Nucleotide sequence analysis of the delta beta-globin gene region in humans

The Role of Quantitative Polymerase Chain Reaction in the Management of Follicular Lymphoma Patients

Aims and background

In order to increase the prognostic significance of polymerase chain reaction (PCR) data it has been suggested that quantitative PCR can be used to measure tumor burden. However, this option has not yet been definitely supported or refuted in patients with follicular lymphoma (FL). We decided to evaluate whether knowledge of the quantitative level of minimal residual disease and its variations can be of use in the management of FL patients.

Methods

We used qualitative and competitive PCR to study 11 patients with refractory or relapsed FL harboring the t(14;18) translocation who underwent autologous (nine patients) or allogeneic (two patients) stem cell transplantation (SCT). Competitive PCR was performed with a multiple competitor carrying specific sequences including Bcl2/lgH MBR and mcr, and the β-globin gene.

Results

After a median post-SCT follow-up of 44 months (range, 12-62), overall survival was 91% and disease-free survival 82%. The quantitative PCR data showed that: 1) effective chemotherapy before SCT substantially (1-2 log) reduced the tumor burden in the bone marrow (BM); 2) the increase in rearranged DNA detected in BM was associated with disease progression and relapse; 3) a PCR-negative autograft seemed to lead to lasting molecular remission even when it was performed in patients with a low level of BM infiltration before transplant; and 4) allo-SCT made and maintained the BM PCR negative even in the presence of a greater tumor burden before SCT. Six of the nine patients having CR after SCT (four auto and two allo) are in continuous molecular remission.

Conclusions

In FL patients qualitative and quantitative PCR may provide data that can be helpful for the prognostic evaluation of tumor progression and the early detection of impending relapse by highlighting biological features such as the quality of the infused material, the tumor burden at transplant, and the behavior of tumor cells after transplant.

Why the DNA self-depurination mechanism operates in HB-β but not in β-globin paralogs HB-δ, HB-ɛ1, HB-γ1 and HB-γ2

The human β-globin, δ-globin and ɛ-globin genes contain almost identical coding strand sequences centered about codon 6 having potential to form a stem-loop with a 5'GAGG loop. Provided with a sufficiently stable stem, such a structure can self-catalyze depurination of the loop 5'G residue, leading to a potential mutation hotspot. Previously, we showed that such a hotspot exists about codon 6 of β-globin, with by far the highest incidence of mutations across the gene, including those responsible for 6 anemias (notably Sickle Cell Anemia) and β-thalassemias. In contrast, we show here that despite identical loop sequences, there is no mutational hotspot in the δ- or ɛ1-globin potential self-depurination sites, which differ by only one or two base pairs in the stem region from that of the β-globin gene. These differences result in either one or two additional mismatches in the potential 7-base pair-forming stem region, thereby weakening its stability, so that either DNA cruciform extrusion from the duplex is rendered ineffective or the lifetime of the stem-loop becomes too short to permit self-catalysis to occur. Having that same loop sequence, paralogs HB-γ1 and HB-γ2 totally lack stem-forming potential. Hence the absence in δ- and ɛ1-globin genes of a mutational hotspot in what must now be viewed as non-functional homologs of the self-depurination site in β-globin. Such stem-destabilizing variants appeared early among vertebrates and remained conserved among mammals and primates. Thus, this study has revealed conserved sequence determinants of self-catalytic DNA depurination associated with variability of mutation incidence among human β-globin paralogs.

Repeated evolution of chimeric fusion genes in the β-globin gene family of laurasiatherian mammals

The evolutionary fate of chimeric fusion genes may be strongly influenced by their recombinational mode of origin and the nature of functional divergence between the parental genes. In the β-globin gene family of placental mammals, the two postnatally expressed δ- and β-globin genes (HBD and HBB, respectively) have a propensity for recombinational exchange via gene conversion and unequal crossing-over. In the latter case, there are good reasons to expect differences in retention rates for the reciprocal HBB/HBD and HBD/HBB fusion genes due to thalassemia pathologies associated with the HBD/HBB "Lepore" deletion mutant in humans. Here, we report a comparative genomic analysis of the mammalian β-globin gene cluster, which revealed that chimeric HBB/HBD fusion genes originated independently in four separate lineages of laurasiatherian mammals: Eulipotyphlans (shrews, moles, and hedgehogs), carnivores, microchiropteran bats, and cetaceans. In cases where an independently derived "anti-Lepore" duplication mutant has become fixed, the parental HBD and/or HBB genes have typically been inactivated or deleted, so that the newly created HBB/HBD fusion gene is primarily responsible for synthesizing the β-type subunits of adult and fetal hemoglobin (Hb). Contrary to conventional wisdom that the HBD gene is a vestigial relict that is typically inactivated or expressed at negligible levels, we show that HBD-like genes often encode a substantial fraction (20-100%) of β-chain Hbs in laurasiatherian taxa. Our results indicate that the ascendancy or resuscitation of genes with HBD-like coding sequence requires the secondary acquisition of HBB-like promoter sequence via unequal crossing-over or interparalog gene conversion.

β-Globin polymorphisms in Amerindian populations from the Brazilian Amazon

OBJECTIVES

This investigation was performed to examine genetic variation at the β-globin locus in a sample of 30 healthy individuals from native populations in South America. The patterns of haplotypic variation were compared with those of previous studies including samples for various worldwide populations in an attempt to make inferences about the occupation of the Americas from a deeper temporal perspective than is typically available with haploid markers.

METHODS

A 2.67-kb segment containing the β-globin gene and its flanking regions was examined for genetic variation in a sample of 60 chromosomes from native populations in South America. The fragment was PCR-amplified and directly sequenced. To determine linkage relationships in compound heterozygotes, we used the amplification refractory mutation system. In addition, we assessed genetic variability and differentiation among populations, and we performed tests of selective neutrality. These analyses were performed for Brazilian Amerindian group and other worldwide populations previously studied.

RESULTS

Eleven polymorphic sites were found in the studied fragment, which distinguished eight different haplotypes, three recombinants haplotypes (present as single copies) and five previously described haplotypes, including some of those most highly differentiated. Genetic variation found in the pooled sample is substantial.

CONCLUSIONS

Although only five known haplotypes are observed in Amazonia, some of these are highly divergent, resulting in patterns of molecular polymorphism equal to or higher than those from other world regions.

The repair of melphalan-induced DNA adducts in the transcribed strand of active genes is subject to a strong polarity effect

To investigate the mechanisms of the therapeutic action and drug resistance to the nitrogen mustard melphalan, melphalan-induced DNA damage repair and chromatin structure were examined along the p53, N-ras and d-globin gene loci in cells carrying different repair activities. In nucleotide excision repair-deficient XP-A cells, similar levels of adducts were found in all fragments examined, indicating uniform distribution of DNA damage. In both, repair-proficient CS-B and XP-C cells, faster repair was observed in regions inside the transcribed N-ras and p53 genes, compared to regions on both sides outside of the genes, while no such difference was observed for the inactive d-globin gene. Moreover, very fast adduct repair on the transcribed strand of the active genes was seen immediately downstream of the transcription start site, together with a steeply decreasing gradient of repair efficiency along the gene towards the 3'-end. In all cells analyzed, the above variation in DNA repair efficiency was paralleled exactly by the variation in the degree of local chromatin condensation, more relaxed chromatin being associated with faster repair. Similar results were obtained using peripheral blood mononuclear cells from healthy volunteers, suggesting that the existence of a repair gradient along transcribed genes may be a universal phenomenon. In conclusion, these findings demonstrate that the repair of melphalan adducts in the transcribed strand of active genes is subject to a strong polarity effect arising from variations in the chromatin structure.

Preferential in vivo DNA repair of melphalan-induced damage in human genes is greatly affected by the local chromatin structure

To investigate the molecular mechanisms of action of the nitrogen mustard melphalan in patients treated for multiple myeloma, the in vivo induction and repair of melphalan-induced DNA damage was measured in genes with different transcriptional activity (b-actin>p53>N-ras>d-globin) from leukocytes of 20 multiple myeloma patients following chemotherapeutic administration of high-dose melphalan (200mg/m(2)) and autologous blood stem cell transplantation. Heterogeneous repair was found among the studied genes. The extent of repair was always in the order: b-actin>p53>N-ras>d-globin, correlating with the gene transcriptional state. Similar findings were obtained using peripheral blood mononuclear cells (PBMC) from healthy volunteers following in vitro treatment with melphalan, indicating that these results are not malignant disease-specific. Following in vitro treatment of PBMC from healthy volunteers with alpha-amanitin, an inhibitor of RNA polymerase II that can also induce condensation of chromatin structure, a significant inhibition of the removal of melphalan-induced damage in the three active genes but not in the silent d-globin gene was found, suggesting that transcription and/or chromatin structure may play important roles in the preferential DNA repair. When the in vivo DNA damage formation and repair in multiple myeloma patients following chemotherapeutic administration of melphalan was measured in the two strands of the active genes, no strand bias was found, indicating that the global genome repair subpathway of nucleotide excision repair may play a crucial role in the repair of these adducts. These results were also confirmed in PBMC from healthy volunteers following in vitro treatment with melphalan. Using micrococcal nuclease digestion of nuclei isolated from PBMC of multiple myeloma patients before the chemotherapeutic treatment, as well as from PBMC of healthy volunteers, we probed the chromatin structure in each gene and found that the "looseness" of the chromatin structure correlated with the levels of the gene-specific repair, being again in the order: b-actin>p53>N-ras>d-globin. To conclude, the in vivo gene-specific repair of melphalan-induced damage in humans is greatly affected by the local chromatin structure.

A novel delta beta fusion gene expresses hemoglobin A (HbA) not Hb Lepore: Senegalese delta(0)beta(+) thalassemia

This study identified and characterized a novel delta beta fusion gene in which the delta-globin gene promoter is linked to intact beta-globin coding sequences in a Senegalese family. It results from a 7.4-kb deletion that removes the delta-globin coding sequences, the delta beta intergenic region as well as the beta-globin gene promoter and causes delta(0)beta(+) thalassemia with hemoglobin A expressed at the 11% to 15% range. The phenotype of this naturally occurring delta beta hybrid gene not only clarifies, in an in vivo context, the respective strength of delta- and beta-globin gene promoters, but also emphasizes the importance of beta-globin intragenic sequences in the expression of beta-globin chains. (Blood. 2001;98:1261-1263)

Substrate specificity plays an important role in uncoupling the catalytic and scaffolding activities of rat testis DNA topoisomerase IIalpha

Topoisomerase II (topo II) is a dyadic enzyme found in all eukaryotic cells. Topo II is involved in a number of cellular processes related to DNA metabolism, including DNA replication, recombination and the maintenance of genomic stability. We discovered a correlation between the development of postnatal testis and increased binding of topo IIalpha to the chromatin fraction. We used this observation to characterize DNA-binding specificity and catalytic properties of purified testis topo IIalpha. The results indicate that topo IIalpha binds a substrate containing the preferred site with greater affinity and, consequently, catalyzes the conversion of form I to form IV DNA more efficiently in contrast to substrates lacking such a site. Interestingly, topo IIalpha displayed high-affinity and cooperativity in binding to the scaffold associated region. In contrast to the preferred site, however, high-affinity binding of topo IIalpha to the scaffold-associated region failed to result in enhanced catalytic activity. Intriguingly, competition assays involving scaffold-associated region revealed an additional DNA-binding site within the dyadic topo IIalpha. These results implicate a dual role for topo IIalpha in vivo consistent with the notion that its sequestration to the chromatin might play a role in chromosome condensation and decondensation during spermatogenesis.

Scanning method to identify the molecular heterogeneity of delta-globin gene especially in delta-thalassemias: detection of three novel substitutions in the promoter region of the gene

A scanning strategy for the detection of delta-globin gene mutations and polymorphisms is presented. This procedure is based on the denaturing gradient gel electrophoresis (DGGE) of four different artificially amplified DNA fragments which cover the promoter, the exons, as well as IVS I of the reported gene. To estimate the efficiency and sensitivity of the proposed procedure, we analysed the appropriate controls of delta-thalassemic carriers, uncharacterised delta-thalassemias and cases with normal hematological phenotype, but slightly increased (up to 3.5%) HbA2. DGGE results permitted the identification of delta-globin gene mutations and the polymorphism -199 (T-->C). Three novel base substitutions inside the promoter region of the gene [-65 (A-->G), -55 (T-->C), -36 (C-->A)], were also revealed. These changes are either linked in cis with other mutations or are responsible for thalassemias or for positive regulatory effect in delta-globin gene expression. The proposed experimental strategy consists of an accurate, rapid, safe and inexpensive screening procedure for establishing the molecular basis of delta-globin gene defects, suitable for the application for both research and diagnostics.

A rare mutation [IVS-I-130 (G-A)] in a Turkish beta-thalassemia major patient

Here we describe the identification of the rare beta-thalassemia mutation IVS-I-130 (G-A) for the first time in Turkey. The hematological evaluation of the patient showed classical signs of beta-thalassemia major requiring regular blood transfusions every 30-35 days. DNA analysis was carried out using reverse dot-blot hybridization and restriction endonuclease digestion, as well as genomic sequencing. The patient was found to be heterozygous for the IVS-I-6 (T-C) and IVS-I-130 (G-A) mutations. In order to deduce a possible origin for the IVS-I-130 (G-A) mutation, the sequence polymorphisms in the DNA of the patient and her family were characterized. The method included the analysis of nine polymorphic nucleotides and the hypervariable microsatellite of composite sequence (AT)(x)T(y) 5' to the beta-globin gene by DNA sequencing. The sequence haplotype (HT4) carrying the IVS-I-130 (G-A) mutation is also observed in Algeria. This favors a Northeastern African origin for this allele. The observed results agree well with a recent introduction of this mutation to Turkey from Egypt toward the end of the 19th century.

Statistical properties of open reading frames in complete genome sequences

Some statistical properties of open reading frames in all currently available complete genome sequences are analyzed (seventeen prokatyotic genomes, and 16 chromosome sequences from the yeast genome). The size distribution of open reading frames is characterized by various techniques, such as quantile tables, QQ-plots, rank-size plots (Zipf's plots), and spatial densities. The issue of the influence of CG% on the size distribution is addressed. When yeast chromosomes are compared with archaeal and eubacterial genomes, they tend to have more long open reading frames. There is little or no evidence to reject the null hypothesis that open reading frames on six different reading frames and two strands distribute similarly. A topic of current interest, the base composition asymmetry in open reading frames between the two strands, is studied using regression analysis. The base composition asymmetry at three codon positions is analyzed separately. It was shown in these genome sequences that the first codon position is G- and A-rich (i.e. purine-rich); there is a co-existence of A- and T-rich branches at the second codon position; and the third codon position is weakly T-rich.

A long terminal repeat of the human endogenous retrovirus ERV-9 is located in the 5' boundary area of the human beta-globin locus control region

Transcription of the human beta-like globin genes in erythroid cells is regulated by the far-upstream locus control region (LCR). In an attempt to define the 5' border of the LCR, we have cloned and sequenced 5 kb of new upstream DNA. We found an LTR retrotransposon belonging to the ERV-9 family of human endogenous retroviruses in the apparent 5' boundary area of the LCR. This ERV-9 LTR contains an unusual U3 enhancer region composed of 14 tandem repeats with recurrent GATA, CACCC, and CCAAT motifs. This LTR is conserved in human and gorilla, indicating its evolutionary stability in the genomes of the higher primates. In both recombinant constructs and the endogenous human genome, the LTR enhancer and promoter activate the transcription of cis-linked DNA preferentially in erythroid cells. Our findings suggest the possibility that this LTR retrotransposon may serve a relevant host function in regulating the transcription of the beta-globin LCR.

HbS/beta(del)-thalassemia associated with high levels of hemoglobins A2 and F in a Turkish family

Beta-thalassemia and sickle cell disease (SCD) are common disorders in Turkey. Compound heterozygosity for these two disorders (betaS/beta-thalassemia) is encountered frequently. In this report we present hematological and molecular data of two Turkish siblings with betaS/beta(del)-thalassemia caused by a 290 base pair (bp) deletion and associated with increased levels of hemoglobin A2 (HbA2) and hemoglobin F (HbF). Clinical analysis of the two patients showed a mild course of the disease. Haplotypic factors involved in increasing the levels of HbF were analyzed. The two patients showed no changes from the normal sequences at the XmnI site of Ggamma-globin promoter and the (AT)xTy microsatellite 5' to the beta-globin mRNA cap site. The removal of the region between positions -125 to +78 relative to the beta-globin gene mRNA cap site by the 290 bp deletion is thought to allow the beta-locus control region to interact with the promoters of the delta- and gamma-globin genes, leading to increased HbA2 and HbF levels.

Expression studies of delta-globin gene alleles associated with reduced hemoglobin A2 levels in Greek Cypriots

We previously identified five delta-globin gene alleles associated with reduced hemoglobin (Hb) A2 (Trifillis, P., Ioannou, P., Schwartz, E., and Surrey, S. (1991) Blood 78, 3298-3305). We have now evaluated functional consequences of the changes after expression in COS-1 cells to monitor effects on RNA splicing. In addition, variant Hb A2 tetramers were expressed in yeast to assess effects of amino acid changes on oxygen binding and stability to heat and mechanical agitation. The G --> T change at codon 27 and the A --> G change in IVS-2 both affect RNA splicing, whereas the C --> T change at codon 97 and the AT deletion in IVS-2 have no effect. Oxygen equilibrium curves of the Hb A2 variants expressed in yeast were similar to that of wild type Hb A2. None of the three variant Hb A2 tetramers (Thr --> Ile at codon 4 (Hb deltaT4I), Ala --> Ser at codon 27 (Hb deltaA27S), and Arg --> Cys at codon 116 (Hb deltaR116C)) showed decreased heat stability compared with Hb A2, whereas the Hb deltaT4I variant showed highest instability to mechanical agitation. Co-expression in yeast of alpha-globin chain and the delta-chain variant containing a Leu --> Pro change at codon 141 yielded no identifiable tetramers, suggesting lack of assembly or severe tetramer instability. These studies show the probable cause for decreased Hb A2 for two alleles is due to defective splicing, whereas decreased protein stability, increased tetramer association with red cell membranes, increased interdisulfide bond formation of delta-chains, which inhibits assembly with alpha-chains, and/or reduced assembly is suggested for the other three alleles.

Molecular detection and differentiation of enteroviruses in endomyocardial biopsies and pericardial effusions from dilated cardiomyopathy and myocarditis

Enteroviruses (EVs), especially group B coxsackieviruses, have been implicated in the pathogenesis of myocarditis and dilated cardiomyopathy (DCM). To determine whether a specific type of EV is present in DCM hearts, we examined the genotypes of EVs detected in endomyocardial biopsies and pericardial effusions by polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) analysis. Positive PCR results were obtained from biopsies in 6 (19 percent) of 31 patients with DCM, 5 (18 percent) of 28 with myocarditis, 5 (22 percent) of 23 with other cardiac diseases, and from pericardial effusions in 4 (57 percent) of 7 patients with pericarditis. SSCP profiles of most of the clinical samples were different and were not identical to any of the standard group B coxsackie viruses. Our findings suggest that EV genomes are involved in the myocardium of patients with various cardiac conditions and that a particular type of EV is not present in DCM hearts.

Coordinate regulation of HLA class II genes: a novel DNA binding complex

We have characterized a nuclear protein complex from B lymphoblastoid cell lines that binds to HLA class II promoters as detected by electrophoretic gel mobility shift assays (EMSA). This complex (C1) binds to three independent sites in the proximal DRA promoter which have not been identified previously as cis-acting elements. C1 is very abundant in Burkitt's lymphoma cell lines, but less abundant in "normal" B lymphoblastoid cell lines. The binding specificity of the C1 complex was analysed using competition experiments and chemical footprinting methods. Complexes with specificity similar to C1 also bind the DPA and DQA promoters. Though mutation of the sequences in the DRA promoter that severely reduced binding of the C1 complex had no effect on the ability of the DRA fragment to drive transcription of the reporter gene in transient expression or in vitro transcription assays, this conservation of binding sites among all class II promoters tested suggests functional relevance in transcription. In addition, complexes similar to C1 were observed in nuclear extracts from all cell lines examined, but minor differences in mobility appeared to correlate with class II expression. Thus, the C1 complex may act as a trans-acting factor in MHC class II expression.

Sequence of the sheep fetal beta globin gene and flanking region

The sheep beta F globin gene has been sequenced completely, including 829 bases of 5' flanking region and 1368 bases 3' to the stop codon. In evolutionary terms, this gene is a homolog of the adult beta-like globin genes, including human beta. Over the course of evolution of Bovidae (comprised of sheep, goats, and cattle) the expression of beta F has become restricted to the fetal compartment of development. Comparisons between beta F and other closely related Bovidae beta globin genes indicate repetitive sequences that were inserted in these genes over the course of their divergence and a region which may be functionally significant to the developmentally regulated expression of beta F.

Homeodomain protein binding sites, inverted repeats, and nuclear matrix attachment regions along the human beta-globin gene complex

beta-Globin genes in primates arose during evolution by duplication of an ancestral gene, and their order of arrangement along the DNA is related to their timing of expression during development. We believe that nuclear matrix anchorage sites (MARs) along the beta-globin gene complex considered to be mass binding sites for transcription protein factors, some of which are developmental stage specific and others ubiquitous, play a decisive role in cell memory by determining the developmental stage-specific expression of the genes. The AT-rich class of MARs appears to possess a significant number of ATTA and ATTTA motifs known to be mass binding sites for homeodomain proteins that determine body formation in development. MARs also appear to harbor origins of replication, to be enriched in inverted repeats (dyad symmetry motifs) and were proposed to include the DNase I hypersensitive sites of a particular gene determined at the chromatin level. This study is an attempt to finely identify MARs at the nucleotide level along the beta-globin gene complex. Searches of a contiguous stretch of about 73.3 kb of human sequences comprising and surrounding the epsilon, gamma G-, gamma A-, delta-, and beta-globin genes of the human beta-globin gene complex for homeotic protein binding sites as well as for inverted repeats has shown that these elements are clustered nonrandomly at particular sites within the beta-globin gene complex. These sites are presumed to be the AT-rich class of MARs of the beta-globin gene complex. The inverted repeats which are characteristic of origins of replication and some promoter/enhancer regions and the homeotic protein sites seem to include the DNase I hypersensitive sites of the gene complex. Indeed, dyad symmetry sequences are present close to the four DNase I HS sites in the locus control region (LCR) of the gene complex as well as in the 5' flanking regions and the large introns of the delta- and beta-globin genes. A search of the putative MAR regions of the gene complex suggests that, in addition to their enrichment in ATTA motifs, palindromes, and DNase I hypersensitive sites, these regions may comprise TG-rich motifs and potential Z-DNA as well as polypurine and polypyrimidine blocks. From the positions of palindromes and clusters of homeodomain protein sites along the complex we propose that an extended origin of replication able to initiate at several sites is present in the LCR and two others surrounding the delta- and beta-globin genes.(ABSTRACT TRUNCATED AT 400 WORDS)

Detection of polymorphisms using thermal cycling with a single oligonucleotide on a DNA sequencing gel

A method is described for the detection of restriction fragment length polymorphisms (RFLPs) in single copy genes in mammalian cells using one 5'-labelled oligonucleotide. This linear amplification (LA) method employs a single oligonucleotide as primer, which is extended by Taq DNA polymerase up to a restriction enzyme cleavage site. The products are arithmetically amplified by thermal cycling. The size of the products are determined by the sequence of the oligonucleotide and the position of the restriction enzyme cleavage site. Hence, an RFLP can be observed by measuring the size of the products. Polymorphisms which differ in size by a small number of base pairs, as are found in (CA)n repeats, are especially suitable for analysis by the LA procedure since the products are run on DNA sequencing gels. A number of genes were examined by the procedure and all produced a satisfactory signal including GC-rich template. It is proposed that the LA method would be suitable for large-scale genetic linkage analysis. The LA procedure has many advantages including the ability to multiplex signals under the same conditions, and lower cost since only one primer is needed.

The association of the human epsilon-globin gene with the nuclear matrix: a reconsideration

The association of the human epsilon-globin gene with the nuclear matrix was studied in erythroid and non-erythroid cell lines. Using a high salt method to prepare histone depleted nuclei we studied the association of variety of fragments covering a 7.8 kb region which contains the human epsilon-globin gene. We furthermore studied the association of a set of DNA fragments covering the 13 kb human G gamma/A gamma-globin gene domain, the 16 kb psi beta/delta-globin gene domain and the 10 kb beta-globin gene domain with the nuclear matrix of K562 and Raji cells. The results show that all fragments studied are easily released from the nuclear matrix, indicating no specific association. Summarizing our results we could say that a region starting 5.7 kb 5' to the human epsilon-globin gene and ending 4 kb 3' to the human beta-globin gene seems to contain no attachment sites with the nuclear matrix of both erythroid and non-erythroid cells.

Pre-B lymphocyte-specific transcriptional control of the mouse VpreB gene

The VpreB genes, which encode surrogate immunoglobulin light chain molecules, are expressed as RNA almost exclusively in pre-B cells. We have investigated the transcriptional control mechanisms which are responsible for the pre-B cell-specific RNA expression of the mouse VpreB1 and VpreB2 genes. Nuclear run-on analyses demonstrate that the pre-B cell-specific expression of both VpreB genes is controlled primarily at the level of initiation of transcription. S1 nuclease protection-mapping defined two or three major start sites of transcription for the VpreB genes. To find a promoter and other potential cis-acting regulatory elements, a 700-bp fragment 5' of the transcription start sites of the VpreB1 gene was used in gene transfer experiments and found to act as a promoter in pre-B lymphocytes. Deletion experiments showed that 191 bp upstream of the most 5' transcription start site is required for the pre-B cell promoter activity. DNA sequence analysis of the 5' region of the mouse VpreB1, VpreB2 and human VpreB genes reveal that this region of approximately 200 bp is strongly conserved. This 200-bp promoter region contains several conserved nucleotide sequence motifs which may act to mediate the pre-B cell-specific transcription of the VpreB genes.

Evolution of the primate beta-globin gene region: nucleotide sequence of the delta-beta-globin intergenic region of gorilla and phylogenetic relationships between African apes and man

A 6.0-kb DNA fragment from Gorilla gorilla including the 5' part of the beta-globin gene and about 4.5 kb of its upstream flanking region was cloned and sequenced. The sequence was compared to the human, chimpanzee, and macaque delta-beta intergenic region. This analysis reveals four tandemly repeated sequences (RS), at the same location in the four species, showing a variable number of repeats generating both intraspecific (polymorphism) and interspecific variability. These tandem arrays delimit five regions of unique sequence called IG for intergenic. The divergence for these IG sequences is 1.85 +/- 0.22% between human and gorilla, which is not significantly different from the value estimated in the same region between chimpanzee and human (1.62 +/- 0.21%). The CpG and TpA dinucleotides are avoided. CpGs evolve faster than other sequence sites but do not confuse phylogenetic inferences by producing parallel mutations in different lineages. About 75% of CpG doublets have become TpG or CpA since the common ancestor, in agreement with the methylation/deamination pattern. Comparison of this intergenic region gives information on branching order within Hominoidea. Parsimony and distance-based methods when applied to the delta-beta intergenic region provide evidence (although not statistically significant) that human and chimpanzee are more closely related to each other than to gorilla. CpG sites are indeed rich in information by carrying substitutions along the short internal branch. Combining these results with those on the psi eta-delta intergenic region, shows in a statistically significant way that chimpanzee is the closest relative of human.

Characterization of the breakpoint of a 3.5-kb deletion of the beta-globin gene

The precise extent and breakpoints of a deletion of the beta-globin gene in a Thai patient have been determined using direct sequencing of a PCR product. This lesion is not detectable by current screening methods using PCR to analyze the beta-globin genes and is, therefore, a potential source of error in the diagnosis and prenatal detection of beta-thalassemia.

Amplification of Epstein-Barr virus genomic sequences in blood cells, lacrimal glands, and tears from primary Sjögren's syndrome patients

Based on observations of primary Sjögren's syndrome (SS) following acute Epstein-Barr virus (EBV) infection, the authors hypothesized that EBV may play a role in the pathogenesis of SS. This hypothesis was tested by evaluating ten peripheral blood mononuclear (PBMN) cell specimens, ten lacrimal gland biopsies, and five tear specimens from 15 EBV-seropositive primary SS patients for EBV genomic sequences using polymerase chain reaction (PCR). Epstein-Barr virus DNA sequences were detected in 50% of SS PBMN cell specimens and 80% of SS lacrimal gland and tear specimens. In six SS patients, specimens were obtained from two or more sites (i.e., PBMN cell and lacrimal gland and/or tears), and EBV genomic sequences were amplified in the PBMN cells and the lacrimal gland or tears in three of these subjects. The authors previously detected EBV genomes in 32% (11/34) of normal human lacrimal glands from EBV-seropositive donors using PCR and concluded that the normal human lacrimal gland may be a site of EBV persistence; however, they were unable to amplify EBV sequences in DNA from PBMN cells or tear specimens from normal donors. Amplification of EBV DNA in PBMN cells, lacrimal glands, and tears of primary SS patients at a greater frequency (P less than 0.01) than normal controls suggests that EBV may be a risk factor in the pathogenesis of SS.

Molecular basis of HbE-beta-thalassemia and the origin of HbE in northeast Thailand: identification of one novel mutation using amplified DNA from buffy coat specimens

Amplification of DNA via polymerase chain reaction directly from a small amount of a buffy coat fraction was used to study the molecular basis of HbE-beta-thalassemia in the northeastern Thai population. Eight different mutations including the new one causing a beta o-thalassemia phenotype were detected. This novel mutation is an amber mutation at codon 26, which occurs at the same position as that of HbE; the most common hemoglobin variant in Southeast Asian countries. A pitfall in detection of the HbE mutation by restriction enzyme analysis was pointed out and differential diagnosis of the HbE mutation and the novel one by using allele specific oligonucleotide probes were described. Analysis of polymorphic restriction sites in the beta-globin gene cluster containing the beta E gene revealed two previously undescribed haplotypes in the Southeast Asian populations, which provide evidence for the multiple origins of beta E gene in Southeast Asian populations.

A single nucleotide deletion in codon 123 of the beta-globin gene causes an inclusion body beta-thalassaemia trait: a novel elongated globin chain beta Makabe

The beta-globin gene from a Japanese individual with an inclusion body beta-thalassaemia trait has been characterized by gene cloning and DNA sequencing. An adenine deletion was detected at the first position of codon 123 (ACCCC) of one allele whereas the other allele had a normal sequence. Heterozygosity for this mutation in the patient was confirmed by Southern blots of the genomic DNA digested with HphI, the recognition site of which is eliminated by this deletion. This one base deletion results in the shift of a reading frame in such a manner that the normal termination codon is out of phase. This frameshift mutation results in the synthesis of an elongated beta-globin chain with 10 extra amino acid residues and with an altered C-terminus. Analysis of labelled globin chains using CM-cellulose column chromatography failed to demonstrate any abnormal protein, thereby suggesting that the beta-globin chain variant is highly unstable and probably degrades rapidly after synthesis. This event will lead to an accumulation of free alpha-chains precipitating in the red blood cells and an inclusion body beta-thalassaemia phenotype would ensue.

Molecular analysis of deletions in the human beta-globin gene cluster: deletion junctions and locations of breakpoints

DNA fragments that contain the deletion junction regions of four independent deletions involving the human beta-globin gene cluster have been isolated and cloned. The fragments were isolated from individuals with the conditions referred to as Sicilian (delta beta)zero-thalassemia, Turkish G gamma+(A gamma delta beta)zero-thalassemia, Black G gamma+(A gamma delta beta)zero-thalassemia, and HPFH-2. The sequences of the deletion junctions and of the normal DNA surrounding their 3' breakpoints were determined and compared to the previously determined sequences of normal DNA surrounding their 5' breakpoints. These comparisons show that the deletions were the result of nonhomologous recombinational events. Two of the deletion junctions contain "orphan" nucleotides, while the other two show very limited amounts of "junctional homology." Both types of junctions are common among recombination events in mammalian cells and we discuss a simple joining scheme that could account for the junctions reported here. Unlike other deletions in this cluster and in other gene clusters, none of the eight deletion breakpoints examined here occurred within Alu family repeats. To examine the significance of deletion breakpoints within various sequence categories, we analyzed the data from a well-defined set of deletions within this locus. In contrast to deletions in the alpha-globin gene cluster, the occurrence of breakpoints in Alu family repetitive sequences is not statistically significant within the beta-globin gene cluster. However, breakpoints do occur within transcriptional units of the beta-globin gene cluster more frequently than expected by chance alone. We conclude from our analysis that the mechanisms of DNA joining are not locus or location specific, but at least a portion of the mechanisms of chromosomal breakages do show locus specificity.

Molecular basis of beta-thalassemia in Thailand: analysis of beta-thalassemia mutations using the polymerase chain reaction

beta-Thalassemia mutations in 71 chromosomes of Thai patients from the northeast, the middle and the south of the country were investigated using dot blot hybridization of PCR (polymerase chain reaction)-amplified DNA with allele-specific oligonucleotide probes. Eight different known molecular defects were detected, at different frequencies. There was an amber mutation in codon 17, a C-T transversion at position 654 of IVS-2, a frameshift mutation between codons 71 and 72, an A-G transition at nucleotide -28 within the TATA box (known as Chinese mutations), a G-T transversion at position 1 of IVS-1 (an Indian mutation), a 4 bp deletion in codons 41/42 and a G-C transversion at position 5 of IVS-1 (described as both Chinese and Indian mutations) and a Thai original mutation, an ochre mutation in codon 35. Analysis of the three unknown alleles by DNA sequencing of the cloned DNA fragment amplified by PCR revealed an A-G substitution at the second position of the codon for amino acid 19 (AAC-AGC). The analytic approach used in the present study and the characteristic distribution of mutations in each region of Thailand will prove useful for setting up a prenatal diagnosis program.

Evolution and transcription of old world monkey globin genes

Although apparently inactive in the whole animal, the delta globin genes from three species of Old World monkey (rhesus, baboon and green monkey) are all functional in an in vitro transcription assay. Their activities in vitro are similar to that of the functional human delta gene. A fourth monkey gene, from the colobus monkey, is transcribed approximately fivefold less efficiently than the others. This reduced in vitro activity results from a 20 base-pair deletion, which removes the normal site of mRNA initiation. When the deletion is repaired by site-directed mutagenesis, transcriptional activity increases to the level observed for the other delta genes. We also report the complete nucleotide sequences of the colobus beta, colobus delta, and rhesus delta genes. Sequence comparisons show that the delta and beta genes in the same species have not exchanged genetic information since the divergence of the human and monkey lineages. Phylogenetic analysis of these sequences affirms that the Old World monkey delta genes are evolving more rapidly than their functional counterparts. Moreover, the rate of replacement substitutions has risen to equal that of non-coding DNA, as expected for genes no longer under selective constraint.

Positive and negative regulation of the gene for transcription factor IIIA in Xenopus laevis oocytes

Expression of the positively acting 5S gene-specific transcription factor, TFIIIA, is regulated during development, with highest levels of mRNA and protein occurring during oogenesis. By analysis of TFIIIA promoter mutants microinjected into late stage Xenopus oocytes, we have determined DNA sequences required for the transcription of this gene and we have identified proteins that bind to these regulatory sequences. A negative element lies between positions -306 and -289. Three positive-acting sequences are located between positions -289 and -253, -250 and -173, and -144 and -101. Gel shift analyses of TFIIIA promoter fragments incubated with Xenopus oocyte extracts have identified two DNA-protein complexes. One complex, designated B1, requires sequences within the promoter region extending from -271 to -253 while the second complex, designated B2, involves promoter sequences from -235 to -221. The protein involved in formation of the B1 complex has been found to be related to the human adenovirus major late transcription factor, USF.

The human calbindin 27-kDa gene: structural organization of the 5' and 3' regions, chromosomal assignment, and restriction fragment length polymorphism

The 5' and 3' regions of the human gene coding for calbindin 27 kDa were cloned and sequenced. Structural features of the 5' region included the presence of an Alu repeat and two elements regularly associated with eukaryotic promoters: an alternating purine-pyrimidine element and a homopurine-homopyrimidine box. The 3' region contained a second Alu family member and a degenerate 1.4-kb L1 repeat. A comparison with the chicken promoter was made in order to define regions conserved in evolution and potentially important in gene expression regulation. The greater similarity is located around the TATA box, but strongly conserved elements were not found. The gene was assigned to chromosome 8 by using human-rodent hybrid cell lines. Two restriction fragment length polymorphisms (HindIII and SacI) were detected with a cDNA probe recognizing the 3' end of the gene.

The distribution of interspersed repetitive DNA sequences in the human genome

The distribution of interspersed repetitive DNA sequences in the human genome has been investigated, using a combination of biochemical, cytological, computational, and recombinant DNA approaches. "Low-resolution" biochemical experiments indicate that the general distribution of repetitive sequences in human DNA can be adequately described by models that assume a random spacing, with an average distance of 3 kb. A detailed "high-resolution" map of the repetitive sequence organization along 400 kb of cloned human DNA, including 150 kb of DNA fragments isolated for this study, is consistent with this general distribution pattern. However, a higher frequency of spacing distances greater than 9.5 kb was observed in this genomic DNA sample. While the overall repetitive sequence distribution is best described by models that assume a random distribution, an analysis of the distribution of Alu repetitive sequences appearing in the GenBank sequence database indicates that there are local domains with varying Alu placement densities. In situ hybridization to human metaphase chromosomes indicates that local density domains for Alu placement can be observed cytologically. Centric heterochromatin regions, in particular, are at least 50-fold underrepresented in Alu sequences. The observed distribution for repetitive sequences in human DNA is the expected result for sequences that transpose throughout the genome, with local regions of "preference" or "exclusion" for integration.

Complete nucleotide sequence of the rabbit beta-like globin gene cluster. Analysis of intergenic sequences and comparison with the human beta-like globin gene cluster

The nucleotide sequence of the entire beta-like globin gene cluster of rabbits has been determined. This sequence of a continuous stretch of 44.5 x 10(3) base-pairs (bp) starts about 6 x 10(3) bp upstream from epsilon (the 5'-most gene) and ends about 12 x 10(3) bp downstream from beta (the 3'-most gene). Analysis of the sequence reveals that: (1) the sequence is relatively A + T rich (about 60%); (2) regions with high G + C content are associated with OcC repeats, a short interspersed repeated DNA in rabbits; (3) the distribution of polypurines, polypyrimidines and alternating purine/pyrimidine tracts is not random within the cluster; (4) most open reading frames are associated with known globin coding regions, OcC repeats or long interspersed repeats (L1 repeats); (5) the most prominent open reading frames are found in the L1 repeats; (6) different strand asymmetries in base composition are associated with embyronic and adult genes as well as the tandem L1 repeats at the 3' end of the cluster; and (7) essentially all the repeats appear to have been inserted by a transposon mechanism. A comparison of the sequence with itself by a dot-plot analysis has revealed nine new members of the OcC family of repeats in addition to the six previously reported. The OcC repeats tend to be clustered, particularly in the epsilon-gamma and gamma-psi delta intergenic regions. Dot-plot comparisons between the rabbit and the human clusters have revealed extensive sequence matches. Homology starts about 6 x 10(3) bp 5' to epsilon or as far upstream as the rabbit sequence is available. It continues throughout the entire cluster and stops about 0.7 x 10(3) bp 3' to beta, at which point several repeats have inserted in both rabbits and humans. Throughout the gene cluster, the homology is interrupted mainly by insertions or deletions in either the rabbit or the human genome. Almost all of the insertions are of known short or long repeated DNAs. The positions of the insertions are different in the two gene clusters, which indicates that both short and long repeats have been transposing throughout the genome for the time since the mammalian radiation. An alignment of rabbit and human sequences allows the calculation of the substitution rate around epsilon. Sequences far removed from the gene are evolving at a rate equivalent to the pseudogene rate, although some short regions show an apparently higher rate.(ABSTRACT TRUNCATED AT 400 WORDS)

Characterization of three types of beta zero-thalassemia resulting from a partial deletion of the beta-globin gene

Three patients heterozygous for a partial deletion of the beta-globin gene were studied: an American Black with an approximately 1.35 kb deletion, a Turkish patient with an approximately 300 nucleotide deletion, and a Greek patient with a newly discovered deletion of 44 nucleotides. The DNA was amplified by the polymerase chain reaction procedure and sequenced; only the DNA with the deletion was amplified for the patients with the approximately 1.35 kb and approximately 300 bp deletion, facilitating the interpretation of the sequencing gels. The amplified DNA fragments from these two chromosomes were also cloned into a plasmid vector and sequenced. The size of the deletion found in the Turkish patient is 290 nucleotides and includes 123, 124 or 125 nucleotides 5' to the Cap site, the 5' untranslated region, exon 1, and 25, 24, or 23 nucleotides of the first intron. The total size of the deletion of the Black patient is 1393 nucleotides including 485 (484) bp 5' to the Cap site, exon 1, intron 1, exon 2, and 413 (414) nucleotides of the second intron. The new deletion in the Greek beta-thalassemic patient was detected by direct sequencing of amplified DNA; the 44 bp deletion begins within codon 24 or between codons 24 and 25, and includes the first 26 or 27 nucleotides of intron 1. This deletion was confirmed by hybridization of amplified DNA with a specific oligonucleotide probe and by sequence analysis of amplified DNA cloned in a plasmid. A 7 bp homology sequence (GACAGGT) was found at both sides of the 290 bp deletion, while only 3 nucleotides were repeated at both sides of the 44 nucleotide deletion (GGT). No homology was found between the breakpoints of the 1393 nucleotide deletion.

Hemoglobin Pasadena: identification of the gene mutant by DNA analysis using synthetic DNA probes

Hemoglobin Pasadena [beta 75(E19)Leu----Arg] was found in a boy who had an acute episode of anemia and rapid splenic enlargement. His father was the only other member of a large family with this hemoglobinopathy. We have used gene mapping techniques for direct identification of the beta-globin gene mutation. To correlate the DNA findings with the structural identification of this variant, we have also performed globin chain separation and analysis of the tryptic peptides using high performance liquid chromatography and secondary ion mass spectral analysis.

A beta+-thalassemia (codon 24, GGT----GGA) found in a Japanese

A beta+-thalassemia mutation at codon 24 (GGT----GGA) was discovered in a Japanese; this is the third type of beta-thalassemia found in this population. The case, as well as the data from DNA sequencing analysis, are presented.

A two-state conformational equilibrium for alternating (A-T)n sequences in negatively supercoiled DNA

We have made a study of the pattern of osmium tetroxide modification in supercoiled plasmids containing alternating (A-T)n tracts. Two distinct alternative patterns may be obtained, depending upon conditions. At moderate salt concentrations, or at low temperature, only thymine bases close to the centres of the tracts were modified, consistent with the presence of a cruciform structure. At higher temperatures in the absence of cations, uniform modification throughout the tracts was observed. The cationic concentration required to stabilize cruciform structure depends markedly on its charge, and a number of transition metal ions were totally ineffective. The results are interpreted in terms of a two-state equilibrium between the cruciform and a perturbed helical structure, the position of which is temperature- and salt-dependent. For longer (A-T)n tracts, a third pattern of osmium tetroxide modification is found at intermediate salt concentrations, consistent with a cruciform having an extensively disrupted four-way junction.