonstrated deletion of the beta-globin gene from the affected chromosome. Using a DNA fragment that maps greater than 40 kilobases (kb) 5' to the epsilon-gene as a probe, reduced amounts of normal fragments were found in the DNA of affected family members. Similar analysis using radiolabeled DNA fragments located 3' to the beta-globin cluster has shown that the deletion extends more than 17 kb 3' to the beta-gene, but terminates before the 3' endpoint of the Ghanian HPFH deletion. Hence, this gamma delta beta-thalassemia deletion eliminates over 105 kb of DNA and is the first report of a deletion of the entire beta-globin gene cluster.

Specific transcription and RNA splicing defects in five cloned beta-thalassaemia genes

Transcriptional analysis of five different cloned beta-thalassaemia genes introduced into cultured mammalian cells revealed specific defects in transcription and RNA splicing. A single base change 87 base pairs to the 5' side of the mRNA cap site significantly lowers the level of transcription and therefore appears to represent a promoter mutation. Three genes contain different single base changes in the first intervening sequence (IVS) 5' splice site. One mutation, at IVS1 position 1, inactivates the splice site completely; the other two, at IVS1 positions 5 and 6, reduce its activity. Each mutation activates the same three cryptic splice sites. The fifth gene contains a single base change within IVS2 at position 745, which results in the formation of abnormal beta-globin RNA that contains an extra exon.

Direct detection of the common Mediterranean beta-thalassemia gene with synthetic DNA probes. An alternative approach for prenatal diagnosis

The most common form of beta-thalassemia among Mediterraneans results from a single nucleotide substitution within the first intervening sequence (IVS-1) of the beta-globin gene. This particular mutation is not detectable in uncloned DNA by restriction enzyme analysis. Using synthetic DNA of 19-nucleotides in length corresponding to the normal and mutant IVS-1 sequences as probes, we have developed a direct assay for this gene defect. Under carefully controlled experimental conditions these synthetic probes detect only their homologous sequences in restriction digests of both cloned and uncloned DNA samples. The method is sufficiently sensitive to establish the genotype of individuals with respect to this defect using approximately 20 micrograms total DNA. This assay provides an alternative to fetal blood and DNA linkage analysis for the prenatal diagnosis of this variety of beta-thalassemia, particularly among Greek families where it is especially common.

Isolation and DNA sequence of a full-length cDNA clone for human X chromosome-encoded phosphoglycerate kinase

Phosphoglycerate kinase (PGK), a major enzyme in glycolysis, is encoded by the X chromosome in mammals. We have initiated molecular analysis of the PGK structural gene by isolating a full-length cDNA clone from a human fetal liver cDNA library. Synthetic oligonucleotide mixtures encoding two different portions of PGK were used as direct in situ hybridization probes for the cDNA library. Several classes of clones were obtained based on their hybridization at different stringencies to one or both of the PGK oligonucleotide mixtures. One clone, designated pHPGK-7e, which hybridized at high stringency to each of the synthetic probes, encoded the complete PGK protein sequence as well as 82 base pairs of 5' and 437 base pairs of 3' untranslated regions. Southern blot analysis of human genomic DNAs revealed a complex pattern of hybridizing fragments, two of which were non-X in origin. These results suggest that the human genome contains a small family of dispersed PGK or PGK-like genes.

Isolation of DNA fragments from chromosome 13

A number of patients with retinoblastoma have a deletion of chromosome 13. Comparison of the deleted segments from different individuals reveals that all deletions involve chromosome band 13q14. This observation has lead to the hypothesis that in this region is a gene of genes important in the etiology of retinoblastoma. As a first step toward understanding those genes, the authors successfully isolated five DNA fragments from chromosome 13 using recombinant DNA techniques. The DNA fragments from chromosome 13 will be useful in identifying DNA polymorphic sites that are linked to the retinoblastoma locus tentatively assigned to 13q14. Such DNA polymorphisms will be important in the genetic counselling of families with retinoblastoma. These chromosome 13q14 fragments also may be useful in searching for microdeletions of 13q14.

Abnormal RNA processing due to the exon mutation of beta E-globin gene

As is typical of all beta-thalassaemias, the erythroid cells of individuals with the variant haemoglobin E (alpha 2 beta 2(26Glu leads to Lys)) exhibit a quantitative deficiency in their content of beta-globin (in this case beta E-globin) and its messenger RNA2,3. To determine the molecular basis of this phenotype, we have investigated the structure and expression of cloned beta E-globin genes. We report here that the complete nucleotide sequence of a beta E-gene revealed the expected GAG leads to AAG change in codon 26 but no other mutations. Expression of beta E-globin genes introduced into HeLa cells revealed two abnormalities of RNA processing: slow excision of intervening sequence-1 (IVS-1) and alternative splicing into exon-1 at a cryptic donor sequence within which the codon 26 nucleotide substitution resides. These results demonstrate a disturbance in the expression of the beta E-gene attributable solely to the exon mutation-a novel mechanism for gene dysfunction.

Duplication followed by deletion accounts for the structure of an Indian deletion beta (0)-thalassemia gene

Nucleotide sequence analysis of a cloned deletion beta-globin gene from a patient with beta(0)-thalassemia demonstrates a 619 nucleotide deletion extending from the 3' third of the second intervening sequence through 209 bases of 3' flanking DNA. However, an additional novel heptanucleotide was identified between the deletion endpoints, suggesting a complex etiology for this rearrangement.

Evidence for multiple origins of the beta E-globin gene in Southeast Asia

To investigate whether recurrent mutation has contributed to the high frequency of the beta E-globin gene in Southeast Asia, we used the haplotypes at three polymorphic restriction sites within and to the 3' side of the beta-globin gene to predict the framework of 23 beta E-globin genes. These haplotypes suggested that beta E-globin genes are present in two different beta-globin gene frameworks. DNA sequence determination of one gene representing each framework demonstrated that the same mutation (GAG leads to AAG at codon 26) was present in both frameworks. Moreover, the frameworks differed at three nucleotide positions known to be polymorphic in Mediterraneans. These polymorphic sites are located 70 nucleotides to the 5' side of the beta E mutation and 382 and 1032 nucleotides to the 3' side of it. The existence of the beta E mutation in these two beta-globin gene frameworks can be explained by (i) recurrent mutation giving rise to beta E-globin, (ii) a double crossing-over event, or (iii) two single crossing-over events. Mathematical analysis suggests that the first alternative, recurrent mutation of G leads to A at the first nucleotide of codon 26, is most likely.

Abnormal RNA splicing causes one form of alpha thalassemia

The alpha 2-globin gene from a patient with alpha thalassemia contains a pentanucleotide deletion in intron 1 immediately adjacent to exon 1. We tested the functional consequences of this mutation by introducing the thalassemic gene, along with its normal counterpart as a control, into cultured monkey cells on SV40 plasmid vectors. Both genes are expressed, at similar levels, into globin RNA with the correct 5' and 3' ends. However, while most of the normal transcripts are appropriately processed, the thalassemic transcripts are abnormally spliced from a 5' donor site in the middle of exon 1 to the normal 3' acceptor site. This results in the synthesis of a truncated RNA incapable of encoding a normal globin polypeptide. The alternative donor, also used at a low level in monkey cells transfected with the normal gene, shows strong homology to the consensus donor sequence characteristic of many eucaryotic splice junctions. No unspliced or partially spliced thalassemic RNA was detected, indicating that recognition of this site is efficient and does not block removal of intron 2. The alternatively spliced RNA was also found in bone marrow RNA from the alpha-thalassemic patient, although not in that from a normal individual or a beta +-thalassemic patient. The thalassemic phenotype of the patient therefore results from abnormal RNA splicing owing to the deletion of the first splice donor signal.

Isolation of mouse x-chromosome specific DNA from an x-enriched lambda phage library derived from flow sorted chromosomes

A lambda phage library enriched in X(7) chromosomal material has been constructed from flow sorted chromosomes isolated from mice carrying the Cattanach translocation T(X;7)1Ct. The flow sorted fraction that was cloned contained 40% X(7) chromosomes, so that the resulting lambda phage library should be more than 10-fold enriched for X chromosomal DNA. Approximately 100,000 lambda phage clones were obtained; of these, at least 80% were recombinant. Three quarters of recombinants were positive for mouse repetitive DNA as detected either by phage plaque filter hybridization or by Southern blotting. Recombinant DNA inserts were prepared from some of the remaining nonrepetitive phage fraction. The X-chromosome specificity of cloned DNA inserts was tested by hybridization to DNA from mouse-hamster somatic cell hybrids that had retained all or most of the mouse X as the only mouse chromosome and by comparison of the extent of hybridization to DNA from male and female mice. Out of nine cloned unique sequence segments successfully examined thus far, two were presumably derived from the X. Possession of phage library highly enriched for mouse X DNA should facilitate molecular studies of the control of X chromosome gene expression.

Nonsense and frameshift mutations in beta 0-thalassemia detected in cloned beta-globin genes

The molecular basis for deficiency of beta-globin synthesis in beta-thalassemia was investigated by gene cloning and DNA sequencing. beta-Globin genes of two patients with beta 0-thalassemia were cloned in a phage lambda vector. Both beta-genes transcribed normally in vitro. The gene of an Italian individual had a single nucleotide substitution (C leads to T) in the codon for amino acid 39 that resulted in formation of a nonsense codon. In a Turkish individual, the cloned beta-globin gene had a dinucleotide deletion in the codon for amino acid 8. This frameshift mutation produced a termination codon at the position of the new 21st codon. Mutations that lead to premature termination of beta-globin synthesis appear to be among the common causes of beta 0-thalassemia in man.

Mutation in an intervening sequence splice junction in man

The alpha 2-globin gene of an individual with alpha-thalassemia associated with the absence of alpha 2 mRNA was cloned in bacteriophage. This mutant globin gene was normally active in transcription in vitro. The DNA sequence of the gene, however, revealed a pentanucleotide deletion within the 5' splice junction of the first intervening sequence. Following the G of the invariant G-T dinucleotide normally located within such junctions, a deletion of T-G-A-G-G was found. No other sequence abnormalities within the mutant gene were present. We speculate therefore that this deletion within the splice junction is the primary genetic defect in this individual with thalassemia and that loss of a functional splice junction results in failure of stable mRNA formation.

The duplicated human alpha-globin genes: their relative expression as measured by RNA analysis

The human alpha-globin genes are duplicated and encode identical polypeptides. Recently we detected in cloned genomic DNAs characteristic sequence differences between the 3' untranslated regions of the 5' (alpha 2) and 3' (alpha 1) genes, not previously recognized by direct analysis of mRNA and cDNA transcripts. Based on these untranslated region differences, we have now used S1 nuclease mapping of RNA to detect and quantitate the two predicted alpha-mRNA species. With this assay we have examined the relative expression of the alpha-globin genes during normal development and in alpha-thalassemia syndromes. In normal adult reticulocytes, alpha 2 RNA is slightly more abundant than the alpha 1 species (ratio 60:40). This relative abundance of the alpha RNAs was consistently observed in fetal blood and liver RNA samples from 10 weeks of gestation to birth. In both deletion and nondeletion forms of alpha thalassemia, only the alpha 1 RNA and establish the normal pattern of relative alpha-gene expression during development independent of protein variants. RNA analysis also permits for the first time identification of the mutant genes in nondeletion forms of thalassemia.

Heterogeneity of DNA deletion in gamma delta beta-thalassemia

By restriction endonuclease mapping, gene cloning, and DNA sequencing we have determined the region of DNA that is deleted in a family with gamma delta beta-thalassemia. The deletion removes the linked epsilon, gamma-, and delta-globin structural genes and terminates within the coding portion of the beta-globin gene. Since the extent of DNA deletion in this family differs from that reported in another family, we conclude that gamma delta beta-thalassemia is heterogeneous at the molecular level.

The 3' untranslated regions of the duplicated human alpha-globin genes are unexpectedly divergent

DNA sequence analysis of a cloned partially deleted human alpha-thalassemia globin gene revealed a novel 3' untranslated region displaying at least nineteen differences when compared with previously published alpha mRNA sequences. Restriction enzyme mapping established the origin of the alpha-thalassemia gene as the more 3' of the normal, duplicated alpha genes (alpha 1). DNA sequencing of a previously isolated alpha 1 gene revealed a 3' untranslated region identical to that of the alpha-thalassemia gene. The sequence of the corresponding region of the more 5' alpha gene (alpha 2) was consistent with published mRNA sequences except in three probably polymorphic positions. Therefore the 3' untranslated regions of the highly homologous alpha-globin genes differ significantly. The recognition that the duplicated alpha genes differ in a region expressed in mature mRNA should not permit direct assessment of relative gene output in various normal and pathologic states. The divergence of the alpha gene 3' untranslated regions in the face of minimal coding sequence differences must be reconciled with current models for matching homologous gene sequences by recombination events.

Cloning and direct examination of a structurally abnormal human beta 0-thalassemia globin gene

Restriction endonuclease mapping permitted identification of a form of beta 0-thalassemia in which a partial deletion of the beta-globin structural gene occurred [Orkin, S. H., Old, J. M., Weatherall, D. J. & Nathan, D. G. (1979) Proc. Natil. Acad. Sci. USA 76, 2400-2404]. To analyze its structure more directly, this abnormal human gene has now been cloned in bacteriophage lambda gtWES. Restriction mapping of the cloned gene and of a normal beta-globin gene contained in the phage H beta G1 confirmed previous findings regarding the presence of a deletion toward the 3' end of the gene but could not establish its position more accurately. Electron microscopy of the hybrid of the beta-thalassemia gene with globin RNA (R-loop analysis) provided unequivocal evidence for a deletion with the beta-globin structural gene. Hybridization of restriction fragments of the mutant gene with homologous fragments of H beta G1 (heteroduplex analysis) revealed a continuous, internal deletion of about 0.6 kilobase of DNA in the mutant gene and permitted its localization within the beta-globin gene region. This deletion removed the terminal third of the large intervening sequence within the beta-globin gene, the entire 3' coding block (extending from codon 105 to the end of the gene), and approximately 150 base pairs of DNA past the end of the normal globin gene.

Precise localization of human beta-globin gene complex on chromosome 11

Cloned DNA probes were used in combination with a panel of five hybrid cell clones containing a series of different terminal deletions in human chromosome 11 to map precisely the human hemoglobin beta and delta chain structural genes contained on this chromosome. The region of deletion in each clone of the panel has been defined by biochemical, immunologic, and cytogenetic markers. DNA from clones containing successively larger terminal deletions was tested with appropriate DNA probes to determine the point on the chromosome at which DNA for these two closely linked hemoglobin genes is deleted. These genes, and by inference the closely linked G gamma and A gamma globin genes as well, have been assigned to the intraband region 11p1205 leads to 11p1208 on the short arm of chromosome 11, an interval containing approximately 4500 kilobases of DNA. The approach appears to have potential for even greater resolution and reasonably wide applicability for gene mapping.

Deletion of the A gamma-globin gene in G gamma-delta beta-thalassemia

In an individual homozygous for G gamma-delta beta-thalassemia, a physical alteration in gamma-globin gene organization was detected by restriction enzyme mapping. The data indicated that the absence of A gamma-globin chains resulted from extension of the DNA deletion from the delta beta-globin gene region into the gamma-globin gene region rather than a functional disturbance of gamma-gene expression.

Partial deletion of beta-globin gene DNA in certain patients with beta 0-thalassemia

We have used restriction endonuclease mapping of cell DNA to investigate the structure of the beta-globin gene in beta-thalassemias. Among 17 individuals with beta +- and beta 0-thalassemia, we observed three patients of Indian origin with beta 0-thalassemia whose DNA revealed a consistent mapping abnormality. In one beta allele in each diploid cell, 0.6 kilobase of DNA was deleted from beta-specific Pst I and Bgl II restriction fragments. This deletion involved 3' beta-globin gene sequences and eliminated the EcoRI site normally present at codons 121/122, but it did not extend to the BamHI site at codons 98--100 on the 5' side of the 0.90-kilobase intervening sequence normally present in beta-globin genes. Partial beta-globin gene deletion appears, therefore, to be a primary molecular defect seen in certain patients with beta 0-thalassemia.

The molecular basis of alpha-thalassemias: frequent occurrence of dysfunctional alpha loci among non-Asians with Hb H disease

Study of Asians has previously indicated that deletion of alpha-globin structural genes is the predominant lesion in alpha-thalassemias and that Hb H disease occurs when three of four normal alpha loci per cell are deleted. To test the generality of this model, Hb H disease DNAs of both Asian and non-Asian origin were analyzed by restriction endonuclease mapping using the technique of Southern (1975). Whereas in normal DNA, alpha sequences are present in a single Eco Rl fragment of cellular DNA approximately 22.5 kb long, fragments of 22.5, 20 and 2.6 kb were found in various Hb H disease DNAs. The 20 kb Eco Rl fragment alone, in which a single alpha-globin structural locus resides, was found in Asian Hb H disease DNA. This finding is consistent with the deletion model of alpha-thalassemia. In contrast, seven of eight non-Asian Hb H disease DNAs displayed a more complex molecular composition. The fragment patterns observed were 22.5 kb alone, 22.5 plus 2.6 kb, 20 plus 2.6 kb and 20 kb alone. Non-Asian Hb H disease DNAs contained one, two or three alpha loci per cell in contrast to the one locus predicted by the simple deletion model of alpha-thalassemia. The data are best explained by the existence of defective alpha loci in certain individuals with alpha-thalassemia, particularly outside the Asian population. Restriction mapping of the 20 kb Eco Rl fragment found in Asian and some non-Asian Hb H disease DNAs demonstrated a striking similarity in the placement of restriction sites about the single alpha gene compared with sites about the two genes in the 22.5 kb Eco Rl fragment seen in normal DNA. These data are consistent with origin of the 20 kb fragment from the 22.5 kb normal Eco Rl fragment by either unequal crossing-over or a deletion event. The molecular heterogeneity and frequent occurrence of defective alpha loci in non-Asian Hb H disease DNAs described here may explain, in part, the clinical heterogeneity of alpha-thalassemias and the absence of the homozygous deletion state (hydrops fetalis) in non-Asians. Further study of cellular DNA fragments containing the defective alpha loci identified in this work may indicate the types of specific mutations responsible for abnormal globin gene expression and complement similar studies on abnormal beta genes in beta-thalassemias.

The duplicated human alpha globin genes lie close together in cellular DNA

The organization of alpha globin genes in normal human DNA was examined by restriction endonuclease mapping, alpha globin-specific fragments in endonuclease digests of total cell DNA were identified after electrophoresis by hybridization with [32P]cDNA following the blotting procedure of Southern [(1975) J. Mol. Biol. 98, 503--517]. The data provide direct evidence for the duplication of alpha genes and further indicate that these loci are closely linked within a single restriction fragment. The HindIII sites (codons 90/91) of these duplicated genes lie approximately 3.7 kilobases apart in the physical map proposed for this region. This organization of alpha genes can be altered in DNA of individuals with alpha-thalassemia.

Application of endonuclease mapping to the analysis and prenatal diagnosis of thalassemias caused by globin-gene deletion

We applied a recently developed and more direct technic to diagnose thalassemia syndromes associated with deletion of particular globin structural genes and to assess a fetus at risk for one of those conditions, deltabeta-thalassemia. The method allows assessment of the globin genes present in total cellular DNA and is applicable to amniotic-fluid cell DNA. Cellular DNA fragments produced by cleavage using two specific restriction endonucleases are separated on the basis of size by agarose-gel electrophoresis, and the distribution of specific sequences among the DNA fragments determined by molecular hybridization. We observed the total deletion of alpha-globin genes in homozygous alpha-thalassemia (hydrops fetalis with hemoglobin Bart's) and the deletion of particular beta and beta-like sequences in cases homozygous for hereditary persistence of fetal hemoglobin and deltabeta-thalassemia. Analysis of amniotic-fluid cell DNA from a fetus at risk for deltabeta-thalassemia demonstrated the feasibility of these improved methods for antenatal diagnosis. The molecular studies confirmed the diagnosis predicted by analysis of fetal blood and established at birth.