Linkage of adult alpha- and beta-globin genes in X. laevis and gene duplication by tetraploidization

Spatial and biological characterisation of the complete quinic acid utilisation gene cluster in Aspergillus nidulans

Heterologous probing of restriction digests of chromosomal DNA from Aspergillus nidulans with radioactively labelled probes encoding dehydroshikimate dehydratase (QA-4) and a repressor gene (QA1-S) from Neurospora crassa revealed a pattern of hybridisation inconsistent with an equivalent single copy of each gene in A. nidulans. Screening of size-selected and total genome A. nidulans DNA libraries allowed the isolation of four unique classes of sequence, two of which hybridised to the QA-4 probe, and two of which hybridised to the QA1-S probe. In each case, one of each pair of unique sequences was able to complement the equivalent mutations qutC (= QA-4) and qutR (= QA1-S) in A. nidulans, whereas the second of each pair was unable to complement the same mutation. The complementing sequences were physically mapped relative to the previously cloned A. nidulans QUT gene cluster, demonstrating that QUTR is distal and divergently transcribed from QUTA with approximately 3.6 kb between the ATG translational start codons, and that QUTC is transcribed in the same direction as QUTD on the other side of the cluster, approximately 1.65 kb downstream of the QUTD TAA translational stop signal. The physical and genetic maps of the QUT gene cluster correlate precisely. The non-complementing A. nidulans DNA sequences that hybridise to the N. crassa QA-4 (= QUTC) and QA1-S (= QUTR) fulfill many of the criteria characteristic of pseudogenes.(ABSTRACT TRUNCATED AT 250 WORDS)

Sequence analysis of the upstream regions of Xenopus laevis beta-globin genes and arrangement of repetitive elements within the globin gene clusters

The globin gene clusters of Xenopus laevis are interspersed by various different repetitive DNA elements. A specific repeat, the JH12 element, has been mapped by Southern analysis and some of its locations have been subsequently confirmed by nucleotide sequencing. JH12 family members seem to represent mobile genetic elements and display a high degree of divergence. The nucleotide sequences upstream to the adult beta I-globin gene and to the two coordinately expressed larval beta I- and beta II-globin genes have been determined and compared to those of the adult alpha-genes. Besides some repetitive DNA elements and a short sequence of rather weak homology we have found no characteristic sequence motifs to be common to the adult alpha- and beta-genes. The two larval beta-genes share one short sequence element being absent from the adult genes. This might reflect completely different sequence requirements for protein interactions and for the regulation of adult and larval globin gene expression.

Selective overexpression of the QUTE gene encoding catabolic 3-dehydroquinase in multicopy transformants of Aspergillus nidulans

The three enzymes necessary to catabolize quinate to protocatechuate are inducible by quinic acid, and transcription of their corresponding genes is controlled by the action of a positively acting activator gene and a negatively acting repressor gene. Transformed strains of Aspergillus nidulans containing multiple copies of the activator gene (QUTA) but single copies of the other QUT genes retain normal regulation of the gene cluster and do not show any overexpression of the three quinic acid catabolic enzymes. Transformed strains containing equal multiple copies of the activator gene (QUTA) and QUTE (encoding catabolic 3-dehydroquinase), but single copies of the other QUT genes, retain normal regulation of the QUT gene cluster, but selectively overexpress the QUTE gene upon quinic acid induction. Data are presented that strongly suggested that the gene QUTG, which is physically located within the QUT gene cluster and for which no function has been identified, is not required for expression of the gene cluster and does not encode a chlorogenic acid esterase.

Duplicated homeobox genes in Xenopus

Multiple kinds of clones and restriction fragment polymorphisms are frequently encountered when analyzing genes of the tetraploid frog Xenopus laevis. Two types of cDNA clone have been isolated for homeobox gene 2. Analysis of their corresponding genomic clones confirmed the existence of clearly distinct restriction maps; in addition the nearby presence of two additional homeoboxes suggests that this region is homologous to the Hox 2 gene complex of mammals. We asked whether the genetic polymorphism in Xenopus results from increased allelic differences due to tetraploidy or from having duplicated Hox 2 complexes. Using X. laevis/Xenopus borealis interspecies hybrids we show that the two types of X. laevis homeobox gene 2 transcripts result from two different genetic loci. They cannot represent alleles of the same gene because they do not segregate independently in the F1 hybrid progeny. Most other X. laevis homeobox genes studied so far are also found in two versions. Thus X. laevis seems to have two homeobox genes, both of which are expressed, for each one present in mammals or other vertebrates.

Erythroid specific activation of the Xenopus laevis adult alpha-globin promoter in transient heterokaryons

Insertion of 1.5 kb of the 5' flanking region of the adult alpha-globin gene of X. laevis in front of the CAT structural gene promotes synthesis of CAT in transiently transfected X. laevis kidney cells. Fusion of transiently transfected kidney cells with erythroblasts isolated from anaemic frogs stimulates CAT expression 3-4 fold in the resulting transient heterokaryons. The stimulation is specific for the alpha-globin promoter and is obtained after fusion with erythroid cells but not with hepatocytes or kidney cells. Stably transfected kidney cells express drastically reduced CAT activity as compared with transiently transfected cells. Nevertheless, fusion of stably transfected kidney cells with erythroblasts leads to a 10-17 fold stimulation of CAT expression. The experiments suggest that erythroid specific transacting factors stimulate expression of CAT controlled by the adult alpha-globin promoter.

Primary structure and evolutionary relationship between the adult alpha-globin genes and their 5'-flanking regions of Xenopus laevis and Xenopus tropicalis

To investigate the evolution of globin genes in the genus Xenopus, we have determined the primary structure of the related adult alpha I- and alpha II-globin genes of X. laevis and of the adult alpha-globin gene of X. tropicalis, including their 5'-flanking regions. All three genes are comprised of three exons and two introns at homologous positions. The exons are highly conserved and code for 141 amino acids. By contrast, the corresponding introns vary in length and show considerable divergence. Comparison of 900 bp of the 5'-flanking region revealed that the X. tropicalis gene contains a conserved proximal 310-bp promoter sequence, comprised of the canonical TATA and CCAAT motifs at homologous positions, and five conserved elements in the same order and at similar positions as previously shown for the corresponding genes of X. laevis. We therefore conclude that these conserved upstream elements may represent regulatory sequences for cell-specific regulation of the adult Xenopus globin genes.

Fingerprinting cell lines: use of human hypervariable DNA probes to characterize mammalian cell cultures

Hypervariable DNA sequences may be used as probes to derive DNA "finger-prints" for individuals. To assess the use of the human 33.15 and 33.6 probes (isolated by Jeffreys and coworkers) for characterizing cell lines of nonhuman origin, DNA from different stocks of Chinese hamster (CH) cells was screened. All CHO (ovary) sublines could be readily distinguished from CH-V79 sublines by their fingerprints, but where two stocks had been derived recently from the same line, their fingerprints were nearly identical. Similarly fingerprints of HPRT-deficient mutants derived from one cell stock were identical. A V79 x CHO fusion hybrid showed equal fingerprint band-sharing with each parent line, while early-passage diploid CH cells had a fingerprint closer to CHO than to V79. Thus these data introduce a simple means of typing cell lines to avoid cross-contamination, of checking cell hybrids, and of assessing the divergence of cell stocks from one another.

Multilocus molecular mapping of the mouse X chromosome

Using restriction fragment length polymorphisms (RFLPs) and enzymatic variants between distantly related mouse species, we have assigned three genes to the mouse X chromosome and concurrently mapped a total of eight genes spanning an estimated 50 cM of the chromosome. Segregation of RFLPs in over 200 male progeny from interspecies backcrosses between the inbred strain C57BL/6JRos and either wild-derived Mus musculus or Mus spretus was followed for the murine genes Timp (tissue inhibitor of metalloproteinases), Cf-8 (coagulation factor VIII), and Rsvp (red-sensitive visual pigment) and the known X-linked markers Otc, Hprt, Cf-9, G6pd, and Ags. From the centromere, the gene order was defined as Otc, Timp, Hprt, Cf-9, (Cf-8/Rsvp/G6pd), Ags, by minimizing the number of multiple recombinational events. No significant differences in map order or frequency of recombination were observed between the two backcross series studied. The use of Southern analysis has allowed us to add new genes to the map in a cumulative manner, and as probes become available, additional markers can be mapped, using the same set of mice, by utilizing existing blots or resampling the DNAs. The use of probes for functional genes has allowed us to directly compare the X chromosomes of mouse and man and has provided insight into chromosomal rearrangements which have occurred during the evolutionary divergence of these species, as well as to define the extent of linkage homologies.

Molecular organisation of the quinic acid utilization (QUT) gene cluster in Aspergillus nidulans

The functional integrity of the QUTB gene (encoding quinate dehydrogenase) has been confirmed by transformation of a qutB mutant strain. The DNA sequence of the contiguous genes QUTD (quinate permease), QUTB and QUTG (function unknown) has been determined and analysed, together with that of QUTE (catabolic 3-dehydroquinase). The QUTB sequence shows significant homology with the shikimate dehydrogenase function of the complex AROM locus of Aspergillus nidulans, and with the QA-3 quinate dehydrogenase and QA-1S (repressor) genes of Neurospora crassa. The QUTD gene shows strong homology with the N. crassa QA-Y gene and QUTG with the QA-X gene. QUTD, QUTB, and QUTG, QUTE form two pairs of divergently transcribed genes, and conserved sequence motifs identified in the two common 5' non-coding regions show significant homology with UASGAL and UASQA sequences of the Saccharomyces cerevisiae and N. crassa Gal and QA systems. In addition, conserved 5' sequences homologous to the mammalian CAAT box are noted and a previously unreported conserved 22 nucleotide motif is presented.

Structure and expression of the guinea-pig alpha-lactalbumin gene

The entire guinea-pig alpha-lactalbumin gene was isolated from a genomic DNA library constructed in the bacteriophage lambda L47. The complete nucleotide sequence of the gene and its immediate 5' and 3' flanking sequences were determined and compared with those of the human and rat alpha-lactalbumin genes. This demonstrates that the size, organization and sequence of the exons is highly conserved between species, and reveals the presence of the highly conserved potential regulatory 'milk box' consensus sequence [RGAAGRAAA(N)TGGACAGAAATCAA(CG)TTTCTA] between positions -140 and -110 relative to the transcriptional start point. A guinea-pig LINE repeat sequence was also present in the 5' flanking region between positions -520 and -1195. Transfection of the alpha-lactalbumin gene cloned in a bovine papilloma virus vector into the mouse C127 and human MCF-7 mammary tumour cell-lines gave rise to stable but seemingly constitutive expression of alpha-lactalbumin. Expression was from the correct transcriptional start point, resulting in the accumulation of correctly processed mRNA and the secretion of alpha-lactalbumin into the culture medium.

A third striated muscle actin gene is expressed during early development in the amphibian Xenopus laevis

During early embryonic development in the frog Xenopus laevis, several muscle-specific actin genes encoding distinct actin protein isoforms are activated in cells of the embryonic muscle. In addition to the cardiac (or alpha 1) and skeletal (or alpha 2) actin genes, a third muscle-specific actin gene is expressed in the same embryonic tissue. We have determined the complete nucleotide sequence of this third gene and examined its expression in embryonic and adult tissues. During embryogenesis, this femoral (alpha 3) actin gene is activated several hours later than its cardiac and skeletal counterparts and its transcripts are first detected after neurulation. The gene encodes a skeletal-type actin protein and is expressed exclusively in skeletal muscle in the adult frog. Two copies of this gene have been isolated from the tetraploid species Xenopus laevis, differing by only a few nucleotides in their protein-coding sequence. The related, diploid species, Xenopus tropicalis, possesses a single copy of the alpha 3 gene and its transcript is similarly conserved in nucleotide sequence. However, the X. tropicalis gene is expressed exclusively in embryonic stages of development. Comparison of the X. laevis and X. tropicalis alpha 3 gene promoters reveals extensive sequence homology, including several copies of a repeated motif that is common to other vertebrate striated-muscle actin gene promoters.

5' structural motifs and Xenopus beta globin gene activation

We have analysed the structure of the Xenopus beta globin gene 5' flanking region in erythroid and non-erythroid chromatin, in supercoiled plasmids and in minichromosomes assembled in HeLa cell transfections. We have identified two erythroid chromatin-specific, nuclease-hypersensitive sites (HSs), one centred on the cap site, the other located 1000 base-pairs further upstream. An (AT)n tract is located 200 base-pairs upstream from each of these sites. In supercoiled plasmids, the (AT)n tracts, and not the chromatin HSs, are preferentially cleaved by single strand and double strand-specific nucleases. Using restriction enzymes, we have looked at the structure of the cap site HS in minichromosomes assembled in HeLa cell transfections. We find that the structure is indistinguishable from that found in erythroid chromatin, thus reinforcing our previous suggestion, based only on DNase I studies, that the formation of this HS is not dependent on erythroid-specific factors. In view of this close structural mimicry of the situation in vivo, we have used the HeLa cell model system to study the sequences required for cap site HS formation. We find that deletion of the (AT)n tract immediately upstream influenced neither the formation of the HS nor transcription of the globin gene. Indeed, these features remained unaffected by further deletion of upstream sequences, including 50 base-pairs of the HS itself. In this construct, the dimensions of the HS remained the same as in the undeleted construct, with the plasmid sequences that replaced the deleted Xenopus sequences becoming hypersensitive. Thus, HS formation is directed by sequences downstream from --116 acting over a distance of at least 50 base-pairs.

Sequence organization and developmentally regulated transcription of a family of repetitive DNA sequences of Xenopus laevis

Members of a family of DNA sequences of Xenopus laevis have been cloned and sequenced. Molecular analyses revealed that these sequences are moderately repetitive and dispersed throughout the genome. The sequences of seven clones were compared. Two of the clones lie in the globin gene cluster; one 5' to the adult alpha 1 gene, and the other in the first intron of the tadpole alpha 1 gene. In all clones, the homologous region begins at the same site, but the lengths of the common regions vary from 123 bp to over 320 bp due to heterogeneous 3' ends. Some of the repeats are bracketed by direct and/or inverted repeats, and relatively large palindromes were found 5' to the common region in some clones. These characteristics, and the presence of a repeat 5' to one of a pair of duplicated alpha genes suggests that some family members may be capable of transposition. A number of interesting features were found in the sequences, including multiple elements similar to the yeast autonomously replicating sequence, and a sequence which is about 80% homologous to the first 30 bases of the SV40 enhancer. Transcription studies revealed that homologous transcripts are detectable beginning at neurulation, increase in concentration up to stage 45, and disappear by metamorphosis. Implications of these data are discussed.

Isolation and characterization of the positively acting regulatory gene QUTA from Aspergillus nidulans

The positively acting regulator gene QUTA from Aspergillus nidulans has been identified and located within a cluster of quinic acid utilisation (QUT) genes isolated within a recombinant phage lambda (lambda Q1). The DNA sequence of the QUTA gene reveals a single uninterrupted reading frame coding for a protein of mw 90.416 Kd. The QUTA protein sequence has a protein motif in the form of a putative "DNA finger" that shows strong homology to other such motifs in the GAL4, PPR1, ARGRII, LAC9 and QA1F regulatory gene products of S. cerevisiae, K. lactis and N. crassa. The data presented confirm the view deduced by genetical analysis that the QUTA gene of A. nidulans encodes a protein capable of interacting with QUT specific DNA sequences.

Organization and sequence of the human alpha-lactalbumin gene

A recombinant bacteriophage containing the entire alpha-lactalbumin gene was isolated from a human genomic library constructed in bacteriophage lambda L47. Within this recombinant the 2.5 kb alpha-lactalbumin gene is flanked by about 5 kb of sequence on either side. The complete nucleotide sequence of the gene and its immediate flanking sequences were determined and compared with those of the rat alpha-lactalbumin gene. These studies showed that the size, organization and sequence of the exons have been highly conserved, whereas the introns have diverged considerably. In particular, the first intron of the human gene was found to contain an Alu repetitive sequence not present in the rat. A high degree of homology (67%) was also observed in the 5' flanking regions, extending as far as 655 nucleotide residues upstream of the transcriptional initiation site. Comparison of the 5' flanking sequences of these two alpha-lactalbumin genes with those of five casein genes has revealed the presence of a highly conserved region [consensus sequence: RGAAGRAAA(N)TGGACAGAAATCAA(CG)TTTCTA], extending from position -140 to -110 in all seven sequences examined, suggesting a possible regulatory role in the hormonal control or tissue-specific expression of milk protein genes in the mammary gland.

Sequence analysis and transformation by the catabolic 3-dehydroquinase (QUTE) gene from Aspergillus nidulans

The induction of catabolic 3-dehydroquinase by quinic acid in Aspergillus nidulans has been shown to involve transcriptional control and yields a single major 0.8 kb mRNA. The nucleotide sequence of the catabolic 3-dehydroquinase QUTE gene has been determined and contains a single uninterrupted open reading frame of 462 bases encoding a 16,505 Da protein of 153 residues. Comparison with the corresponding QA2 gene of Neurospora crassa reveals the absence of 75 nucleotides encoding 25 amino acids from the centre of the QUTE gene of A. nidulans and the presence of 21 additional nucleotides at its 3' end. There is no nucleotide or amino acid homology between these two elements. A 16 bp inverted repeat (5' GGCAGAGCGTTCTGCC) shows similarity to such repeats found in other fungal promoters. The functional integrity of the QUTE gene was demonstrated by the transformation of a qutE mutant strain which regains growth on quinic acid as sole carbon source. Four of the twelve transformed strains examined contained vector sequences integrated at the qutE locus, and these strains all exhibited normal regulation of 3-dehydroquinase even when 16 copies of the QUTE gene were present.

Globin evolution in the genus Xenopus: comparative analysis of cDNAs coding for adult globin polypeptides of Xenopus borealis and Xenopus tropicalis

Globin mRNAs of Xenopus borealis and Xenopus tropicalis have been cloned and sequenced. The nucleotide and derived amino acid sequences were compared with each other and with already available data from Xenopus laevis. This analysis rendered clear evidence that the common ancestor of X. laevis and X. borealis, but not of X. tropicalis, had lost one amino acid of the beta-globins prior to a genome duplication event that preceded the segregation of the former two species. Replacement-site substitutions were used to calculate a rough time scale of genome duplication and species segregation. The results suggest an ancient separation between the X. laevis and the X. tropicalis groups occurring approximately 110-120 million years ago. Analysis of the amino acid chains demonstrated various alterations. However, some functional domains, like heme-binding sites and alpha 1 beta 2 contact sites, were subject to a high degree of conservation, indicating the existence of functional constraints on them also in the genus Xenopus.

Conserved sequences and cell-specific DNase I hypersensitive sites upstream from the co-ordinately expressed alpha I- and alpha II-globin genes of Xenopus laevis

The globin gene family of Xenopus laevis comprises pairs of closely related genes that are arranged in two clusters, each pair of genes being co-ordinately and stage-specifically expressed. To get information on putative regulatory elements, we compared the DNA sequences and the chromatin conformation 5' to the co-ordinately expressed adult alpha-globin genes. Sequence analysis revealed a relatively conserved region from the cap site up to position -289, and further upstream seven distinct boxes of homology, separated by more diverged sequences or deletions/insertions. The homology boxes comprise 22 to 194 base-pairs showing 78 to 95% homology. Analysis of chromatin conformation showed that DNase I preferentially cuts the upstream region of both genes at similar positions, 5' to the T-A-T-A and the C-C-A-A-T boxes, only in chromatin of adult erythroblasts and erythrocytes, where adult globin genes are expressed, but not in chromatin of adult liver cells or larval erythrocytes, where these genes are silent. This suggests that cell- and stage-specific activation of these genes coincides with specific changes in chromatin conformation within the proximal upstream region. No difference was found in the nucleotide sequence within the DNase I hypersensitive region proximal to the adult alpha 1-globin gene in DNA from embryonic cells, in which this gene is inactive, and adult erythrocytes, expressing this gene.

The isolation and nucleotide sequence of the complex AROM locus of Aspergillus nidulans

The AROM locus of A. nidulans, which governs five consecutive steps in pre-chorismate aromatic amino acid biosynthesis, has been cloned in a bacteriophage vector. The nucleotide sequence of the locus reveals a single, open reading-frame of 4,812 base-pairs, apparently without introns. An internal segment of the A. nidulans AROM sequence has extensive homology with the E. coli aroA gene that encodes the 5-enolpyruvylshikimate 3-phosphate synthase.

Isolation and characterization of sarcomeric actin genes expressed in Xenopus laevis embryos

A Xenopus laevis complementary DNA (cDNA) library prepared from messenger RNAs extracted from embryos has been screened for actin-coding sequences. Two cDNA clones corresponding to an alpha cardiac and an alpha skeletal muscle actin mRNA have been identified and characterized. From a genomic library, we have furthermore isolated the genes that correspond to the characterized cDNAs. In addition we have identified an actin processed gene which seems to be derived from a second type of skeletal muscle actin gene. Southern blot analysis of X. laevis DNA reveals that each of the three genes is present in at least two copies. In Xenopus tropicalis, a similar Southern blot analysis demonstrates that the three alpha actin genes exist as single copy. This result correlates with the genome duplication that has been proposed to have occurred recently in a X. laevis ancestor. A sequence comparison of the X. laevis cardiac and skeletal muscle actin cDNAs shows that the encoded peptides are highly conserved. Nevertheless, the numerous nucleotide changes at silent mutation sites suggest that the genes originated before the amphibia/reptile-bird divergence, more than 350 million years ago. Comparison of the promoters of the cardiac and skeletal actin genes, which are co-expressed in embryos, reveals a few common structural sequence elements.

Sequence analysis of the larval beta II-globin gene of Xenopus laevis

The 1822 bp sequence of the larval Xenopus laevis beta II-globin gene is reported together with 240 bp upstream of the gene and 190 bp beyond the site of polyadenylation. The mRNA start point was determined by primer extension as well as nuclease S1 mapping and the polyadenylation site by comparison of the gene sequence to the mRNA sequence derived from a corresponding cDNA clone. Like other vertebrate globin genes, this gene comprises three exons interrupted by two intervening sequences (IVS). IVS I spans over 582 nucleotides and interrupts the exon sequences within codon 30. IVS II is located between the codons 104/105 and spans over 617 nucleotides. The 5' region of the gene contains the canonical TATAA homology at position -31. Comparison of the upstream sequence to that of Xenopus laevis larval beta I-globin gene revealed a conserved sequence, located between nucleotide positions -60 and -87, which might function as regulatory element of transcription. Whereas the upstream region of the larval beta II-globin gene does not contain a CAAT box, we notice a reiterated AAATGA motif and discuss its possible significance.

Cloning and sequencing of mRNAs coding for two adult alpha globin chains of the salamander Pleurodeles waltlii

A cDNA library of erythrocyte mRNAs was established from immature red blood cells of the adult amphibian, Pleurodeles waltlii (urodele; salamander). The cDNA clones corresponding to the four adult globin chains were first identified and characterized by positive selection and the cDNAs derived from the two (major and minor) alpha-globin chains sequenced. The sequences presented contain both the complete 3'-noncoding region and the coding region of both chains, with the exception of the first nine codons of the minor alpha-chain, and a portion of the 5'-noncoding region of the major chain. The amino acid sequences of the encoded alpha-globin polypeptides have been deduced and compared with those of Xenopus laevis and of man. These comparative studies suggest that the alpha-globins of Pleurodeles waltlii and Xenopus laevis may have diverged from a common ancestral gene at the time when mammalian and amphibian lines diverged, and that they then evolved separately. Duplication of the alpha-gene, which is responsible for the polypeptide heterogeneity, appears to have occurred earlier in Pleurodeles waltlii than in Xenopus laevis.

Analysis of a deleted MC29 provirus: gag sequences are not required for fibroblast transformation

Recovered avian myelocytomatosis virus HBI is an MC29-related virus that induces lymphoid tumors in chickens rather than the predominant neoplastic disease induced by wild-type MC29 (namely, endotheliomas). An analysis of the structure of the HBI provirus(es) in the tumors demonstrated that the provirus(es) could be either full size or deleted. One tumor was found to be clonal in that it contained a single provirus which had been partially deleted; this raised a question concerning the role of this provirus in the maintenance of tumor growth. To characterize the detailed structure of this provirus and determine its biological activity, it was molecularly cloned from tumor DNA. Sequencing confirmed that the provirus contained a deletion which effectively removed the whole gag gene. However, the provirus was shown to encode a myc-specific protein, presumably initiating from within the myc gene, and to be biologically active when it was transfected onto quail embryo fibroblasts. Our results suggest that myc alone is sufficient to transform quail embryo fibroblasts and to maintain tumor growth in vivo.

Cloning and chromosomal location of the alpha- and beta-globin genes from a marsupial

The cDNA sequences encoding the adult alpha- and beta-globin polypeptides of a marsupial, the native cat Dasyurus viverrinus, have been cloned and their nucleotide sequences have been determined. Using these cDNA clones we have determined the chromosomal location of the native cat alpha- and beta-globin genes by in situ hybridization to fixed metaphase chromosomes and by hybridization to DNA extracted from chromosomes purified by a fluorescence-activated cell sorter. Using two independent methods of gene assignment we have shown the alpha- and beta-globin-like gene sequences to be asyntenic in the native cat, the alpha-globin-like sequences being on chromosome 2 and the beta-globin-like sequences being on chromosome 4.

Comparative nucleotide sequence analysis of two types of larval beta-globin mRNAs of Xenopus laevis

The complete nucleotide sequence of the cDNA insert of the clone pXGL25 derived from the larval beta II-globin mRNA of Xenopus laevis has been determined. The sequence of 593 nucleotides represents part of the 5'nontranslated region, the coding region for 146 amino acids and the entire 3'nontranslated region. It diverges from the related larval beta I-sequence by 24.9% in the coding region. Alignment of the 5' and 3'nontranslated regions of the two related larval beta-sequences to maximum matching resulted in 31.2% and 46.7% divergence, respectively. Divergence between the corresponding adult and larval sequences considerably exceeds that of related larval sequences, suggesting that larval genes may have arisen by gene duplication prior to genome duplication. In contrast to mammalian beta-globin mRNAs, replacement and silent base substitutions are equally abundant, thus indicating less functional constraint on the larval Xenopus laevis beta-globin chains. The larval beta I- and beta II-globins diverge by 30.8% and show most variation in the alpha 1/beta 2-chain interaction sites.

Developmental changes in the pattern of larval beta-globin gene expression in Xenopus laevis. Identification of two early larval beta-globin mRNA sequences

We have analysed beta-globin mRNA sequences in total RNA extracted from embryos and tadpoles of Xenopus laevis at different stages of development and we have identified the most abundantly transcribed beta-globin mRNA (beta T1). The entire nucleotide sequence of a cDNA clone corresponding to this mRNA is known. We have now identified the gene corresponding to this mRNA and we have determined the nucleotide sequences of its immediate 5'-flanking region. Using a DNA fragment from within the coding region of the cloned beta T1 cDNA we show, by primer extension analysis, that beta T1 mRNA is first detectable at stage 28-32 of development. This is the time at which the first presumptive erythropoietic tissue, the ventral blood island, becomes observable histologically. We show that two minor beta-globin genes, distinct from beta T1, are expressed during early stages of development, and that their expression ceases shortly after the beginning of the feeding stage. We term these two early larval genes beta E1 and beta E2. A third minor beta-globin gene is expressed during early development but, unlike beta E1 and beta E2, it is also expressed throughout subsequent larval development. We term this gene beta T2 and show that it corresponds to a gene previously termed beta LII. Finally, using a primer derived from the major adult beta-globin gene (beta 1), we have analysed the accumulation of the major adult beta-globin mRNA during larval development, and we show that this sequence does not accumulate to any significant level before metamorphosis.

The pattern of expression of the Xenopus laevis tadpole alpha-globin genes and the amino acid sequence of the three major tadpole alpha-globin polypeptides

We have isolated cDNA clones derived from three tadpole alpha-globin mRNAs of Xenopus laevis. The entire nucleotide sequence of the three mRNAs has been determined from the cDNA clones and is presented together with the deduced amino acid sequence of the encoded polypeptides. Two of the three polypeptide sequences are 96% homologous whilst the third sequence is highly diverged, with only a 72% homology. The three tadpole alpha-globin genes are all similarly diverged from the two X. laevis adult alpha-globin genes with which they display approximately 50% homology. Analysis of several independent clones from each class of tadpole alpha-globin sequence reveals a very high degree of coding region polymorphism for each of the three corresponding genes. Using the cloned DNA sequences as hybridisation probes, we have analysed the expression of the corresponding genes during larval development. We show that all three genes are activated simultaneously early in development and that thereafter all three are expressed at an approximately equivalent level. A fourth tadpole alpha-globin mRNA sequence, for which we do not have a cDNA clone, accumulates co-ordinately with the three major mRNA sequences but to a much lower concentration. This pattern of gene expression differs significantly from that of the tadpole beta-globin genes of X. laevis, despite the two classes of genes being closely linked in the genome.

A 78-kilobase region of mouse chromosome 3 contains salivary and pancreatic amylase genes and a pseudogene

Genetic studies have demonstrated that salivary and pancreatic amylase genes are closely linked in human and mouse. To analyze the arrangement of genes within the amylase cluster, a library of YBR mouse genomic DNA was cloned in the cosmid vector pJB8. Clones containing amylase genes were identified by hybridization with amylase cDNA probes. Salivary and pancreatic amylase genes were isolated on separate cosmid clones, but no overlapping clones were evident from the initial screening. A strategy for the rapid isolation of terminal noncoding fragments from the cosmid clones was developed. By using these terminal fragments for chromosome "walking," a map of 78 kilobases of the amylase gene region was constructed. The salivary and pancreatic amylase genes are present within this region in the same 5'-to-3' orientation, separated by 22 kilobases of genomic DNA. A truncated amylase pseudogene is located 10 kilobases downstream from the pancreatic amylase gene.

Molecular cloning of the 3-phosphoglycerate kinase (PGK) gene from Aspergillus nidulans

The Aspergillus nidulans 3-phosphoglycerate kinase gene (PGK) has been isolated from a phage lambda genomic library, using the equivalent yeast gene as a hybridization probe. The location of the PGK gene within the cloned DNA has been physically mapped. The DNA sequence of a small region of the putative PGK has been determined and found to code for amino acids corresponding to the N-terminal end of the PGK protein. In contrast to the yeast PGK gene the Aspergillus gene contains a 57 base pair intron occurring between the coding sequences for amino acid 22 and 23. A DNA fragment encompassing the PGK gene was shown to hybridize a 1,700 base poly(A) mRNA, sufficient to encode the PGK polypeptide.

Cloning and characterization of the three enzyme structural genes QUTB, QUTC and QUTE from the quinic acid utilization gene cluster in Aspergillus nidulans

Heterologous DNA probes from the quinic acid gene cluster (QA) in Neurospora crassa (Schweizer 1981) have been used to isolate the corresponding gene cluster (QUT) from Aspergillus nidulans cloned in a phage lambda vector. N. crassa probes for each of the three enzyme structural genes in the cluster have been used to identify the corresponding genes within the A. nidulans cloned DNA. The three genes are in the same relative sequence [dehydrogenase (1), QA-3 = QUTB; dehydratase (3), QA-4 = QUTC; dehydroquinase (2), QA-2 = QUTE] though contained within a 3.4 kb DNA sequence in Aspergillus compared to a 5.4 kb sequence in Neurospora. The A. nidulans dehydroquinase (2) gene QUTE has been shown to complement an auxotrophic mutant aroD6 of Escherichia coli lacking biosynthetic dehydroquinase when tested for growth at 30 degrees C. A mutant of A. nidulans lacking catabolic dehydroquinase (2) and designated qutE208 has been isolated and shown to be tightly linked to the gene cluster, which maps between the ornB and fwA loci in linkage group VIII.

Hypervariable 'minisatellite' regions in human DNA

The human genome contains many dispersed tandem-repetitive 'minisatellite' regions detected via a shared 10-15-base pair 'core' sequence similar to the generalized recombination signal (chi) of Escherichia coli. Many minisatellites are highly polymorphic due to allelic variation in repeat copy number in the minisatellite. A probe based on a tandem-repeat of the core sequence can detect many highly variable loci simultaneously and can provide an individual-specific DNA 'fingerprint' of general use in human genetic analysis.

A mouse gene family associated with a major submaxillary-gland glycoprotein

A gene family encoding msp36 (mouse submaxillary protein 36), a major product of the mouse submaxillary gland, was shown by Southern analysis and genomic cloning to contain approx. 10 related genes. Heteroduplex mapping has elucidated the structure of one of the genes. Close physical linkage of four of the genes in this family has been demonstrated by the use of specific oligonucleotide probes.

Fidelity of transcription of Xenopus laevis globin genes injected into Xenopus laevis oocytes and unfertilized eggs

The Xenopus laevis alpha 1- and beta 1-globin genes were injected into oocytes and unfertilized eggs of X. laevis. In oocytes, the injected globin genes were actively transcribed, but the majority of the transcripts were incorrectly initiated. In unfertilized eggs, the injected genes were transcribed at a low level but only from the correct start sites. In oocytes, the injected circular plasmid DNA containing the cloned globin genes persisted but did not replicate. In contrast, DNA injected into unfertilized eggs replicated up to 15-fold within a 22-h period. We suggest that the ability of the egg to selectively transcribe the injected X. laevis globin genes from the correct promoter sites may be related to differences in chromatin structure between the oocyte and the unfertilized egg.

The primate psi beta 1 gene. An ancient beta-globin pseudogene

The human beta-globin gene cluster contains five functional genes plus a single pseudogene termed psi beta 1. Hybridization and comparative sequence analysis show that this pseudogene is not the product of a recent gene duplication, but is ancient and has been maintained in all major primate groups ranging from prosimians to anthropoids, at the same position as in man, between gamma- and delta-globin genes. In the lemur, a prosimian, the central exons of the psi beta 1 and delta-globin genes have undergone an unequal exchange, which has resulted in a contraction of the beta-globin gene cluster and the formation of a Lepore-type psi beta 1-delta globin pseudogene. Comparisons of defects shared by prosimian, New World monkey and human psi beta 1 sequences suggest that the ancestral primate gene was probably a pseudogene with an abnormal initiation codon but few if any additional defects, and that most contemporary pseudogene defects were accumulated relatively recently by slow neutral drift. We suggest that psi beta 1 arose early in primate evolution by silencing of a pre-existing discrete functional gene, and show that psi beta 1-related sequences are also present in other mammalian orders. In view of the antiquity of psi beta 1-related sequences, we propose that this gene be renamed the eta-globin gene.

The primary structure of the larval beta 1-globin gene of Xenopus laevis and its flanking regions

We present the complete nucleotide sequence of the larval beta I-globin gene of Xenopus laevis including 240 nucleotides of the 5' flanking region and 594 nucleotides beyond the polyadenylation site. The site of transcription initiation was mapped by S1 nuclease, and the site of polyadenylation was determined by comparison with corresponding cDNA clones. The larval Xenopus beta I-gene shows the same internal structure as the beta-globin genes of higher vertebrates, viz. 3 exons interrupted by 2 intervening sequences. The first intervening sequence, which is of exceptional length, spans over 564 nucleotides and interrupts the coding sequence at amino acid 30, whereas the second one comprises 968 nucleotides and is located between the amino acids 104 and 105. The second intervening sequence contains a long inverted repeat of almost perfect homology. The 5' flanking region contains a TATA- and a CAAT-box at positions -33 and -58, respectively. An additional TATA-box is located at -197 and two more CAAT-boxes occur at positions -105 and -237.

Fidelity of transcription of Xenopus laevis globin genes injected into Xenopus laevis oocytes and unfertilized eggs

The Xenopus laevis alpha 1- and beta 1-globin genes were injected into oocytes and unfertilized eggs of X. laevis. In oocytes, the injected globin genes were actively transcribed, but the majority of the transcripts were incorrectly initiated. In unfertilized eggs, the injected genes were transcribed at a low level but only from the correct start sites. In oocytes, the injected circular plasmid DNA containing the cloned globin genes persisted but did not replicate. In contrast, DNA injected into unfertilized eggs replicated up to 15-fold within a 22-h period. We suggest that the ability of the egg to selectively transcribe the injected X. laevis globin genes from the correct promoter sites may be related to differences in chromatin structure between the oocyte and the unfertilized egg.

Self tolerance is H-2-restricted

H-2 restriction is an established characteristic of T-cell behaviour and, in effect, it means that mouse T cells are activated against foreign antigens only if those antigens are presented in a membrane association with molecules of the mouse major histocompatibility complex, H-2. Whether T-cell inactivation or tolerance is also H-2-restricted is a question which has been tested directly and indirectly several times in the past. In each case the answer was 'No' but in each case the answer was inconclusive. Doubts arose because of the observation that activation of T cells, in vivo, is an H-2-restricted event which appears unrestricted because of antigen processing by the host. If antigen processing is involved in the induction of tolerance, then tolerance might also be an H-2-restricted process disguised to appear unrestricted. We report here a study designed to minimize antigen processing in which we find that T-cell tolerance induction to 'self' minor histocompatibility (H) antigens is indeed H-2-restricted.

The human myoglobin gene: a third dispersed globin locus in the human genome

Human myoglobin is specified by a single gene. Unique sequence DNA probes were isolated from the cloned gene and used to test for the presence of the human myoglobin gene in a series of human rodent somatic cell hybrids containing various complements of human chromosomes. The myoglobin gene cosegregated with human chromosome 22. Somatic cell hybrids containing translocation chromosomes carrying part of chromosome 22 were used to locate the myoglobin gene to the region 22q11----22q13. The myoglobin gene is therefore not linked to the alpha-globin gene cluster on chromosome 16 or the beta-globin cluster on chromosome 11, and represents a third dispersed globin locus in the human genome.

Comparative analysis of the cDNA sequences derived from the larval and the adult alpha 1-globin mRNAs of Xenopus laevis

The complete nucleotide sequences of cloned cDNA segments derived from the larval and the adult alpha 1-globin mRNA of Xenopus laevis have been determined. These sequences comprise part of the 5' noncoding region, the entire coding region and the 3' noncoding region, including the polyadenylation site. The larval sequence differs from the adult one by a much longer 3' noncoding region. The sequences diverge by 47%, but codon usage is similar. Comparison of the amino acid sequences of vertebrates shows that the sites of heme contact are highly conserved, whereas the alpha 1/beta 1- and the alpha 1/beta 11-interfaces diverge to different degrees. In these regions the larval alpha 1-globin diverges less from embryonic than from adult alpha-like globins of vertebrates. This suggests that these sites are mainly responsible for the functional peculiarities of the larval amphibian hemoglobins.

The methylation pattern of tRNA genes in Xenopus laevis

The methylation sensitive restriction enzymes Hha I and Hpa II were used to analyse the methylation pattern of a tRNA gene cluster in germ line and somatic DNA of Xenopus laevis. A single tDNA repeat containing 8 tRNA genes was studied and all copies were found to be fully modified in sperm DNA. In the DNA from erythroid cells, hepatocytes, kidney and brain, most tDNA repeats were found to be fully modified. However, in a fraction of the repeats, specific demethylated sites can be detected, giving rise to a pattern which does not vary significantly from one tissue to another. Although our results do not allow a straightforward correlation between hypomethylation and tRNA gene transcription, they are in agreement with the observation that hypomethylation accompanies differentiation and development.

The evolution of a plant globin gene family

We have analyzed the sequences of soybean leghemoglobin genes as an initial step toward understanding their mode of evolution. Alignment of the sequences of plant globin genes with those of animals reveals that based on the proportion of nucleotide substitutions that have occurred at the first, second, and third codon positions, the time of divergence of plant and animal globin gene families appears to be extremely remote (between 900 million and 1.4 billion years ago, if one assumes constancy of evolutionary rate in both the plant and animal lineages) and in addition to the normal regulatory sequences on the 5' end, an approximately 30-base-pair sequence, specific to globin genes, that surrounds the cap site is conserved between the plant and animal globin genes. Comparison of the leghemoglobin sequences with one another shows that the relative amount of sequence divergence in various coding and noncoding regions is roughly similar to that found for animal globin genes and as in animal globin genes, the positions of insertions and deletions in the intervening sequences often coincide with the locations of direct repeats. Thus, the mode of evolution of the plant globin genes appears to resemble, in many ways, that of their animal counterparts. We contrast the overall intergenic organization of the plant globin genes with that of animal genes, and discuss the possibility of the concerted evolution of the leghemoglobin genes.

A recovered avian myelocytomatosis virus that induces lymphomas in chickens: pathogenic properties and their molecular basis

The avian myelocytomatosis virus MC29 induces neoplastic diseases in chicken, including myelocytomas and tumors of kidney and liver, which are due to the action of the v-myc gene. However, MC29 has never been reported to cause lymphoid tumors, the disease associated with activation of the c-myc gene by the insertion of a lymphoid leukosis virus genome. We have analyzed a recovered MC29 virus, HBI, which has a myc gene containing c-myc sequences, acquired by recombination with the cellular gene, and some v-myc sequences. Inoculation of HBI into chickens resulted in lymphoid tumors independent of the bursa. Antigenically these tumors were made up of T and B cells. Molecular analysis showed HBI proviral DNA in 36 of 39 tumors analyzed, with no obvious alteration of c-myc, and the HBI gag-myc fusion protein, p 108, could be detected in tumor cells. These data are discussed in terms of the mechanism of target-cell specificity for transformation by the myc gene.