Allele specific oligonucleotide probes for mouse I-A region and gene: I-A beta

MHC Class II gene expression is being intensively studied in vitro. In vivo class II gene expression that occurs during G.V.H.R. and allograft reaction has not been studied as well as the gene expression in vitro because such studies require unambiguous detection of graft or host specific MHC class II genes. Although this is possible by using allele specific oligonucleotide probes for individual class II genes, such probes for class II genes in mice have not been described before. We compared the nucleotide sequences of I-A beta genes from various haplotypes and selected a region of minimal homology in the 2nd exon of this gene. We synthesized two oligonucleotide probes corresponding to a 20 nucleotide stretch in the hypervariable region of the I-A beta 1 genes of H-2k and H-2d haplotype mice. These probes specifically detect I-A beta mRNA from mice of appropriate haplotypes. These allele-specific probes should help study the in vivo expression of graft or host specific I-A genes in G.V.H.R. or allograft reaction.

In vitro galactosylation of a 110-kDa glycoprotein by an endogenous cell surface galactosyltransferase correlates with the invasiveness of adrenal carcinoma cells

We have examined the role of a cell surface galactosyltransferase, laminin, and laminin-binding protein (receptor) in the invasion of clonal derivatives of a murine adrenal carcinoma cell line. Although a 10-fold variation was found in the ability to invade a reconstituted basement membrane matrix, levels of intracellular laminin and the laminin-binding protein were shown to be present and secreted equally in all lines. Of the eight lines tested, seven showed a correlation between invasion and the incorporation of [3H]galactose from UDP-[3H]galactose into a 90- to 110-kDa protein. One noninvasive line (clone HSR), however, retained high galactosyltransferase activity yet could not galactosylate the endogenous 90- to 110-kDa substrate. Interestingly, this clone was unable to attach to laminin. Although high galactosyltransferase activity can be consistent with cells of high invasiveness, our results suggest that the galactosylation status of a 90- to 110-kDa Y1 cell surface glycoprotein is most indicative of invasion potential.

Characterization of a nondeleterious L1 insertion in an intron of the human factor VIII gene and further evidence of open reading frames in functional L1 elements

We have characterized an insertional event in IVS-10 of the factor VIII gene in a pedigree containing a hemophilia A patient (JH-25). The inserted DNA is a 5' truncated L1 element that is 681 bp long followed by a 3'66-bp poly(A) tract. The L1 element is inserted 154 bp 5' to the start of exon 11 and is flanked by a 13- to 17-bp target site duplication. The L1 insertion is present in four generations of the patient's family. The maternal grandfather who carries the insertion does not have hemophilia A, indicating that the insertion is not the cause of hemophilia A in the patient. We have sequenced this insertion and two previously reported de novo L1 insertions in the factor VIII gene in patients JH-27 (3785 bp) and JH-28 (2132 bp). The three nucleotide sequences differ by 0.2-0.8%. All three of these L1 insertions have open reading frames (ORFs) (1192, 642, and 157 aa) and the three derived amino acid sequences are 98-99% identical. The previously reported sequence similarity between L1 3' ORFs and the polymerase domain of reverse transcriptases is maintained in the ORFs of the JH-27 and JH-28 L1 insertions. The presence of open reading frames and the close sequence similarity of these recently inserted L1 elements provide indirect evidence for the existence of a set of functional L1 elements that encode one or more proteins necessary for their retrotransposition.

Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man

L1 sequences are a human-specific family of long, interspersed, repetitive elements, present as approximately 10(5) copies dispersed throughout the genome. The full-length L1 sequence is 6.1 kilobases, but the majority of L1 elements are truncated at the 5' end, resulting in a fivefold higher copy number of 3' sequences. The nucleotide sequence of L1 elements includes an A-rich 3' end and two long open reading frames (orf-1 and orf-2), the second of which encodes a potential polypeptide having sequence homology with the reverse transcriptases. This structure suggests that L1 elements represent a class of non-viral retrotransposons. A number of L1 complementary DNAs, including a nearly full-length element, have been isolated from an undifferentiated teratocarcinoma cell line. We now report insertions of L1 elements into exon 14 of the factor VIII gene in two of 240 unrelated patients with haemophilia A. Both of these insertions (3.8 and 2.3 kilobases respectively) contain 3' portions of the L1 sequence, including the poly (A) tract, and create target site duplications of at least 12 and 13 nucleotides of the factor VIII gene. In addition, their 3'-trailer sequences following orf-2 are nearly identical to the consensus sequence of L1 cDNAs (ref. 6). These results indicate that certain L1 sequences in man can be dispersed, presumably by an RNA intermediate, and cause disease by insertional mutation.

Origin of the human L1 elements: proposed progenitor genes deduced from a consensus DNA sequence

A consensus sequence for the human long interspersed repeated DNA element, L1Hs (LINE or KpnI sequence), is presented. The sequence contains two open reading frames (ORFs) which are homologous to ORFs in corresponding regions of L1 elements in other species. The L1Hs ORFs are separated by a small evolutionarily nonconserved region. The 5' end of the consensus contains frequent terminators in all three reading frames and has a relatively high GC content with numerous stretches of weak homology with AluI repeats. The 5' ORF extends for a minimum of 723 bp (241 codons). The 3' ORF is 3843 bp (1281 codons) and predicts a protein of 149 kD which has regions of weak homology to the polymerase domain of various reverse transcriptases. The 3' end of the consensus has a 208-bp nonconserved region followed by an adenine-rich end. The organization of the L1Hs consensus sequence resembles the structure of eukaryotic mRNAs except for the noncoding region between ORFs. However, due to base substitutions or truncation most elements appear incapable of producing mRNA that can be translated. Our observation that individual elements cluster into subfamilies on the basis of the presence or absence of blocks of sequence, or by the linkage of alternative bases at multiple positions, suggests that most L1 sequences were derived from a small number of structural genes. An estimate of the mammalian L1 substitution rate was derived and used to predict the age of individual human elements. From this it follows that the majority of human L1 sequences have been generated within the last 30 million years. The human elements studied here differ from each other, yet overall the L1Hs sequences demonstrate a pattern of species-specificity when compared to the L1 families of other mammals. Possible mechanisms that may account for the origin and evolution of the L1 family are discussed. These include pseudogene formation (retroposition), transposition, gene conversion, and RNA recombination.

Structure and expression of amplified cKi-ras gene sequences in Y1 mouse adrenal tumor cells

A recombinant library of double minute chromosomal DNA, enriched in specific sequences that are amplified in Y1 mouse adrenal tumor cells, was used as a source of material to explore the structure and expression of amplified cKi-ras genes in these cells. From DNA sequence analysis of these cloned fragments, we found no evidence for the presence of point mutations previously demonstrated to be associated with activation of the transforming potential of ras genes. A comparison of the mouse gene with that of the homologous human cKi-ras2 gene reveals 94% nucleotide sequence homology within the coding regions and 97% homology for the predicted amino acid composition. Like the human gene, the mouse cKi-ras gene contains alternative 3' coding exons. Blot hybridization analyses of RNA revealed a preferential utilization of the more 3' of the two fourth coding exons in the generation of Y1 cKi-ras transcripts.

The sequence of the gorilla fetal globin genes: evidence for multiple gene conversions in human evolution

Two fetal globin genes (G gamma and A gamma) from one chromosome of a lowland gorilla (Gorilla gorilla gorilla) have been sequenced and compared to three human loci (a G gamma-gene and two A gamma-alleles). A comparison of regions of local homology among these five sequences indicates that long after the duplication that produced the two nonallelic gamma-globin loci of catarrhine primates, about 35 million years (Myr) ago, at least one gene conversion event occurred between these loci. This conversion occurred not long before the ancestral divergence (about 6 Myr ago) of Homo and Gorilla. After this ancestral divergence, a minimum of three more gene conversion events occurred in the human lineage. Each human A gamma-allele shares specific sequence features with the gorilla A gamma-gene; one such distinctive allelic feature involves the simple repeated sequence in IVS 2. This suggests that early in the human lineage the A gamma-genes may have undergone a crossing-over event mediated by this simple repeated sequence. The DNA sequences from coding regions of both G gamma- and A gamma-loci, a comparison of 292 codons in the corresponding gorilla and human genes, show an unusually low evolutionary rate, with only two nonsilent differences and, surprisingly, not even one silent substitution. The two nonsynonymous substitutions observed predict a glycine at codon 73 and an arginine at codon 104 in the gorilla A gamma-sequence rather than aspartic acid and lysine, respectively, in human A gamma. Because only arginine has been found at position 104 in gamma-chains of Old World monkeys, it may represent the ancestral residue lost in gorilla and human G gamma-chains and in the human A gamma-chain. Possibly the arginine codon (AGG) was replaced by the lysine codon (AAG) in the G gamma-gene of a common ancestor of Homo and Gorilla and then was transferred to the A gamma-gene by subsequent conversions in the human lineage. DNA sequence conversions, similar to that attributed to the fetal gamma-globin genes, appear to be relatively frequent phenomena and, if widespread throughout the genome, may have profound evolutionary consequences.

Amplified DNA in Y1 mouse adrenal tumor cells: isolation of cDNAs complementary to an amplified c-Ki-ras gene and localization of homologous sequences to mouse chromosome 6

We have isolated cDNA clones complementary to a c-Ki-ras cellular oncogene that is amplified in Y1 mouse adrenal tumor cells, with the amplified sequences located on double-minute chromatin bodies (DMs) and homogeneously staining chromosomal regions (HSRs). Characterization of the cDNAs included the isolation of corresponding genomic clones, Northern blot analysis of RNA, and DNA sequence analysis. Our studies demonstrate that the c-Ki-ras gene amplified in the Y1 cells is homologous to the human c-Ki-ras2 gene. We have also obtained evidence that, in addition to c-Ki-ras, at least one other transcription unit has been amplified in the mouse adrenal tumor cells. Moreover, by Southern blot analysis of Chinese hamster-mouse somatic cell hybrids, we have determined that the amplified DNA sequences associated with DMs and HSRs, including the c-Ki-ras gene, are present in normal mouse cells on chromosome 6.

beta-Thalassemia in American Blacks: novel mutations in the "TATA" box and an acceptor splice site

beta-Thalassemia genes, although often mild in their effects, are common among American Blacks. We have begun a systematic molecular analysis of beta-thalassemia mutations in this group. DNA polymorphisms in the beta-globin gene cluster were examined among 22 beta-thalassemia chromosomes. Six different haplotypes were observed. beta-globin genes of two of these were cloned, and their phenotypes were examined both in heterologous cells upon transient expression and in vivo. The gene found in the most common haplotype (9 of 22 chromosomes) contained a single base substitution (A----G) at position -29 within the highly conserved proximal promoter element (the "TATA" box). This mutant gene directed beta-globin RNA at 25% of normal levels both in heterologous cells and in vivo. It was associated with a mild beta +-thalassemia phenotype. A different gene, isolated from an apparently rare haplotype (1 of 22 chromosomes), had a single base substitution (A----G) within the acceptor splice site of the second intervening sequence. This mutation abolished normal RNA splicing so that the only RNA made from the gene in vitro was an alternatively spliced RNA, which could not encode beta-globin. The mild deficit in beta-globin production attributable to the -29 A----G mutant allele most likely accounts for the frequently mild nature of beta-thalassemia among American Blacks.

Transcripts homologous to a long repeated DNA element in the human genome

Using three cloned DNA fragments from a 6.4-kb (kilobase pair) DNA element repeated several thousand times in the human genome (Adams, J. W., Kaufman, R. E., Kretschmer, P. J., Harrison, M. and Nienhuis, A. W. (1980) Nucleic Acids Res. 8, 6113-6128) and DNA/RNA hybridization, we show that transcripts homologous to this DNA family exist in total cellular RNA from human blood cells and from a mouse-human hybrid cell line with one human chromosome, the X. No such transcripts were detected in RNA from rabbit blood or a mouse cell line. For each DNA fragment studied, we found that blood transcripts and X-chromosome transcripts were indistinguishable in electrophoretic mobility and very heterogeneous in length; in addition, prominent hybridization bands were seen at 4.7 and 1.9 kb. Transcription from this DNA family likely occurs from heterogeneous templates. The existence of RNAs smaller than 6.4 kb suggests that part of the repeat unit can be transcribed and/or there exists a cellular mechanism to make these short RNAs from longer precursors. The vast majority of the RNAs homologous to the long repeat are not polyadenylated. In blood RNA there are a few hundred copies of beta-globin mRNA for every transcript homologous to this 6.4 kb repeat.

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.

Population heterogeneity of the Hpa I restriction site associated with the beta globin gene: implications for prenatal diagnosis

The Hpa I restriction endonuclease site polymorphism that results in some human beta globin genes being contained in a 13-kilobase (kb) DNA restriction fragment rather than in the usual 7.6-kb fragment has been reported to be in linkage disequilibrium with the beta S mutation. The frequency of the 13-kb fragment among Baltimore black sickle cell (SS) disease patients (58%) is lower than that reported for San Francisco black SS disease patients (87%) and similar to that reported for such New York patients (59%). There is, then, considerable heterogeneity among American black populations. Therefore, for the purposes of prenatal diagnosis, the frequency in the particular population at risk should be established. When the frequency of association of the 13-kb fragment and the beta S mutation is low, the linkage phase must also be established. When the linkage phase is known, the Hpa I pattern alone can exclude SS disease 54% of the time for Baltimore AS X AS couples.

The molecular basis of hemoglobin Grady

DNA from individuals heterozygous for the extended alpha-chain variant Hb Grady were studied by gene counting and restriction enzyme analysis. Neither method indicated the presence of an extra (fifth) alpha gene, which argues that if this variant arose by unequal crossing over, the event most likely involved mispairing between alleles rather than between the separate alpha 1 and alpha 2 loci.

Unequal crossing-over: a common basis of single alpha-globin genes in Asians and American blacks with hemoglobin-H disease

The alpha-globin genes of five black Americans, two Chinese, and five Filipinos with HbH disease (an alpha-thalassemia state in which there is a single functional alpha gene) were analyzed by restriction endonuclease techniques. All subjects were found to have one chromosome 16, lacking both alpha genes, and another containing a single alpha gene (--/-alpha). Restriction endonuclease patterns of the DNA obtained from all 12 subjects were identical and compatible with unequal crossing-over as the mechanism of origin of the single alpha gene in these individuals.

Prenatal diagnosis of sickle cell anemia by restriction and endonuclease analysis: HindIII polymorphisms in gamma-globin genes extend test applicability

Polymorphism for a Hpa I restriction endonuclease site associated with about 60% of beta S genes in American Blacks allows exact prenatal diagnosis of sickle cell anemia by amniocentesis in 36% of couples at risk. In three families in whom exact diagnosis by Hpa I sites was impossible, we found analysis for the presence of polymorphic HindIII sites in the G gamma and A gamma intervening sequences would allow an exact prenatal diagnosis of sickle cell status in all three. In one of these families, the presence of an A gamma HindIII site in amniocyte DNA confirmed the diagnosis (sickle cell trait) made by synthetic studies using fetal erythrocytes obtained at fetoscopy. Studies of other Black families and individuals provide evidence for linkage disequilibrium in the G gamma-A gamma-delta-beta gene complex involving the four sites, G gamma HindIII, A gamma HindIII, beta S, and Hpa I, which span 33 kilobases (kb). Ten of 14 chromosomes bearing a beta S gene in a 7.6-kb Hpa I fragment contained a G gamma but not an A gamma HindIII site, whereas 16 of 16 chromosomes bearing a beta S gene in a 13-kb Hpa I fragment lacked both the G gamma and A gamma HindIII sites. Two-thirds of beta A-bearing chromosomes lacked both G gamma and A gamma sites, whereas one-third contained either the G gamma or both G gamma and A gamma sites. These data demonstrate that combined analysis of both Hpa I and HindIII polymorphisms and verification of their linkage phase should increase the fraction of couples for whom amniocentesis can provide an exact diagnosis of sickle cell status from 36% to greater than 80%.

A molecular basis for hemoglobin-H disease in American blacks

We have applied gene counting and restriction endonuclease mapping techniques to the study of two American black families in which there were one or more cases of HbH disease. We found deletions of three of the four normal alpha-globin genes in individuals with HbH disease. In two of these individuals, the chromosome containing the single alpha gene could have originated by crossing over between mispaired alpha genes, resulting in a deletion of about 4.2 kilobases (kb).

DNA restriction endonuclease analysis for localization of human beta- and delta-globin genes on chromosome 11

DNA from a clone of a mouse-human hybrid that retained a human chromosome consisting of the major part of chromosome 11 and region q25-26-qter of the X chromosome was digested with various restriction endonucleases, subjected to electrophoresis in agarose gels, and transferred to nitrocellulose filters. The restriction digest pattern of the clone, when hybridized with a 32P-labeled plasmid fragment containing human beta-globin gene sequences, was a composite of the normal human and mouse (A9) patterns. When back-selected in 6-thioguanine to eliminate the 11 translocation chromosome, the hybrid cells showed only the A9 restriction pattern. These results substantiate the localization of beta- and delta-globin genes to human chromosome 11 and exclude the region 11q23-qter as the site.

The proportion of all point mutations which are unacceptable: an estimate based on hemoglobin amino acid and nucleotide sequences

Statistical analysis of the distribution of 156 kinds of human hemoglobin beta (Hbbeta) chain variants suggests that mutations are essentially random in their location. Thus differential fitness, not differential mutability, is the principal source of nonrandom distribution of interspecies differences in Hbbeta amino acid sequence. Similar analyses of both the location and the kind of interspecies differences detected among primates support this viewpoint and lead us to estimate that at least 95% of all amino acid subsitutions,i.e., nonsynonymous mutations, in Hbbeta are functionally unacceptable in homozygous state. Through the combined use of this estimate and the number of nonsynonymous and synonymous substitutions per nucleotide site inferred from comparisons of entire human and rabbit HbbetamRNA nucleotide sequences, we calculate (a) approximately 70% of synonymous Hbbeta mutations are adaptively undersirable and (b) the mutation rate underlying all changes is lesser than or equal to 10(-8) nucleotide substitutions per nucleotide site per year. Apart from such calculations, analyses of nucleotide patterns in HbbetamRNA as well as in rat preproinsulin mRNA reinforce the notion that a large portion of synonymous mutations are functionally unacceptable and rendered so by selective constraint, at a pretranslational level, of the abundance of particular nucleotide doublets such as CpG.

The phylogenetic distribution of red cell 2,3 diphosphoglycerate and its interaction with mammalian hemoglobins

In order to better understand the extent to which 2,3 diphosphoglycerate (DPG) contributes to red cell function in the mammals, we assayed DPG levels in blood from a taxonomically diverse set of 71 species representing 14 orders. In addition, for 66 species and 4 hemoglobin phenotypes of the sheep, the effect of DPG on oxygen affinity was measured by determining P 50 values for hemoglobin in the absence of DPG and at 0.2 mM and 1.0 mM concentrations. Most mammals had high levels of red cell DPG and phosphate-free hemoglobins with a relatively high oxygen affinity. In contrast, two taxonomically unrelated groups had both very low intra-erythrocytic DPG concentrations as well as hemoglobins of native low oxygen affinity that interacted weakly with DPG. This latter group includes the Feloidea (order Carnivora) and the Bovoidea (order Artiodactyla). The relationship between DPG concentration, hemoglobin oxygen affinity and the interaction of DPG with hemoglobin is treated quantitatively to provide a model of mammalian red cell function. This derived expression is compared with descriptive allometric equations for whole blood P 50 and is shown to provide statistically reasonable predictions.

Functional aspects of hemoglobin evolution in the mammals

Comparative studies of red cells 2, 3 Diphosphoglycerate (DPG) and its effect on hemoglobin oxygen affinity from a taxonomically diverse set of mammals indicate two anomalous groups: members of the superfamilies Bovoidea (Actiodactyla) and Feloidea (Carnivora). In both taxa all of the individuals assayed had very low or unmeasurable quantities of DPG and red cell lysates with little, if any, DPG effect as measured by the change in oxygen affinity in the absence and presence of the phosphate. However, in both groups compensatory changes have occurred in hemoglobin structure and function so as to reduce the native oxygen affinity and thus cause them to resemble the hemoglobins of DPG-utilizing mammals as they occur in the setting of the red cell. We conclude that this parallelism of function is the result of convergent evolution.