Mapping through somatic cell hybrids and cDNA probes of protein C to chromosome 2, factor X to chromosome 13, and alpha 1-acid glycoprotein to chromosome 9

Maternal thrombophilias are associated with specific placental lesions

Maternal floor infarction (MFI), massive perivillous fibrin deposition (MPVFD), and fetal thrombotic vasculopathy (FTV) are specific placental lesions with associations to recurrent adverse fetal outcomes and with maternal thrombophilia. We studied the frequency of a range of acquired and genetic maternal thrombophilias in MFI (40 cases), MPVFD (87 cases), FTV (7 cases), and FTV+MPVFD (4 cases). Thrombophilias were identified in 16 (40%), 20 (23%), 5 (71%), and 2 (50%) of these lesions, respectively. Seventy-seven percent of the identified thrombophilias were genetic, and 23% were acquired. The most common genetic thrombophilia was protein S deficiency, which constituted 14 of the 36 genetic thrombophilias (39%). We advocate full maternal thrombophilia testing when the diagnosis of MFI, MPVFD, and FTV is made by placental pathology examination. Because of the possible contribution of paternal thrombophilic mutations to the fetal genotype, it would be desirable to test the whole family as well.

Human chromosomes 9, 12, and 15 contain the nucleation sites of stress-induced nuclear bodies

We previously reported the identification of a novel nuclear compartment detectable in heat-shocked HeLa cells that we termed stress-induced Src-activated during mitosis nuclear body (SNB). This structure is the recruitment center for heat shock factor 1 and for a number of RNA processing factors, among a subset of Serine-Arginine splicing factors. In this article, we show that stress-induced SNBs are detectable in human but not in hamster cells. By means of hamster>human cell hybrids, we have identified three human chromosomes (9, 12, and 15) that are individually able to direct the formation of stress bodies in hamster cells. Similarly to stress-induced SNB, these bodies are sites of accumulation of hnRNP A1-interacting protein and heat shock factor 1, are usually associated to nucleoli, and consist of clusters of perichromatin granules. We show that the p13-q13 region of human chromosome 9 is sufficient to direct the formation of stress bodies in hamster>human cell hybrids. Fluorescence in situ hybridization experiments demonstrate that the pericentromeric heterochromatic q12 band of chromosome 9 and the centromeric regions of chromosomes 12 and 15 colocalize with stress-induced SNBs in human cells. Our data indicate that human chromosomes 9, 12, and 15 contain the nucleation sites of stress bodies in heat-shocked HeLa cells.

Selection and mapping of replication origins from a 500-kb region of the human X chromosome and their relationship to gene expression

In higher eukaryotes the mechanism controlling initiation of DNA replication remains largely unknown. New technologies are needed to shed light on how DNA replication initiates along the genome in specific regions. To identify the human DNA sequence requirements for initiation of replication, we developed a new method that allows selection of replication origins starting from large genomic regions of human DNA. We repeatedly isolated 15 new putative replication origins (PROs) from a human DNA region of 500 kb in which 17 genes have previously been characterized. Fine-mapping of these PROs showed that DNA replication can initiate at many specific points along actively transcribed DNA in the cell lines used for our selection. In conclusion, in this paper we describe a new method to identify PROs that suggests that the availability of initiation sites is dependent on the transcriptional state of the DNA.

The molecular genetics of familial venous thrombosis

In the past few years, important advances have been made in the identification of factors predisposing to familial thrombophilia. Particular attention has been paid to the characterization of known inherited defects and their genotype-phenotype relationship, and to studying the interaction between single or multiple inherited conditions and acquired risk factors for venous thrombosis. The recent discovery of 'new' and very common genetic lesions predisposing to thrombosis has greatly expanded the interest in this field. Hereditary predisposition to venous thrombosis may be related to lesions in one or more of 10-15 genes encoding antithrombin, Protein C, Protein S, Factor V, prothrombin, enzymes of the homocysteine metabolic pathway, fibrinogen, heparin cofactor II, plasminogen and thrombomodulin. About 500 different gene lesions (substitutions, deletions, insertions) have so far been reported to affect these genes in patients with thrombotic disease. Because there are potentially multiple interactions between genetic and environmental factors, familial thrombophilia is now considered to be a multifactorial disease. The aim of this chapter is to review aspects of the molecular genetics of familial thrombophilia. In particular, those gene/protein defects for which there is convincing evidence of an association with familial thrombosis will be examined in detail.

Mutations of SURF-1 in Leigh disease associated with cytochrome c oxidase deficiency

Leigh disease associated with cytochrome c oxidase deficiency (LD[COX-]) is one of the most common disorders of the mitochondrial respiratory chain, in infancy and childhood. No mutations in any of the genes encoding the COX-protein subunits have been identified in LD(COX-) patients. Using complementation assays based on the fusion of LD(COX-) cell lines with several rodent/human rho0 hybrids, we demonstrated that the COX phenotype was rescued by the presence of a normal human chromosome 9. Linkage analysis restricted the disease locus to the subtelomeric region of chromosome 9q, within the 7-cM interval between markers D9S1847 and D9S1826. Candidate genes within this region include SURF-1, the yeast homologue (SHY-1) of which encodes a mitochondrial protein necessary for the maintenance of COX activity and respiration. Sequence analysis of SURF-1 revealed mutations in numerous DNA samples from LD(COX-) patients, indicating that this gene is responsible for the major complementation group in this important mitochondrial disorder.

Interphase cytogenetic and AgNOR analyses of hydatidiform moles

AIM

To determine the potential value of interphase cytogenetic and argyrophilic nucleolar organiser region (AgNOR) analyses in the diagnosis and classification of hydatidiform moles.

METHODS

Serial tissue sections from 37 hydatidiform moles, histologically classified as 11 complete and 15 partial, and from 11 hydropic abortuses were examined by in situ hybridisation using digoxigenin labelled probes specific for chromosomes 1, X, and Y, and a one step silver staining method. The percentages of diploid and triploid nuclei, and the mean number of AgNORs for each tissue were determined.

RESULTS

Interphase cytogenetics showed that eight of the 11 cases (73%) each of complete mole and hydropic abortus had diploid pattern and the three remaining cases (27%) of each group were triploid. Two of the triploid complete moles and one of the triploid hydropic abortuses were revised to partial moles and one remaining triploid complete mole was revised to hydropic abortus. Of the 15 partial moles, nine (60%) were triploid, and six (40%) were diploid. These diploid cases were revised to three complete moles and three hydropic abortuses. There was a significant difference (p < 0.0001) between the mean (SD) AgNOR count in partial mole (5.11 (0.91)) versus hydropic abortus (3.79 (0.90)) and complete mole (3.39 (0.97)). The total of 15 triploid cases showed a high mean AgNOR count of 5.24 (0.73). Also, after reclassification, eight of the nine partial moles (89%) had a mean AgNOR count of > or = 5. The results of analyses by the two methods were closely correlated.

CONCLUSIONS

Interphasecytogeneticanalysis using chromosome specific probes and AgNOR count provides a valuable approach for ploidy analysis in histological sections of hydatidiform moles and helps to resolve difficult cases.

Characterization and genomic mapping of chimeric ERV9 endogenous retroviruses-host gene transcripts

ERV9 is a low repeated family of human endogenous retroviral elements, which has close to 50 members, in addition to at least 4000 solitary LTRs. Previous work has shown that randomly selected LTRs can promote transcription of reporter genes, raising the possibility that these sequences may affect the expression of adjacent cellular genes. We performed Northern blot experiments using sequences from ERV9-LTR, and we observed a different pattern of expression in several different hemopoietic tumor cell lines. It is possible that by the result of a somatic integration event, or by virtue of their original dispersal in the genome, ERV9-LTRs may specifically induce the expression of different cellular sequences in different cell lineages. Here, we describe the identification and analysis of four chimeric cDNA clones isolated from the T-lymphoma Peer cell line, having a structure consistent with transcription initiation from an ERV9-LTR. All the cDNA clones represent transcripts derived from unique cellular sequences. We also report the genomic localization of these cDNA clones.

Chromosomal localization of mitochondrial transcription factor A (TCF6), single-stranded DNA-binding protein (SSBP), and endonuclease G (ENDOG), three human housekeeping genes involved in mitochondrial biogenesis

By using a PCR-based screening of a somatic cell hybrid panel and FISH, we have assigned the loci of mitochondrial single-stranded DNA-binding protein (SSBP), mitochondrial transcription factor A (TCF6), and mitochondrial endonuclease G (ENDOG) genes to human chromosomes 7q34, 10q21, and 9q34.1, respectively. The products of these three genes are involved in fundamental aspects of mitochondrial biogenesis, such as replication and transcription of the mitochondrial genome. The chromosomal localization of these genes is important to testing whether the corresponding proteins may play a role in the etiopathogenesis of human disorders associated with qualitative or quantitative abnormalities of mitochondrial DNA.

Hereditary Protein C Deficiency: The Australian Experience

Hereditary protein C deficiency (HPCD) is a recognized risk factor for thrombotic disease. To examine the underlying genetic defect in more detail, the protein C gene was examined in eight families from Australia. All exons and intron/exon boundaries containing the trans lated sequence of the protein C gene were amplified using the polymerase chain reaction (PCR) and sequenced di rectly. All families were identified because of a throm botic event in the proband. Six families had type I defi ciency and two had type II. Seven mutations were found in eight different families (two apparently unrelated fam ilies shared the same mutation). Five of them were point mutations leading to amino acid substitutions, most of which occurred in the serine protease domain of the ma ture protein. One mutation produced a premature stop codon, and another led to a putative splice site mutation. All of these mutations could be detected using restriction enzyme digestion or single-strand conformation polymor phism (SSCP) analysis of PCR-derived DNA. These re sults confirm the genetic heterogeneity of HPCD. Genetic diagnosis is feasible in families in whom the defect in the proband has been identified; it overcomes some of the limitations of protein-based diagnostic methods.

Cloning and comparative mapping of recently evolved human chromosome 22-specific alpha satellite DNA

We have isolated and characterized a new alphoid probe, named p190.22. Its chromosomal location was investigated using fluorescence in situ hybridization. Under high stringency conditions p190.22 recognizes specifically the centromere of chromosome 22. A chromosome 22-specific alphoid subset has been previously reported in the literature (p22/1:2.1). The partial sequence and the genomic organization comparison strongly suggests that they recognize distinct subsets both specific for chromosome 22. The comparative mapping of probes p190.22 and p22/1:2.1 on chimpanzee (PTR and PPA) and gorilla (GGO) chromosomes was investigated. The two probes showed different hybridization results. p190.22, in particular, did not show any hybridization signal in these three species, suggesting a recent evolution.

Protein C, antithrombin III and plasminogen: effect of age, sex and blood group

We conducted a cross-sectional study of antithrombin III (ATIII), protein C (PC) and plasminogen (Plg) concentrations in a population of healthy plasma donors in the Trent Region. The distribution of values for protein C was log normal whereas for ATIII and Plg the distributions were positively skewed and differed significantly from normal and log normal. Males had higher antithrombin III concentrations (mean 1.10 iu/ml, range 0.72-1.65) than females (mean 1.07 iu/ml, range 0.75-1.69) (P = 0.001) and levels increased with age in women. Younger women aged 25-34 had significantly lower plasma concentrations of ATIII compared to males of similar age. For protein C, concentrations were higher in males (mean 1.07 u/ml, range 0.37-2.11) than in females (mean 1.01 u/ml, range 0.59-1.61) (P < 0.001) and levels increased with age in both sexes P < 0.001). In women, a novel difference in protein C concentration between ABO blood groups was noted. There was no significant difference in plasminogen concentration between males and females, and in women plasminogen decreased with age (r = -0.205, P < 0.001). We conclude that these variations in ATIII and protein C with age and sex are important considerations in the determination of reference ranges for these proteins.

A comparative study of partial primary structures of the catalytic region of mammalian protein C

Protein C (PROC) is a plasma vitamin K-dependent zymogen of a serine protease which regulates blood-clotting cascade through proteolytic inactivation of the non-enzymatic cofactors of blood coagulation, Va and VIIIa. We characterized the partial nucleotide and amino acid sequences for the catalytic domain of PROC in six mammalian species, rhesus monkey, dog, cat, goat, horse and mouse, and compared these sequences with known ones from humans, the bovine and rat. By using a pair of primers based on the nucleotide sequences from human and bovine PROC cDNA, the PROC gene fragments were enzymatically amplified from their genomic DNAs and were sequenced by the dideoxy-termination method. The cloned PROC gDNA encoded a part of the heavy chain of PROC including the lesions of active site residues corresponding to human PROC Asp-257 and Ser-360. Comparison of the sequences from these species revealed that there was a high degree of homology at the nucleotide and amino acid levels; from 69% to 96% of the amino acids in the catalytic region were identical among the nine species including humans, the bovine and rat. The locations of five Cys residues as well as the putative carbohydrate attachment sites were evolutionally conserved. All the amino acids recognized in the human abnormal PROC variants were conserved across species, suggesting their functional importance, and a comparison of the conserved residues among PROC from multiple species will provide considerable information in the investigations of PROC functions.

Acceptor splice site mutation in the invariant AG of intron 5 of the protein C gene, causing type I protein C deficiency

An acceptor splice-site mutation (3318, A-->G) in the invariant AG of intron 5 of the human protein C gene has been identified in a Spanish family with heterozygous type I protein C (PC) deficiency and thromboembolic disease. Family studies confirmed cosegregation of the mutation with type I PC deficiency. Computer analysis of the mutated sequence predicted the normal splicing site to be abolished by this mutation, whereas a cryptic splice site located two nucleotides downstream, in exon 6, is probably activated. According to this, 3318, A-->G should result in a frameshift with a stop at codon 119, in agreement with the presence of a type I or quantitative PC deficient phenotype in the affected members of the family.

Cloning of human and rat cDNAs encoding the mitochondrial single-stranded DNA-binding protein (SSB)

We have retro-transcribed and amplified by PCR the full-length cDNAs specifying the rat and human precursors of the single-stranded mitochondrial DNA (mtDNA)-binding protein (mtSSB). Each deduced sequence is composed of a 16-amino-acid (aa) N-terminal basic pre-sequence and a mature protein (132 aa in humans and 135 aa in the rat). The mature proteins are highly conserved among themselves and with the mtSSB from Xenopus laevis (Xl). Moreover, three regions of the protein are similar to corresponding domains of the SSB of Escherichia coli and to the E. coli F-sex factor SSB, indicating the existence of a broad class of DNA-binding proteins with structural and functional similarities both in prokaryotes and in prokaryote-derived organelles of higher organisms.

Lamin A/C gene and a related sequence map to human chromosomes 1q12.1-q23 and 10

Lamins A and C are products of alternate splicing of one transcript from a single gene. We have isolated a partial cDNA, cE1-2, whose 800-bp sequence is 99% identical to the 3' untranslated region of the lamin A/C gene. We report here the mapping of this gene and a closely related sequence to human chromosomes 1 and 10, more specifically, to 1q12.1-q23. The localization of cE1-2 hybridizing sequences to two different chromosomes suggests that one of these loci represents an as yet unknown member of the lamin gene family, either a pseudogene or an expressed gene.

An alphoid DNA sequence conserved in all human and great ape chromosomes: evidence for ancient centromeric sequences at human chromosomal regions 2q21 and 9q13

Using vector-CENP-B box polymerase chain reaction (PCR) we isolated and cloned from a human chromosome 21-specific plasmid library, a 1 kb DNA sequence, named p alpha H21. In in situ hybridization experiments, p alpha H21 hybridized, under high stringency conditions, to the centromeric region of all the human, chimpanzee, gorilla and orangutan chromosomes. On human chromosomes p alpha H21 also identified non-centromeric sequences at 2q21 (locus D2F33S1) and 9q13 (locus D9F33S2). The possible derivation of these sequences from ancestral centromeres is discussed. Sequence analysis confirmed the alphoid nature of the whole p alpha H21 insert.

Molecular organization and chromosomal location of human GC-rich heterochromatic blocks

From the sequencing of three genomic DNA fragments and PCR amplification products from total human DNA, we have derived the sequence of a 545-bp Sau3A fragment (68% GC), representative of a family of human DNA repeats. Since previous studies suggested its linkage with unrelated Sau3A repeats of 68 bp (54% GC) (beta-satellite sequences), this feature was further investigated by in situ hybridization experiments and by Southern blot analysis of a panel of DNAs from human-Chinese hamster somatic cell hybrids. Both DNA repeats are preferentially localized on the heterochromatic regions of acrocentric chromosomes, on the pericentromeric heterochromatin of chromosome 1, 3 and 9, and on the proximal euchromatic region of the chromosome Y q arm. On chromosome 9, both repeats are part of a 2.7-kb higher-order repeat unit. These results and the Southern blot analysis on partial digests of total DNA, suggest that the linkage between the two repetitive DNA sequences is a constant feature throughout the genome. Furthermore, Southern blot analysis of HpaII-digested and MspI-digested DNA from different human tissues and tumor cell lines indicates that the investigated heterochromatic blocks appear to be subjected to changes in their methylation pattern.

A novel X-linked member of the human zinc finger protein gene family: isolation, mapping, and expression

We report the partial characterization of a novel putative zinc finger gene of the Krüppel-type (ZNF81), isolated from an X Chromosome (Chr) specific library. The pattern of segregation in human-hamster somatic cell hybrids of sequences homologous to the ZNF81 finger domain has established that it resides within the Xp22.1-Xp11 region. ZNF81 represents yet another example, together with ZFX, ZNF41, and ZNF21, of members of the zinc finger gene family residing within the short arm of the human X Chr. Sequence analysis showed that ZNF81 may encode a polypeptide(s) containing tandem arrays of 12 canonical C2H2 zinc fingers of the Krüppel-type at the C-terminus. Northern analysis indicated that probes from the ZNF81 finger domain hybridize to polyadenylated transcripts present in several cell lines, a result that supports the hypothesis that it is an expressed, functional member of this multigene family.

Characterization by yeast artificial chromosome cloning of the linked apolipoprotein(a) and plasminogen genes and identification of the apolipoprotein(a) 5' flanking region

The apoprotein(a) [apo(a)] gene encodes a protein component of the circulating lipoprotein(a) [Lp(a)]. The apo(a) gene is highly homologous to the plasminogen gene. It encodes one of the most polymorphic human proteins, due to variability in the number of repetitions of structures called kringles. In addition, Lp(a) levels vary among individuals by more than two orders of magnitude, the high levels being highly correlated with predisposition to early atherosclerotic disease. To better understand the genetics and function of the apo(a) gene, we have cloned in yeast artificial chromosome vectors DNA fragments comprising the linked apo(a) and plasminogen genes and other members of the plasminogen family. By a combination of pulsed-field gel electrophoresis and genome walking experiments, we have identified the 5' portion and flanking regions of the apo(a) gene.

Impaired secretion of the elongated mutant of protein C (protein C-Nagoya). Molecular and cellular basis for hereditary protein C deficiency

Genetic analysis of a heterozygous protein C-deficient patient revealed a novel deletion of a single guanine residue (8857G) among four consecutive guanine nucleotides [380Trp(TGG)-381Gly(GGT)] in exon IX, which encodes the carboxyl-terminal region of protein C. This deletion results in a frameshift mutation and substitution of the last 39 amino acids (381Gly-419Pro) with 81 abnormal amino acid residues, and we have designated this elongated variant as Protein C-Nagoya. A mutagenic primer was designed which replaced the third guanine residue upstream from the deletion with cytosine, thereby creating a new AvaI site in an otherwise normal allele. Analysis of the polymerase chain reaction products derived from this mutagenic primer showed that the abnormal allele has been inherited in this family. To elucidate how this molecular abnormality leads to protein C deficiency, an expression plasmid containing this mutation was transfected into COS 7, BHK, and psi-2 cells, and the secretory process of the expressed Protein C-Nagoya was analyzed. ELISA and immunoprecipitation analysis with [35S]methionine labeling indicated that the mutant protein C, which was larger in size than normal, was mostly retained within the cells, and only a small portion of it was secreted into the medium. These results suggest that most of Protein C-Nagoya undergoes degradation within the producing cells, and this frameshift mutation apparently leads to protein C deficiency by impairment of secretion of the elongated protein C into plasma.

Coexistence of congenital afibrinogenemia and protein C deficiency in a patient

A rare association of congenital afibrinogenemia and hereditary protein C deficiency is described in a 37-year-old female who suffered from ischemic necrosis in the left first toe. The diagnosis of afibrinogenemia was assessed by the absence of fibrinogen in clotting and immunological assays. The diagnosis of hereditary heterozygous type I protein C deficiency was based on the evidence of proportional decreases of activity and antigen of plasma protein C in the propositus, her mother, and two maternal aunts.

Isolation of a zinc finger motif (ZNF75) mapping on chromosome Xq26

We report here the partial characterization of a new human zinc finger (ZNF75) gene of the Kruppel type mapping to the long arm of the X chromosome. A cosmid clone was isolated from a library specific to the Xq24-qter region by hybridization to a degenerate oligonucleotide representing the link between two contigous fingers of the C2H2 type. The sequence of the pertinent cosmid fragments demonstrated five consecutive zinc finger motifs, all pertaining to the Kruppel family. A reading frame starting at least 75 amino acids before the first zinc finger and ending 11 amino acids after the last one was identified; comparison with other ZF genes suggests that this genomic fragment represents the carboxy-terminal exon of the gene. Homology of approximately 55% in the zinc finger region was detected with many zinc finger genes including mouse Zfp-35 and human ZFN7 cDNA clones. Mapping using a panel of sematic cell hybrids and chromosomal in situ hybridization localized the gene to Xq26, in a region not previously known to contain zinc finger genes.

In situ mapping of the gene coding for a leucine zipper DNA binding protein (CDR62) to 16p12-16p13.1

A cDNA clone encoding the major antigen (CDR62) associated with the antibody-induced paraneoplastic cerebellar degeneration has been used to identify the chromosomal location of the corresponding structural gene(s) by screening for its retention in a panel of rodent-human somatic cell hybrids. Having established the synteny of the gene with the autosome 16, we proceeded to its precise subregional mapping by in situ fluorescence hybridization with a recombinant lambda phage containing the genomic region homologous to the cDNA gene. The latter studies pin-pointed the chromosomal localization of the structural CDR62 gene within the interval 16p12-16p13.1.

Assignment of eight loci to bovine syntenic groups by use of PCR: extension of a comparative gene map

The polymerase chain reaction (PCR) has been combined with hybrid somatic cell technology to extend the bovine physical map. Eight bovine loci--glycoprotein hormone alpha (CGA), coagulation factor X (F10), chromogranin A (CHGA), low-density lipoprotein receptor (LDLR), human prochymosin pseudogene (CYM), oxytocin (OXT), arginine-vasopressin (ARVP), and cytochrome oxidase c subunit IV pseudogene (COXP)--were assigned to bovine syntenic groups with this approach. CGA was assigned to bovine syntenic group U2, F10 to U27, CHGA to U4 [bovine Chromosome (Chr) 21], LDLR to U22, CYM to U6, OXT and ARVP to U11, and COXP to U3 (bovine Chr 5). Seven of these genes, CGA, F10, CHGA, LDLR, OXT, ARVP, and CYM, further delineate regions of chromosomal conservation on human Chrs 6, 13, 14, 19, 20, 20, and 1, respectively. CHGA, OXT, and ARVP are unmapped in the mouse. Comparative mapping predicts the mouse CHGA will map to Chr 12, and mouse OXT and ARVP will map to mouse Chr 2. Furthermore, human CYM is predicted to be sublocalized to 1p32-q21. The primers developed for these eight loci will be useful for the development of hybrid somatic cell panels in the future as well as establishing a collection of bovine expressed sequence tags.

The NM23 gene maps to human chromosome band 17q22 and shows a restriction fragment length polymorphism with BglII

The NM23-Hl gene is a putative tumor suppressor gene that may be important in the metastasic process. Recent genetic and immunological data indicate that the NM23-Hl gene encodes a protein with nucleoside diphosphate (NDP) kinase activity. The mapping of NM23-Hl by panels of rodent-human somatic cell hybrids and in situ hybridization showed that the gene is located in human chromosome band 17q22. A two-allele polymorphism with BglII was demonstrated.

Protein C deficiency: identification of a novel two-base pair insertion and two point mutations in exon 7 of the protein C gene in Spanish families

We have applied single-strand conformation polymorphism (SSCP) to the analysis of exon 7 of the anticoagulant protein C (PC) gene, in 13 PC-deficient Spanish families. Abnormal patterns were visualized in three samples from type I or quantitative PC deficient proposita. A previously undescribed mutation due to a TT insertion after nucleotide 6139, between codons Gly-142 and Arg-143 was found in one family. The mutation (6139,ins TT) should result in a frameshift with a stop at codon 156, which agrees with the presence of a type I or quantitative PC deficiency in the affected members of the family. The second mutation identified was a C to T transition at nucleotide 6274, 9 base pairs into intron G. This mutation (6274,C-->T), found for the first time in a Spanish family, is identical to the previously characterized PC Sant Louis. The third mutation was a G to A transition that replaces arginine 178 with glutamine (178,R-->Q). This is the third case of 178,R-->Q mutation in 17 apparently unrelated Spanish families with type I PC deficiency. Furthermore, SSCP analysis allowed the detection of another previously described mutation in a PC-deficient Spanish family (178,R-->W).

Two novel mutations responsible for hereditary type I protein C deficiency: characterization by denaturing gradient gel electrophoresis

Hereditary protein C (PC) deficiency is usually associated with a high risk of thrombosis. We report the results of a study undertaken to screen for molecular defects in families with hereditary quantitative PC deficiency. Using a strategy combining polymerase chain reaction amplification of selected gene fragments, denaturing gradient gel electrophoresis of the amplification products, and direct sequencing of fragments with altered melting behavior, we studied the PC gene exons and exon/intron junctions of subjects with hereditary type I PC deficiency. Computer simulation of DNA melting was used to design several sets of primers, each containing a GC-clamp, permitting the complete analysis of each amplified exon sequence. Using this procedure, we identified two previously undescribed mutations located in exon VII: a C-to-T substitution generating a nonsense codon in place of Arg 157 in the mature PC and a G-to-A substitution converting Arg 178 to GIn. The two mutations were detected in, respectively, 3 and 2 apparently independent families. This strategy is therefore a valuable tool for screening patients, and the results emphasize its advantages over plasma assays in individuals with a family history of thrombosis.

Two novel sequence polymorphisms of the human protein C gene

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Polymorphism in the protein C gene detected by denaturing gradient gel electrophoresis

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Isolation and sub-chromosomal localization of a DNA fragment of the human choline acetyltransferase gene

A DNA fragment of 219 bp was obtained by polymerase chain reaction (PCR) on human genomic DNA using two oligonucleotide mixtures derived from peptide sequences of human placenta choline acetyltransferase (ChAT) and from partially conserved amino acid sequences of rat, porcine and Drosophila ChAT. Sequence homology with porcine ChAT demonstrated that this fragment is part of the human ChAT gene. This gene was assigned to chromosome 10 by hybridization of the 219 bp DNA probe with DNA from human-hamster somatic cell hybrids, and to region 10q11.2-10qter by PCR experiments.

Isolation and expression analysis of a human zinc finger gene (ZNF41) located on the short arm of the X chromosome

We have isolated a novel human zinc finger gene, ZNF41, from a human X-chromosome-specific library. Nucleotide sequence analysis reveals that ZNF41 potentially encodes a polypeptide featuring an array of 18 contiguous zinc fingers of the C2H2 type. Multiple polyadenylated transcripts homologous to ZNF41 are present at different levels in several distinct cell types. Southern analyses of somatic cell hybrids containing either intact or rearranged X chromosomes confirm the genomic origin of the isolated gene and establish that it is localized between Xcen and Xp22.1.

The molecular genetics of familial venous thrombosis

Inherited defects of antithrombin III, protein C, protein S, heparin cofactor II, plasminogen and the fibrinogens are thought to be responsible for between 10 and 15% of all patients presenting with recurrent venous thrombosis. The structure, function and expression of these genes and the nature of the gene lesions underlying the deficiency states are reviewed in detail.

Translocation breakpoint of acute promyelocytic leukemia lies within the retinoic acid receptor alpha locus

Acute promyelocytic leukemias (APLs) are characterized by a reciprocal balanced translocation that involves chromosomes 15 and 17 [t(15;17)]. We report the isolation and characterization of one of the two reciprocal break sites and demonstrate that the chromosome 17 breakpoint lies within the retinoic acid receptor alpha locus. Nucleotide sequencing of the 15;17 cross-over junction on 15q+ showed that the retinoic acid receptor alpha gene is truncated within its first intron, 370 base pairs upstream from the splicing donor site of exon II. Such a recombination would be expected to generate abnormal RAR alpha mRNA and protein. Southern blot analysis of a number of APLs with chromosome 15- and 17-derived DNA probes revealed similar 15;17 recombinations in the majority of other APLs. Our data are strong evidence that the retinoic acid receptor alpha gene plays a crucial role in the leukemogenesis of APL.

cDNA cloning, sequence analysis, and chromosomal localization of the gene for human carnitine palmitoyltransferase

We have cloned and sequenced a cDNA encoding human liver carnitine palmitoyltransferase (CPTase; palmitoyl-CoA:L-carnitine O-palmitoyltransferase, EC 2.3.1.21), an inner mitochondrial membrane enzyme that plays a major role in the fatty acid oxidation pathway. Mixed oligonucleotide primers whose sequences were deduced from one tryptic peptide obtained from purified CPTase were used in a polymerase chain reaction, allowing the amplification of a 0.12-kilobase fragment of human genomic DNA encoding such a peptide. A 60-base-pair (bp) oligonucleotide synthesized on the basis of the sequence from this fragment was used for the screening of a cDNA library from human liver and hybridized to a cDNA insert of 2255 bp. This cDNA contains an open reading frame of 1974 bp that encodes a protein of 658 amino acid residues including 25 residues of an NH2-terminal leader peptide. The assignment of this open reading frame to human liver CPTase is confirmed by matches to seven different amino acid sequences of tryptic peptides derived from pure human CPTase and by the 82.2% homology with the amino acid sequence of rat CPTase. The NH2-terminal region of CPTase contains a leucine-proline motif that is shared by carnitine acetyl- and octanoyltransferases and by choline acetyltransferase. The gene encoding CPTase was assigned to human chromosome 1, region 1q12-1pter, by hybridization of CPTase cDNA with a DNA panel of 19 human-hamster somatic cell hybrids.

Chromosome-specific subsets of human alphoid DNA identified by a chromosome 2-derived clone

We have cloned an alphoid DNA fragment, pBS4D, from the DNA of a human-hamster hybrid cell line containing chromosome 2 as its only cytologically detectable human component. Under high stringency conditions, pBS4D hybridized in situ mostly to chromosome 2 and to a lesser extent to chromosomes 18 and 20. Restriction analysis using the DNA from selected somatic hybrid cell lines revealed that the genomic organization of this alphoid DNA differs on each of these three chromosomes.

Probes for CpG islands on the distal long arm of the human X chromosome are clustered in Xq24 and Xq28

We have isolated and characterized 55 EagI-containing genomic DNA clones from the distal long arm of the human X chromosome. The presence of additional sites for rare-cutter restriction enzymes and the demethylation of the corresponding genomic DNA demonstrate that at least 30 clones correspond to CpG islands of the Xq24-Xqter region. All clones were regionally mapped with a hybrid panel. The majority are in Xq28 and Xq24 (18 and 14 clones, respectively), 15 are in the Xq26-Xq27 interval, and none is in Xq25. This analysis demonstrates a nonuniform distribution of CpG islands that may reflect the distribution of coding regions in this part of the genome.

Superficial thrombophlebitis. I. Primary hypercoagulable states

This review concentrates on those disorders in which superficial thrombophlebitis can be a significant or presenting clinical sign. Primary hypercoagulable states are those conditions associated with an increased risk of thrombosis caused by a specific measurable defect in the proteins of coagulation and/or fibrinolytic systems. These disorders are frequently inherited and include deficiencies of antithrombin III, heparin cofactor 2, protein C, protein S, abnormal fibrinolytic activity, dysfibrinogenemia, and Hageman trait. Patients with a lupus anticoagulant and anticardiolipin antibody syndrome with thrombotic episodes are also considered to have a primary hypercoagulable state. The physiology, pathophysiology, clinical characteristics, and treatment of primary hypercoagulable states are reviewed.

Physical mapping of the human chromosome 11q23 region containing the ataxia-telangiectasia locus

Two breakpoints within chromosome 11q23 were characterized with 29 DNA probes to establish a physical map of the region. This region is notable in that it contains at least 14 functional genes which are also syntenic in the mouse (chromosome 9). Chromosome 11q23 includes these markers: STMY, CLG, NCAM, DRD2, APOA1, APOC3, APOA4, CD3E, CD3D, CD3G, PBGD, THY1, ets-1, and cbl-2. The two breakpoints, herein called "X;11" and "4;11," defined a region of approximately 8 cM containing the APO and CD3 complexes as well as the polymorphic marker D11S29. DRD2 localized centromeric to the X;11 breakpoint despite evidence for close genetic linkage to D11S29, suggesting that DRD2 lies close to the X;11 breakpoint. THY1, PBGD, and cbl-2 localized telomeric to the 4;11 breakpoint and thus to the [D11S29--APO--CD3] grouping as well. The physical map helps to correlate the cytogenetic and linkage maps of this region. It also suggests that the human 11q23 syntenic grouping is inverted with respect to its murine counterpart. Based on this physical map and on our primary linkage map of the 11q23 region, we are able to confirm a preliminary localization of the gene for ataxia-telangiectasia group A (ATA) to a region centromeric to the interval defined by D11S144 (pYNB3.12) and THY1.

Site-specific integration by adeno-associated virus

Cellular sequences flanking integrated copies of the adeno-associated virus (AAV) genome were isolated from a latently infected clonal human cell line and used to probe genomic blots derived from an additional 21 independently derived clones of human cells latently infected with AAV. In genomic blots of uninfected human cell lines and of primary human tissue, each flanking-sequence probe hybridized to unique bands, but in 15 of the 22 latently infected clones the flanking sequences hybridized not only to the original fragments but also to a total of 36 additional species. AAV probes also hybridized to 22 of these new bands, representing 11 of the 15 positive clones, but never to the fragment characteristic of uninfected cell DNA. From these data we conclude that the AAV genome preferentially integrates into a specific region of the cellular genome. We have determined that the integration site is unique to chromosome 19 by somatic cell hybrid mapping, and this sequence has been isolated from uninfected human DNA.

Use of transgenic mice for the characterization of human alpha 1-acid glycoprotein (orosomucoid) variants

Sera from transgenic mice (TM) carrying human genes of alpha 1-acid glycoprotein (orosomucoid or ORM) have been analyzed by isoelectrofocusing and subsequent immunoblotting with antihuman ORM antibodies. With this technique it is possible to reveal selectively the human protein secreted in the TM sera. Orosomucoid bands present in TM sera have been compared with those of the most common human ORM phenotypes to correlate the products of specific genes to previously identified genetic variants. In this paper, we report the identification of the genes encoding for variants ORM1 F1 and ORM2 A, which are genes AGP-A and AGP-B/B' respectively. The nucleotide sequences of these genes are known; therefore a direct correlation between variants and specific amino acid sequences can be established.

A human alphoid DNA clone from the EcoRI dimeric family: genomic and internal organization and chromosomal assignment

We isolated an alpha satellite DNA clone (pC1.8), 17 kb long, which is composed exclusively of tandemly repeated 340-bp EcoRI fragments. Hybridization studies using 37 random EcoRI dimers subcloned from pC1.8 showed that they are heterogeneous. The sequence of 5 dimers, 3 of them adjacent, confirmed this observation and showed that the heterogeneity is more accentuated among the second monomers. The chromosomal assignment under high stringency conditions showed that this alphoid subset is located on chromosomes 1, 5, and 19. No conditions that eliminate the hybridization on any one of those chromosomes were found. This suggests that, in contrast to many other chromosome-specific alpha satellite subsets, the single chromosome subsets of this family are virtually indistinguishable by hybridization techniques.

MspI RFLP in intron 8 of the human protein C gene

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Assignment of human aldolase C gene to chromosome 17, region cen----q21.1

The mapping of the gene coding for human aldolase C has been studied using a specific cDNA probe and genomic blots from a panel of human-hamster somatic cell hybrids. The results show that the aldolase C gene is on chromosome 17. In situ experiments have restricted the mapping to the region 17cen----q21.1. Using the same panel of human-hamster somatic cell hybrids, we have confirmed the localization of aldolase A and B on chromosomes 16 and 9, respectively.

Regional mapping of RBP4 to 10q23----q24 and RBP1 to 3q21----q22 in man

The human gene coding for RBP4 has been assigned to 10q23----24 using a panel of somatic cell hybrids and in situ hybridization experiments. The mapping of the human RBP1, previously assigned by our group to chromosome 3 using a panel of somatic cell hybrids, was restricted to the region 3q21----22 using in situ experiments and Southern blots of genomic DNA from a hybrid retaining a portion of chromosome 3.